,Query,Hit type,PSSM-ID,From,To,E-Value,Bitscore,Accession,Short name,Incomplete,Superfamily,Definition,simple_id,full_fasta_name,My_Category,subfam,orf,simple_genome,frame,Incomplete_meaning
0,Q#3 - >seq2,non-specific,335182,153,250,1.3662899999999999e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,marg,CompleteHit
1,Q#3 - >seq2,superfamily,335182,153,250,1.3662899999999999e-46,152.842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,marg,CompleteHit
2,Q#3 - >seq2,non-specific,340205,253,317,1.6240499999999997e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,marg,CompleteHit
3,Q#3 - >seq2,superfamily,340205,253,317,1.6240499999999997e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,marg,CompleteHit
4,Q#3 - >seq2,non-specific,340204,109,150,1.7992400000000002e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs3_orang,marg,CompleteHit
5,Q#3 - >seq2,superfamily,340204,109,150,1.7992400000000002e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs3_orang,marg,CompleteHit
6,Q#3 - >seq2,non-specific,235175,52,153,0.00714219,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
7,Q#3 - >seq2,superfamily,235175,52,153,0.00714219,38.1212,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
8,Q#3 - >seq2,non-specific,274009,39,201,0.00741542,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
9,Q#3 - >seq2,superfamily,274009,39,201,0.00741542,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
10,Q#3 - >seq2,non-specific,222878,28,194,0.00916522,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
11,Q#3 - >seq2,superfamily,222878,28,194,0.00916522,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
12,Q#3 - >seq2,non-specific,224117,34,209,0.00958031,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
13,Q#3 - >seq2,superfamily,224117,34,209,0.00958031,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
14,Q#3 - >seq2,non-specific,225288,40,149,0.00978422,37.3764,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
15,Q#3 - >seq2,superfamily,331991,40,149,0.00978422,37.3764,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1HS.ORF1.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs3_orang,marg,BothTerminiTruncated
16,Q#6 - >seq5,specific,238827,510,772,3.3322799999999994e-66,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
17,Q#6 - >seq5,superfamily,295487,510,772,3.3322799999999994e-66,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
18,Q#6 - >seq5,specific,197310,9,236,1.7240299999999997e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
19,Q#6 - >seq5,superfamily,351117,9,236,1.7240299999999997e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
20,Q#6 - >seq5,non-specific,197306,9,236,2.4417599999999996e-54,188.84400000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
21,Q#6 - >seq5,specific,333820,516,772,4.1106299999999996e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
22,Q#6 - >seq5,superfamily,333820,516,772,4.1106299999999996e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
23,Q#6 - >seq5,non-specific,197307,9,236,1.6411600000000002e-25,106.21799999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
24,Q#6 - >seq5,non-specific,223780,9,238,2.3008700000000002e-24,103.447,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
25,Q#6 - >seq5,non-specific,197321,7,236,2.6968300000000002e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
26,Q#6 - >seq5,non-specific,197320,8,236,3.1665900000000006e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
27,Q#6 - >seq5,non-specific,273186,9,237,2.89294e-19,88.1048,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
28,Q#6 - >seq5,specific,335306,10,229,4.31246e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
29,Q#6 - >seq5,non-specific,272954,9,236,8.226900000000001e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
30,Q#6 - >seq5,non-specific,197319,8,236,3.6706599999999996e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
31,Q#6 - >seq5,non-specific,197336,7,235,1.7404e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
32,Q#6 - >seq5,non-specific,238828,516,737,2.28801e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
33,Q#6 - >seq5,non-specific,197322,9,236,2.06628e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
34,Q#6 - >seq5,non-specific,275209,467,799,2.64118e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
35,Q#6 - >seq5,superfamily,275209,467,799,2.64118e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
36,Q#6 - >seq5,non-specific,236970,9,238,1.96133e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
37,Q#6 - >seq5,non-specific,339261,108,232,4.80621e-09,55.0359,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
38,Q#6 - >seq5,non-specific,197311,7,236,5.1154199999999994e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,pars,CompleteHit
39,Q#6 - >seq5,non-specific,197317,139,229,3.6856e-06,49.1376,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,pars,N-TerminusTruncated
40,Q#6 - >seq5,non-specific,238185,656,772,3.50457e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs3_orang,pars,CompleteHit
41,Q#6 - >seq5,non-specific,226098,138,239,0.00024097799999999998,43.9284,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,pars,N-TerminusTruncated
42,Q#6 - >seq5,non-specific,197314,7,192,0.00149027,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF2,hs3_orang,pars,C-TerminusTruncated
43,Q#6 - >seq5,non-specific,274009,305,453,0.00205236,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,pars,C-TerminusTruncated
44,Q#6 - >seq5,superfamily,274009,305,453,0.00205236,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,pars,C-TerminusTruncated
45,Q#6 - >seq5,non-specific,235175,295,464,0.00814107,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,pars,BothTerminiTruncated
46,Q#6 - >seq5,superfamily,235175,295,464,0.00814107,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,pars,BothTerminiTruncated
47,Q#9 - >seq8,specific,238827,510,772,4.210599999999999e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
48,Q#9 - >seq8,superfamily,295487,510,772,4.210599999999999e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
49,Q#9 - >seq8,specific,197310,9,236,1.6185799999999996e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
50,Q#9 - >seq8,superfamily,351117,9,236,1.6185799999999996e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
51,Q#9 - >seq8,non-specific,197306,9,236,1.38373e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
52,Q#9 - >seq8,specific,333820,516,772,4.50684e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
53,Q#9 - >seq8,superfamily,333820,516,772,4.50684e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
54,Q#9 - >seq8,non-specific,197307,9,236,1.58949e-25,106.988,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
55,Q#9 - >seq8,non-specific,223780,9,238,2.6287500000000004e-24,103.447,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
56,Q#9 - >seq8,non-specific,197320,8,236,3.10125e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
57,Q#9 - >seq8,non-specific,197321,7,236,4.7575499999999996e-21,93.7708,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
58,Q#9 - >seq8,non-specific,273186,9,237,3.2359999999999996e-19,88.49,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
59,Q#9 - >seq8,specific,335306,10,229,5.72756e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
60,Q#9 - >seq8,non-specific,272954,9,236,8.296330000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
61,Q#9 - >seq8,non-specific,197319,8,236,4.72226e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
62,Q#9 - >seq8,non-specific,197336,7,235,2.41109e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
63,Q#9 - >seq8,non-specific,238828,516,737,2.31083e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
64,Q#9 - >seq8,non-specific,197322,9,236,2.7799e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
65,Q#9 - >seq8,non-specific,275209,467,799,3.4815e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
66,Q#9 - >seq8,superfamily,275209,467,799,3.4815e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
67,Q#9 - >seq8,non-specific,236970,9,238,1.8301099999999998e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
68,Q#9 - >seq8,non-specific,339261,108,232,3.8392700000000005e-09,55.4211,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
69,Q#9 - >seq8,non-specific,197311,7,236,5.64342e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs3_orang,marg,CompleteHit
70,Q#9 - >seq8,non-specific,197317,139,229,4.54226e-06,49.5228,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,marg,N-TerminusTruncated
71,Q#9 - >seq8,non-specific,238185,656,772,4.8001400000000004e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs3_orang,marg,CompleteHit
72,Q#9 - >seq8,non-specific,226098,138,239,0.000318524,43.9284,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs3_orang,marg,N-TerminusTruncated
73,Q#9 - >seq8,non-specific,274009,305,453,0.00107797,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,C-TerminusTruncated
74,Q#9 - >seq8,superfamily,274009,305,453,0.00107797,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,C-TerminusTruncated
75,Q#9 - >seq8,non-specific,197314,7,192,0.00200022,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF2,hs3_orang,marg,C-TerminusTruncated
76,Q#9 - >seq8,specific,311990,1238,1256,0.00213025,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs3_orang,marg,CompleteHit
77,Q#9 - >seq8,superfamily,311990,1238,1256,0.00213025,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs3_orang,marg,CompleteHit
78,Q#9 - >seq8,non-specific,235175,295,464,0.00387367,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,BothTerminiTruncated
79,Q#9 - >seq8,superfamily,235175,295,464,0.00387367,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,BothTerminiTruncated
80,Q#9 - >seq8,non-specific,274008,157,500,0.00533529,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,N-TerminusTruncated
81,Q#9 - >seq8,superfamily,274008,157,500,0.00533529,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs3_orang,marg,N-TerminusTruncated
82,Q#9 - >seq8,non-specific,293702,337,451,0.00927613,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1HS,ORF2,hs3_orang,marg,C-TerminusTruncated
83,Q#9 - >seq8,superfamily,293702,337,451,0.00927613,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs3_orang.marg.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1HS,ORF2,hs3_orang,marg,C-TerminusTruncated
84,Q#12 - >seq11,non-specific,335182,154,251,3.80203e-49,159.776,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
85,Q#12 - >seq11,superfamily,335182,154,251,3.80203e-49,159.776,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
86,Q#12 - >seq11,non-specific,335182,154,251,3.80203e-49,159.776,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
87,Q#12 - >seq11,non-specific,340205,254,318,1.5871299999999998e-34,120.51899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
88,Q#12 - >seq11,superfamily,340205,254,318,1.5871299999999998e-34,120.51899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
89,Q#12 - >seq11,non-specific,340205,254,318,1.5871299999999998e-34,120.51899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,pars,CompleteHit
90,Q#12 - >seq11,specific,340204,109,151,1.14833e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,pars,CompleteHit
91,Q#12 - >seq11,superfamily,340204,109,151,1.14833e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,pars,CompleteHit
92,Q#12 - >seq11,non-specific,340204,109,151,1.14833e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,pars,CompleteHit
93,Q#12 - >seq11,non-specific,335623,34,146,0.0007841580000000001,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
94,Q#12 - >seq11,superfamily,335623,34,146,0.0007841580000000001,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
95,Q#12 - >seq11,non-specific,335623,34,146,0.0007841580000000001,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
96,Q#12 - >seq11,non-specific,274008,39,209,0.0012202,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
97,Q#12 - >seq11,superfamily,274008,39,209,0.0012202,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
98,Q#12 - >seq11,non-specific,274008,39,209,0.0012202,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
99,Q#12 - >seq11,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
100,Q#12 - >seq11,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
101,Q#12 - >seq11,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs0_human,pars,C-TerminusTruncated
102,Q#12 - >seq11,non-specific,235175,52,140,0.00177899,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
103,Q#12 - >seq11,superfamily,235175,52,140,0.00177899,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
104,Q#12 - >seq11,non-specific,235175,52,140,0.00177899,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
105,Q#12 - >seq11,non-specific,313022,21,151,0.00608831,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,pars,N-TerminusTruncated
106,Q#12 - >seq11,superfamily,313022,21,151,0.00608831,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,pars,N-TerminusTruncated
107,Q#12 - >seq11,non-specific,313022,21,151,0.00608831,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,pars,N-TerminusTruncated
108,Q#12 - >seq11,non-specific,316375,34,136,0.00624582,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
109,Q#12 - >seq11,superfamily,316375,34,136,0.00624582,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
110,Q#12 - >seq11,non-specific,316375,34,136,0.00624582,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
111,Q#12 - >seq11,non-specific,335556,47,130,0.0074719999999999995,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
112,Q#12 - >seq11,superfamily,335556,47,130,0.0074719999999999995,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
113,Q#12 - >seq11,non-specific,335556,47,130,0.0074719999999999995,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,pars,BothTerminiTruncated
114,Q#15 - >seq14,non-specific,335182,154,251,3.80203e-49,159.776,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
115,Q#15 - >seq14,superfamily,335182,154,251,3.80203e-49,159.776,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
116,Q#15 - >seq14,non-specific,335182,154,251,3.80203e-49,159.776,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
117,Q#15 - >seq14,non-specific,340205,254,318,1.5871299999999998e-34,120.51899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
118,Q#15 - >seq14,superfamily,340205,254,318,1.5871299999999998e-34,120.51899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
119,Q#15 - >seq14,non-specific,340205,254,318,1.5871299999999998e-34,120.51899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs0_human,marg,CompleteHit
120,Q#15 - >seq14,specific,340204,109,151,1.14833e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,marg,CompleteHit
121,Q#15 - >seq14,superfamily,340204,109,151,1.14833e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,marg,CompleteHit
122,Q#15 - >seq14,non-specific,340204,109,151,1.14833e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs0_human,marg,CompleteHit
123,Q#15 - >seq14,non-specific,335623,34,146,0.0007841580000000001,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
124,Q#15 - >seq14,superfamily,335623,34,146,0.0007841580000000001,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
125,Q#15 - >seq14,non-specific,335623,34,146,0.0007841580000000001,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
126,Q#15 - >seq14,non-specific,274008,39,209,0.0012202,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
127,Q#15 - >seq14,superfamily,274008,39,209,0.0012202,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
128,Q#15 - >seq14,non-specific,274008,39,209,0.0012202,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
129,Q#15 - >seq14,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
130,Q#15 - >seq14,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
131,Q#15 - >seq14,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs0_human,marg,C-TerminusTruncated
132,Q#15 - >seq14,non-specific,235175,52,140,0.00177899,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
133,Q#15 - >seq14,superfamily,235175,52,140,0.00177899,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
134,Q#15 - >seq14,non-specific,235175,52,140,0.00177899,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
135,Q#15 - >seq14,non-specific,313022,21,151,0.00608831,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,marg,N-TerminusTruncated
136,Q#15 - >seq14,superfamily,313022,21,151,0.00608831,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,marg,N-TerminusTruncated
137,Q#15 - >seq14,non-specific,313022,21,151,0.00608831,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs0_human,marg,N-TerminusTruncated
138,Q#15 - >seq14,non-specific,316375,34,136,0.00624582,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
139,Q#15 - >seq14,superfamily,316375,34,136,0.00624582,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
140,Q#15 - >seq14,non-specific,316375,34,136,0.00624582,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
141,Q#15 - >seq14,non-specific,335556,47,130,0.0074719999999999995,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
142,Q#15 - >seq14,superfamily,335556,47,130,0.0074719999999999995,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
143,Q#15 - >seq14,non-specific,335556,47,130,0.0074719999999999995,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs0_human,marg,BothTerminiTruncated
144,Q#17 - >seq16,specific,238827,510,772,7.80121e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
145,Q#17 - >seq16,superfamily,295487,510,772,7.80121e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
146,Q#17 - >seq16,non-specific,238827,510,772,7.80121e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
147,Q#17 - >seq16,specific,197310,9,236,3.39823e-64,217.604,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
148,Q#17 - >seq16,superfamily,351117,9,236,3.39823e-64,217.604,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
149,Q#17 - >seq16,non-specific,197310,9,236,3.39823e-64,217.604,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
150,Q#17 - >seq16,non-specific,197306,9,236,2.0043599999999995e-56,195.393,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
151,Q#17 - >seq16,non-specific,197306,9,236,2.0043599999999995e-56,195.393,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
152,Q#17 - >seq16,specific,333820,516,772,1.6545e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
153,Q#17 - >seq16,superfamily,333820,516,772,1.6545e-35,133.572,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
154,Q#17 - >seq16,non-specific,333820,516,772,1.6545e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
155,Q#17 - >seq16,non-specific,197307,9,236,6.993520000000001e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
156,Q#17 - >seq16,non-specific,197307,9,236,6.993520000000001e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
157,Q#17 - >seq16,non-specific,223780,9,238,6.94118e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
158,Q#17 - >seq16,non-specific,223780,9,238,6.94118e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
159,Q#17 - >seq16,non-specific,197320,8,236,1.68453e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
160,Q#17 - >seq16,non-specific,197320,8,236,1.68453e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
161,Q#17 - >seq16,non-specific,197321,7,236,2.4878299999999997e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
162,Q#17 - >seq16,non-specific,197321,7,236,2.4878299999999997e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
163,Q#17 - >seq16,specific,335306,10,229,1.5930300000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
164,Q#17 - >seq16,non-specific,335306,10,229,1.5930300000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
165,Q#17 - >seq16,non-specific,273186,9,237,3.56182e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
166,Q#17 - >seq16,non-specific,273186,9,237,3.56182e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
167,Q#17 - >seq16,non-specific,272954,9,236,8.47706e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
168,Q#17 - >seq16,non-specific,272954,9,236,8.47706e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
169,Q#17 - >seq16,non-specific,197336,7,235,9.59217e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
170,Q#17 - >seq16,non-specific,197336,7,235,9.59217e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
171,Q#17 - >seq16,non-specific,197319,8,236,1.01146e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
172,Q#17 - >seq16,non-specific,197319,8,236,1.01146e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
173,Q#17 - >seq16,non-specific,238828,516,737,1.91992e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
174,Q#17 - >seq16,non-specific,238828,516,737,1.91992e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
175,Q#17 - >seq16,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
176,Q#17 - >seq16,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
177,Q#17 - >seq16,non-specific,275209,467,800,1.6734300000000003e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
178,Q#17 - >seq16,superfamily,275209,467,800,1.6734300000000003e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
179,Q#17 - >seq16,non-specific,275209,467,800,1.6734300000000003e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
180,Q#17 - >seq16,non-specific,197322,9,236,1.17086e-08,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
181,Q#17 - >seq16,non-specific,197322,9,236,1.17086e-08,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
182,Q#17 - >seq16,non-specific,339261,108,232,6.787869999999999e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs0_human,pars,CompleteHit
183,Q#17 - >seq16,non-specific,339261,108,232,6.787869999999999e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs0_human,pars,CompleteHit
184,Q#17 - >seq16,non-specific,197311,7,236,5.35175e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
185,Q#17 - >seq16,non-specific,197311,7,236,5.35175e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,pars,CompleteHit
186,Q#17 - >seq16,non-specific,197317,139,229,6.47675e-07,51.833999999999996,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,N-TerminusTruncated
187,Q#17 - >seq16,non-specific,197317,139,229,6.47675e-07,51.833999999999996,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,N-TerminusTruncated
188,Q#17 - >seq16,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
189,Q#17 - >seq16,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
190,Q#17 - >seq16,non-specific,274009,305,453,0.0007642269999999999,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
191,Q#17 - >seq16,superfamily,274009,305,453,0.0007642269999999999,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
192,Q#17 - >seq16,non-specific,274009,305,453,0.0007642269999999999,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
193,Q#17 - >seq16,specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,pars,CompleteHit
194,Q#17 - >seq16,superfamily,311990,1241,1259,0.00199368,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,pars,CompleteHit
195,Q#17 - >seq16,non-specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,pars,CompleteHit
196,Q#17 - >seq16,non-specific,226098,138,239,0.00282967,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,N-TerminusTruncated
197,Q#17 - >seq16,non-specific,226098,138,239,0.00282967,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,pars,N-TerminusTruncated
198,Q#17 - >seq16,non-specific,239569,525,748,0.00312522,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
199,Q#17 - >seq16,non-specific,239569,525,748,0.00312522,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs0_human,pars,CompleteHit
200,Q#17 - >seq16,non-specific,224117,311,428,0.00913062,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
201,Q#17 - >seq16,superfamily,224117,311,428,0.00913062,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
202,Q#17 - >seq16,non-specific,224117,311,428,0.00913062,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.pars.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,pars,C-TerminusTruncated
203,Q#20 - >seq19,specific,238827,510,772,7.80121e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
204,Q#20 - >seq19,superfamily,295487,510,772,7.80121e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
205,Q#20 - >seq19,non-specific,238827,510,772,7.80121e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
206,Q#20 - >seq19,specific,197310,9,236,3.39823e-64,217.604,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
207,Q#20 - >seq19,superfamily,351117,9,236,3.39823e-64,217.604,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
208,Q#20 - >seq19,non-specific,197310,9,236,3.39823e-64,217.604,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
209,Q#20 - >seq19,non-specific,197306,9,236,2.0043599999999995e-56,195.393,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
210,Q#20 - >seq19,non-specific,197306,9,236,2.0043599999999995e-56,195.393,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
211,Q#20 - >seq19,specific,333820,516,772,1.6545e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
212,Q#20 - >seq19,superfamily,333820,516,772,1.6545e-35,133.572,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
213,Q#20 - >seq19,non-specific,333820,516,772,1.6545e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
214,Q#20 - >seq19,non-specific,197307,9,236,6.993520000000001e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
215,Q#20 - >seq19,non-specific,197307,9,236,6.993520000000001e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
216,Q#20 - >seq19,non-specific,223780,9,238,6.94118e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
217,Q#20 - >seq19,non-specific,223780,9,238,6.94118e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
218,Q#20 - >seq19,non-specific,197320,8,236,1.68453e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
219,Q#20 - >seq19,non-specific,197320,8,236,1.68453e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
220,Q#20 - >seq19,non-specific,197321,7,236,2.4878299999999997e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
221,Q#20 - >seq19,non-specific,197321,7,236,2.4878299999999997e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
222,Q#20 - >seq19,specific,335306,10,229,1.5930300000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
223,Q#20 - >seq19,non-specific,335306,10,229,1.5930300000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
224,Q#20 - >seq19,non-specific,273186,9,237,3.56182e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
225,Q#20 - >seq19,non-specific,273186,9,237,3.56182e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
226,Q#20 - >seq19,non-specific,272954,9,236,8.47706e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
227,Q#20 - >seq19,non-specific,272954,9,236,8.47706e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
228,Q#20 - >seq19,non-specific,197336,7,235,9.59217e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
229,Q#20 - >seq19,non-specific,197336,7,235,9.59217e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
230,Q#20 - >seq19,non-specific,197319,8,236,1.01146e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
231,Q#20 - >seq19,non-specific,197319,8,236,1.01146e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
232,Q#20 - >seq19,non-specific,238828,516,737,1.91992e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
233,Q#20 - >seq19,non-specific,238828,516,737,1.91992e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
234,Q#20 - >seq19,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
235,Q#20 - >seq19,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
236,Q#20 - >seq19,non-specific,275209,467,800,1.6734300000000003e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
237,Q#20 - >seq19,superfamily,275209,467,800,1.6734300000000003e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
238,Q#20 - >seq19,non-specific,275209,467,800,1.6734300000000003e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
239,Q#20 - >seq19,non-specific,197322,9,236,1.17086e-08,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
240,Q#20 - >seq19,non-specific,197322,9,236,1.17086e-08,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
241,Q#20 - >seq19,non-specific,339261,108,232,6.787869999999999e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs0_human,marg,CompleteHit
242,Q#20 - >seq19,non-specific,339261,108,232,6.787869999999999e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs0_human,marg,CompleteHit
243,Q#20 - >seq19,non-specific,197311,7,236,5.35175e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
244,Q#20 - >seq19,non-specific,197311,7,236,5.35175e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs0_human,marg,CompleteHit
245,Q#20 - >seq19,non-specific,197317,139,229,6.47675e-07,51.833999999999996,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,N-TerminusTruncated
246,Q#20 - >seq19,non-specific,197317,139,229,6.47675e-07,51.833999999999996,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,N-TerminusTruncated
247,Q#20 - >seq19,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
248,Q#20 - >seq19,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
249,Q#20 - >seq19,non-specific,274009,305,453,0.0007642269999999999,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
250,Q#20 - >seq19,superfamily,274009,305,453,0.0007642269999999999,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
251,Q#20 - >seq19,non-specific,274009,305,453,0.0007642269999999999,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
252,Q#20 - >seq19,specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,marg,CompleteHit
253,Q#20 - >seq19,superfamily,311990,1241,1259,0.00199368,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,marg,CompleteHit
254,Q#20 - >seq19,non-specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs0_human,marg,CompleteHit
255,Q#20 - >seq19,non-specific,226098,138,239,0.00282967,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,N-TerminusTruncated
256,Q#20 - >seq19,non-specific,226098,138,239,0.00282967,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs0_human,marg,N-TerminusTruncated
257,Q#20 - >seq19,non-specific,239569,525,748,0.00312522,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
258,Q#20 - >seq19,non-specific,239569,525,748,0.00312522,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs0_human,marg,CompleteHit
259,Q#20 - >seq19,non-specific,224117,311,428,0.00913062,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
260,Q#20 - >seq19,superfamily,224117,311,428,0.00913062,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
261,Q#20 - >seq19,non-specific,224117,311,428,0.00913062,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF2.hs0_human.marg.frame3,1909122130_L1HS.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs0_human,marg,C-TerminusTruncated
262,Q#22 - >seq21,non-specific,335182,153,250,1.3662899999999999e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,pars,CompleteHit
263,Q#22 - >seq21,superfamily,335182,153,250,1.3662899999999999e-46,152.842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,pars,CompleteHit
264,Q#22 - >seq21,non-specific,340205,253,317,1.6240499999999997e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,pars,CompleteHit
265,Q#22 - >seq21,superfamily,340205,253,317,1.6240499999999997e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs3_orang,pars,CompleteHit
266,Q#22 - >seq21,non-specific,340204,109,150,1.7992400000000002e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs3_orang,pars,CompleteHit
267,Q#22 - >seq21,superfamily,340204,109,150,1.7992400000000002e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs3_orang,pars,CompleteHit
268,Q#22 - >seq21,non-specific,235175,52,153,0.00714219,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
269,Q#22 - >seq21,superfamily,235175,52,153,0.00714219,38.1212,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
270,Q#22 - >seq21,non-specific,274009,39,201,0.00741542,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
271,Q#22 - >seq21,superfamily,274009,39,201,0.00741542,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
272,Q#22 - >seq21,non-specific,222878,28,194,0.00916522,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
273,Q#22 - >seq21,superfamily,222878,28,194,0.00916522,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
274,Q#22 - >seq21,non-specific,224117,34,209,0.00958031,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
275,Q#22 - >seq21,superfamily,224117,34,209,0.00958031,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
276,Q#22 - >seq21,non-specific,225288,40,149,0.00978422,37.3764,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
277,Q#22 - >seq21,superfamily,331991,40,149,0.00978422,37.3764,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1HS.ORF1.hs3_orang.pars.frame3,1909122130_L1HS.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs3_orang,pars,BothTerminiTruncated
278,Q#26 - >seq25,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
279,Q#26 - >seq25,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
280,Q#26 - >seq25,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
281,Q#26 - >seq25,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
282,Q#26 - >seq25,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
283,Q#26 - >seq25,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,pars,CompleteHit
284,Q#26 - >seq25,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,pars,CompleteHit
285,Q#26 - >seq25,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,pars,CompleteHit
286,Q#26 - >seq25,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,pars,CompleteHit
287,Q#26 - >seq25,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
288,Q#26 - >seq25,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
289,Q#26 - >seq25,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
290,Q#26 - >seq25,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
291,Q#26 - >seq25,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
292,Q#26 - >seq25,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
293,Q#26 - >seq25,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
294,Q#26 - >seq25,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
295,Q#26 - >seq25,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
296,Q#26 - >seq25,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
297,Q#26 - >seq25,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
298,Q#26 - >seq25,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
299,Q#26 - >seq25,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
300,Q#26 - >seq25,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
301,Q#26 - >seq25,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
302,Q#26 - >seq25,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,pars,N-TerminusTruncated
303,Q#26 - >seq25,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,pars,N-TerminusTruncated
304,Q#26 - >seq25,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,pars,N-TerminusTruncated
305,Q#26 - >seq25,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
306,Q#26 - >seq25,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
307,Q#26 - >seq25,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,pars,C-TerminusTruncated
308,Q#26 - >seq25,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
309,Q#26 - >seq25,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
310,Q#26 - >seq25,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
311,Q#26 - >seq25,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
312,Q#26 - >seq25,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.pars.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,pars,BothTerminiTruncated
313,Q#29 - >seq28,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
314,Q#29 - >seq28,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
315,Q#29 - >seq28,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
316,Q#29 - >seq28,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
317,Q#29 - >seq28,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
318,Q#29 - >seq28,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs1_chimp,marg,CompleteHit
319,Q#29 - >seq28,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,marg,CompleteHit
320,Q#29 - >seq28,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,marg,CompleteHit
321,Q#29 - >seq28,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs1_chimp,marg,CompleteHit
322,Q#29 - >seq28,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
323,Q#29 - >seq28,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
324,Q#29 - >seq28,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
325,Q#29 - >seq28,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
326,Q#29 - >seq28,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
327,Q#29 - >seq28,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
328,Q#29 - >seq28,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
329,Q#29 - >seq28,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
330,Q#29 - >seq28,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
331,Q#29 - >seq28,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
332,Q#29 - >seq28,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
333,Q#29 - >seq28,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
334,Q#29 - >seq28,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
335,Q#29 - >seq28,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
336,Q#29 - >seq28,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
337,Q#29 - >seq28,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,marg,N-TerminusTruncated
338,Q#29 - >seq28,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,marg,N-TerminusTruncated
339,Q#29 - >seq28,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1HS,ORF1,hs1_chimp,marg,N-TerminusTruncated
340,Q#29 - >seq28,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
341,Q#29 - >seq28,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
342,Q#29 - >seq28,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1HS,ORF1,hs1_chimp,marg,C-TerminusTruncated
343,Q#29 - >seq28,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
344,Q#29 - >seq28,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
345,Q#29 - >seq28,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
346,Q#29 - >seq28,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
347,Q#29 - >seq28,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs1_chimp.marg.frame3,1909122130_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs1_chimp,marg,BothTerminiTruncated
348,Q#33 - >seq32,specific,238827,510,772,4.24841e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
349,Q#33 - >seq32,superfamily,295487,510,772,4.24841e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
350,Q#33 - >seq32,specific,197310,9,236,1.2619999999999997e-64,218.76,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
351,Q#33 - >seq32,superfamily,351117,9,236,1.2619999999999997e-64,218.76,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
352,Q#33 - >seq32,non-specific,197306,9,236,1.2320499999999998e-55,193.082,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
353,Q#33 - >seq32,specific,333820,516,772,2.8072599999999996e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
354,Q#33 - >seq32,superfamily,333820,516,772,2.8072599999999996e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
355,Q#33 - >seq32,non-specific,197307,9,236,7.571699999999999e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
356,Q#33 - >seq32,non-specific,223780,9,238,2.3027200000000002e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
357,Q#33 - >seq32,non-specific,197320,8,236,2.4124e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
358,Q#33 - >seq32,non-specific,197321,7,236,2.32723e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
359,Q#33 - >seq32,specific,335306,10,229,1.57365e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
360,Q#33 - >seq32,non-specific,273186,9,237,9.226579999999999e-18,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
361,Q#33 - >seq32,non-specific,272954,9,236,2.73693e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
362,Q#33 - >seq32,non-specific,197319,8,236,6.095359999999999e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
363,Q#33 - >seq32,non-specific,197336,7,235,1.40558e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
364,Q#33 - >seq32,non-specific,238828,516,737,2.13293e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
365,Q#33 - >seq32,non-specific,197322,9,236,2.5296400000000006e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
366,Q#33 - >seq32,non-specific,236970,9,238,2.8562099999999995e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
367,Q#33 - >seq32,non-specific,275209,467,800,1.94463e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
368,Q#33 - >seq32,superfamily,275209,467,800,1.94463e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
369,Q#33 - >seq32,non-specific,339261,108,232,1.68512e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
370,Q#33 - >seq32,non-specific,197317,139,229,7.38615e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,marg,N-TerminusTruncated
371,Q#33 - >seq32,non-specific,197311,7,236,2.76503e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
372,Q#33 - >seq32,non-specific,238185,656,772,0.000139863,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
373,Q#33 - >seq32,non-specific,274009,305,453,0.00035013199999999996,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,marg,C-TerminusTruncated
374,Q#33 - >seq32,superfamily,274009,305,453,0.00035013199999999996,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,marg,C-TerminusTruncated
375,Q#33 - >seq32,non-specific,226098,138,239,0.0005172019999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,marg,N-TerminusTruncated
376,Q#33 - >seq32,non-specific,197314,7,236,0.00246255,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
377,Q#33 - >seq32,non-specific,239569,525,748,0.00352502,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,marg,CompleteHit
378,Q#33 - >seq32,non-specific,235175,301,469,0.00784832,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,marg,BothTerminiTruncated
379,Q#33 - >seq32,superfamily,235175,301,469,0.00784832,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,marg,BothTerminiTruncated
380,Q#35 - >seq34,non-specific,335182,154,251,2.73001e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
381,Q#35 - >seq34,superfamily,335182,154,251,2.73001e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
382,Q#35 - >seq34,non-specific,340205,254,318,9.65213e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
383,Q#35 - >seq34,superfamily,340205,254,318,9.65213e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
384,Q#35 - >seq34,specific,340204,109,151,1.1832e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
385,Q#35 - >seq34,superfamily,340204,109,151,1.1832e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1HS,ORF1,hs2_gorilla,pars,CompleteHit
386,Q#35 - >seq34,non-specific,337663,48,139,0.00157217,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
387,Q#35 - >seq34,superfamily,337663,48,139,0.00157217,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
388,Q#35 - >seq34,non-specific,335623,66,146,0.00173701,39.465,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
389,Q#35 - >seq34,superfamily,335623,66,146,0.00173701,39.465,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
390,Q#35 - >seq34,non-specific,235175,52,140,0.00206345,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
391,Q#35 - >seq34,superfamily,235175,52,140,0.00206345,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
392,Q#35 - >seq34,non-specific,274008,39,209,0.00276658,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
393,Q#35 - >seq34,superfamily,274008,39,209,0.00276658,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
394,Q#35 - >seq34,non-specific,316375,53,136,0.00666166,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
395,Q#35 - >seq34,superfamily,316375,53,136,0.00666166,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
396,Q#35 - >seq34,non-specific,335556,47,130,0.00804698,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
397,Q#35 - >seq34,superfamily,335556,47,130,0.00804698,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF1,hs2_gorilla,pars,BothTerminiTruncated
398,Q#35 - >seq34,non-specific,273690,53,194,0.0086014,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
399,Q#35 - >seq34,superfamily,355611,53,194,0.0086014,37.3253,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1HS.ORF1.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1HS,ORF1,hs2_gorilla,pars,C-TerminusTruncated
400,Q#36 - >seq35,specific,238827,510,772,1.4747399999999997e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
401,Q#36 - >seq35,superfamily,295487,510,772,1.4747399999999997e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
402,Q#36 - >seq35,specific,197310,9,236,3.525599999999999e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
403,Q#36 - >seq35,superfamily,351117,9,236,3.525599999999999e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
404,Q#36 - >seq35,non-specific,197306,9,236,8.30303e-56,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
405,Q#36 - >seq35,specific,333820,516,772,1.5339799999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
406,Q#36 - >seq35,superfamily,333820,516,772,1.5339799999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
407,Q#36 - >seq35,non-specific,197307,9,236,2.15392e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
408,Q#36 - >seq35,non-specific,223780,9,238,5.75328e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
409,Q#36 - >seq35,non-specific,197320,8,236,7.87246e-23,98.7413,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
410,Q#36 - >seq35,non-specific,197321,7,236,5.51318e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
411,Q#36 - >seq35,specific,335306,10,229,1.36121e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
412,Q#36 - >seq35,non-specific,273186,9,237,3.33219e-18,85.4084,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
413,Q#36 - >seq35,non-specific,272954,9,236,1.1098399999999999e-16,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
414,Q#36 - >seq35,non-specific,197319,8,236,1.59673e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
415,Q#36 - >seq35,non-specific,197336,7,235,9.42374e-13,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
416,Q#36 - >seq35,non-specific,238828,516,737,1.23233e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
417,Q#36 - >seq35,non-specific,236970,9,238,1.8509999999999999e-10,62.6042,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
418,Q#36 - >seq35,non-specific,197322,9,236,2.1734900000000002e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
419,Q#36 - >seq35,non-specific,275209,467,800,6.545509999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
420,Q#36 - >seq35,superfamily,275209,467,800,6.545509999999999e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
421,Q#36 - >seq35,non-specific,339261,108,232,1.6579e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
422,Q#36 - >seq35,non-specific,197317,139,229,5.66918e-08,54.9156,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,pars,N-TerminusTruncated
423,Q#36 - >seq35,non-specific,197311,7,236,1.71476e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
424,Q#36 - >seq35,non-specific,238185,656,772,8.81306e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
425,Q#36 - >seq35,non-specific,274009,305,453,0.00042360699999999994,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,pars,C-TerminusTruncated
426,Q#36 - >seq35,superfamily,274009,305,453,0.00042360699999999994,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,pars,C-TerminusTruncated
427,Q#36 - >seq35,non-specific,226098,138,239,0.00044866,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs2_gorilla,pars,N-TerminusTruncated
428,Q#36 - >seq35,non-specific,197314,7,236,0.0020635000000000002,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
429,Q#36 - >seq35,non-specific,239569,525,748,0.00290383,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs2_gorilla,pars,CompleteHit
430,Q#36 - >seq35,non-specific,235175,301,469,0.00639873,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,pars,BothTerminiTruncated
431,Q#36 - >seq35,superfamily,235175,301,469,0.00639873,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs2_gorilla.pars.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs2_gorilla,pars,BothTerminiTruncated
432,Q#38 - >seq37,non-specific,130141,277,387,0.00830271,39.8029,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs2_gorilla.marg.frame1,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1HS,ORF2,hs2_gorilla,marg,N-TerminusTruncated
433,Q#38 - >seq37,superfamily,130141,277,387,0.00830271,39.8029,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs2_gorilla.marg.frame1,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1HS,ORF2,hs2_gorilla,marg,N-TerminusTruncated
434,Q#39 - >seq38,non-specific,130141,277,387,0.00900369,39.8029,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs2_gorilla.pars.frame1,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1HS,ORF2,hs2_gorilla,pars,N-TerminusTruncated
435,Q#39 - >seq38,superfamily,130141,277,387,0.00900369,39.8029,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs2_gorilla.pars.frame1,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1HS,ORF2,hs2_gorilla,pars,N-TerminusTruncated
436,Q#40 - >seq39,non-specific,335182,154,251,2.73001e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
437,Q#40 - >seq39,superfamily,335182,154,251,2.73001e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
438,Q#40 - >seq39,non-specific,340205,254,318,9.65213e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
439,Q#40 - >seq39,superfamily,340205,254,318,9.65213e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
440,Q#40 - >seq39,specific,340204,109,151,1.1832e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
441,Q#40 - >seq39,superfamily,340204,109,151,1.1832e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1HS,ORF1,hs2_gorilla,marg,CompleteHit
442,Q#40 - >seq39,non-specific,337663,48,139,0.00157217,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
443,Q#40 - >seq39,superfamily,337663,48,139,0.00157217,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
444,Q#40 - >seq39,non-specific,335623,66,146,0.00173701,39.465,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
445,Q#40 - >seq39,superfamily,335623,66,146,0.00173701,39.465,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
446,Q#40 - >seq39,non-specific,235175,52,140,0.00206345,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
447,Q#40 - >seq39,superfamily,235175,52,140,0.00206345,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
448,Q#40 - >seq39,non-specific,274008,39,209,0.00276658,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
449,Q#40 - >seq39,superfamily,274008,39,209,0.00276658,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
450,Q#40 - >seq39,non-specific,316375,53,136,0.00666166,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
451,Q#40 - >seq39,superfamily,316375,53,136,0.00666166,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_GAS,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
452,Q#40 - >seq39,non-specific,335556,47,130,0.00804698,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
453,Q#40 - >seq39,superfamily,335556,47,130,0.00804698,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF1,hs2_gorilla,marg,BothTerminiTruncated
454,Q#40 - >seq39,non-specific,273690,53,194,0.0086014,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
455,Q#40 - >seq39,superfamily,355611,53,194,0.0086014,37.3253,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1HS.ORF1.hs2_gorilla.marg.frame3,1909122130_L1HS.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1HS,ORF1,hs2_gorilla,marg,C-TerminusTruncated
456,Q#46 - >seq45,non-specific,335182,65,161,3.70204e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
457,Q#46 - >seq45,superfamily,335182,65,161,3.70204e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
458,Q#46 - >seq45,non-specific,335182,65,161,3.70204e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
459,Q#46 - >seq45,non-specific,340205,165,227,3.4452699999999997e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
460,Q#46 - >seq45,superfamily,340205,165,227,3.4452699999999997e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
461,Q#46 - >seq45,non-specific,340205,165,227,3.4452699999999997e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.pars.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,pars,CompleteHit
462,Q#48 - >seq47,non-specific,335182,65,161,3.70204e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
463,Q#48 - >seq47,superfamily,335182,65,161,3.70204e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
464,Q#48 - >seq47,non-specific,335182,65,161,3.70204e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
465,Q#48 - >seq47,non-specific,340205,165,227,3.4452699999999997e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
466,Q#48 - >seq47,superfamily,340205,165,227,3.4452699999999997e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
467,Q#48 - >seq47,non-specific,340205,165,227,3.4452699999999997e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs2_gorilla.marg.frame3,1909122131_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs2_gorilla,marg,CompleteHit
468,Q#49 - >seq48,non-specific,335182,66,162,1.8202099999999998e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
469,Q#49 - >seq48,superfamily,335182,66,162,1.8202099999999998e-28,103.15100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
470,Q#49 - >seq48,non-specific,335182,66,162,1.8202099999999998e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
471,Q#49 - >seq48,non-specific,340205,166,228,3.53036e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
472,Q#49 - >seq48,superfamily,340205,166,228,3.53036e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
473,Q#49 - >seq48,non-specific,340205,166,228,3.53036e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.marg.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,marg,CompleteHit
474,Q#51 - >seq50,non-specific,335182,66,162,1.8202099999999998e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
475,Q#51 - >seq50,superfamily,335182,66,162,1.8202099999999998e-28,103.15100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
476,Q#51 - >seq50,non-specific,335182,66,162,1.8202099999999998e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
477,Q#51 - >seq50,non-specific,340205,166,228,3.53036e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
478,Q#51 - >seq50,superfamily,340205,166,228,3.53036e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
479,Q#51 - >seq50,non-specific,340205,166,228,3.53036e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs1_chimp.pars.frame3,1909122131_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs1_chimp,pars,CompleteHit
480,Q#56 - >seq55,non-specific,335182,66,162,8.41915e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs6_sqmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,marg,CompleteHit
481,Q#56 - >seq55,superfamily,335182,66,162,8.41915e-27,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs6_sqmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,marg,CompleteHit
482,Q#56 - >seq55,non-specific,340205,166,228,2.5353400000000002e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs6_sqmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,marg,CompleteHit
483,Q#56 - >seq55,superfamily,340205,166,228,2.5353400000000002e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs6_sqmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,marg,CompleteHit
484,Q#59 - >seq58,non-specific,335182,65,161,6.53669e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
485,Q#59 - >seq58,superfamily,335182,65,161,6.53669e-27,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
486,Q#59 - >seq58,non-specific,335182,65,161,6.53669e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
487,Q#59 - >seq58,non-specific,340205,165,227,1.37077e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
488,Q#59 - >seq58,superfamily,340205,165,227,1.37077e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
489,Q#59 - >seq58,non-specific,340205,165,227,1.37077e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.pars.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,pars,CompleteHit
490,Q#62 - >seq61,non-specific,335182,65,161,6.53669e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
491,Q#62 - >seq61,superfamily,335182,65,161,6.53669e-27,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
492,Q#62 - >seq61,non-specific,335182,65,161,6.53669e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
493,Q#62 - >seq61,non-specific,340205,165,227,1.37077e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
494,Q#62 - >seq61,superfamily,340205,165,227,1.37077e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
495,Q#62 - >seq61,non-specific,340205,165,227,1.37077e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs0_human.marg.frame3,1909122132_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs0_human,marg,CompleteHit
496,Q#63 - >seq62,non-specific,340205,242,293,1.1334799999999997e-16,72.75399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs1_chimp,pars,CompleteHit
497,Q#63 - >seq62,superfamily,340205,242,293,1.1334799999999997e-16,72.75399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs1_chimp,pars,CompleteHit
498,Q#64 - >seq63,non-specific,335182,162,241,3.1300400000000003e-21,86.2026,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs1_chimp,pars,CompleteHit
499,Q#64 - >seq63,superfamily,335182,162,241,3.1300400000000003e-21,86.2026,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs1_chimp,pars,CompleteHit
500,Q#67 - >seq66,non-specific,335182,157,243,3.08304e-20,83.8915,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs1_chimp,marg,CompleteHit
501,Q#67 - >seq66,superfamily,335182,157,243,3.08304e-20,83.8915,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs1_chimp,marg,CompleteHit
502,Q#67 - >seq66,non-specific,340205,246,309,3.08382e-19,80.0728,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs1_chimp,marg,CompleteHit
503,Q#67 - >seq66,superfamily,340205,246,309,3.08382e-19,80.0728,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs1_chimp,marg,CompleteHit
504,Q#68 - >seq67,non-specific,238827,458,697,4.30947e-24,101.214,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a1,ORF2,hs1_chimp,pars,CompleteHit
505,Q#68 - >seq67,superfamily,295487,458,697,4.30947e-24,101.214,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a1,ORF2,hs1_chimp,pars,CompleteHit
506,Q#68 - >seq67,non-specific,333820,573,674,1.3811500000000002e-10,61.1542,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a1,ORF2,hs1_chimp,pars,N-TerminusTruncated
507,Q#68 - >seq67,superfamily,333820,573,674,1.3811500000000002e-10,61.1542,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a1,ORF2,hs1_chimp,pars,N-TerminusTruncated
508,Q#68 - >seq67,non-specific,238828,550,674,0.000219007,43.3437,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a1.ORF2.hs1_chimp.pars.frame1,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a1,ORF2,hs1_chimp,pars,N-TerminusTruncated
509,Q#69 - >seq68,non-specific,197310,86,144,2.32881e-08,55.4353,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2a1,ORF2,hs1_chimp,pars,BothTerminiTruncated
510,Q#69 - >seq68,superfamily,351117,86,144,2.32881e-08,55.4353,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,BothTerminiTruncated
511,Q#69 - >seq68,non-specific,197306,86,144,0.000475793,42.4685,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,BothTerminiTruncated
512,Q#69 - >seq68,non-specific,197320,97,144,0.00745538,39.0354,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs1_chimp.pars.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,BothTerminiTruncated
513,Q#70 - >seq69,non-specific,197310,7,201,1.76692e-18,85.4809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs1_chimp,pars,CompleteHit
514,Q#70 - >seq69,superfamily,351117,7,201,1.76692e-18,85.4809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,CompleteHit
515,Q#70 - >seq69,non-specific,238827,494,567,5.78026e-11,63.07899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
516,Q#70 - >seq69,superfamily,295487,494,567,5.78026e-11,63.07899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
517,Q#70 - >seq69,specific,335306,8,128,8.265139999999999e-07,50.7066,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
518,Q#70 - >seq69,non-specific,197306,7,76,2.4707900000000003e-06,49.4021,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
519,Q#70 - >seq69,non-specific,197321,5,45,0.000137704,44.08,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
520,Q#70 - >seq69,non-specific,273186,7,72,0.000166565,44.192,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
521,Q#70 - >seq69,non-specific,223780,7,78,0.00021409400000000001,43.7411,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
522,Q#70 - >seq69,non-specific,197307,7,76,0.00373119,39.9637,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
523,Q#70 - >seq69,non-specific,272954,7,72,0.00946952,38.5181,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs1_chimp.pars.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs1_chimp,pars,C-TerminusTruncated
524,Q#72 - >seq71,specific,197310,23,222,9.641529999999999e-32,124.001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a1,ORF2,hs1_chimp,marg,CompleteHit
525,Q#72 - >seq71,superfamily,351117,23,222,9.641529999999999e-32,124.001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,CompleteHit
526,Q#72 - >seq71,non-specific,197306,20,198,2.38999e-15,76.7512,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,CompleteHit
527,Q#72 - >seq71,non-specific,197320,26,198,3.89048e-09,58.2954,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,C-TerminusTruncated
528,Q#72 - >seq71,specific,335306,26,205,7.91692e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,CompleteHit
529,Q#72 - >seq71,non-specific,197307,34,198,2.39982e-07,53.0605,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,C-TerminusTruncated
530,Q#72 - >seq71,non-specific,223780,26,198,4.987699999999999e-07,52.2155,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2a1,ORF2,hs1_chimp,marg,C-TerminusTruncated
531,Q#72 - >seq71,non-specific,272954,29,200,6.921189999999999e-06,48.5333,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a1,ORF2,hs1_chimp,marg,C-TerminusTruncated
532,Q#72 - >seq71,non-specific,273186,29,198,0.000855109,42.266000000000005,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a1,ORF2,hs1_chimp,marg,C-TerminusTruncated
533,Q#72 - >seq71,non-specific,235175,299,456,0.0009945569999999999,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M2a1,ORF2,hs1_chimp,marg,BothTerminiTruncated
534,Q#72 - >seq71,superfamily,235175,299,456,0.0009945569999999999,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M2a1,ORF2,hs1_chimp,marg,BothTerminiTruncated
535,Q#72 - >seq71,non-specific,235175,233,466,0.00126134,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M2a1,ORF2,hs1_chimp,marg,BothTerminiTruncated
536,Q#72 - >seq71,non-specific,197311,40,211,0.00855201,38.8121,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a1,ORF2,hs1_chimp,marg,CompleteHit
537,Q#72 - >seq71,non-specific,227608,211,422,0.00918795,39.9107,COG5283,COG5283,N,cl34972,"Phage-related tail protein  [Mobilome: prophages, transposons]; Phage-related tail protein [Function unknown].",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
538,Q#72 - >seq71,superfamily,227608,211,422,0.00918795,39.9107,cl34972,COG5283 superfamily,N, - ,"Phage-related tail protein  [Mobilome: prophages, transposons]; Phage-related tail protein [Function unknown].",L1M2a1.ORF2.hs1_chimp.marg.frame2,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
539,Q#73 - >seq72,non-specific,238827,556,729,1.07769e-21,94.6654,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
540,Q#73 - >seq72,superfamily,295487,556,729,1.07769e-21,94.6654,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
541,Q#73 - >seq72,non-specific,333820,572,711,1.6429000000000003e-11,64.2358,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
542,Q#73 - >seq72,superfamily,333820,572,711,1.6429000000000003e-11,64.2358,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
543,Q#73 - >seq72,non-specific,238828,530,711,7.85849e-07,51.0476,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a1.ORF2.hs1_chimp.marg.frame3,1909122132_L1M2a1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs1_chimp,marg,N-TerminusTruncated
544,Q#76 - >seq75,non-specific,335182,65,161,8.128949999999999e-27,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs6_sqmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,pars,CompleteHit
545,Q#76 - >seq75,superfamily,335182,65,161,8.128949999999999e-27,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs6_sqmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,pars,CompleteHit
546,Q#76 - >seq75,non-specific,340205,165,227,2.5064900000000001e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs6_sqmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,pars,CompleteHit
547,Q#76 - >seq75,superfamily,340205,165,227,2.5064900000000001e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs6_sqmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs6_sqmonkey,pars,CompleteHit
548,Q#77 - >seq76,non-specific,335182,66,162,5.79051e-27,99.6846,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,pars,CompleteHit
549,Q#77 - >seq76,superfamily,335182,66,162,5.79051e-27,99.6846,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,pars,CompleteHit
550,Q#77 - >seq76,non-specific,340205,166,228,1.8422299999999998e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,pars,CompleteHit
551,Q#77 - >seq76,superfamily,340205,166,228,1.8422299999999998e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,pars,CompleteHit
552,Q#77 - >seq76,non-specific,224117,1,109,0.00778341,37.0012,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
553,Q#77 - >seq76,superfamily,224117,1,109,0.00778341,37.0012,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M1.ORF1.hs5_gmonkey.pars.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1M1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
554,Q#82 - >seq81,non-specific,335182,66,162,4.16237e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
555,Q#82 - >seq81,superfamily,335182,66,162,4.16237e-28,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
556,Q#82 - >seq81,non-specific,335182,66,162,4.16237e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
557,Q#82 - >seq81,non-specific,340205,166,228,1.64302e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
558,Q#82 - >seq81,superfamily,340205,166,228,1.64302e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
559,Q#82 - >seq81,non-specific,340205,166,228,1.64302e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.pars.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,pars,CompleteHit
560,Q#84 - >seq83,non-specific,335182,66,162,4.16237e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
561,Q#84 - >seq83,superfamily,335182,66,162,4.16237e-28,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
562,Q#84 - >seq83,non-specific,335182,66,162,4.16237e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
563,Q#84 - >seq83,non-specific,340205,166,228,1.64302e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
564,Q#84 - >seq83,superfamily,340205,166,228,1.64302e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
565,Q#84 - >seq83,non-specific,340205,166,228,1.64302e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs3_orang.marg.frame3,1909122132_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs3_orang,marg,CompleteHit
566,Q#87 - >seq86,non-specific,335182,65,161,1.74973e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs4_gibbon.pars.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,pars,CompleteHit
567,Q#87 - >seq86,superfamily,335182,65,161,1.74973e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs4_gibbon.pars.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,pars,CompleteHit
568,Q#87 - >seq86,non-specific,340205,165,227,1.7406600000000002e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs4_gibbon.pars.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,pars,CompleteHit
569,Q#87 - >seq86,superfamily,340205,165,227,1.7406600000000002e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs4_gibbon.pars.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,pars,CompleteHit
570,Q#90 - >seq89,non-specific,335182,65,161,2.98706e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs4_gibbon.marg.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,marg,CompleteHit
571,Q#90 - >seq89,superfamily,335182,65,161,2.98706e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs4_gibbon.marg.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,marg,CompleteHit
572,Q#90 - >seq89,non-specific,340205,165,227,2.07415e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs4_gibbon.marg.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,marg,CompleteHit
573,Q#90 - >seq89,superfamily,340205,165,227,2.07415e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs4_gibbon.marg.frame3,1909122132_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs4_gibbon,marg,CompleteHit
574,Q#95 - >seq94,non-specific,335182,66,162,5.79051e-27,99.6846,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,marg,CompleteHit
575,Q#95 - >seq94,superfamily,335182,66,162,5.79051e-27,99.6846,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,marg,CompleteHit
576,Q#95 - >seq94,non-specific,340205,166,228,1.8422299999999998e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,marg,CompleteHit
577,Q#95 - >seq94,superfamily,340205,166,228,1.8422299999999998e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M1,ORF1,hs5_gmonkey,marg,CompleteHit
578,Q#95 - >seq94,non-specific,224117,1,109,0.00778341,37.0012,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
579,Q#95 - >seq94,superfamily,224117,1,109,0.00778341,37.0012,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M1.ORF1.hs5_gmonkey.marg.frame3,1909122132_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1M1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
580,Q#97 - >seq96,non-specific,335182,77,157,8.692210000000001e-26,96.603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,marg,CompleteHit
581,Q#97 - >seq96,superfamily,335182,77,157,8.692210000000001e-26,96.603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,marg,CompleteHit
582,Q#97 - >seq96,non-specific,340205,160,222,1.3573500000000001e-18,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,marg,CompleteHit
583,Q#97 - >seq96,superfamily,340205,160,222,1.3573500000000001e-18,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,marg,CompleteHit
584,Q#100 - >seq99,non-specific,197310,86,223,5.14615e-11,60.8281,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs3_orang,pars,N-TerminusTruncated
585,Q#100 - >seq99,superfamily,351117,86,223,5.14615e-11,60.8281,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs3_orang,pars,N-TerminusTruncated
586,Q#100 - >seq99,non-specific,197306,72,198,0.00112131,39.0017,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs3_orang,pars,N-TerminusTruncated
587,Q#101 - >seq100,non-specific,238827,531,778,2.48274e-13,70.0126,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
588,Q#101 - >seq100,superfamily,295487,531,778,2.48274e-13,70.0126,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
589,Q#101 - >seq100,non-specific,197310,41,242,3.58355e-07,51.9685,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
590,Q#101 - >seq100,superfamily,351117,41,242,3.58355e-07,51.9685,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
591,Q#101 - >seq100,non-specific,224117,230,473,4.40254e-05,47.4016,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
592,Q#101 - >seq100,superfamily,224117,230,473,4.40254e-05,47.4016,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
593,Q#101 - >seq100,non-specific,333820,532,755,0.000895533,41.1238,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
594,Q#101 - >seq100,superfamily,333820,532,755,0.000895533,41.1238,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs3_orang.marg.frame1,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs3_orang,marg,CompleteHit
595,Q#104 - >seq103,non-specific,335182,158,238,1.53249e-23,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
596,Q#104 - >seq103,superfamily,335182,158,238,1.53249e-23,92.3658,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
597,Q#104 - >seq103,non-specific,340205,241,303,1.00278e-18,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
598,Q#104 - >seq103,superfamily,340205,241,303,1.00278e-18,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
599,Q#104 - >seq103,non-specific,340204,96,133,0.000354647,37.3872,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
600,Q#104 - >seq103,superfamily,340204,96,133,0.000354647,37.3872,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M2a1.ORF1.hs4_gibbon.pars.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1M2a1,ORF1,hs4_gibbon,pars,CompleteHit
601,Q#106 - >seq105,non-specific,335182,179,259,8.362649999999999e-23,90.825,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs4_gibbon.marg.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,marg,CompleteHit
602,Q#106 - >seq105,superfamily,335182,179,259,8.362649999999999e-23,90.825,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs4_gibbon.marg.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,marg,CompleteHit
603,Q#106 - >seq105,non-specific,340205,262,324,2.7565e-18,77.7616,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs4_gibbon.marg.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,marg,CompleteHit
604,Q#106 - >seq105,superfamily,340205,262,324,2.7565e-18,77.7616,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs4_gibbon.marg.frame1,1909122133_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs4_gibbon,marg,CompleteHit
605,Q#110 - >seq109,non-specific,227709,384,611,0.000952406,42.9559,COG5422,ROM1,C,cl34999,"RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].",L1M2a1.ORF2.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
606,Q#110 - >seq109,superfamily,227709,384,611,0.000952406,42.9559,cl34999,ROM1 superfamily,C, - ,"RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].",L1M2a1.ORF2.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
607,Q#110 - >seq109,non-specific,236304,305,583,0.00720468,39.7711,PRK08581,PRK08581,C,cl35718,N-acetylmuramoyl-L-alanine amidase; Validated,L1M2a1.ORF2.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
608,Q#110 - >seq109,superfamily,236304,305,583,0.00720468,39.7711,cl35718,PRK08581 superfamily,C, - ,N-acetylmuramoyl-L-alanine amidase; Validated,L1M2a1.ORF2.hs3_orang.marg.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs3_orang,marg,C-TerminusTruncated
609,Q#112 - >seq111,non-specific,197310,10,203,2.73708e-21,93.5701,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a1,ORF2,hs2_gorilla,marg,CompleteHit
610,Q#112 - >seq111,superfamily,351117,10,203,2.73708e-21,93.5701,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs2_gorilla,marg,CompleteHit
611,Q#112 - >seq111,non-specific,238827,524,798,1.27654e-14,73.8646,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs2_gorilla,marg,CompleteHit
612,Q#112 - >seq111,superfamily,295487,524,798,1.27654e-14,73.8646,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs2_gorilla,marg,CompleteHit
613,Q#112 - >seq111,non-specific,197306,10,214,1.96518e-05,46.7057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs2_gorilla,marg,CompleteHit
614,Q#112 - >seq111,non-specific,333820,623,757,0.0006690239999999999,41.50899999999999,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
615,Q#112 - >seq111,superfamily,333820,623,757,0.0006690239999999999,41.50899999999999,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
616,Q#112 - >seq111,non-specific,225240,231,389,0.00696829,38.9648,COG2365,Oca4,N,cl25999,Protein tyrosine/serine phosphatase  [Signal transduction mechanisms]; Protein tyrosine/serine phosphatase [Signal transduction mechanisms].,L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
617,Q#112 - >seq111,superfamily,225240,231,389,0.00696829,38.9648,cl25999,Oca4 superfamily,N, - ,Protein tyrosine/serine phosphatase  [Signal transduction mechanisms]; Protein tyrosine/serine phosphatase [Signal transduction mechanisms].,L1M2a1.ORF2.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
618,Q#114 - >seq113,non-specific,335182,67,147,3.76304e-26,97.3734,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,pars,CompleteHit
619,Q#114 - >seq113,superfamily,335182,67,147,3.76304e-26,97.3734,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,pars,CompleteHit
620,Q#114 - >seq113,non-specific,340205,150,212,1.11435e-18,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,pars,CompleteHit
621,Q#114 - >seq113,superfamily,340205,150,212,1.11435e-18,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs3_orang.pars.frame3,1909122133_L1M2a1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs3_orang,pars,CompleteHit
622,Q#115 - >seq114,non-specific,340205,142,204,9.3049e-21,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs2_gorilla,pars,CompleteHit
623,Q#115 - >seq114,superfamily,340205,142,204,9.3049e-21,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs2_gorilla,pars,CompleteHit
624,Q#115 - >seq114,non-specific,335182,57,139,1.05865e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs2_gorilla,pars,CompleteHit
625,Q#115 - >seq114,superfamily,335182,57,139,1.05865e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a1,ORF1,hs2_gorilla,pars,CompleteHit
626,Q#117 - >seq116,non-specific,335182,175,257,4.0512e-20,83.5063,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs2_gorilla,marg,CompleteHit
627,Q#117 - >seq116,superfamily,335182,175,257,4.0512e-20,83.5063,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs2_gorilla,marg,CompleteHit
628,Q#117 - >seq116,non-specific,340205,260,322,4.80761e-20,82.384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs2_gorilla,marg,CompleteHit
629,Q#117 - >seq116,superfamily,340205,260,322,4.80761e-20,82.384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs2_gorilla.marg.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs2_gorilla,marg,CompleteHit
630,Q#121 - >seq120,non-specific,238827,485,545,0.00359602,39.1966,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
631,Q#121 - >seq120,superfamily,295487,485,545,0.00359602,39.1966,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs2_gorilla.pars.frame2,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
632,Q#122 - >seq121,non-specific,197310,8,192,5.6808199999999996e-24,100.889,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs2_gorilla,pars,CompleteHit
633,Q#122 - >seq121,superfamily,351117,8,192,5.6808199999999996e-24,100.889,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs2_gorilla,pars,CompleteHit
634,Q#122 - >seq121,non-specific,197306,8,203,2.7137099999999997e-10,60.9581,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs2_gorilla,pars,CompleteHit
635,Q#122 - >seq121,non-specific,223780,8,191,0.000202198,43.3559,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
636,Q#122 - >seq121,non-specific,238827,618,679,0.00221982,39.967,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
637,Q#122 - >seq121,superfamily,295487,618,679,0.00221982,39.967,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
638,Q#122 - >seq121,specific,335306,9,203,0.00504582,39.1506,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs2_gorilla,pars,CompleteHit
639,Q#122 - >seq121,non-specific,197307,8,191,0.00563204,39.1933,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs2_gorilla.pars.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a1,ORF2,hs2_gorilla,pars,CompleteHit
640,Q#124 - >seq123,non-specific,339523,201,424,0.0005417859999999999,43.3295,pfam15712,NPAT_C,NC,cl25855,NPAT C-terminus; NPAT C-terminus.  ,L1M2a1.ORF2.hs2_gorilla.marg.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
641,Q#124 - >seq123,superfamily,339523,201,424,0.0005417859999999999,43.3295,cl25855,NPAT_C superfamily,NC, - ,NPAT C-terminus; NPAT C-terminus.  ,L1M2a1.ORF2.hs2_gorilla.marg.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
642,Q#124 - >seq123,non-specific,313469,296,441,0.00385893,40.614000000000004,pfam10243,MIP-T3,NC,cl25761,"Microtubule-binding protein MIP-T3; This protein, which interacts with both microtubules and TRAF3 (tumor necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.",L1M2a1.ORF2.hs2_gorilla.marg.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
643,Q#124 - >seq123,superfamily,313469,296,441,0.00385893,40.614000000000004,cl25761,MIP-T3 superfamily,NC, - ,"Microtubule-binding protein MIP-T3; This protein, which interacts with both microtubules and TRAF3 (tumor necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.",L1M2a1.ORF2.hs2_gorilla.marg.frame3,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
644,Q#126 - >seq125,non-specific,315458,300,388,0.00276854,39.9288,pfam12787,EcsC,C,cl15090,EcsC protein family; Proteins in this family are related to EcsC from B. subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system. The function of this protein is unknown.,L1M2a1.ORF2.hs2_gorilla.pars.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
645,Q#126 - >seq125,superfamily,315458,300,388,0.00276854,39.9288,cl15090,EcsC superfamily,C, - ,EcsC protein family; Proteins in this family are related to EcsC from B. subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system. The function of this protein is unknown.,L1M2a1.ORF2.hs2_gorilla.pars.frame1,1909122133_L1M2a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
646,Q#127 - >seq126,non-specific,238827,617,735,2.2174400000000003e-24,101.984,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
647,Q#127 - >seq126,superfamily,295487,617,735,2.2174400000000003e-24,101.984,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
648,Q#127 - >seq126,non-specific,333820,599,702,2.6198299999999998e-12,66.1618,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
649,Q#127 - >seq126,superfamily,333820,599,702,2.6198299999999998e-12,66.1618,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
650,Q#127 - >seq126,non-specific,197310,7,224,7.84881e-09,56.9761,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a1,ORF2,hs0_human,pars,CompleteHit
651,Q#127 - >seq126,superfamily,351117,7,224,7.84881e-09,56.9761,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,pars,CompleteHit
652,Q#127 - >seq126,non-specific,238828,578,702,8.54083e-06,47.9661,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
653,Q#127 - >seq126,specific,335306,8,217,0.00010858200000000001,44.5434,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,pars,CompleteHit
654,Q#127 - >seq126,non-specific,129694,286,461,0.00309077,41.1857,TIGR00606,rad50,NC,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M2a1,ORF2,hs0_human,pars,BothTerminiTruncated
655,Q#127 - >seq126,superfamily,129694,286,461,0.00309077,41.1857,cl31018,rad50 superfamily,NC, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M2a1,ORF2,hs0_human,pars,BothTerminiTruncated
656,Q#127 - >seq126,non-specific,238185,618,695,0.00782877,36.56,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a1,ORF2,hs0_human,pars,C-TerminusTruncated
657,Q#127 - >seq126,non-specific,197306,7,224,0.00923581,38.6165,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,pars,CompleteHit
658,Q#129 - >seq128,non-specific,238827,497,554,8.107820000000001e-16,77.3314,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
659,Q#129 - >seq128,superfamily,295487,497,554,8.107820000000001e-16,77.3314,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
660,Q#129 - >seq128,non-specific,333820,503,552,5.74716e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
661,Q#129 - >seq128,superfamily,333820,503,552,5.74716e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
662,Q#130 - >seq129,specific,197310,9,239,1.7445999999999998e-40,149.424,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
663,Q#130 - >seq129,superfamily,351117,9,239,1.7445999999999998e-40,149.424,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
664,Q#130 - >seq129,non-specific,238827,674,782,1.97858e-21,93.895,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs0_human,marg,N-TerminusTruncated
665,Q#130 - >seq129,superfamily,295487,674,782,1.97858e-21,93.895,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs0_human,marg,N-TerminusTruncated
666,Q#130 - >seq129,non-specific,197306,9,239,3.40162e-19,87.92200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
667,Q#130 - >seq129,specific,335306,10,216,1.43955e-12,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
668,Q#130 - >seq129,non-specific,333820,631,760,4.7491999999999994e-11,62.695,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs0_human,marg,N-TerminusTruncated
669,Q#130 - >seq129,superfamily,333820,631,760,4.7491999999999994e-11,62.695,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs0_human,marg,N-TerminusTruncated
670,Q#130 - >seq129,non-specific,223780,9,240,1.9125799999999998e-10,62.6159,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
671,Q#130 - >seq129,non-specific,197320,9,197,8.374969999999999e-10,60.6066,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
672,Q#130 - >seq129,non-specific,197307,9,197,1.91587e-08,56.5273,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a1,ORF2,hs0_human,marg,CompleteHit
673,Q#130 - >seq129,non-specific,272954,9,197,1.3019400000000001e-05,47.7629,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
674,Q#130 - >seq129,non-specific,238828,635,760,2.40773e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a1,ORF2,hs0_human,marg,N-TerminusTruncated
675,Q#130 - >seq129,non-specific,236970,9,197,0.000269031,43.7294,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1M2a1.ORF2.hs0_human.marg.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a1,ORF2,hs0_human,marg,C-TerminusTruncated
676,Q#131 - >seq130,non-specific,340205,242,305,3.34562e-27,100.874,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs1_chimp.marg.frame1,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs1_chimp,marg,CompleteHit
677,Q#131 - >seq130,superfamily,340205,242,305,3.34562e-27,100.874,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs1_chimp.marg.frame1,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs1_chimp,marg,CompleteHit
678,Q#131 - >seq130,non-specific,335182,143,239,4.62408e-13,63.8611,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs1_chimp.marg.frame1,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs1_chimp,marg,CompleteHit
679,Q#131 - >seq130,superfamily,335182,143,239,4.62408e-13,63.8611,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs1_chimp.marg.frame1,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs1_chimp,marg,CompleteHit
680,Q#135 - >seq134,non-specific,238827,491,536,3.7905699999999996e-10,60.7678,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs0_human,pars,C-TerminusTruncated
681,Q#135 - >seq134,superfamily,295487,491,536,3.7905699999999996e-10,60.7678,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs0_human,pars,C-TerminusTruncated
682,Q#135 - >seq134,non-specific,333820,497,534,0.0039413,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs0_human,pars,C-TerminusTruncated
683,Q#135 - >seq134,superfamily,333820,497,534,0.0039413,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a1,ORF2,hs0_human,pars,C-TerminusTruncated
684,Q#137 - >seq136,non-specific,197310,85,183,1.99856e-14,73.5397,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
685,Q#137 - >seq136,superfamily,351117,85,183,1.99856e-14,73.5397,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
686,Q#137 - >seq136,non-specific,197320,91,179,4.62911e-07,51.747,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a1,ORF2,hs0_human,pars,BothTerminiTruncated
687,Q#137 - >seq136,non-specific,197306,85,182,0.00015382700000000002,44.0093,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
688,Q#137 - >seq136,non-specific,223780,91,179,0.00176696,41.0447,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a1,ORF2,hs0_human,pars,BothTerminiTruncated
689,Q#137 - >seq136,non-specific,272954,91,179,0.003836,40.0589,TIGR00195,exoDNase_III,NC,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a1,ORF2,hs0_human,pars,BothTerminiTruncated
690,Q#137 - >seq136,non-specific,197307,87,179,0.00418102,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a1.ORF2.hs0_human.pars.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a1,ORF2,hs0_human,pars,N-TerminusTruncated
691,Q#138 - >seq137,non-specific,340205,159,222,8.31421e-28,100.488,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs1_chimp.pars.frame3,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs1_chimp,pars,CompleteHit
692,Q#138 - >seq137,superfamily,340205,159,222,8.31421e-28,100.488,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs1_chimp.pars.frame3,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs1_chimp,pars,CompleteHit
693,Q#138 - >seq137,non-specific,335182,52,156,8.22201e-15,67.3279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs1_chimp.pars.frame3,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs1_chimp,pars,CompleteHit
694,Q#138 - >seq137,superfamily,335182,52,156,8.22201e-15,67.3279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs1_chimp.pars.frame3,1909122134_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs1_chimp,pars,CompleteHit
695,Q#139 - >seq138,non-specific,340205,258,304,6.57626e-16,70.828,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a1,ORF1,hs0_human,marg,N-TerminusTruncated
696,Q#139 - >seq138,superfamily,340205,258,304,6.57626e-16,70.828,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs0_human.marg.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a1,ORF1,hs0_human,marg,N-TerminusTruncated
697,Q#140 - >seq139,non-specific,197310,31,187,1.6044e-18,80.0881,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs4_gibbon.pars.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a1,ORF2,hs4_gibbon,pars,CompleteHit
698,Q#140 - >seq139,superfamily,351117,31,187,1.6044e-18,80.0881,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs4_gibbon.pars.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs4_gibbon,pars,CompleteHit
699,Q#143 - >seq142,non-specific,238827,527,616,8.6237e-10,59.6122,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
700,Q#143 - >seq142,superfamily,295487,527,616,8.6237e-10,59.6122,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
701,Q#143 - >seq142,non-specific,197310,10,81,1.12615e-06,50.4277,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
702,Q#143 - >seq142,superfamily,351117,10,81,1.12615e-06,50.4277,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
703,Q#143 - >seq142,non-specific,333820,528,573,0.00379211,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
704,Q#143 - >seq142,superfamily,333820,528,573,0.00379211,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a1.ORF2.hs4_gibbon.marg.frame1,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
705,Q#144 - >seq143,non-specific,197310,75,234,8.39658e-13,68.5321,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a1.ORF2.hs4_gibbon.marg.frame2,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
706,Q#144 - >seq143,superfamily,351117,75,234,8.39658e-13,68.5321,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs4_gibbon.marg.frame2,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
707,Q#144 - >seq143,non-specific,197306,82,234,0.00053092,42.4685,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a1.ORF2.hs4_gibbon.marg.frame2,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
708,Q#144 - >seq143,non-specific,238827,621,636,0.00204823,40.3522,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a1.ORF2.hs4_gibbon.marg.frame2,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
709,Q#144 - >seq143,superfamily,295487,621,636,0.00204823,40.3522,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a1.ORF2.hs4_gibbon.marg.frame2,1909122134_L1M2a1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
710,Q#148 - >seq147,non-specific,337033,44,109,0.00196441,39.4845,pfam08385,DHC_N1,NC,cl20356,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1M2a1.ORF1.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a1,ORF1,hs0_human,pars,BothTerminiTruncated
711,Q#148 - >seq147,superfamily,337033,44,109,0.00196441,39.4845,cl20356,DHC_N1 superfamily,NC, - ,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1M2a1.ORF1.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a1,ORF1,hs0_human,pars,BothTerminiTruncated
712,Q#148 - >seq147,specific,214625,17,103,0.00783817,36.9693,smart00332,PP2Cc,NC,cl00120,"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.",L1M2a1.ORF1.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a1,ORF1,hs0_human,pars,BothTerminiTruncated
713,Q#148 - >seq147,superfamily,350908,17,103,0.00783817,36.9693,cl00120,PP2Cc superfamily,NC, - ,"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.",L1M2a1.ORF1.hs0_human.pars.frame2,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a1,ORF1,hs0_human,pars,BothTerminiTruncated
714,Q#149 - >seq148,non-specific,335182,141,223,2.32188e-21,86.2026,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs0_human,pars,CompleteHit
715,Q#149 - >seq148,superfamily,335182,141,223,2.32188e-21,86.2026,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs0_human,pars,CompleteHit
716,Q#149 - >seq148,non-specific,340205,226,287,2.0066099999999997e-20,82.7692,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs0_human,pars,CompleteHit
717,Q#149 - >seq148,superfamily,340205,226,287,2.0066099999999997e-20,82.7692,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a1.ORF1.hs0_human.pars.frame3,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a1,ORF1,hs0_human,pars,CompleteHit
718,Q#150 - >seq149,non-specific,335182,174,250,4.32945e-15,70.0243,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs0_human.marg.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs0_human,marg,CompleteHit
719,Q#150 - >seq149,superfamily,335182,174,250,4.32945e-15,70.0243,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a1.ORF1.hs0_human.marg.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a1,ORF1,hs0_human,marg,CompleteHit
720,Q#150 - >seq149,non-specific,337033,51,135,0.00781038,37.9437,pfam08385,DHC_N1,NC,cl20356,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1M2a1.ORF1.hs0_human.marg.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M2a1,ORF1,hs0_human,marg,BothTerminiTruncated
721,Q#150 - >seq149,superfamily,337033,51,135,0.00781038,37.9437,cl20356,DHC_N1 superfamily,NC, - ,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1M2a1.ORF1.hs0_human.marg.frame1,1909122134_L1M2a1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M2a1,ORF1,hs0_human,marg,BothTerminiTruncated
722,Q#151 - >seq150,non-specific,335023,56,124,0.00314331,38.2357,pfam02646,RmuC,N,cl25857,"RmuC family; This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures",L1M2a.ORF1.hs2_gorilla.marg.frame3,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
723,Q#151 - >seq150,superfamily,355456,56,124,0.00314331,38.2357,cl25857,RmuC superfamily,N, - ,"RmuC family; This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures",L1M2a.ORF1.hs2_gorilla.marg.frame3,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
724,Q#154 - >seq153,non-specific,340205,245,307,9.00628e-26,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,pars,CompleteHit
725,Q#154 - >seq153,superfamily,340205,245,307,9.00628e-26,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,pars,CompleteHit
726,Q#154 - >seq153,non-specific,335182,164,241,4.9773699999999994e-18,77.7283,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,pars,CompleteHit
727,Q#154 - >seq153,superfamily,335182,164,241,4.9773699999999994e-18,77.7283,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,pars,CompleteHit
728,Q#154 - >seq153,non-specific,222878,45,144,0.00291904,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
729,Q#154 - >seq153,superfamily,222878,45,144,0.00291904,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
730,Q#154 - >seq153,non-specific,289056,85,247,0.00523117,38.3271,pfam12252,SidE,N,cl26680,Dot/Icm substrate protein; This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 1543 amino acids in length. This family is the SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
731,Q#154 - >seq153,superfamily,289056,85,247,0.00523117,38.3271,cl26680,SidE superfamily,N, - ,Dot/Icm substrate protein; This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 1543 amino acids in length. This family is the SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.,L1M2a.ORF1.hs2_gorilla.pars.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
732,Q#156 - >seq155,non-specific,340205,231,293,5.97798e-26,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs2_gorilla.marg.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,marg,CompleteHit
733,Q#156 - >seq155,superfamily,340205,231,293,5.97798e-26,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs2_gorilla.marg.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,marg,CompleteHit
734,Q#156 - >seq155,non-specific,335182,147,227,5.06913e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs2_gorilla.marg.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,marg,CompleteHit
735,Q#156 - >seq155,superfamily,335182,147,227,5.06913e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs2_gorilla.marg.frame2,1909122135_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs2_gorilla,marg,CompleteHit
736,Q#157 - >seq156,specific,238827,528,786,3.36704e-39,144.741,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
737,Q#157 - >seq156,superfamily,295487,528,786,3.36704e-39,144.741,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
738,Q#157 - >seq156,non-specific,333820,534,752,1.80872e-18,83.8809,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
739,Q#157 - >seq156,superfamily,333820,534,752,1.80872e-18,83.8809,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
740,Q#157 - >seq156,non-specific,238828,620,741,1.5719900000000002e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,N-TerminusTruncated
741,Q#157 - >seq156,non-specific,238185,675,753,0.00333255,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs1_chimp.marg.frame2,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
742,Q#161 - >seq160,non-specific,197310,17,206,3.91824e-19,85.8661,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs1_chimp,pars,CompleteHit
743,Q#161 - >seq160,superfamily,351117,17,206,3.91824e-19,85.8661,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs1_chimp,pars,CompleteHit
744,Q#161 - >seq160,non-specific,197306,6,206,4.443229999999999e-09,56.3357,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs1_chimp,pars,CompleteHit
745,Q#161 - >seq160,specific,335306,41,199,0.00116244,39.921,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs1_chimp,pars,N-TerminusTruncated
746,Q#161 - >seq160,non-specific,197307,99,206,0.00143617,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a,ORF2,hs1_chimp,pars,N-TerminusTruncated
747,Q#161 - >seq160,non-specific,223780,61,199,0.00354984,38.7335,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs1_chimp.pars.frame1,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a,ORF2,hs1_chimp,pars,N-TerminusTruncated
748,Q#162 - >seq161,non-specific,197310,9,285,5.99503e-17,80.8585,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs1_chimp.marg.frame3,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
749,Q#162 - >seq161,superfamily,351117,9,285,5.99503e-17,80.8585,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs1_chimp.marg.frame3,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
750,Q#162 - >seq161,non-specific,197306,9,285,6.53832e-06,48.2465,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs1_chimp.marg.frame3,1909122135_L1M2a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs1_chimp,marg,CompleteHit
751,Q#163 - >seq162,specific,238827,555,808,1.90461e-27,111.229,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
752,Q#163 - >seq162,superfamily,295487,555,808,1.90461e-27,111.229,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
753,Q#163 - >seq162,non-specific,197310,53,280,9.29537e-19,86.2513,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
754,Q#163 - >seq162,superfamily,351117,53,280,9.29537e-19,86.2513,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
755,Q#163 - >seq162,non-specific,333820,575,781,3.2641e-12,65.7766,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
756,Q#163 - >seq162,superfamily,333820,575,781,3.2641e-12,65.7766,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs2_gorilla,marg,CompleteHit
757,Q#163 - >seq162,non-specific,197306,153,280,1.1718299999999999e-08,56.7209,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs2_gorilla.marg.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
758,Q#164 - >seq163,non-specific,240420,334,450,0.00127089,42.2585,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1M2a.ORF2.hs2_gorilla.marg.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M2a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
759,Q#164 - >seq163,superfamily,240420,334,450,0.00127089,42.2585,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1M2a.ORF2.hs2_gorilla.marg.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M2a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
760,Q#166 - >seq165,non-specific,238827,502,690,1.1100700000000001e-12,67.7014,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs2_gorilla.pars.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
761,Q#166 - >seq165,superfamily,295487,502,690,1.1100700000000001e-12,67.7014,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs2_gorilla.pars.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
762,Q#166 - >seq165,non-specific,333820,546,673,1.12934e-06,49.213,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs2_gorilla.pars.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
763,Q#166 - >seq165,superfamily,333820,546,673,1.12934e-06,49.213,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs2_gorilla.pars.frame2,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
764,Q#167 - >seq166,non-specific,240420,362,426,0.000252336,44.1845,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1M2a.ORF2.hs2_gorilla.pars.frame1,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
765,Q#167 - >seq166,superfamily,240420,362,426,0.000252336,44.1845,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1M2a.ORF2.hs2_gorilla.pars.frame1,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
766,Q#167 - >seq166,non-specific,238827,481,531,0.0007514860000000001,41.5078,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs2_gorilla.pars.frame1,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
767,Q#167 - >seq166,superfamily,295487,481,531,0.0007514860000000001,41.5078,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs2_gorilla.pars.frame1,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
768,Q#168 - >seq167,non-specific,197310,33,235,1.8399e-11,64.2949,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs2_gorilla.pars.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
769,Q#168 - >seq167,superfamily,351117,33,235,1.8399e-11,64.2949,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs2_gorilla.pars.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
770,Q#168 - >seq167,non-specific,197306,37,235,6.059300000000001e-07,50.9429,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs2_gorilla.pars.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
771,Q#168 - >seq167,specific,335306,33,228,0.00704679,38.3802,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs2_gorilla.pars.frame3,1909122137_L1M2a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs2_gorilla,pars,CompleteHit
772,Q#169 - >seq168,non-specific,335182,155,246,9.234129999999999e-25,95.8326,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs3_orang.pars.frame1,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs3_orang,pars,CompleteHit
773,Q#169 - >seq168,superfamily,335182,155,246,9.234129999999999e-25,95.8326,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs3_orang.pars.frame1,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs3_orang,pars,CompleteHit
774,Q#169 - >seq168,non-specific,340205,249,311,4.5000100000000003e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs3_orang.pars.frame1,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs3_orang,pars,CompleteHit
775,Q#169 - >seq168,superfamily,340205,249,311,4.5000100000000003e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs3_orang.pars.frame1,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs3_orang,pars,CompleteHit
776,Q#174 - >seq173,non-specific,335182,159,250,2.48072e-24,94.677,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs3_orang.marg.frame3,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs3_orang,marg,CompleteHit
777,Q#174 - >seq173,superfamily,335182,159,250,2.48072e-24,94.677,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs3_orang.marg.frame3,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs3_orang,marg,CompleteHit
778,Q#174 - >seq173,non-specific,340205,253,315,5.427579999999999e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs3_orang.marg.frame3,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs3_orang,marg,CompleteHit
779,Q#174 - >seq173,superfamily,340205,253,315,5.427579999999999e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs3_orang.marg.frame3,1909122142_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs3_orang,marg,CompleteHit
780,Q#175 - >seq174,specific,197310,9,235,1.5308299999999999e-40,149.039,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
781,Q#175 - >seq174,superfamily,351117,9,235,1.5308299999999999e-40,149.039,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
782,Q#175 - >seq174,non-specific,197306,9,235,3.63958e-21,93.3148,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
783,Q#175 - >seq174,specific,335306,10,228,2.3077599999999997e-10,61.107,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
784,Q#175 - >seq174,non-specific,223780,7,236,4.6378300000000005e-10,61.0751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
785,Q#175 - >seq174,non-specific,197307,9,235,9.081049999999999e-08,53.8309,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
786,Q#175 - >seq174,non-specific,197320,7,228,3.1327e-07,52.5174,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
787,Q#175 - >seq174,non-specific,272954,7,235,1.6368499999999998e-05,46.9925,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
788,Q#175 - >seq174,non-specific,197321,7,235,1.80335e-05,46.7764,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
789,Q#175 - >seq174,non-specific,197319,7,235,8.843639999999999e-05,44.9601,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
790,Q#175 - >seq174,non-specific,273186,7,236,0.00010915799999999999,44.5772,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs3_orang.marg.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,marg,CompleteHit
791,Q#176 - >seq175,non-specific,238827,530,664,1.7388100000000001e-09,58.4566,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs3_orang.marg.frame1,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a,ORF2,hs3_orang,marg,BothTerminiTruncated
792,Q#176 - >seq175,superfamily,295487,530,664,1.7388100000000001e-09,58.4566,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs3_orang.marg.frame1,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a,ORF2,hs3_orang,marg,BothTerminiTruncated
793,Q#176 - >seq175,non-specific,333820,535,664,1.0340199999999999e-07,52.6798,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs3_orang.marg.frame1,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a,ORF2,hs3_orang,marg,BothTerminiTruncated
794,Q#176 - >seq175,superfamily,333820,535,664,1.0340199999999999e-07,52.6798,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs3_orang.marg.frame1,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2a,ORF2,hs3_orang,marg,BothTerminiTruncated
795,Q#179 - >seq178,specific,197310,9,240,2.04822e-36,137.09799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
796,Q#179 - >seq178,superfamily,351117,9,240,2.04822e-36,137.09799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
797,Q#179 - >seq178,non-specific,197306,9,240,4.69254e-22,95.626,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
798,Q#179 - >seq178,non-specific,238827,443,608,3.6786300000000005e-12,66.1606,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs3_orang,pars,C-TerminusTruncated
799,Q#179 - >seq178,superfamily,295487,443,608,3.6786300000000005e-12,66.1606,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs3_orang,pars,C-TerminusTruncated
800,Q#179 - >seq178,non-specific,223780,7,241,7.38748e-10,60.3047,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
801,Q#179 - >seq178,specific,335306,10,233,3.16107e-09,57.6402,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
802,Q#179 - >seq178,non-specific,333820,453,610,1.0729799999999998e-08,55.3762,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs3_orang,pars,C-TerminusTruncated
803,Q#179 - >seq178,superfamily,333820,453,610,1.0729799999999998e-08,55.3762,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs3_orang,pars,C-TerminusTruncated
804,Q#179 - >seq178,non-specific,197307,9,240,3.42232e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
805,Q#179 - >seq178,non-specific,272954,7,240,7.845740000000001e-07,50.8445,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
806,Q#179 - >seq178,non-specific,273186,7,241,5.29692e-05,45.3476,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
807,Q#179 - >seq178,non-specific,197319,7,240,7.376939999999999e-05,44.9601,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
808,Q#179 - >seq178,non-specific,197321,7,240,0.00172321,40.6132,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs3_orang.pars.frame3,1909122143_L1M2a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs3_orang,pars,CompleteHit
809,Q#181 - >seq180,non-specific,238827,682,794,9.516960000000001e-12,65.3902,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
810,Q#181 - >seq180,superfamily,295487,682,794,9.516960000000001e-12,65.3902,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
811,Q#181 - >seq180,non-specific,333820,622,736,0.0020945,40.3534,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
812,Q#181 - >seq180,superfamily,333820,622,736,0.0020945,40.3534,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
813,Q#183 - >seq182,non-specific,197310,165,399,1.14968e-23,100.889,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
814,Q#183 - >seq182,superfamily,351117,165,399,1.14968e-23,100.889,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
815,Q#183 - >seq182,non-specific,340205,16,68,2.2282e-12,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
816,Q#183 - >seq182,superfamily,340205,16,68,2.2282e-12,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
817,Q#183 - >seq182,non-specific,197306,160,399,6.17366e-11,63.6545,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
818,Q#183 - >seq182,non-specific,197307,180,399,0.0006677489999999999,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
819,Q#183 - >seq182,specific,335306,173,392,0.00175718,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs4_gibbon.marg.frame1,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,marg,CompleteHit
820,Q#184 - >seq183,non-specific,197310,110,253,2.2566800000000002e-15,75.4657,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs4_gibbon.pars.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
821,Q#184 - >seq183,superfamily,351117,110,253,2.2566800000000002e-15,75.4657,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs4_gibbon.pars.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
822,Q#184 - >seq183,specific,335306,118,243,0.00101257,40.6914,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs4_gibbon.pars.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
823,Q#185 - >seq184,non-specific,197310,160,307,1.6051499999999999e-18,84.7105,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
824,Q#185 - >seq184,superfamily,351117,160,307,1.6051499999999999e-18,84.7105,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
825,Q#185 - >seq184,non-specific,197306,160,307,3.04738e-08,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
826,Q#185 - >seq184,non-specific,340205,19,49,3.30987e-05,41.5528,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF2.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
827,Q#185 - >seq184,superfamily,340205,19,49,3.30987e-05,41.5528,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF2.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
828,Q#187 - >seq186,non-specific,340205,124,188,5.817780000000001e-23,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,CompleteHit
829,Q#187 - >seq186,superfamily,340205,124,188,5.817780000000001e-23,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,CompleteHit
830,Q#187 - >seq186,non-specific,335182,68,121,2.27732e-14,65.4019,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
831,Q#187 - >seq186,superfamily,335182,68,121,2.27732e-14,65.4019,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame2,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
832,Q#190 - >seq189,non-specific,335182,40,99,1.35733e-07,47.2975,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
833,Q#190 - >seq189,superfamily,335182,40,99,1.35733e-07,47.2975,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.pars.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
834,Q#191 - >seq190,non-specific,335182,150,243,9.170520000000001e-25,95.4474,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,marg,CompleteHit
835,Q#191 - >seq190,superfamily,335182,150,243,9.170520000000001e-25,95.4474,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,marg,CompleteHit
836,Q#191 - >seq190,non-specific,340205,246,310,6.79243e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,marg,CompleteHit
837,Q#191 - >seq190,superfamily,340205,246,310,6.79243e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs4_gibbon.marg.frame3,1909122144_L1M2a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs4_gibbon,marg,CompleteHit
838,Q#195 - >seq194,non-specific,335182,189,283,2.87022e-25,97.7586,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs5_gmonkey.marg.frame3,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs5_gmonkey,marg,CompleteHit
839,Q#195 - >seq194,superfamily,335182,189,283,2.87022e-25,97.7586,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs5_gmonkey.marg.frame3,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs5_gmonkey,marg,CompleteHit
840,Q#195 - >seq194,non-specific,340205,286,350,2.1943699999999997e-21,86.236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs5_gmonkey.marg.frame3,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs5_gmonkey,marg,CompleteHit
841,Q#195 - >seq194,superfamily,340205,286,350,2.1943699999999997e-21,86.236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs5_gmonkey.marg.frame3,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2a,ORF1,hs5_gmonkey,marg,CompleteHit
842,Q#197 - >seq196,non-specific,335182,162,255,3.46351e-24,94.2918,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs5_gmonkey.pars.frame1,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs5_gmonkey,pars,CompleteHit
843,Q#197 - >seq196,superfamily,335182,162,255,3.46351e-24,94.2918,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs5_gmonkey.pars.frame1,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs5_gmonkey,pars,CompleteHit
844,Q#197 - >seq196,non-specific,340205,258,322,8.40115e-22,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs5_gmonkey.pars.frame1,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs5_gmonkey,pars,CompleteHit
845,Q#197 - >seq196,superfamily,340205,258,322,8.40115e-22,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs5_gmonkey.pars.frame1,1909122145_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2a,ORF1,hs5_gmonkey,pars,CompleteHit
846,Q#200 - >seq199,specific,197310,11,239,3.0132e-45,162.52100000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
847,Q#200 - >seq199,superfamily,351117,11,239,3.0132e-45,162.52100000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
848,Q#200 - >seq199,non-specific,197306,11,239,4.909229999999999e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
849,Q#200 - >seq199,specific,335306,12,232,1.4168200000000002e-14,73.4333,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
850,Q#200 - >seq199,non-specific,197307,11,239,2.00033e-14,73.8613,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
851,Q#200 - >seq199,non-specific,223780,9,232,3.5451199999999996e-13,70.3199,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
852,Q#200 - >seq199,non-specific,197320,9,232,9.20412e-12,65.9994,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
853,Q#200 - >seq199,non-specific,273186,9,240,1.24375e-09,59.6,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
854,Q#200 - >seq199,non-specific,197321,9,239,1.4085099999999999e-08,56.4064,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
855,Q#200 - >seq199,non-specific,197311,9,239,2.8102799999999997e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
856,Q#200 - >seq199,non-specific,272954,9,188,3.9942500000000004e-07,52.0001,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
857,Q#200 - >seq199,non-specific,197314,9,187,0.000155638,43.8715,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_DNARepair,L1M2a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
858,Q#200 - >seq199,non-specific,197336,9,187,0.00172474,40.6735,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
859,Q#200 - >seq199,non-specific,339261,110,235,0.0017795999999999999,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2a.ORF2.hs5_gmonkey.marg.frame1,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M2a,ORF2,hs5_gmonkey,marg,CompleteHit
860,Q#201 - >seq200,non-specific,238827,461,652,1.5199199999999999e-15,76.1758,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs5_gmonkey.marg.frame2,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
861,Q#201 - >seq200,superfamily,295487,461,652,1.5199199999999999e-15,76.1758,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs5_gmonkey.marg.frame2,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
862,Q#201 - >seq200,non-specific,333820,576,650,0.00325559,39.1978,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs5_gmonkey.marg.frame2,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
863,Q#201 - >seq200,superfamily,333820,576,650,0.00325559,39.1978,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs5_gmonkey.marg.frame2,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
864,Q#204 - >seq203,specific,197310,9,232,1.23466e-46,160.595,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
865,Q#204 - >seq203,superfamily,351117,9,232,1.23466e-46,160.595,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
866,Q#204 - >seq203,non-specific,197306,9,232,7.69553e-27,107.56700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
867,Q#204 - >seq203,specific,335306,10,225,6.94657e-17,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
868,Q#204 - >seq203,non-specific,197307,9,232,3.12112e-15,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
869,Q#204 - >seq203,non-specific,223780,7,225,3.36925e-15,74.9423,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
870,Q#204 - >seq203,non-specific,197320,7,225,4.81596e-14,71.3922,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
871,Q#204 - >seq203,non-specific,273186,7,233,1.13104e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
872,Q#204 - >seq203,non-specific,197321,7,232,9.672289999999999e-10,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
873,Q#204 - >seq203,non-specific,272954,7,182,2.32795e-07,51.6149,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
874,Q#204 - >seq203,non-specific,197311,7,232,2.90982e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
875,Q#204 - >seq203,non-specific,197319,7,232,3.2865899999999997e-06,48.0417,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
876,Q#204 - >seq203,non-specific,197314,7,232,4.6805e-06,47.3383,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
877,Q#204 - >seq203,non-specific,197336,7,181,8.921360000000001e-06,46.8367,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
878,Q#204 - >seq203,non-specific,339261,107,228,0.00199749,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
879,Q#204 - >seq203,non-specific,197318,9,232,0.00751796,37.6611,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2a.ORF2.hs5_gmonkey.pars.frame3,1909122146_L1M2a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs5_gmonkey,pars,CompleteHit
880,Q#210 - >seq209,non-specific,197310,37,204,4.08337e-13,67.7617,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs7_bushaby,marg,CompleteHit
881,Q#210 - >seq209,superfamily,351117,37,204,4.08337e-13,67.7617,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs7_bushaby,marg,CompleteHit
882,Q#210 - >seq209,non-specific,197306,68,181,2.0940099999999996e-06,48.2465,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs7_bushaby,marg,BothTerminiTruncated
883,Q#210 - >seq209,non-specific,339261,100,140,0.00094601,38.4723,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2a.ORF2.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M2a,ORF2,hs7_bushaby,marg,C-TerminusTruncated
884,Q#210 - >seq209,non-specific,197320,96,138,0.00340472,38.265,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs7_bushaby,marg,BothTerminiTruncated
885,Q#214 - >seq213,non-specific,340205,140,208,9.040219999999999e-10,53.1088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs7_bushaby,marg,CompleteHit
886,Q#214 - >seq213,superfamily,340205,140,208,9.040219999999999e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs7_bushaby,marg,CompleteHit
887,Q#214 - >seq213,non-specific,335182,58,137,1.6391600000000002e-09,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs7_bushaby,marg,CompleteHit
888,Q#214 - >seq213,superfamily,335182,58,137,1.6391600000000002e-09,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs7_bushaby.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2a,ORF1,hs7_bushaby,marg,CompleteHit
889,Q#216 - >seq215,non-specific,340205,239,302,2.2006900000000005e-26,98.5624,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs0_human.marg.frame2,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs0_human,marg,CompleteHit
890,Q#216 - >seq215,superfamily,340205,239,302,2.2006900000000005e-26,98.5624,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs0_human.marg.frame2,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs0_human,marg,CompleteHit
891,Q#216 - >seq215,non-specific,335182,156,236,9.710799999999999e-25,95.4474,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs0_human.marg.frame2,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs0_human,marg,CompleteHit
892,Q#216 - >seq215,superfamily,335182,156,236,9.710799999999999e-25,95.4474,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs0_human.marg.frame2,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs0_human,marg,CompleteHit
893,Q#219 - >seq218,non-specific,340205,243,306,4.8516500000000006e-26,97.792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs0_human.pars.frame3,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs0_human,pars,CompleteHit
894,Q#219 - >seq218,superfamily,340205,243,306,4.8516500000000006e-26,97.792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs0_human.pars.frame3,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs0_human,pars,CompleteHit
895,Q#219 - >seq218,non-specific,335182,160,240,4.07011e-24,93.9066,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs0_human.pars.frame3,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs0_human,pars,CompleteHit
896,Q#219 - >seq218,superfamily,335182,160,240,4.07011e-24,93.9066,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs0_human.pars.frame3,1909122148_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs0_human,pars,CompleteHit
897,Q#220 - >seq219,non-specific,340205,60,126,2.51525e-12,57.7312,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs7_bushaby.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs7_bushaby,pars,CompleteHit
898,Q#220 - >seq219,superfamily,340205,60,126,2.51525e-12,57.7312,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs7_bushaby.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs7_bushaby,pars,CompleteHit
899,Q#220 - >seq219,non-specific,335182,1,57,9.34726e-07,44.2159,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs7_bushaby.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs7_bushaby,pars,N-TerminusTruncated
900,Q#220 - >seq219,superfamily,335182,1,57,9.34726e-07,44.2159,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs7_bushaby.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs7_bushaby,pars,N-TerminusTruncated
901,Q#224 - >seq223,non-specific,340205,135,199,6.62449e-27,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs6_sqmonkey,pars,CompleteHit
902,Q#224 - >seq223,superfamily,340205,135,199,6.62449e-27,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs6_sqmonkey,pars,CompleteHit
903,Q#224 - >seq223,non-specific,335182,48,132,1.29996e-16,71.5651,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs6_sqmonkey,pars,CompleteHit
904,Q#224 - >seq223,superfamily,335182,48,132,1.29996e-16,71.5651,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2a,ORF1,hs6_sqmonkey,pars,CompleteHit
905,Q#226 - >seq225,non-specific,340205,166,230,8.80433e-28,100.488,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs6_sqmonkey,marg,CompleteHit
906,Q#226 - >seq225,superfamily,340205,166,230,8.80433e-28,100.488,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2a.ORF1.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs6_sqmonkey,marg,CompleteHit
907,Q#226 - >seq225,non-specific,335182,79,163,7.39405e-16,70.4095,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs6_sqmonkey,marg,CompleteHit
908,Q#226 - >seq225,superfamily,335182,79,163,7.39405e-16,70.4095,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2a.ORF1.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2a,ORF1,hs6_sqmonkey,marg,CompleteHit
909,Q#229 - >seq228,non-specific,197310,75,113,0.000554335,41.1829,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs6_sqmonkey.pars.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
910,Q#229 - >seq228,superfamily,351117,75,113,0.000554335,41.1829,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.pars.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
911,Q#230 - >seq229,non-specific,197310,98,222,1.7940799999999997e-08,55.0501,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
912,Q#230 - >seq229,superfamily,351117,98,222,1.7940799999999997e-08,55.0501,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
913,Q#230 - >seq229,non-specific,197306,98,222,0.00036899199999999995,42.0833,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.pars.frame3,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
914,Q#231 - >seq230,non-specific,197310,74,303,4.0206000000000003e-22,95.8813,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,CompleteHit
915,Q#231 - >seq230,superfamily,351117,74,303,4.0206000000000003e-22,95.8813,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,CompleteHit
916,Q#231 - >seq230,non-specific,197306,74,285,7.32429e-13,69.0473,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,CompleteHit
917,Q#231 - >seq230,specific,335306,75,278,0.000102649,44.5434,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,CompleteHit
918,Q#231 - >seq230,non-specific,197307,74,213,0.00240777,40.3489,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
919,Q#231 - >seq230,non-specific,197321,72,153,0.00308186,40.228,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
920,Q#231 - >seq230,non-specific,273186,74,142,0.00355277,39.9548,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs6_sqmonkey.marg.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
921,Q#232 - >seq231,non-specific,238827,690,754,6.16762e-10,59.9974,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
922,Q#232 - >seq231,superfamily,295487,690,754,6.16762e-10,59.9974,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
923,Q#232 - >seq231,non-specific,333820,633,757,1.28191e-06,49.5982,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
924,Q#232 - >seq231,superfamily,333820,633,757,1.28191e-06,49.5982,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
925,Q#232 - >seq231,non-specific,197310,129,167,0.00045359800000000004,42.7237,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
926,Q#232 - >seq231,superfamily,351117,129,167,0.00045359800000000004,42.7237,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
927,Q#232 - >seq231,non-specific,238828,633,754,0.00299958,39.8769,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2a.ORF2.hs6_sqmonkey.marg.frame2,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
928,Q#234 - >seq233,non-specific,197310,39,88,1.7959299999999998e-06,48.8869,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs6_sqmonkey.pars.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
929,Q#234 - >seq233,superfamily,351117,39,88,1.7959299999999998e-06,48.8869,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs6_sqmonkey.pars.frame1,1909122148_L1M2a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
930,Q#236 - >seq235,specific,197310,9,234,4.636729999999999e-59,197.959,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
931,Q#236 - >seq235,superfamily,351117,9,234,4.636729999999999e-59,197.959,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
932,Q#236 - >seq235,non-specific,197306,9,234,6.27338e-30,117.96799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
933,Q#236 - >seq235,non-specific,197307,9,234,1.11756e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
934,Q#236 - >seq235,specific,335306,10,227,2.00957e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
935,Q#236 - >seq235,non-specific,197320,7,207,2.2469e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
936,Q#236 - >seq235,non-specific,197321,7,234,4.84503e-17,81.0592,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
937,Q#236 - >seq235,non-specific,223780,7,227,6.10043e-16,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
938,Q#236 - >seq235,non-specific,273186,7,235,5.23019e-14,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
939,Q#236 - >seq235,non-specific,197319,7,234,4.65504e-12,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
940,Q#236 - >seq235,non-specific,272954,7,234,4.2157599999999997e-10,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
941,Q#236 - >seq235,non-specific,197311,26,234,1.07656e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
942,Q#236 - >seq235,non-specific,197336,7,193,1.3800000000000002e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
943,Q#236 - >seq235,non-specific,236970,9,206,6.22723e-05,44.885,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
944,Q#236 - >seq235,non-specific,339261,107,230,0.0007812889999999999,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
945,Q#236 - >seq235,non-specific,197318,9,234,0.00120632,40.7427,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2c.ORF2.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
946,Q#237 - >seq236,non-specific,238827,343,563,6.989189999999999e-13,68.0866,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs1_chimp.marg.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
947,Q#237 - >seq236,superfamily,295487,343,563,6.989189999999999e-13,68.0866,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs1_chimp.marg.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs1_chimp,marg,CompleteHit
948,Q#239 - >seq238,specific,197310,9,216,4.8390800000000004e-54,179.855,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
949,Q#239 - >seq238,superfamily,351117,9,216,4.8390800000000004e-54,179.855,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
950,Q#239 - >seq238,non-specific,197306,9,222,3.1401499999999997e-28,111.419,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
951,Q#239 - >seq238,non-specific,197307,9,216,6.692430000000001e-18,82.7209,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
952,Q#239 - >seq238,non-specific,197320,7,207,1.05849e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
953,Q#239 - >seq238,non-specific,197321,7,206,1.9993599999999998e-16,78.3628,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
954,Q#239 - >seq238,specific,335306,10,209,3.93978e-16,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
955,Q#239 - >seq238,non-specific,223780,7,206,4.3942899999999996e-16,77.6387,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
956,Q#239 - >seq238,non-specific,273186,7,207,2.80996e-12,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
957,Q#239 - >seq238,non-specific,272954,7,206,2.89657e-10,60.0893,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
958,Q#239 - >seq238,non-specific,197319,7,216,3.4424000000000004e-10,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
959,Q#239 - >seq238,non-specific,197336,7,193,7.65818e-08,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
960,Q#239 - >seq238,non-specific,197311,26,145,1.3900899999999998e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs1_chimp,pars,C-TerminusTruncated
961,Q#239 - >seq238,non-specific,236970,9,206,5.2216800000000005e-05,44.4998,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs1_chimp,pars,CompleteHit
962,Q#239 - >seq238,non-specific,339261,107,147,0.00724521,36.1611,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs1_chimp.pars.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M2c,ORF2,hs1_chimp,pars,C-TerminusTruncated
963,Q#242 - >seq241,non-specific,340205,69,132,7.68716e-21,80.0728,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs1_chimp,marg,CompleteHit
964,Q#242 - >seq241,superfamily,340205,69,132,7.68716e-21,80.0728,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs1_chimp,marg,CompleteHit
965,Q#242 - >seq241,non-specific,335182,4,66,1.24497e-17,72.7207,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs1_chimp,marg,N-TerminusTruncated
966,Q#242 - >seq241,superfamily,335182,4,66,1.24497e-17,72.7207,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs1_chimp,marg,N-TerminusTruncated
967,Q#242 - >seq241,non-specific,163678,28,86,0.00498725,35.5019,cd07940,DRE_TIM_IPMS,NC,cl21457,"2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis.  This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein.  This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein.  AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin.  AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-hydroxy-1,2,6- hexanetricarboxylic acid.  This family belongs to the DRE-TIM metallolyase superfamily.  DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM"".",L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2c,ORF1,hs1_chimp,marg,BothTerminiTruncated
968,Q#242 - >seq241,superfamily,354814,28,86,0.00498725,35.5019,cl21457,DRE_TIM_metallolyase superfamily,NC, - ,"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM"".",L1M2c.ORF1.hs1_chimp.marg.frame3,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2c,ORF1,hs1_chimp,marg,BothTerminiTruncated
969,Q#244 - >seq243,specific,238827,471,726,4.5354799999999996e-39,144.741,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs0_human.marg.frame2,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs0_human,marg,CompleteHit
970,Q#244 - >seq243,superfamily,295487,471,726,4.5354799999999996e-39,144.741,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs0_human.marg.frame2,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs0_human,marg,CompleteHit
971,Q#244 - >seq243,non-specific,333820,477,703,1.4045e-12,66.9322,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs0_human.marg.frame2,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs0_human,marg,CompleteHit
972,Q#244 - >seq243,superfamily,333820,477,703,1.4045e-12,66.9322,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs0_human.marg.frame2,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2a,ORF2,hs0_human,marg,CompleteHit
973,Q#245 - >seq244,non-specific,340205,69,132,4.45277e-21,80.0728,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs1_chimp,pars,CompleteHit
974,Q#245 - >seq244,superfamily,340205,69,132,4.45277e-21,80.0728,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs1_chimp,pars,CompleteHit
975,Q#245 - >seq244,non-specific,335182,4,66,1.58526e-17,71.9503,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs1_chimp,pars,N-TerminusTruncated
976,Q#245 - >seq244,superfamily,335182,4,66,1.58526e-17,71.9503,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs1_chimp,pars,N-TerminusTruncated
977,Q#245 - >seq244,non-specific,163678,28,86,0.00279229,36.2723,cd07940,DRE_TIM_IPMS,NC,cl21457,"2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis.  This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein.  This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein.  AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin.  AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-hydroxy-1,2,6- hexanetricarboxylic acid.  This family belongs to the DRE-TIM metallolyase superfamily.  DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM"".",L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2c,ORF1,hs1_chimp,pars,BothTerminiTruncated
978,Q#245 - >seq244,superfamily,354814,28,86,0.00279229,36.2723,cl21457,DRE_TIM_metallolyase superfamily,NC, - ,"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM"".",L1M2c.ORF1.hs1_chimp.pars.frame2,1909122149_L1M2c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2c,ORF1,hs1_chimp,pars,BothTerminiTruncated
979,Q#247 - >seq246,specific,197310,9,237,3.4167099999999997e-42,154.046,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
980,Q#247 - >seq246,superfamily,351117,9,237,3.4167099999999997e-42,154.046,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
981,Q#247 - >seq246,non-specific,197306,9,237,8.63565e-26,106.79700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
982,Q#247 - >seq246,specific,335306,10,230,2.4671400000000003e-12,67.2702,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
983,Q#247 - >seq246,non-specific,197307,9,237,3.49337e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
984,Q#247 - >seq246,non-specific,223780,7,230,6.38778e-11,63.7715,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
985,Q#247 - >seq246,non-specific,197320,7,230,1.3207499999999998e-10,62.9178,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
986,Q#247 - >seq246,non-specific,273186,7,238,3.7236e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
987,Q#247 - >seq246,non-specific,197321,7,237,1.03912e-07,54.0952,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
988,Q#247 - >seq246,non-specific,197319,7,237,3.73045e-07,52.2789,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2a.ORF2.hs0_human.marg.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2a,ORF2,hs0_human,marg,CompleteHit
989,Q#249 - >seq248,specific,238827,461,712,3.36314e-29,115.851,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs0_human,pars,CompleteHit
990,Q#249 - >seq248,superfamily,295487,461,712,3.36314e-29,115.851,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs0_human,pars,CompleteHit
991,Q#249 - >seq248,non-specific,333820,467,689,1.67735e-10,60.769,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs0_human,pars,CompleteHit
992,Q#249 - >seq248,superfamily,333820,467,689,1.67735e-10,60.769,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2a,ORF2,hs0_human,pars,CompleteHit
993,Q#249 - >seq248,non-specific,197310,9,57,0.00121278,41.1829,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2a,ORF2,hs0_human,pars,C-TerminusTruncated
994,Q#249 - >seq248,superfamily,351117,9,57,0.00121278,41.1829,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs0_human.pars.frame3,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,pars,C-TerminusTruncated
995,Q#251 - >seq250,specific,197310,20,216,2.30807e-30,119.764,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs0_human,pars,CompleteHit
996,Q#251 - >seq250,superfamily,351117,20,216,2.30807e-30,119.764,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,pars,CompleteHit
997,Q#251 - >seq250,non-specific,197306,34,216,1.22516e-16,80.218,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
998,Q#251 - >seq250,non-specific,197320,86,209,7.73272e-08,54.0582,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
999,Q#251 - >seq250,non-specific,223780,48,209,1.07917e-05,47.5931,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
1000,Q#251 - >seq250,non-specific,273186,87,217,2.8216999999999998e-05,46.5032,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
1001,Q#251 - >seq250,specific,335306,25,209,5.78811e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2a,ORF2,hs0_human,pars,CompleteHit
1002,Q#251 - >seq250,non-specific,197307,86,216,0.00032862900000000004,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
1003,Q#251 - >seq250,non-specific,197319,86,216,0.000374647,43.0341,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
1004,Q#251 - >seq250,non-specific,197321,153,216,0.00509416,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2a.ORF2.hs0_human.pars.frame1,1909122149_L1M2a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2a,ORF2,hs0_human,pars,N-TerminusTruncated
1005,Q#254 - >seq253,specific,197310,24,236,8.23272e-51,178.699,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1006,Q#254 - >seq253,superfamily,351117,24,236,8.23272e-51,178.699,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1007,Q#254 - >seq253,non-specific,197306,23,236,6.839189999999999e-26,107.182,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1008,Q#254 - >seq253,non-specific,197320,30,229,4.36196e-16,79.0961,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1009,Q#254 - >seq253,non-specific,197307,23,236,2.0002800000000002e-15,76.9429,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1010,Q#254 - >seq253,specific,335306,26,229,3.3659100000000003e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1011,Q#254 - >seq253,non-specific,197321,23,236,8.88164e-15,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1012,Q#254 - >seq253,non-specific,223780,30,229,2.9177200000000002e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1013,Q#254 - >seq253,non-specific,197319,23,236,8.87869e-12,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1014,Q#254 - >seq253,non-specific,273186,23,237,1.6556599999999997e-10,62.2964,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1015,Q#254 - >seq253,non-specific,238827,549,669,7.67882e-09,56.9158,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1016,Q#254 - >seq253,superfamily,295487,549,669,7.67882e-09,56.9158,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1017,Q#254 - >seq253,non-specific,272954,24,236,5.40265e-07,52.0001,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1018,Q#254 - >seq253,non-specific,197311,29,236,9.304609999999999e-07,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1019,Q#254 - >seq253,non-specific,339261,108,232,0.000750115,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1020,Q#254 - >seq253,non-specific,197336,22,194,0.0008336880000000001,42.2143,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1021,Q#254 - >seq253,non-specific,333820,433,597,0.00243556,39.9682,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1022,Q#254 - >seq253,superfamily,333820,433,597,0.00243556,39.9682,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs2_gorilla.marg.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs2_gorilla,marg,CompleteHit
1023,Q#258 - >seq257,specific,197310,24,236,7.81856e-54,175.232,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1024,Q#258 - >seq257,superfamily,351117,24,236,7.81856e-54,175.232,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1025,Q#258 - >seq257,non-specific,197306,23,236,8.217339999999999e-28,107.56700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1026,Q#258 - >seq257,non-specific,197320,30,229,3.98623e-17,79.0961,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1027,Q#258 - >seq257,non-specific,197307,23,236,1.6530499999999998e-16,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1028,Q#258 - >seq257,specific,335306,26,229,3.94215e-16,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1029,Q#258 - >seq257,non-specific,197321,23,236,1.26966e-15,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1030,Q#258 - >seq257,non-specific,223780,30,229,3.2002399999999997e-13,68.0087,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1031,Q#258 - >seq257,non-specific,197319,23,236,1.24127e-12,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1032,Q#258 - >seq257,non-specific,273186,23,237,2.22423e-11,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1033,Q#258 - >seq257,non-specific,272954,24,236,4.64574e-08,52.7705,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1034,Q#258 - >seq257,non-specific,197311,29,236,3.82559e-07,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1035,Q#258 - >seq257,non-specific,197336,22,194,0.000173206,42.2143,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1036,Q#258 - >seq257,non-specific,339261,108,232,0.000866184,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M2c,ORF2,hs2_gorilla,pars,CompleteHit
1037,Q#258 - >seq257,non-specific,197317,126,229,0.00717817,37.1964,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2c.ORF2.hs2_gorilla.pars.frame2,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1038,Q#260 - >seq259,non-specific,340205,171,236,4.06228e-18,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs2_gorilla.marg.frame1,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs2_gorilla,marg,CompleteHit
1039,Q#260 - >seq259,superfamily,340205,171,236,4.06228e-18,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs2_gorilla.marg.frame1,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs2_gorilla,marg,CompleteHit
1040,Q#260 - >seq259,non-specific,335182,92,168,1.39002e-16,72.3355,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs2_gorilla.marg.frame1,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
1041,Q#260 - >seq259,superfamily,335182,92,168,1.39002e-16,72.3355,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs2_gorilla.marg.frame1,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
1042,Q#261 - >seq260,non-specific,340205,114,179,1.00553e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs2_gorilla.pars.frame3,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs2_gorilla,pars,CompleteHit
1043,Q#261 - >seq260,superfamily,340205,114,179,1.00553e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs2_gorilla.pars.frame3,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs2_gorilla,pars,CompleteHit
1044,Q#261 - >seq260,non-specific,335182,35,111,1.17854e-17,73.8763,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs2_gorilla.pars.frame3,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1045,Q#261 - >seq260,superfamily,335182,35,111,1.17854e-17,73.8763,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs2_gorilla.pars.frame3,1909122150_L1M2c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1046,Q#265 - >seq264,non-specific,340205,117,181,7.1011400000000005e-25,91.6288,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,CompleteHit
1047,Q#265 - >seq264,superfamily,340205,117,181,7.1011400000000005e-25,91.6288,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,CompleteHit
1048,Q#265 - >seq264,non-specific,335182,65,114,9.849019999999999e-08,47.6827,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,N-TerminusTruncated
1049,Q#265 - >seq264,superfamily,335182,65,114,9.849019999999999e-08,47.6827,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,N-TerminusTruncated
1050,Q#266 - >seq265,non-specific,335182,22,75,3.9303800000000003e-07,46.1419,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,C-TerminusTruncated
1051,Q#266 - >seq265,superfamily,335182,22,75,3.9303800000000003e-07,46.1419,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,marg,C-TerminusTruncated
1052,Q#268 - >seq267,non-specific,238827,499,548,0.00243036,39.967,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs4_gibbon.pars.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1053,Q#268 - >seq267,superfamily,295487,499,548,0.00243036,39.967,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs4_gibbon.pars.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1054,Q#269 - >seq268,non-specific,197310,9,85,8.915260000000001e-13,68.5321,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1055,Q#269 - >seq268,superfamily,351117,9,85,8.915260000000001e-13,68.5321,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1056,Q#269 - >seq268,non-specific,197306,9,108,5.58698e-05,45.1649,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1057,Q#269 - >seq268,non-specific,238827,595,700,0.00028467200000000003,42.6634,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1058,Q#269 - >seq268,superfamily,295487,595,700,0.00028467200000000003,42.6634,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1059,Q#270 - >seq269,non-specific,340205,117,181,2.6846799999999998e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,CompleteHit
1060,Q#270 - >seq269,superfamily,340205,117,181,2.6846799999999998e-24,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,CompleteHit
1061,Q#270 - >seq269,non-specific,335182,65,114,1.36809e-07,47.2975,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,N-TerminusTruncated
1062,Q#270 - >seq269,superfamily,335182,65,114,1.36809e-07,47.2975,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,N-TerminusTruncated
1063,Q#271 - >seq270,specific,197310,206,433,1.14963e-39,147.113,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1064,Q#271 - >seq270,superfamily,351117,206,433,1.14963e-39,147.113,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1065,Q#271 - >seq270,non-specific,197306,206,425,3.63461e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1066,Q#271 - >seq270,non-specific,340205,57,122,1.21088e-13,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1067,Q#271 - >seq270,superfamily,340205,57,122,1.21088e-13,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1068,Q#271 - >seq270,specific,335306,207,426,5.6072e-11,63.8034,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1069,Q#271 - >seq270,non-specific,197320,204,406,7.979609999999999e-09,57.525,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1070,Q#271 - >seq270,non-specific,197307,206,426,6.9539e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1071,Q#271 - >seq270,non-specific,223780,204,405,3.7292099999999995e-07,52.6007,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1072,Q#271 - >seq270,non-specific,197319,204,433,2.514e-05,47.2713,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1073,Q#271 - >seq270,non-specific,339261,306,405,0.009038899999999999,37.3167,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs4_gibbon.marg.frame1,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M2c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1074,Q#272 - >seq271,non-specific,238827,681,916,2.68497e-15,76.1758,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1075,Q#272 - >seq271,superfamily,295487,681,916,2.68497e-15,76.1758,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1076,Q#272 - >seq271,non-specific,333820,680,880,0.0005800590000000001,41.8942,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1077,Q#272 - >seq271,superfamily,333820,680,880,0.0005800590000000001,41.8942,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs4_gibbon.marg.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs4_gibbon,marg,CompleteHit
1078,Q#273 - >seq272,non-specific,238827,656,740,0.000630418,42.2782,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs4_gibbon.marg.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1079,Q#273 - >seq272,superfamily,295487,656,740,0.000630418,42.2782,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs4_gibbon.marg.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1080,Q#274 - >seq273,specific,197310,82,229,3.29045e-27,110.51899999999999,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1081,Q#274 - >seq273,superfamily,351117,82,229,3.29045e-27,110.51899999999999,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1082,Q#274 - >seq273,non-specific,197306,75,221,4.0802e-14,72.5141,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1083,Q#274 - >seq273,non-specific,197320,100,202,1.65764e-08,55.9842,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1084,Q#274 - >seq273,specific,335306,63,222,1.18073e-05,47.2398,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1085,Q#274 - >seq273,non-specific,197307,100,222,0.00017568,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1086,Q#274 - >seq273,non-specific,223780,100,201,0.00035596900000000003,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1087,Q#274 - >seq273,non-specific,339261,102,142,0.00930704,36.5463,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs4_gibbon.pars.frame2,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M2c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1088,Q#276 - >seq275,non-specific,335182,27,78,1.0412200000000002e-06,44.9863,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1089,Q#276 - >seq275,superfamily,335182,27,78,1.0412200000000002e-06,44.9863,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs4_gibbon.pars.frame3,1909122151_L1M2c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1090,Q#277 - >seq276,specific,197310,73,231,1.1662899999999999e-30,120.919,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1091,Q#277 - >seq276,superfamily,351117,73,231,1.1662899999999999e-30,120.919,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1092,Q#277 - >seq276,non-specific,238827,544,778,1.2107999999999999e-15,76.9462,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs3_orang,marg,CompleteHit
1093,Q#277 - >seq276,superfamily,295487,544,778,1.2107999999999999e-15,76.9462,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs3_orang,marg,CompleteHit
1094,Q#277 - >seq276,non-specific,197306,65,231,7.66525e-15,75.2104,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1095,Q#277 - >seq276,non-specific,197320,86,216,1.7136700000000001e-12,68.3106,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1096,Q#277 - >seq276,non-specific,197307,101,224,5.3503e-08,54.9865,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1097,Q#277 - >seq276,non-specific,223780,101,224,1.20545e-07,53.7563,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1098,Q#277 - >seq276,specific,335306,107,224,2.18086e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1099,Q#277 - >seq276,non-specific,197319,101,231,5.49468e-05,45.7305,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1100,Q#277 - >seq276,non-specific,197321,101,231,0.00138005,41.3836,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,marg,N-TerminusTruncated
1101,Q#278 - >seq277,non-specific,197310,9,105,1.1272200000000002e-16,80.0881,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1102,Q#278 - >seq277,superfamily,351117,9,105,1.1272200000000002e-16,80.0881,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1103,Q#278 - >seq277,non-specific,197306,9,115,7.51684e-11,63.2693,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1104,Q#278 - >seq277,non-specific,223780,7,96,1.2675000000000002e-07,53.7563,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1105,Q#278 - >seq277,non-specific,197321,7,146,8.88921e-07,51.0136,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1106,Q#278 - >seq277,non-specific,197336,7,43,9.33515e-06,47.9923,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1107,Q#278 - >seq277,specific,335306,10,76,1.5385799999999998e-05,46.8546,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1108,Q#278 - >seq277,non-specific,273186,7,75,6.0720299999999995e-05,45.3476,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1109,Q#278 - >seq277,non-specific,197307,9,64,0.000134383,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1110,Q#278 - >seq277,non-specific,197320,7,75,0.00023150299999999998,43.6578,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1111,Q#278 - >seq277,non-specific,272954,7,75,0.00057636,42.3701,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1112,Q#278 - >seq277,non-specific,197319,7,43,0.00875791,38.7969,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,marg,C-TerminusTruncated
1113,Q#279 - >seq278,non-specific,335182,32,98,1.92153e-13,63.0907,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.pars.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs3_orang,pars,C-TerminusTruncated
1114,Q#279 - >seq278,superfamily,335182,32,98,1.92153e-13,63.0907,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.pars.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs3_orang,pars,C-TerminusTruncated
1115,Q#281 - >seq280,non-specific,335182,46,112,5.102939999999999e-13,62.3203,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.marg.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs3_orang,marg,C-TerminusTruncated
1116,Q#281 - >seq280,superfamily,335182,46,112,5.102939999999999e-13,62.3203,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.marg.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs3_orang,marg,C-TerminusTruncated
1117,Q#283 - >seq282,non-specific,340205,121,184,3.5083699999999995e-26,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,pars,CompleteHit
1118,Q#283 - >seq282,superfamily,340205,121,184,3.5083699999999995e-26,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,pars,CompleteHit
1119,Q#283 - >seq282,non-specific,335182,93,118,6.29174e-05,40.3639,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,pars,N-TerminusTruncated
1120,Q#283 - >seq282,superfamily,335182,93,118,6.29174e-05,40.3639,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,pars,N-TerminusTruncated
1121,Q#283 - >seq282,non-specific,224556,77,162,0.00820994,36.167,COG1641,COG1641,N,cl03398,"Uncharacterized conserved protein, DUF111 family [Function unknown]; Uncharacterized conserved protein [Function unknown].",L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M2c,ORF1,hs3_orang,pars,N-TerminusTruncated
1122,Q#283 - >seq282,superfamily,351986,77,162,0.00820994,36.167,cl03398,DUF111 superfamily,N, - ,Protein of unknown function DUF111; This prokaryotic family has no known function.,L1M2c.ORF1.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M2c,ORF1,hs3_orang,pars,N-TerminusTruncated
1123,Q#284 - >seq283,non-specific,238827,507,564,4.016859999999999e-08,54.2194,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs3_orang.pars.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1124,Q#284 - >seq283,superfamily,295487,507,564,4.016859999999999e-08,54.2194,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs3_orang.pars.frame1,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1125,Q#285 - >seq284,specific,197310,73,230,9.785419999999999e-30,117.838,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1126,Q#285 - >seq284,superfamily,351117,73,230,9.785419999999999e-30,117.838,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1127,Q#285 - >seq284,non-specific,197306,62,230,9.817760000000001e-14,71.3585,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1128,Q#285 - >seq284,non-specific,197320,100,215,4.09304e-12,66.7698,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1129,Q#285 - >seq284,non-specific,197307,100,223,3.1255000000000004e-08,55.3717,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1130,Q#285 - >seq284,non-specific,223780,100,223,4.18152e-08,54.9119,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1131,Q#285 - >seq284,specific,335306,106,223,1.67967e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1132,Q#285 - >seq284,non-specific,197319,100,230,2.98762e-05,46.1157,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1133,Q#285 - >seq284,non-specific,197321,100,230,0.0008874639999999999,41.7688,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1134,Q#285 - >seq284,non-specific,238827,611,716,0.00881425,38.4262,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1135,Q#285 - >seq284,superfamily,295487,611,716,0.00881425,38.4262,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs3_orang.pars.frame2,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2c,ORF2,hs3_orang,pars,N-TerminusTruncated
1136,Q#286 - >seq285,non-specific,197310,9,94,8.297979999999999e-17,80.0881,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1137,Q#286 - >seq285,superfamily,351117,9,94,8.297979999999999e-17,80.0881,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1138,Q#286 - >seq285,non-specific,197306,9,104,6.61542e-10,60.1877,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1139,Q#286 - >seq285,non-specific,223780,7,75,1.89599e-07,52.9859,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1140,Q#286 - >seq285,non-specific,197321,7,79,1.4069e-06,50.2432,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1141,Q#286 - >seq285,non-specific,197336,7,43,7.81252e-06,47.9923,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1142,Q#286 - >seq285,specific,335306,10,76,1.293e-05,46.8546,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1143,Q#286 - >seq285,non-specific,273186,7,75,5.0879e-05,45.3476,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1144,Q#286 - >seq285,non-specific,197307,9,64,0.000129043,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1145,Q#286 - >seq285,non-specific,197320,7,75,0.000194165,43.6578,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1146,Q#286 - >seq285,non-specific,272954,7,75,0.000792756,41.5997,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1147,Q#286 - >seq285,non-specific,197319,7,43,0.00889016,38.4117,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs3_orang.pars.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs3_orang,pars,C-TerminusTruncated
1148,Q#288 - >seq287,non-specific,340205,135,199,6.698330000000001e-24,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,marg,CompleteHit
1149,Q#288 - >seq287,superfamily,340205,135,199,6.698330000000001e-24,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,marg,CompleteHit
1150,Q#288 - >seq287,non-specific,335182,107,132,0.00015507700000000002,39.2083,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,marg,N-TerminusTruncated
1151,Q#288 - >seq287,superfamily,335182,107,132,0.00015507700000000002,39.2083,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs3_orang.marg.frame3,1909122151_L1M2c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs3_orang,marg,N-TerminusTruncated
1152,Q#290 - >seq289,non-specific,335182,20,102,1.39087e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs6_sqmonkey,pars,CompleteHit
1153,Q#290 - >seq289,superfamily,335182,20,102,1.39087e-15,68.0983,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs6_sqmonkey,pars,CompleteHit
1154,Q#290 - >seq289,non-specific,340205,106,169,1.42438e-11,56.9608,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs6_sqmonkey,pars,CompleteHit
1155,Q#290 - >seq289,superfamily,340205,106,169,1.42438e-11,56.9608,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs6_sqmonkey,pars,CompleteHit
1156,Q#292 - >seq291,non-specific,335182,55,138,7.11134e-15,67.7131,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs6_sqmonkey,marg,CompleteHit
1157,Q#292 - >seq291,superfamily,335182,55,138,7.11134e-15,67.7131,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs6_sqmonkey,marg,CompleteHit
1158,Q#292 - >seq291,non-specific,340205,142,206,1.8396099999999998e-09,52.3384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs6_sqmonkey,marg,CompleteHit
1159,Q#292 - >seq291,superfamily,340205,142,206,1.8396099999999998e-09,52.3384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2c,ORF1,hs6_sqmonkey,marg,CompleteHit
1160,Q#295 - >seq294,non-specific,238827,461,504,2.26451e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
1161,Q#295 - >seq294,superfamily,295487,461,504,2.26451e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
1162,Q#295 - >seq294,non-specific,197310,9,68,0.00120286,40.7977,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
1163,Q#295 - >seq294,superfamily,351117,9,68,0.00120286,40.7977,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs6_sqmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
1164,Q#296 - >seq295,non-specific,340205,5,49,8.88615e-06,43.864,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs6_sqmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1165,Q#296 - >seq295,superfamily,340205,5,49,8.88615e-06,43.864,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs6_sqmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1166,Q#297 - >seq296,non-specific,238827,694,960,2.1563800000000001e-07,52.6786,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs6_sqmonkey,marg,CompleteHit
1167,Q#297 - >seq296,superfamily,295487,694,960,2.1563800000000001e-07,52.6786,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs6_sqmonkey.marg.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M2c,ORF2,hs6_sqmonkey,marg,CompleteHit
1168,Q#298 - >seq297,non-specific,197310,227,368,1.3202799999999999e-20,91.6441,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1169,Q#298 - >seq297,superfamily,351117,227,368,1.3202799999999999e-20,91.6441,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1170,Q#298 - >seq297,non-specific,197306,234,368,8.01938e-10,60.1877,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1171,Q#298 - >seq297,non-specific,197320,253,370,5.5836700000000004e-09,57.525,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1172,Q#298 - >seq297,non-specific,223780,221,354,0.00037800199999999995,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1173,Q#298 - >seq297,non-specific,197307,253,368,0.00130007,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1174,Q#298 - >seq297,non-specific,272954,195,354,0.00759838,38.9033,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs6_sqmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs6_sqmonkey,marg,CompleteHit
1175,Q#299 - >seq298,non-specific,197310,68,208,2.5538400000000003e-21,93.1849,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1176,Q#299 - >seq298,superfamily,351117,68,208,2.5538400000000003e-21,93.1849,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1177,Q#299 - >seq298,non-specific,197306,78,208,4.70896e-10,60.1877,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1178,Q#299 - >seq298,non-specific,197320,93,210,3.55103e-09,57.525,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1179,Q#299 - >seq298,non-specific,223780,78,194,0.000267586,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1180,Q#299 - >seq298,non-specific,197307,78,208,0.0007191610000000001,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs6_sqmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1181,Q#301 - >seq300,non-specific,340205,166,230,9.376700000000001e-23,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,marg,CompleteHit
1182,Q#301 - >seq300,superfamily,340205,166,230,9.376700000000001e-23,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,marg,CompleteHit
1183,Q#301 - >seq300,non-specific,335182,86,163,8.209189999999999e-16,70.4095,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
1184,Q#301 - >seq300,superfamily,335182,86,163,8.209189999999999e-16,70.4095,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
1185,Q#303 - >seq302,non-specific,340205,139,203,2.1108300000000002e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,pars,CompleteHit
1186,Q#303 - >seq302,superfamily,340205,139,203,2.1108300000000002e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,pars,CompleteHit
1187,Q#303 - >seq302,non-specific,335182,59,136,1.98081e-16,71.1799,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
1188,Q#303 - >seq302,superfamily,335182,59,136,1.98081e-16,71.1799,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2c,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
1189,Q#305 - >seq304,non-specific,197310,203,437,2.36178e-18,85.4809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs5_gmonkey,marg,CompleteHit
1190,Q#305 - >seq304,superfamily,351117,203,437,2.36178e-18,85.4809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,marg,CompleteHit
1191,Q#305 - >seq304,non-specific,238827,719,989,5.00538e-17,81.1834,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,marg,CompleteHit
1192,Q#305 - >seq304,superfamily,295487,719,989,5.00538e-17,81.1834,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,marg,CompleteHit
1193,Q#305 - >seq304,non-specific,197306,313,437,1.84064e-05,47.4761,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1194,Q#305 - >seq304,non-specific,197320,331,408,5.15125e-05,45.968999999999994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1195,Q#305 - >seq304,non-specific,333820,725,782,0.000169701,43.8202,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1196,Q#305 - >seq304,superfamily,333820,725,782,0.000169701,43.8202,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1197,Q#305 - >seq304,specific,335306,310,430,0.000752981,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs5_gmonkey.marg.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1198,Q#308 - >seq307,non-specific,197310,112,233,2.0269900000000002e-19,87.7921,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1199,Q#308 - >seq307,superfamily,351117,112,233,2.0269900000000002e-19,87.7921,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1200,Q#308 - >seq307,non-specific,197320,131,205,5.26575e-07,51.3618,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1201,Q#308 - >seq307,non-specific,197306,113,233,6.20119e-07,50.9429,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1202,Q#308 - >seq307,specific,335306,69,226,2.2138299999999998e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1203,Q#308 - >seq307,non-specific,197307,119,226,0.00101885,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1204,Q#308 - >seq307,non-specific,235943,335,576,0.00146897,41.727,PRK07133,PRK07133,N,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1205,Q#308 - >seq307,superfamily,235943,335,576,0.00146897,41.727,cl35548,PRK07133 superfamily,N, - ,DNA polymerase III subunits gamma and tau; Validated,L1M2c.ORF2.hs5_gmonkey.pars.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2c,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
1206,Q#309 - >seq308,non-specific,197310,42,119,1.41555e-05,46.9609,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs5_gmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1207,Q#309 - >seq308,superfamily,351117,42,119,1.41555e-05,46.9609,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.pars.frame2,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1208,Q#310 - >seq309,non-specific,238827,457,597,1.60721e-18,84.6502,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1209,Q#310 - >seq309,superfamily,295487,457,597,1.60721e-18,84.6502,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1210,Q#310 - >seq309,non-specific,333820,459,599,1.5377900000000002e-07,51.9094,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1211,Q#310 - >seq309,superfamily,333820,459,599,1.5377900000000002e-07,51.9094,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1212,Q#310 - >seq309,non-specific,197310,17,63,0.000237148,43.1089,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1213,Q#310 - >seq309,superfamily,351117,17,63,0.000237148,43.1089,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.pars.frame3,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1214,Q#311 - >seq310,non-specific,340205,57,112,2.38475e-08,51.568000000000005,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1215,Q#311 - >seq310,superfamily,340205,57,112,2.38475e-08,51.568000000000005,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1216,Q#311 - >seq310,non-specific,197310,254,329,0.00017853099999999998,44.2645,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1217,Q#311 - >seq310,superfamily,351117,254,329,0.00017853099999999998,44.2645,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1218,Q#311 - >seq310,non-specific,335182,16,54,0.00953866,36.5119,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1219,Q#311 - >seq310,superfamily,335182,16,54,0.00953866,36.5119,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF2.hs5_gmonkey.marg.frame1,1909122152_L1M2c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1220,Q#314 - >seq313,non-specific,335182,64,160,2.6807899999999996e-29,105.848,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs1_chimp.marg.frame3,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs1_chimp,marg,CompleteHit
1221,Q#314 - >seq313,superfamily,335182,64,160,2.6807899999999996e-29,105.848,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs1_chimp.marg.frame3,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs1_chimp,marg,CompleteHit
1222,Q#314 - >seq313,non-specific,340205,163,226,7.45463e-28,100.874,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs1_chimp.marg.frame3,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs1_chimp,marg,CompleteHit
1223,Q#314 - >seq313,superfamily,340205,163,226,7.45463e-28,100.874,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs1_chimp.marg.frame3,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs1_chimp,marg,CompleteHit
1224,Q#318 - >seq317,non-specific,335182,58,154,2.2591499999999997e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs1_chimp.pars.frame2,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs1_chimp,pars,CompleteHit
1225,Q#318 - >seq317,superfamily,335182,58,154,2.2591499999999997e-28,103.15100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs1_chimp.pars.frame2,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs1_chimp,pars,CompleteHit
1226,Q#318 - >seq317,non-specific,340205,157,220,3.1404299999999998e-27,99.3327,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs1_chimp.pars.frame2,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs1_chimp,pars,CompleteHit
1227,Q#318 - >seq317,superfamily,340205,157,220,3.1404299999999998e-27,99.3327,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs1_chimp.pars.frame2,1909122153_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs1_chimp,pars,CompleteHit
1228,Q#320 - >seq319,specific,197310,122,320,9.58702e-34,129.00799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1229,Q#320 - >seq319,superfamily,351117,122,320,9.58702e-34,129.00799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1230,Q#320 - >seq319,non-specific,197306,122,326,5.290560000000001e-17,80.9884,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1231,Q#320 - >seq319,non-specific,197320,121,310,6.65792e-12,65.9994,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1232,Q#320 - >seq319,non-specific,223780,156,309,8.24145e-08,53.7563,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1233,Q#320 - >seq319,specific,335306,150,312,2.1233e-07,52.2474,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1234,Q#320 - >seq319,non-specific,197307,156,310,2.2356999999999998e-07,52.2901,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1235,Q#320 - >seq319,non-specific,272954,122,309,0.000287296,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs0_human,marg,CompleteHit
1236,Q#320 - >seq319,non-specific,197311,152,248,0.000522762,41.8937,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1237,Q#320 - >seq319,non-specific,197319,193,320,0.00656968,38.7969,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2c,ORF2,hs0_human,marg,N-TerminusTruncated
1238,Q#321 - >seq320,non-specific,197310,124,172,6.90129e-09,56.9761,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1239,Q#321 - >seq320,superfamily,351117,124,172,6.90129e-09,56.9761,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1240,Q#321 - >seq320,non-specific,340205,3,39,2.2016600000000001e-07,48.1012,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs0_human,marg,N-TerminusTruncated
1241,Q#321 - >seq320,superfamily,340205,3,39,2.2016600000000001e-07,48.1012,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2c,ORF2,hs0_human,marg,N-TerminusTruncated
1242,Q#321 - >seq320,non-specific,238827,417,582,1.0111e-06,49.9822,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2c,ORF2,hs0_human,marg,BothTerminiTruncated
1243,Q#321 - >seq320,superfamily,295487,417,582,1.0111e-06,49.9822,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2c,ORF2,hs0_human,marg,BothTerminiTruncated
1244,Q#321 - >seq320,non-specific,197306,124,181,0.000809892,41.6981,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1245,Q#321 - >seq320,specific,335306,125,169,0.00256236,39.921,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1246,Q#321 - >seq320,non-specific,333820,427,542,0.00312506,39.1978,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2c,ORF2,hs0_human,marg,N-TerminusTruncated
1247,Q#321 - >seq320,superfamily,333820,427,542,0.00312506,39.1978,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2c,ORF2,hs0_human,marg,N-TerminusTruncated
1248,Q#321 - >seq320,non-specific,238828,428,530,0.0040343,39.1065,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M2c,ORF2,hs0_human,marg,BothTerminiTruncated
1249,Q#321 - >seq320,non-specific,197321,122,164,0.00654421,38.6872,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.marg.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,marg,C-TerminusTruncated
1250,Q#322 - >seq321,non-specific,335182,57,140,7.37494e-26,95.8326,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,marg,CompleteHit
1251,Q#322 - >seq321,superfamily,335182,57,140,7.37494e-26,95.8326,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,marg,CompleteHit
1252,Q#322 - >seq321,non-specific,340205,143,207,5.55161e-23,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,marg,CompleteHit
1253,Q#322 - >seq321,superfamily,340205,143,207,5.55161e-23,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs0_human.marg.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,marg,CompleteHit
1254,Q#324 - >seq323,specific,197310,66,270,3.3460199999999994e-44,157.513,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1255,Q#324 - >seq323,superfamily,351117,66,270,3.3460199999999994e-44,157.513,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1256,Q#324 - >seq323,non-specific,197306,66,276,1.03271e-26,108.723,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1257,Q#324 - >seq323,non-specific,197320,64,260,3.5354300000000003e-15,75.6293,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1258,Q#324 - >seq323,specific,335306,67,262,1.9174599999999997e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1259,Q#324 - >seq323,non-specific,223780,64,259,5.689149999999999e-14,72.2459,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1260,Q#324 - >seq323,non-specific,197307,66,260,3.0499400000000002e-12,66.9277,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1261,Q#324 - >seq323,non-specific,197321,64,259,2.22207e-10,61.413999999999994,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1262,Q#324 - >seq323,non-specific,273186,64,260,1.7977100000000002e-09,58.4444,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1263,Q#324 - >seq323,non-specific,272954,64,259,1.90622e-08,55.4669,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1264,Q#324 - >seq323,non-specific,197319,64,270,1.9378e-08,55.3605,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1265,Q#324 - >seq323,non-specific,238827,428,471,5.72159e-05,44.5894,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs0_human,pars,BothTerminiTruncated
1266,Q#324 - >seq323,superfamily,295487,428,471,5.72159e-05,44.5894,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2c,ORF2,hs0_human,pars,BothTerminiTruncated
1267,Q#324 - >seq323,non-specific,197336,64,246,0.000473534,42.2143,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2c,ORF2,hs0_human,pars,CompleteHit
1268,Q#324 - >seq323,non-specific,339261,160,200,0.00524987,36.9315,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2c.ORF2.hs0_human.pars.frame1,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M2c,ORF2,hs0_human,pars,C-TerminusTruncated
1269,Q#327 - >seq326,non-specific,335182,29,111,1.36511e-24,91.5954,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs0_human.pars.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,pars,CompleteHit
1270,Q#327 - >seq326,superfamily,335182,29,111,1.36511e-24,91.5954,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2c.ORF1.hs0_human.pars.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,pars,CompleteHit
1271,Q#327 - >seq326,non-specific,340205,114,178,1.43711e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs0_human.pars.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,pars,CompleteHit
1272,Q#327 - >seq326,superfamily,340205,114,178,1.43711e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2c.ORF1.hs0_human.pars.frame3,1909122153_L1M2c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2c,ORF1,hs0_human,pars,CompleteHit
1273,Q#332 - >seq331,non-specific,340205,159,222,1.27183e-29,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs2_gorilla.marg.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,marg,CompleteHit
1274,Q#332 - >seq331,superfamily,340205,159,222,1.27183e-29,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs2_gorilla.marg.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,marg,CompleteHit
1275,Q#332 - >seq331,non-specific,335182,68,156,1.56092e-28,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs2_gorilla.marg.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,marg,CompleteHit
1276,Q#332 - >seq331,superfamily,335182,68,156,1.56092e-28,103.15100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs2_gorilla.marg.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,marg,CompleteHit
1277,Q#334 - >seq333,non-specific,335182,163,254,1.13119e-29,108.929,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs2_gorilla.pars.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,pars,CompleteHit
1278,Q#334 - >seq333,superfamily,335182,163,254,1.13119e-29,108.929,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs2_gorilla.pars.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,pars,CompleteHit
1279,Q#334 - >seq333,non-specific,340205,257,320,5.2697499999999995e-28,103.57,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs2_gorilla.pars.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,pars,CompleteHit
1280,Q#334 - >seq333,superfamily,340205,257,320,5.2697499999999995e-28,103.57,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs2_gorilla.pars.frame3,1909122154_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs2_gorilla,pars,CompleteHit
1281,Q#338 - >seq337,non-specific,335182,172,266,7.666029999999999e-29,107.00299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs3_orang.pars.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,pars,CompleteHit
1282,Q#338 - >seq337,superfamily,335182,172,266,7.666029999999999e-29,107.00299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs3_orang.pars.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,pars,CompleteHit
1283,Q#338 - >seq337,non-specific,340205,269,333,5.35378e-27,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs3_orang.pars.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,pars,CompleteHit
1284,Q#338 - >seq337,superfamily,340205,269,333,5.35378e-27,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs3_orang.pars.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,pars,CompleteHit
1285,Q#341 - >seq340,non-specific,335182,158,252,2.5286599999999996e-29,108.15899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs3_orang.marg.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,marg,CompleteHit
1286,Q#341 - >seq340,superfamily,335182,158,252,2.5286599999999996e-29,108.15899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs3_orang.marg.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,marg,CompleteHit
1287,Q#341 - >seq340,non-specific,340205,255,318,4.73247e-29,106.266,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs3_orang.marg.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,marg,CompleteHit
1288,Q#341 - >seq340,superfamily,340205,255,318,4.73247e-29,106.266,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs3_orang.marg.frame1,1909122158_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M2,ORF1,hs3_orang,marg,CompleteHit
1289,Q#343 - >seq342,non-specific,340205,178,241,1.23762e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs4_gibbon.pars.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,pars,CompleteHit
1290,Q#343 - >seq342,superfamily,340205,178,241,1.23762e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs4_gibbon.pars.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,pars,CompleteHit
1291,Q#343 - >seq342,non-specific,335182,93,175,1.9453799999999998e-22,88.1286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs4_gibbon.pars.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,pars,CompleteHit
1292,Q#343 - >seq342,superfamily,335182,93,175,1.9453799999999998e-22,88.1286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs4_gibbon.pars.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,pars,CompleteHit
1293,Q#344 - >seq343,non-specific,340205,178,241,1.5386899999999998e-28,102.8,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs4_gibbon.marg.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,marg,CompleteHit
1294,Q#344 - >seq343,superfamily,340205,178,241,1.5386899999999998e-28,102.8,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs4_gibbon.marg.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,marg,CompleteHit
1295,Q#344 - >seq343,non-specific,335182,93,175,2.28109e-22,87.7434,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs4_gibbon.marg.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,marg,CompleteHit
1296,Q#344 - >seq343,superfamily,335182,93,175,2.28109e-22,87.7434,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs4_gibbon.marg.frame3,1909122202_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs4_gibbon,marg,CompleteHit
1297,Q#349 - >seq348,non-specific,335182,161,244,7.8746e-27,101.225,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,marg,CompleteHit
1298,Q#349 - >seq348,superfamily,335182,161,244,7.8746e-27,101.225,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,marg,CompleteHit
1299,Q#349 - >seq348,non-specific,340205,247,311,2.21514e-22,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,marg,CompleteHit
1300,Q#349 - >seq348,superfamily,340205,247,311,2.21514e-22,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,marg,CompleteHit
1301,Q#349 - >seq348,non-specific,275316,48,116,0.00206576,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1M2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
1302,Q#349 - >seq348,superfamily,275316,48,116,0.00206576,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1M2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
1303,Q#349 - >seq348,non-specific,235461,39,113,0.00489892,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1M2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
1304,Q#349 - >seq348,superfamily,235461,39,113,0.00489892,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1M2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
1305,Q#349 - >seq348,non-specific,224117,29,141,0.00579985,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
1306,Q#349 - >seq348,superfamily,224117,29,141,0.00579985,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1M2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
1307,Q#349 - >seq348,non-specific,340016,9,116,0.00624568,37.4349,pfam17300,FIN1,N,cl38584,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
1308,Q#349 - >seq348,superfamily,340016,9,116,0.00624568,37.4349,cl38584,FIN1 superfamily,N, - ,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
1309,Q#349 - >seq348,non-specific,237177,33,115,0.00655113,37.8354,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1M2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
1310,Q#349 - >seq348,superfamily,237177,33,115,0.00655113,37.8354,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1M2.ORF1.hs5_gmonkey.marg.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1M2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
1311,Q#352 - >seq351,non-specific,335182,80,163,2.3477199999999996e-29,105.463,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1312,Q#352 - >seq351,superfamily,335182,80,163,2.3477199999999996e-29,105.463,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1313,Q#352 - >seq351,non-specific,340205,166,230,1.1088e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1314,Q#352 - >seq351,superfamily,340205,166,230,1.1088e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1315,Q#352 - >seq351,non-specific,340204,21,62,0.00641858,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1316,Q#352 - >seq351,superfamily,340204,21,62,0.00641858,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M2.ORF1.hs5_gmonkey.pars.frame3,1909122235_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1M2,ORF1,hs5_gmonkey,pars,CompleteHit
1317,Q#356 - >seq355,non-specific,340205,165,228,4.3862300000000004e-30,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs6_sqmonkey.pars.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,pars,CompleteHit
1318,Q#356 - >seq355,superfamily,340205,165,228,4.3862300000000004e-30,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs6_sqmonkey.pars.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,pars,CompleteHit
1319,Q#356 - >seq355,non-specific,335182,86,162,1.44086e-27,101.225,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs6_sqmonkey.pars.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1320,Q#356 - >seq355,superfamily,335182,86,162,1.44086e-27,101.225,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs6_sqmonkey.pars.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1321,Q#357 - >seq356,non-specific,340205,167,230,2.9467799999999997e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs6_sqmonkey.marg.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,marg,CompleteHit
1322,Q#357 - >seq356,superfamily,340205,167,230,2.9467799999999997e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs6_sqmonkey.marg.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,marg,CompleteHit
1323,Q#357 - >seq356,non-specific,335182,88,164,1.3225999999999999e-27,101.611,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs6_sqmonkey.marg.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1324,Q#357 - >seq356,superfamily,335182,88,164,1.3225999999999999e-27,101.611,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs6_sqmonkey.marg.frame3,1909122246_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1325,Q#362 - >seq361,non-specific,340205,196,263,2.3077699999999997e-19,79.3024,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs7_bushaby.marg.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,marg,CompleteHit
1326,Q#362 - >seq361,superfamily,340205,196,263,2.3077699999999997e-19,79.3024,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs7_bushaby.marg.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,marg,CompleteHit
1327,Q#362 - >seq361,non-specific,335182,110,193,3.49505e-14,66.5575,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.marg.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,marg,CompleteHit
1328,Q#362 - >seq361,superfamily,335182,110,193,3.49505e-14,66.5575,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.marg.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,marg,CompleteHit
1329,Q#364 - >seq363,non-specific,340205,166,233,1.7224400000000002e-20,81.6136,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,pars,CompleteHit
1330,Q#364 - >seq363,superfamily,340205,166,233,1.7224400000000002e-20,81.6136,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,pars,CompleteHit
1331,Q#364 - >seq363,non-specific,335182,119,163,2.60008e-05,41.9047,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
1332,Q#364 - >seq363,superfamily,335182,119,163,2.60008e-05,41.9047,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame2,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
1333,Q#366 - >seq365,non-specific,335182,78,128,3.70965e-08,49.6087,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame1,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs7_bushaby,pars,C-TerminusTruncated
1334,Q#366 - >seq365,superfamily,335182,78,128,3.70965e-08,49.6087,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs7_bushaby.pars.frame1,1909122303_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M2,ORF1,hs7_bushaby,pars,C-TerminusTruncated
1335,Q#367 - >seq366,non-specific,334380,320,394,0.00210445,39.5797,pfam01086,Clathrin_lg_ch,N,cl03091,Clathrin light chain; Clathrin light chain.  ,L1M2.ORF2.hs7_bushaby.pars.frame1,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
1336,Q#367 - >seq366,superfamily,334380,320,394,0.00210445,39.5797,cl03091,Clathrin_lg_ch superfamily,N, - ,Clathrin light chain; Clathrin light chain.  ,L1M2.ORF2.hs7_bushaby.pars.frame1,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
1337,Q#368 - >seq367,non-specific,308206,224,436,0.0011991,41.4961,pfam02463,SMC_N,C,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1M2.ORF2.hs7_bushaby.pars.frame2,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1338,Q#368 - >seq367,superfamily,308206,224,436,0.0011991,41.4961,cl37666,SMC_N superfamily,C, - ,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1M2.ORF2.hs7_bushaby.pars.frame2,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1339,Q#369 - >seq368,non-specific,197310,7,215,7.584949999999999e-20,88.1773,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,pars,CompleteHit
1340,Q#369 - >seq368,superfamily,351117,7,215,7.584949999999999e-20,88.1773,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs7_bushaby,pars,CompleteHit
1341,Q#369 - >seq368,non-specific,197306,7,200,1.1492e-08,55.5653,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs7_bushaby,pars,CompleteHit
1342,Q#369 - >seq368,non-specific,223780,7,42,0.000278784,42.5855,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1343,Q#369 - >seq368,non-specific,197307,7,42,0.000311381,42.2749,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1344,Q#369 - >seq368,non-specific,272954,7,42,0.0007039360000000001,41.2145,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1345,Q#369 - >seq368,non-specific,273186,7,42,0.000813065,41.1104,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1346,Q#369 - >seq368,non-specific,197321,6,48,0.00307763,39.0724,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs7_bushaby.pars.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1347,Q#371 - >seq370,non-specific,197310,145,222,2.32353e-06,48.8869,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs7_bushaby.marg.frame2,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
1348,Q#371 - >seq370,superfamily,351117,145,222,2.32353e-06,48.8869,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs7_bushaby.marg.frame2,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
1349,Q#372 - >seq371,non-specific,197310,9,142,3.28245e-15,75.0805,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1350,Q#372 - >seq371,superfamily,351117,9,142,3.28245e-15,75.0805,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1351,Q#372 - >seq371,non-specific,197306,9,128,2.51038e-07,51.7133,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1352,Q#372 - >seq371,non-specific,197307,9,45,0.00531987,38.4229,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1353,Q#372 - >seq371,non-specific,197321,8,51,0.00842695,37.9168,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1354,Q#372 - >seq371,non-specific,223780,9,45,0.00906649,37.9631,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs7_bushaby.marg.frame3,1909122309_L1M2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1355,Q#373 - >seq372,non-specific,340205,261,324,8.38528e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs0_human.marg.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,marg,CompleteHit
1356,Q#373 - >seq372,superfamily,340205,261,324,8.38528e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs0_human.marg.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,marg,CompleteHit
1357,Q#373 - >seq372,non-specific,335182,166,258,2.8993900000000003e-24,94.677,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs0_human.marg.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,marg,CompleteHit
1358,Q#373 - >seq372,superfamily,335182,166,258,2.8993900000000003e-24,94.677,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs0_human.marg.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,marg,CompleteHit
1359,Q#378 - >seq377,non-specific,340205,241,304,5.38353e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs0_human.pars.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,pars,CompleteHit
1360,Q#378 - >seq377,superfamily,340205,241,304,5.38353e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M2.ORF1.hs0_human.pars.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,pars,CompleteHit
1361,Q#378 - >seq377,non-specific,335182,146,238,1.25284e-24,95.4474,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs0_human.pars.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,pars,CompleteHit
1362,Q#378 - >seq377,superfamily,335182,146,238,1.25284e-24,95.4474,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M2.ORF1.hs0_human.pars.frame3,1909122310_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M2,ORF1,hs0_human,pars,CompleteHit
1363,Q#380 - >seq379,non-specific,340205,145,214,1.0470999999999999e-07,47.3308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs3_orang.marg.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3d,ORF1,hs3_orang,marg,CompleteHit
1364,Q#380 - >seq379,superfamily,340205,145,214,1.0470999999999999e-07,47.3308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs3_orang.marg.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3d,ORF1,hs3_orang,marg,CompleteHit
1365,Q#387 - >seq386,non-specific,197310,73,306,8.55525e-20,89.7181,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3d,ORF2,hs2_gorilla,marg,CompleteHit
1366,Q#387 - >seq386,superfamily,351117,73,306,8.55525e-20,89.7181,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3d,ORF2,hs2_gorilla,marg,CompleteHit
1367,Q#387 - >seq386,non-specific,238827,639,798,2.38728e-11,64.6198,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3d,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1368,Q#387 - >seq386,superfamily,295487,639,798,2.38728e-11,64.6198,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3d,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1369,Q#387 - >seq386,non-specific,197306,73,302,8.46657e-05,45.1649,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3d,ORF2,hs2_gorilla,marg,CompleteHit
1370,Q#388 - >seq387,non-specific,238827,505,538,1.60775e-06,49.9822,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3d,ORF2,hs1_chimp,marg,C-TerminusTruncated
1371,Q#388 - >seq387,superfamily,295487,505,538,1.60775e-06,49.9822,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3d,ORF2,hs1_chimp,marg,C-TerminusTruncated
1372,Q#399 - >seq398,non-specific,197310,62,220,6.64652e-13,68.5321,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs2_gorilla.pars.frame2,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3d,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1373,Q#399 - >seq398,superfamily,351117,62,220,6.64652e-13,68.5321,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs2_gorilla.pars.frame2,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1374,Q#399 - >seq398,non-specific,197306,19,216,0.00019931700000000002,43.2389,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs2_gorilla.pars.frame2,1909122337_L1M3d.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs2_gorilla,pars,CompleteHit
1375,Q#400 - >seq399,non-specific,197310,17,196,1.99646e-17,81.6289,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs3_orang.pars.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3d,ORF2,hs3_orang,pars,CompleteHit
1376,Q#400 - >seq399,superfamily,351117,17,196,1.99646e-17,81.6289,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs3_orang.pars.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs3_orang,pars,CompleteHit
1377,Q#400 - >seq399,non-specific,197306,15,213,1.17026e-08,55.9505,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs3_orang.pars.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs3_orang,pars,CompleteHit
1378,Q#400 - >seq399,specific,335306,18,195,9.38348e-07,49.9362,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3d.ORF2.hs3_orang.pars.frame2,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs3_orang,pars,CompleteHit
1379,Q#401 - >seq400,non-specific,197310,24,194,9.95176e-14,70.4581,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3d,ORF2,hs7_bushaby,pars,CompleteHit
1380,Q#401 - >seq400,superfamily,351117,24,194,9.95176e-14,70.4581,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs7_bushaby,pars,CompleteHit
1381,Q#401 - >seq400,non-specific,197320,117,184,2.97014e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3d,ORF2,hs7_bushaby,pars,N-TerminusTruncated
1382,Q#401 - >seq400,specific,335306,24,186,1.0318199999999999e-05,46.4694,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs7_bushaby,pars,CompleteHit
1383,Q#401 - >seq400,non-specific,339261,92,184,0.00146091,38.0871,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M3d,ORF2,hs7_bushaby,pars,C-TerminusTruncated
1384,Q#401 - >seq400,non-specific,197306,55,205,0.00382175,38.6165,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs7_bushaby,pars,N-TerminusTruncated
1385,Q#403 - >seq402,non-specific,238827,552,708,8.47331e-05,44.9746,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs1_chimp.marg.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3d,ORF2,hs1_chimp,marg,C-TerminusTruncated
1386,Q#403 - >seq402,superfamily,295487,552,708,8.47331e-05,44.9746,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs1_chimp.marg.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3d,ORF2,hs1_chimp,marg,C-TerminusTruncated
1387,Q#407 - >seq406,non-specific,340205,106,139,1.36534e-06,43.0936,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs0_human.marg.frame1,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs0_human,marg,N-TerminusTruncated
1388,Q#407 - >seq406,superfamily,340205,106,139,1.36534e-06,43.0936,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs0_human.marg.frame1,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs0_human,marg,N-TerminusTruncated
1389,Q#407 - >seq406,non-specific,335182,11,68,6.4149e-06,41.9047,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs0_human.marg.frame1,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs0_human,marg,N-TerminusTruncated
1390,Q#407 - >seq406,superfamily,335182,11,68,6.4149e-06,41.9047,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs0_human.marg.frame1,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs0_human,marg,N-TerminusTruncated
1391,Q#409 - >seq408,non-specific,335182,3,53,4.71962e-07,43.8307,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs0_human.pars.frame2,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3d,ORF1,hs0_human,pars,N-TerminusTruncated
1392,Q#409 - >seq408,superfamily,335182,3,53,4.71962e-07,43.8307,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs0_human.pars.frame2,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3d,ORF1,hs0_human,pars,N-TerminusTruncated
1393,Q#413 - >seq412,non-specific,197310,43,265,6.842660000000001e-06,47.7313,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3d,ORF2,hs7_bushaby,marg,CompleteHit
1394,Q#413 - >seq412,superfamily,351117,43,265,6.842660000000001e-06,47.7313,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3d,ORF2,hs7_bushaby,marg,CompleteHit
1395,Q#413 - >seq412,non-specific,238827,604,708,9.83962e-06,47.2858,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3d,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1396,Q#413 - >seq412,superfamily,295487,604,708,9.83962e-06,47.2858,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3d,ORF2,hs7_bushaby,marg,C-TerminusTruncated
1397,Q#413 - >seq412,non-specific,223780,146,216,0.00346729,39.8891,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3d.ORF2.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3d,ORF2,hs7_bushaby,marg,BothTerminiTruncated
1398,Q#416 - >seq415,non-specific,340205,119,167,1.33728e-05,41.1676,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs7_bushaby.marg.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3d,ORF1,hs7_bushaby,marg,C-TerminusTruncated
1399,Q#416 - >seq415,superfamily,340205,119,167,1.33728e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs7_bushaby.marg.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3d,ORF1,hs7_bushaby,marg,C-TerminusTruncated
1400,Q#418 - >seq417,non-specific,335182,48,107,1.12811e-09,53.4607,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs7_bushaby,marg,N-TerminusTruncated
1401,Q#418 - >seq417,superfamily,335182,48,107,1.12811e-09,53.4607,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3d.ORF1.hs7_bushaby.marg.frame1,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs7_bushaby,marg,N-TerminusTruncated
1402,Q#419 - >seq418,non-specific,340205,61,101,0.000517254,35.3896,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3d,ORF1,hs7_bushaby,pars,C-TerminusTruncated
1403,Q#419 - >seq418,superfamily,340205,61,101,0.000517254,35.3896,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs7_bushaby.pars.frame3,1909122337_L1M3d.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3d,ORF1,hs7_bushaby,pars,C-TerminusTruncated
1404,Q#422 - >seq421,non-specific,197310,2,259,1.75582e-20,91.2589,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs3_orang.marg.frame3,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3d,ORF2,hs3_orang,marg,CompleteHit
1405,Q#422 - >seq421,superfamily,351117,2,259,1.75582e-20,91.2589,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs3_orang.marg.frame3,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs3_orang,marg,CompleteHit
1406,Q#422 - >seq421,non-specific,238827,535,624,3.4231900000000004e-07,51.9082,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs3_orang.marg.frame3,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3d,ORF2,hs3_orang,marg,C-TerminusTruncated
1407,Q#422 - >seq421,superfamily,295487,535,624,3.4231900000000004e-07,51.9082,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs3_orang.marg.frame3,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3d,ORF2,hs3_orang,marg,C-TerminusTruncated
1408,Q#422 - >seq421,non-specific,197306,2,242,6.76903e-06,48.2465,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs3_orang.marg.frame3,1909122337_L1M3d.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs3_orang,marg,CompleteHit
1409,Q#425 - >seq424,specific,197310,44,217,6.538629999999999e-33,127.46799999999999,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1410,Q#425 - >seq424,superfamily,351117,44,217,6.538629999999999e-33,127.46799999999999,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1411,Q#425 - >seq424,non-specific,197306,48,214,2.17726e-11,64.8101,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1412,Q#425 - >seq424,non-specific,197320,96,199,8.12471e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1413,Q#425 - >seq424,non-specific,223780,96,218,0.000561116,42.5855,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1414,Q#425 - >seq424,non-specific,197307,96,214,0.00218725,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3d.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3d,ORF2,hs1_chimp,marg,N-TerminusTruncated
1415,Q#426 - >seq425,non-specific,197310,6,254,1.7505e-15,76.2361,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs4_gibbon,marg,CompleteHit
1416,Q#426 - >seq425,superfamily,351117,6,254,1.7505e-15,76.2361,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs4_gibbon,marg,CompleteHit
1417,Q#427 - >seq426,specific,197310,13,209,4.65555e-33,126.697,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1418,Q#427 - >seq426,superfamily,351117,13,209,4.65555e-33,126.697,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1419,Q#427 - >seq426,non-specific,197306,6,209,8.76739e-12,65.1953,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1420,Q#427 - >seq426,non-specific,197307,1,202,9.87722e-07,50.3641,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1421,Q#427 - >seq426,non-specific,197319,1,209,0.00016367,43.4193,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1422,Q#427 - >seq426,non-specific,223780,81,202,0.000515825,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3d,ORF2,hs1_chimp,pars,N-TerminusTruncated
1423,Q#427 - >seq426,specific,335306,6,202,0.000963158,40.6914,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1424,Q#427 - >seq426,non-specific,273186,81,210,0.00111437,40.7252,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3d,ORF2,hs1_chimp,pars,N-TerminusTruncated
1425,Q#427 - >seq426,non-specific,339261,83,204,0.00487012,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M3d,ORF2,hs1_chimp,pars,CompleteHit
1426,Q#427 - >seq426,non-specific,335313,56,149,0.009117499999999999,38.5768,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3d,ORF2,hs1_chimp,pars,N-TerminusTruncated
1427,Q#427 - >seq426,superfamily,354836,56,149,0.009117499999999999,38.5768,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1M3d.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3d,ORF2,hs1_chimp,pars,N-TerminusTruncated
1428,Q#429 - >seq428,non-specific,340205,151,215,1.6891700000000002e-22,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs6_sqmonkey,marg,CompleteHit
1429,Q#429 - >seq428,superfamily,340205,151,215,1.6891700000000002e-22,86.6212,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs6_sqmonkey,marg,CompleteHit
1430,Q#429 - >seq428,non-specific,335182,58,148,3.1342399999999997e-09,52.3051,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs6_sqmonkey,marg,CompleteHit
1431,Q#429 - >seq428,superfamily,335182,58,148,3.1342399999999997e-09,52.3051,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs6_sqmonkey,marg,CompleteHit
1432,Q#430 - >seq429,non-specific,340205,125,189,1.6367e-22,85.8508,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs6_sqmonkey,pars,CompleteHit
1433,Q#430 - >seq429,superfamily,340205,125,189,1.6367e-22,85.8508,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs6_sqmonkey,pars,CompleteHit
1434,Q#430 - >seq429,non-specific,335182,47,122,3.2648200000000004e-18,75.4171,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1435,Q#430 - >seq429,superfamily,335182,47,122,3.2648200000000004e-18,75.4171,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1436,Q#433 - >seq432,non-specific,197310,132,212,1.16395e-07,52.7389,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1437,Q#433 - >seq432,superfamily,351117,132,212,1.16395e-07,52.7389,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1438,Q#433 - >seq432,non-specific,238827,505,583,1.5173199999999999e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1439,Q#433 - >seq432,superfamily,295487,505,583,1.5173199999999999e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1440,Q#435 - >seq434,non-specific,197310,10,76,3.4088199999999996e-06,48.1165,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs5_gmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1441,Q#435 - >seq434,superfamily,351117,10,76,3.4088199999999996e-06,48.1165,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs5_gmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1442,Q#435 - >seq434,non-specific,197306,10,88,0.000201785,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs5_gmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1443,Q#435 - >seq434,non-specific,197307,10,90,0.00608743,38.4229,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs5_gmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3de,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1444,Q#436 - >seq435,non-specific,197310,3,168,2.8611599999999997e-07,50.4277,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs5_gmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs5_gmonkey,pars,CompleteHit
1445,Q#436 - >seq435,superfamily,351117,3,168,2.8611599999999997e-07,50.4277,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs5_gmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs5_gmonkey,pars,CompleteHit
1446,Q#436 - >seq435,non-specific,197306,3,82,8.116939999999999e-07,49.0169,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs5_gmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1447,Q#436 - >seq435,non-specific,223780,1,37,0.00787596,37.1927,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs5_gmonkey.pars.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1448,Q#439 - >seq438,non-specific,340205,116,178,5.36846e-24,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs5_gmonkey,marg,CompleteHit
1449,Q#439 - >seq438,superfamily,340205,116,178,5.36846e-24,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs5_gmonkey,marg,CompleteHit
1450,Q#439 - >seq438,non-specific,335182,20,113,1.1500500000000001e-20,81.5803,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs5_gmonkey,marg,CompleteHit
1451,Q#439 - >seq438,superfamily,335182,20,113,1.1500500000000001e-20,81.5803,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs5_gmonkey,marg,CompleteHit
1452,Q#443 - >seq442,non-specific,335182,40,107,6.05193e-14,63.8611,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame2,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
1453,Q#443 - >seq442,superfamily,335182,40,107,6.05193e-14,63.8611,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame2,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
1454,Q#443 - >seq442,non-specific,340205,110,129,0.007412,33.4636,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame2,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
1455,Q#443 - >seq442,superfamily,340205,110,129,0.007412,33.4636,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame2,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
1456,Q#444 - >seq443,non-specific,340205,123,172,1.43748e-14,64.6648,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,CompleteHit
1457,Q#444 - >seq443,superfamily,340205,123,172,1.43748e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs5_gmonkey.pars.frame1,1909122337_L1M3de.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs5_gmonkey,pars,CompleteHit
1458,Q#445 - >seq444,non-specific,197310,1,206,7.780409999999999e-21,91.6441,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs0_human.pars.frame3,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3d,ORF2,hs0_human,pars,CompleteHit
1459,Q#445 - >seq444,superfamily,351117,1,206,7.780409999999999e-21,91.6441,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs0_human.pars.frame3,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs0_human,pars,CompleteHit
1460,Q#445 - >seq444,non-specific,197306,1,201,2.41819e-05,45.9353,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs0_human.pars.frame3,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs0_human,pars,CompleteHit
1461,Q#447 - >seq446,non-specific,238827,524,640,2.7233299999999996e-20,90.04299999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1462,Q#447 - >seq446,superfamily,295487,524,640,2.7233299999999996e-20,90.04299999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1463,Q#447 - >seq446,non-specific,333820,543,647,1.06095e-05,46.5166,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1464,Q#447 - >seq446,superfamily,333820,543,647,1.06095e-05,46.5166,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1465,Q#447 - >seq446,non-specific,214395,249,480,0.000618637,43.1686,CHL00204,ycf1,NC,cl33340,Ycf1; Provisional,L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M3de,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1466,Q#447 - >seq446,superfamily,214395,249,480,0.000618637,43.1686,cl33340,ycf1 superfamily,NC, - ,Ycf1; Provisional,L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M3de,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1467,Q#447 - >seq446,non-specific,222878,323,513,0.000978182,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3de,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1468,Q#447 - >seq446,superfamily,222878,323,513,0.000978182,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1M3de.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3de,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1469,Q#448 - >seq447,non-specific,197310,6,213,1.52924e-09,58.1317,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs4_gibbon,pars,CompleteHit
1470,Q#448 - >seq447,superfamily,351117,6,213,1.52924e-09,58.1317,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs4_gibbon,pars,CompleteHit
1471,Q#448 - >seq447,non-specific,340095,140,439,4.47589e-05,45.974,pfam17380,DUF5401,N,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3de,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1472,Q#448 - >seq447,superfamily,340095,140,439,4.47589e-05,45.974,cl38662,DUF5401 superfamily,N, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3de,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1473,Q#448 - >seq447,non-specific,238827,499,532,4.84713e-05,44.5894,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1474,Q#448 - >seq447,superfamily,295487,499,532,4.84713e-05,44.5894,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1475,Q#448 - >seq447,non-specific,225087,98,337,0.00123727,41.5357,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3de,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1476,Q#448 - >seq447,superfamily,225087,98,337,0.00123727,41.5357,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3de,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1477,Q#448 - >seq447,non-specific,222878,270,444,0.0013164000000000001,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs4_gibbon,pars,BothTerminiTruncated
1478,Q#448 - >seq447,superfamily,222878,270,444,0.0013164000000000001,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs4_gibbon,pars,BothTerminiTruncated
1479,Q#448 - >seq447,non-specific,197306,6,113,0.00344981,39.0017,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1480,Q#450 - >seq449,non-specific,238827,435,468,9.876940000000001e-07,49.597,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3d,ORF2,hs1_chimp,pars,C-TerminusTruncated
1481,Q#450 - >seq449,superfamily,295487,435,468,9.876940000000001e-07,49.597,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3d,ORF2,hs1_chimp,pars,C-TerminusTruncated
1482,Q#451 - >seq450,non-specific,197310,19,181,0.000193523,40.7977,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3de,ORF2,hs6_sqmonkey,pars,CompleteHit
1483,Q#451 - >seq450,superfamily,351117,19,181,0.000193523,40.7977,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs6_sqmonkey,pars,CompleteHit
1484,Q#456 - >seq455,non-specific,340205,186,227,1.70662e-05,41.1676,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs1_chimp,marg,N-TerminusTruncated
1485,Q#456 - >seq455,superfamily,340205,186,227,1.70662e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3d,ORF1,hs1_chimp,marg,N-TerminusTruncated
1486,Q#457 - >seq456,non-specific,340205,81,136,4.94803e-09,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3d,ORF1,hs1_chimp,pars,CompleteHit
1487,Q#457 - >seq456,superfamily,340205,81,136,4.94803e-09,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3d.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3d.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3d,ORF1,hs1_chimp,pars,CompleteHit
1488,Q#459 - >seq458,non-specific,197310,151,204,0.000752104,41.5681,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs0_human.marg.frame3,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs0_human,marg,N-TerminusTruncated
1489,Q#459 - >seq458,superfamily,351117,151,204,0.000752104,41.5681,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs0_human.marg.frame3,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,marg,N-TerminusTruncated
1490,Q#460 - >seq459,non-specific,197310,35,163,1.0705999999999998e-19,88.5625,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs0_human.marg.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1491,Q#460 - >seq459,superfamily,351117,35,163,1.0705999999999998e-19,88.5625,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs0_human.marg.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1492,Q#460 - >seq459,non-specific,197306,49,182,5.45852e-09,57.1061,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs0_human.marg.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1493,Q#461 - >seq460,non-specific,238827,514,617,4.7935500000000004e-21,91.969,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1494,Q#461 - >seq460,superfamily,295487,514,617,4.7935500000000004e-21,91.969,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1495,Q#461 - >seq460,non-specific,333820,522,631,1.41234e-07,51.9094,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1496,Q#461 - >seq460,superfamily,333820,522,631,1.41234e-07,51.9094,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs0_human,marg,C-TerminusTruncated
1497,Q#463 - >seq462,specific,197310,3,207,3.2411599999999996e-34,125.156,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3de,ORF2,hs0_human,pars,CompleteHit
1498,Q#463 - >seq462,superfamily,351117,3,207,3.2411599999999996e-34,125.156,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,pars,CompleteHit
1499,Q#463 - >seq462,non-specific,197306,3,197,1.32469e-14,72.1289,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,pars,CompleteHit
1500,Q#463 - >seq462,non-specific,197320,96,184,7.343640000000001e-07,49.4358,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3de,ORF2,hs0_human,pars,BothTerminiTruncated
1501,Q#463 - >seq462,non-specific,223780,1,184,2.59381e-06,47.9783,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3de,ORF2,hs0_human,pars,C-TerminusTruncated
1502,Q#463 - >seq462,non-specific,197307,3,184,3.4975699999999994e-06,47.2825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3de,ORF2,hs0_human,pars,CompleteHit
1503,Q#463 - >seq462,specific,335306,4,192,1.2921099999999999e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs0_human,pars,CompleteHit
1504,Q#463 - >seq462,non-specific,272954,1,184,2.4940500000000003e-05,44.6813,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3de.ORF2.hs0_human.pars.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3de,ORF2,hs0_human,pars,C-TerminusTruncated
1505,Q#466 - >seq465,non-specific,340205,153,215,1.70601e-19,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs0_human.marg.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3de,ORF1,hs0_human,marg,CompleteHit
1506,Q#466 - >seq465,superfamily,340205,153,215,1.70601e-19,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs0_human.marg.frame2,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3de,ORF1,hs0_human,marg,CompleteHit
1507,Q#467 - >seq466,non-specific,335182,89,149,7.438560000000001e-16,70.4095,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,marg,N-TerminusTruncated
1508,Q#467 - >seq466,superfamily,335182,89,149,7.438560000000001e-16,70.4095,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs0_human.marg.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,marg,N-TerminusTruncated
1509,Q#470 - >seq469,non-specific,340205,126,187,1.9458e-16,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs0_human.pars.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,pars,CompleteHit
1510,Q#470 - >seq469,superfamily,340205,126,187,1.9458e-16,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs0_human.pars.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,pars,CompleteHit
1511,Q#470 - >seq469,non-specific,335182,49,109,4.4615000000000004e-15,67.3279,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs0_human.pars.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,pars,N-TerminusTruncated
1512,Q#470 - >seq469,superfamily,335182,49,109,4.4615000000000004e-15,67.3279,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs0_human.pars.frame1,1909122337_L1M3de.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs0_human,pars,N-TerminusTruncated
1513,Q#473 - >seq472,non-specific,197310,20,238,0.000125316,43.4941,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3de,ORF2,hs6_sqmonkey,marg,CompleteHit
1514,Q#473 - >seq472,superfamily,351117,20,238,0.000125316,43.4941,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs6_sqmonkey,marg,CompleteHit
1515,Q#473 - >seq472,non-specific,238827,526,610,0.000152616,43.0486,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1516,Q#473 - >seq472,superfamily,295487,526,610,0.000152616,43.0486,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3de.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3de,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1517,Q#477 - >seq476,non-specific,197310,2,242,3.40441e-19,87.4069,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3d.ORF2.hs0_human.marg.frame3,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3d,ORF2,hs0_human,marg,CompleteHit
1518,Q#477 - >seq476,superfamily,351117,2,242,3.40441e-19,87.4069,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3d.ORF2.hs0_human.marg.frame3,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3d,ORF2,hs0_human,marg,CompleteHit
1519,Q#478 - >seq477,non-specific,197310,2,183,4.7088e-06,47.3461,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs6_sqmonkey,marg,CompleteHit
1520,Q#478 - >seq477,superfamily,351117,2,183,4.7088e-06,47.3461,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs6_sqmonkey,marg,CompleteHit
1521,Q#482 - >seq481,non-specific,197310,59,179,1.2514100000000001e-05,44.2645,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs6_sqmonkey.pars.frame2,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3e,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1522,Q#482 - >seq481,superfamily,351117,59,179,1.2514100000000001e-05,44.2645,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs6_sqmonkey.pars.frame2,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3e,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1523,Q#484 - >seq483,non-specific,335182,1,79,5.934739999999999e-17,71.5651,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1524,Q#484 - >seq483,superfamily,335182,1,79,5.934739999999999e-17,71.5651,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1525,Q#484 - >seq483,non-specific,340205,128,155,0.00041668099999999996,36.9304,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1526,Q#484 - >seq483,superfamily,340205,128,155,0.00041668099999999996,36.9304,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs6_sqmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
1527,Q#487 - >seq486,non-specific,335182,1,77,2.1446899999999998e-15,66.9427,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1528,Q#487 - >seq486,superfamily,335182,1,77,2.1446899999999998e-15,66.9427,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1529,Q#487 - >seq486,non-specific,340205,95,146,0.000221145,37.3156,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1530,Q#487 - >seq486,superfamily,340205,95,146,0.000221145,37.3156,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs6_sqmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
1531,Q#490 - >seq489,non-specific,197310,24,213,3.66115e-13,67.3765,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs5_gmonkey,marg,CompleteHit
1532,Q#490 - >seq489,superfamily,351117,24,213,3.66115e-13,67.3765,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs5_gmonkey,marg,CompleteHit
1533,Q#490 - >seq489,non-specific,197320,113,222,0.000288773,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3e.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1534,Q#490 - >seq489,non-specific,197306,24,208,0.00133978,39.3869,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs5_gmonkey,marg,CompleteHit
1535,Q#498 - >seq497,non-specific,335182,69,154,4.43234e-15,68.4835,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs5_gmonkey.marg.frame1,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs5_gmonkey,marg,CompleteHit
1536,Q#498 - >seq497,superfamily,335182,69,154,4.43234e-15,68.4835,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs5_gmonkey.marg.frame1,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs5_gmonkey,marg,CompleteHit
1537,Q#499 - >seq498,non-specific,335182,64,133,5.20205e-05,40.3639,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs0_human.pars.frame1,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3e,ORF1,hs0_human,pars,N-TerminusTruncated
1538,Q#499 - >seq498,superfamily,335182,64,133,5.20205e-05,40.3639,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs0_human.pars.frame1,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3e,ORF1,hs0_human,pars,N-TerminusTruncated
1539,Q#500 - >seq499,non-specific,340205,142,191,0.00376849,34.6192,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs5_gmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs5_gmonkey,pars,CompleteHit
1540,Q#500 - >seq499,superfamily,340205,142,191,0.00376849,34.6192,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs5_gmonkey.pars.frame3,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs5_gmonkey,pars,CompleteHit
1541,Q#504 - >seq503,non-specific,197310,3,57,1.03245e-11,65.8357,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1542,Q#504 - >seq503,superfamily,351117,3,57,1.03245e-11,65.8357,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1543,Q#504 - >seq503,non-specific,197306,3,53,2.2171500000000002e-07,52.8689,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1544,Q#504 - >seq503,non-specific,223780,1,37,2.8920599999999995e-06,49.9043,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1545,Q#504 - >seq503,non-specific,197321,1,54,2.11259e-05,47.1616,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1546,Q#504 - >seq503,non-specific,197320,1,37,4.3047600000000004e-05,46.3542,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1547,Q#504 - >seq503,specific,335306,4,185,4.69985e-05,45.699,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1548,Q#504 - >seq503,non-specific,272954,1,47,7.64167e-05,45.4517,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1549,Q#504 - >seq503,non-specific,197307,3,37,0.000183229,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1550,Q#504 - >seq503,non-specific,197336,1,37,0.000265451,43.7551,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1551,Q#504 - >seq503,non-specific,273186,1,47,0.000362764,43.4216,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1552,Q#504 - >seq503,non-specific,197319,1,37,0.00272369,40.7229,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,C-TerminusTruncated
1553,Q#506 - >seq505,specific,238827,506,752,6.0410599999999995e-46,164.386,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1554,Q#506 - >seq505,superfamily,295487,506,752,6.0410599999999995e-46,164.386,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1555,Q#506 - >seq505,specific,197310,43,222,7.12952e-37,139.024,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1556,Q#506 - >seq505,superfamily,351117,43,222,7.12952e-37,139.024,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1557,Q#506 - >seq505,non-specific,333820,516,752,1.13834e-23,99.2889,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1558,Q#506 - >seq505,superfamily,333820,516,752,1.13834e-23,99.2889,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1559,Q#506 - >seq505,non-specific,197306,50,222,7.28797e-17,80.9884,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1560,Q#506 - >seq505,non-specific,197320,40,195,5.22019e-12,67.155,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1561,Q#506 - >seq505,non-specific,223780,93,215,1.12192e-08,57.2231,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1562,Q#506 - >seq505,non-specific,197307,93,222,1.8652400000000002e-08,56.5273,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1563,Q#506 - >seq505,non-specific,238828,562,717,1.49332e-07,53.3588,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1564,Q#506 - >seq505,non-specific,273186,93,223,9.59175e-07,51.1256,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1565,Q#506 - >seq505,specific,335306,49,215,1.16137e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1566,Q#506 - >seq505,non-specific,197319,93,222,4.31705e-06,49.1973,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1567,Q#506 - >seq505,non-specific,272954,93,194,6.877189999999999e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1568,Q#506 - >seq505,non-specific,197321,93,222,9.41445e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1569,Q#506 - >seq505,non-specific,339261,95,218,0.000608069,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M3f,ORF2,hs1_chimp,marg,CompleteHit
1570,Q#506 - >seq505,non-specific,275209,564,771,0.00107901,42.4448,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1571,Q#506 - >seq505,superfamily,275209,564,771,0.00107901,42.4448,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1572,Q#506 - >seq505,non-specific,197311,58,222,0.00189827,40.7381,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,marg,N-TerminusTruncated
1573,Q#508 - >seq507,specific,238827,506,752,2.50612e-46,165.542,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1574,Q#508 - >seq507,superfamily,295487,506,752,2.50612e-46,165.542,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1575,Q#508 - >seq507,specific,197310,43,222,2.9999299999999997e-37,139.79399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1576,Q#508 - >seq507,superfamily,351117,43,222,2.9999299999999997e-37,139.79399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1577,Q#508 - >seq507,non-specific,333820,516,752,5.84039e-24,100.059,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1578,Q#508 - >seq507,superfamily,333820,516,752,5.84039e-24,100.059,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1579,Q#508 - >seq507,non-specific,197306,50,222,3.2244e-17,82.14399999999999,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1580,Q#508 - >seq507,non-specific,197320,40,195,4.56503e-12,67.155,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1581,Q#508 - >seq507,non-specific,223780,93,215,9.46614e-09,57.2231,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1582,Q#508 - >seq507,non-specific,197307,93,222,1.63414e-08,56.5273,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1583,Q#508 - >seq507,non-specific,238828,562,717,1.229e-07,53.3588,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1584,Q#508 - >seq507,non-specific,273186,93,223,9.047e-07,51.1256,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1585,Q#508 - >seq507,specific,335306,49,215,1.02087e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1586,Q#508 - >seq507,non-specific,197319,93,222,4.9307e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1587,Q#508 - >seq507,non-specific,272954,93,194,6.09426e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1588,Q#508 - >seq507,non-specific,197321,93,222,0.000100844,44.8504,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1589,Q#508 - >seq507,non-specific,339261,95,218,0.000320021,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1590,Q#508 - >seq507,non-specific,197311,58,222,0.00167324,40.7381,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,N-TerminusTruncated
1591,Q#508 - >seq507,non-specific,275209,564,717,0.00227953,41.2892,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,BothTerminiTruncated
1592,Q#508 - >seq507,superfamily,275209,564,717,0.00227953,41.2892,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs1_chimp,pars,BothTerminiTruncated
1593,Q#509 - >seq508,non-specific,197310,4,58,1.39234e-11,65.4505,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1594,Q#509 - >seq508,superfamily,351117,4,58,1.39234e-11,65.4505,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1595,Q#509 - >seq508,non-specific,197306,4,54,2.4262699999999997e-07,52.8689,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1596,Q#509 - >seq508,non-specific,223780,2,38,3.2686099999999998e-06,49.5191,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1597,Q#509 - >seq508,non-specific,197321,2,38,2.5235100000000002e-05,46.7764,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1598,Q#509 - >seq508,non-specific,197320,2,38,3.74606e-05,46.3542,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1599,Q#509 - >seq508,specific,335306,5,186,4.09943e-05,45.699,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs1_chimp,pars,CompleteHit
1600,Q#509 - >seq508,non-specific,272954,2,48,0.000106321,44.6813,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1601,Q#509 - >seq508,non-specific,197307,4,38,0.00022886,43.8157,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1602,Q#509 - >seq508,non-specific,197336,2,38,0.000231207,43.7551,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1603,Q#509 - >seq508,non-specific,273186,2,48,0.00045267800000000003,43.0364,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1604,Q#509 - >seq508,non-specific,197319,2,38,0.00327793,40.3377,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs1_chimp,pars,C-TerminusTruncated
1605,Q#510 - >seq509,non-specific,335182,75,171,1.41035e-29,106.23299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs1_chimp,marg,CompleteHit
1606,Q#510 - >seq509,superfamily,335182,75,171,1.41035e-29,106.23299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs1_chimp,marg,CompleteHit
1607,Q#510 - >seq509,non-specific,340205,175,237,2.5656599999999996e-25,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs1_chimp,marg,CompleteHit
1608,Q#510 - >seq509,superfamily,340205,175,237,2.5656599999999996e-25,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs1_chimp,marg,CompleteHit
1609,Q#514 - >seq513,non-specific,335182,76,172,6.03429e-29,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs1_chimp,pars,CompleteHit
1610,Q#514 - >seq513,superfamily,335182,76,172,6.03429e-29,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs1_chimp,pars,CompleteHit
1611,Q#514 - >seq513,non-specific,340205,176,238,1.46666e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs1_chimp,pars,CompleteHit
1612,Q#514 - >seq513,superfamily,340205,176,238,1.46666e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3f.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs1_chimp,pars,CompleteHit
1613,Q#516 - >seq515,non-specific,197310,7,206,7.25571e-10,59.2873,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs0_human,marg,CompleteHit
1614,Q#516 - >seq515,superfamily,351117,7,206,7.25571e-10,59.2873,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs0_human,marg,CompleteHit
1615,Q#516 - >seq515,non-specific,197306,7,153,1.35137e-06,49.7873,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs0_human,marg,C-TerminusTruncated
1616,Q#516 - >seq515,non-specific,223780,7,44,0.00999863,37.9631,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3e.ORF2.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs0_human,marg,C-TerminusTruncated
1617,Q#522 - >seq521,non-specific,335182,2,38,0.000996982,32.6599,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs0_human,marg,BothTerminiTruncated
1618,Q#522 - >seq521,superfamily,335182,2,38,0.000996982,32.6599,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs0_human.marg.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs0_human,marg,BothTerminiTruncated
1619,Q#524 - >seq523,non-specific,340205,138,192,2.5419000000000003e-07,45.79,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs0_human.pars.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs0_human,pars,CompleteHit
1620,Q#524 - >seq523,superfamily,340205,138,192,2.5419000000000003e-07,45.79,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs0_human.pars.frame3,1909122337_L1M3e.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs0_human,pars,CompleteHit
1621,Q#525 - >seq524,non-specific,238827,552,701,1.9981599999999998e-08,55.7602,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3d.ORF2.hs0_human.marg.frame2,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3d,ORF2,hs0_human,marg,C-TerminusTruncated
1622,Q#525 - >seq524,superfamily,295487,552,701,1.9981599999999998e-08,55.7602,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3d.ORF2.hs0_human.marg.frame2,1909122337_L1M3d.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3d,ORF2,hs0_human,marg,C-TerminusTruncated
1623,Q#527 - >seq526,non-specific,197310,11,220,4.11305e-12,66.2209,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs4_gibbon,marg,CompleteHit
1624,Q#527 - >seq526,superfamily,351117,11,220,4.11305e-12,66.2209,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs4_gibbon,marg,CompleteHit
1625,Q#527 - >seq526,non-specific,197306,73,209,1.22265e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs4_gibbon,marg,N-TerminusTruncated
1626,Q#527 - >seq526,non-specific,197320,108,218,5.6932200000000004e-05,44.8134,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3e.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs4_gibbon,marg,N-TerminusTruncated
1627,Q#527 - >seq526,non-specific,223780,75,217,0.00147686,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3e.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs4_gibbon,marg,N-TerminusTruncated
1628,Q#528 - >seq527,non-specific,197310,7,103,1.20665e-07,51.9685,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3e,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1629,Q#528 - >seq527,superfamily,351117,7,103,1.20665e-07,51.9685,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1630,Q#528 - >seq527,non-specific,197306,7,76,0.00191067,39.3869,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1631,Q#530 - >seq529,non-specific,197310,47,221,2.59667e-17,80.4733,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3e,ORF2,hs2_gorilla,pars,CompleteHit
1632,Q#530 - >seq529,superfamily,351117,47,221,2.59667e-17,80.4733,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,pars,CompleteHit
1633,Q#530 - >seq529,non-specific,197306,71,221,1.50675e-09,57.8765,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1634,Q#530 - >seq529,specific,335306,64,214,0.000654908,40.6914,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3e.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1635,Q#531 - >seq530,non-specific,335182,76,165,1.32471e-11,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs2_gorilla,marg,CompleteHit
1636,Q#531 - >seq530,superfamily,335182,76,165,1.32471e-11,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs2_gorilla,marg,CompleteHit
1637,Q#535 - >seq534,non-specific,335182,64,149,6.740279999999999e-09,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs2_gorilla,pars,CompleteHit
1638,Q#535 - >seq534,superfamily,335182,64,149,6.740279999999999e-09,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs2_gorilla,pars,CompleteHit
1639,Q#539 - >seq538,non-specific,197310,7,219,4.0278799999999997e-07,51.1981,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3e,ORF2,hs1_chimp,marg,CompleteHit
1640,Q#539 - >seq538,superfamily,351117,7,219,4.0278799999999997e-07,51.1981,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3e,ORF2,hs1_chimp,marg,CompleteHit
1641,Q#539 - >seq538,non-specific,197306,7,219,4.64221e-06,48.2465,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3e,ORF2,hs1_chimp,marg,CompleteHit
1642,Q#541 - >seq540,non-specific,307756,65,106,0.00322165,37.9994,pfam01784,NIF3,NC,cl15371,"NIF3 (NGG1p interacting factor 3); This family contains several NIF3 (NGG1p interacting factor 3) protein homologs. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown.",L1M3e.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3e,ORF2,hs1_chimp,pars,BothTerminiTruncated
1643,Q#541 - >seq540,superfamily,326563,65,106,0.00322165,37.9994,cl15371,NIF3 superfamily,NC, - ,"NIF3 (NGG1p interacting factor 3); This family contains several NIF3 (NGG1p interacting factor 3) protein homologs. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown.",L1M3e.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3e,ORF2,hs1_chimp,pars,BothTerminiTruncated
1644,Q#545 - >seq544,non-specific,335182,61,151,1.07202e-08,51.1495,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs1_chimp,marg,CompleteHit
1645,Q#545 - >seq544,superfamily,335182,61,151,1.07202e-08,51.1495,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs1_chimp,marg,CompleteHit
1646,Q#547 - >seq546,non-specific,335182,36,81,4.063209999999999e-06,43.0603,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs1_chimp,pars,BothTerminiTruncated
1647,Q#547 - >seq546,superfamily,335182,36,81,4.063209999999999e-06,43.0603,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3e.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs1_chimp,pars,BothTerminiTruncated
1648,Q#550 - >seq549,non-specific,335182,43,98,4.7621699999999995e-06,43.4455,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs5_gmonkey.pars.frame1,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3e,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
1649,Q#550 - >seq549,superfamily,335182,43,98,4.7621699999999995e-06,43.4455,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs5_gmonkey.pars.frame1,1909122337_L1M3e.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3e,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
1650,Q#559 - >seq558,non-specific,335182,84,169,2.5752e-07,47.6827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs4_gibbon,marg,CompleteHit
1651,Q#559 - >seq558,superfamily,335182,84,169,2.5752e-07,47.6827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs4_gibbon,marg,CompleteHit
1652,Q#559 - >seq558,non-specific,340205,175,242,3.4733899999999996e-05,40.7824,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs4_gibbon,marg,CompleteHit
1653,Q#559 - >seq558,superfamily,340205,175,242,3.4733899999999996e-05,40.7824,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3e,ORF1,hs4_gibbon,marg,CompleteHit
1654,Q#560 - >seq559,non-specific,340205,154,202,0.00103949,36.5452,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs4_gibbon.pars.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1655,Q#560 - >seq559,superfamily,340205,154,202,0.00103949,36.5452,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs4_gibbon.pars.frame3,1909122337_L1M3e.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1656,Q#563 - >seq562,non-specific,197310,101,207,1.72414e-07,52.3537,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs3_orang.marg.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs3_orang,marg,N-TerminusTruncated
1657,Q#563 - >seq562,superfamily,351117,101,207,1.72414e-07,52.3537,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs3_orang.marg.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs3_orang,marg,N-TerminusTruncated
1658,Q#569 - >seq568,non-specific,335182,68,142,1.7404e-12,61.9351,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs3_orang.marg.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs3_orang,marg,N-TerminusTruncated
1659,Q#569 - >seq568,superfamily,335182,68,142,1.7404e-12,61.9351,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs3_orang.marg.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3e,ORF1,hs3_orang,marg,N-TerminusTruncated
1660,Q#572 - >seq571,non-specific,335182,58,129,4.11769e-12,59.6239,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs3_orang.pars.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs3_orang,pars,N-TerminusTruncated
1661,Q#572 - >seq571,superfamily,335182,58,129,4.11769e-12,59.6239,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3e.ORF1.hs3_orang.pars.frame3,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3e,ORF1,hs3_orang,pars,N-TerminusTruncated
1662,Q#573 - >seq572,non-specific,340205,152,189,3.35578e-05,40.3972,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs3_orang.pars.frame2,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs3_orang,pars,N-TerminusTruncated
1663,Q#573 - >seq572,superfamily,340205,152,189,3.35578e-05,40.3972,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3e.ORF1.hs3_orang.pars.frame2,1909122337_L1M3e.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3e,ORF1,hs3_orang,pars,N-TerminusTruncated
1664,Q#574 - >seq573,non-specific,197310,7,247,5.626390000000001e-26,106.28200000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1665,Q#574 - >seq573,superfamily,351117,7,247,5.626390000000001e-26,106.28200000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1666,Q#574 - >seq573,non-specific,197306,7,247,1.7437000000000002e-18,84.8404,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1667,Q#574 - >seq573,specific,335306,13,240,2.075e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1668,Q#574 - >seq573,non-specific,197320,11,240,6.79888e-08,53.673,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1669,Q#574 - >seq573,non-specific,223780,7,240,9.74554e-07,50.2895,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1670,Q#574 - >seq573,non-specific,197307,7,240,0.000174903,43.4305,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1671,Q#574 - >seq573,non-specific,197319,7,247,0.0006914019999999999,41.4933,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3e.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3e.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3e,ORF2,hs2_gorilla,marg,CompleteHit
1672,Q#578 - >seq577,non-specific,238827,573,758,2.2904299999999997e-05,46.1302,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1673,Q#578 - >seq577,superfamily,295487,573,758,2.2904299999999997e-05,46.1302,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1674,Q#578 - >seq577,non-specific,333820,554,672,0.00381849,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1675,Q#578 - >seq577,superfamily,333820,554,672,0.00381849,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
1676,Q#579 - >seq578,non-specific,197306,75,211,5.96066e-07,50.9429,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1677,Q#579 - >seq578,superfamily,351117,75,211,5.96066e-07,50.9429,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1678,Q#579 - >seq578,non-specific,197310,61,208,8.63366e-06,47.7313,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
1679,Q#580 - >seq579,non-specific,197310,64,219,7.55965e-05,44.2645,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3b,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1680,Q#580 - >seq579,superfamily,351117,64,219,7.55965e-05,44.2645,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
1681,Q#585 - >seq584,non-specific,340205,177,243,3.5666800000000003e-12,59.6572,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs6_sqmonkey,marg,CompleteHit
1682,Q#585 - >seq584,superfamily,340205,177,243,3.5666800000000003e-12,59.6572,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs6_sqmonkey,marg,CompleteHit
1683,Q#585 - >seq584,non-specific,335182,76,166,7.2649e-05,40.3639,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs6_sqmonkey,marg,CompleteHit
1684,Q#585 - >seq584,superfamily,335182,76,166,7.2649e-05,40.3639,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs6_sqmonkey,marg,CompleteHit
1685,Q#587 - >seq586,non-specific,340205,150,216,1.43428e-12,60.4276,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs6_sqmonkey.pars.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3b,ORF1,hs6_sqmonkey,pars,CompleteHit
1686,Q#587 - >seq586,superfamily,340205,150,216,1.43428e-12,60.4276,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs6_sqmonkey.pars.frame2,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3b,ORF1,hs6_sqmonkey,pars,CompleteHit
1687,Q#589 - >seq588,specific,197310,80,272,5.803850000000001e-45,162.136,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1688,Q#589 - >seq588,superfamily,351117,80,272,5.803850000000001e-45,162.136,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1689,Q#589 - >seq588,non-specific,197306,90,272,1.69851e-20,91.3888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1690,Q#589 - >seq588,non-specific,197320,95,265,1.12273e-12,68.6958,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1691,Q#589 - >seq588,non-specific,223780,91,265,9.20293e-10,60.3047,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1692,Q#589 - >seq588,non-specific,197307,78,272,4.73707e-09,58.0681,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1693,Q#589 - >seq588,specific,335306,78,265,4.47004e-08,54.5586,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1694,Q#589 - >seq588,non-specific,197321,80,272,3.1282599999999995e-06,49.4728,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1695,Q#589 - >seq588,non-specific,273186,142,272,5.98492e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1696,Q#589 - >seq588,non-specific,197319,142,272,6.11421e-06,48.4269,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1697,Q#589 - >seq588,non-specific,272954,83,272,2.67026e-05,46.6073,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1698,Q#589 - >seq588,non-specific,334125,248,406,0.00011684799999999999,45.6032,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1699,Q#589 - >seq588,superfamily,334125,248,406,0.00011684799999999999,45.6032,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1700,Q#589 - >seq588,non-specific,339261,144,268,0.000119903,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M3b,ORF2,hs5_gmonkey,marg,CompleteHit
1701,Q#589 - >seq588,non-specific,197311,110,272,0.00027811400000000004,43.0493,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1702,Q#589 - >seq588,non-specific,274640,274,383,0.00199246,41.6247,TIGR03545,TIGR03545,NC,cl26850,"TIGR03545 family protein; This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
1703,Q#589 - >seq588,superfamily,274640,274,383,0.00199246,41.6247,cl26850,TIGR03545 superfamily,NC, - ,"TIGR03545 family protein; This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
1704,Q#589 - >seq588,non-specific,214660,253,410,0.00766278,39.8559,smart00434,TOP4c,N,cl29576,"DNA Topoisomerase IV; Bacterial DNA topoisomerase IV, GyrA, ParC",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1705,Q#589 - >seq588,superfamily,214660,253,410,0.00766278,39.8559,cl29576,TOP4c superfamily,N, - ,"DNA Topoisomerase IV; Bacterial DNA topoisomerase IV, GyrA, ParC",L1M3b.ORF2.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1706,Q#590 - >seq589,non-specific,238827,524,717,4.81777e-18,83.8798,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1707,Q#590 - >seq589,superfamily,295487,524,717,4.81777e-18,83.8798,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1708,Q#590 - >seq589,non-specific,333820,574,716,1.0298e-05,46.9018,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1709,Q#590 - >seq589,superfamily,333820,574,716,1.0298e-05,46.9018,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
1710,Q#590 - >seq589,non-specific,313357,365,477,0.006358399999999999,38.7868,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1711,Q#590 - >seq589,superfamily,321788,365,477,0.006358399999999999,38.7868,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1M3b.ORF2.hs5_gmonkey.marg.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M3b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
1712,Q#593 - >seq592,non-specific,238827,584,613,0.000157187,43.4338,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs5_gmonkey.pars.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
1713,Q#593 - >seq592,superfamily,295487,584,613,0.000157187,43.4338,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs5_gmonkey.pars.frame2,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3b,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
1714,Q#594 - >seq593,specific,197310,19,215,1.55764e-47,167.91400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1715,Q#594 - >seq593,superfamily,351117,19,215,1.55764e-47,167.91400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1716,Q#594 - >seq593,non-specific,197306,19,215,5.0742699999999995e-24,101.404,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1717,Q#594 - >seq593,non-specific,197320,19,208,6.60677e-16,77.9405,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1718,Q#594 - >seq593,non-specific,197307,9,215,4.18413e-13,69.6241,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1719,Q#594 - >seq593,non-specific,223780,19,208,9.34742e-13,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1720,Q#594 - >seq593,specific,335306,19,208,4.43025e-11,63.033,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1721,Q#594 - >seq593,non-specific,197321,19,215,3.9282400000000003e-10,60.6436,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1722,Q#594 - >seq593,non-specific,272954,7,215,9.56003e-10,59.7041,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1723,Q#594 - >seq593,non-specific,273186,8,215,7.23388e-08,53.821999999999996,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1724,Q#594 - >seq593,non-specific,238827,496,565,2.93521e-07,51.523,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1725,Q#594 - >seq593,superfamily,295487,496,565,2.93521e-07,51.523,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
1726,Q#594 - >seq593,non-specific,197319,19,215,6.456440000000001e-07,51.1233,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1727,Q#594 - >seq593,non-specific,197311,19,215,1.55954e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1728,Q#594 - >seq593,non-specific,339261,87,211,0.00012330200000000002,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3b.ORF2.hs5_gmonkey.pars.frame1,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M3b,ORF2,hs5_gmonkey,pars,CompleteHit
1729,Q#595 - >seq594,non-specific,340205,166,226,2.28777e-14,65.4352,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,marg,CompleteHit
1730,Q#595 - >seq594,superfamily,340205,166,226,2.28777e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,marg,CompleteHit
1731,Q#595 - >seq594,non-specific,335182,68,156,8.803799999999999e-05,40.3639,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,marg,CompleteHit
1732,Q#595 - >seq594,superfamily,335182,68,156,8.803799999999999e-05,40.3639,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs5_gmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,marg,CompleteHit
1733,Q#598 - >seq597,non-specific,340205,111,171,2.61667e-15,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs5_gmonkey.pars.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,pars,CompleteHit
1734,Q#598 - >seq597,superfamily,340205,111,171,2.61667e-15,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs5_gmonkey.pars.frame3,1909122337_L1M3b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs5_gmonkey,pars,CompleteHit
1735,Q#599 - >seq598,non-specific,197310,10,243,1.48345e-09,58.9021,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs6_sqmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs6_sqmonkey,marg,CompleteHit
1736,Q#599 - >seq598,superfamily,351117,10,243,1.48345e-09,58.9021,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs6_sqmonkey.marg.frame3,1909122337_L1M3b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs6_sqmonkey,marg,CompleteHit
1737,Q#601 - >seq600,non-specific,335182,58,94,0.00185973,35.7415,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs0_human,pars,N-TerminusTruncated
1738,Q#601 - >seq600,superfamily,335182,58,94,0.00185973,35.7415,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs0_human,pars,N-TerminusTruncated
1739,Q#602 - >seq601,non-specific,340205,117,180,2.5286300000000002e-23,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs0_human.pars.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,pars,CompleteHit
1740,Q#602 - >seq601,superfamily,340205,117,180,2.5286300000000002e-23,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs0_human.pars.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,pars,CompleteHit
1741,Q#602 - >seq601,non-specific,335182,19,113,0.000634455,37.2823,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.pars.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,pars,CompleteHit
1742,Q#602 - >seq601,superfamily,335182,19,113,0.000634455,37.2823,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.pars.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,pars,CompleteHit
1743,Q#603 - >seq602,non-specific,197310,41,250,2.89049e-12,67.7617,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs1_chimp,marg,CompleteHit
1744,Q#603 - >seq602,superfamily,351117,41,250,2.89049e-12,67.7617,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs1_chimp,marg,CompleteHit
1745,Q#603 - >seq602,non-specific,238827,537,770,2.89517e-11,64.2346,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3c,ORF2,hs1_chimp,marg,CompleteHit
1746,Q#603 - >seq602,superfamily,295487,537,770,2.89517e-11,64.2346,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3c,ORF2,hs1_chimp,marg,CompleteHit
1747,Q#603 - >seq602,non-specific,197306,41,170,0.00220156,40.9277,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs1_chimp,marg,C-TerminusTruncated
1748,Q#606 - >seq605,non-specific,238827,309,390,3.76163e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3c,ORF2,hs1_chimp,pars,C-TerminusTruncated
1749,Q#606 - >seq605,superfamily,295487,309,390,3.76163e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3c,ORF2,hs1_chimp,pars,C-TerminusTruncated
1750,Q#607 - >seq606,non-specific,238827,440,520,5.2993100000000006e-05,45.3598,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3c,ORF2,hs1_chimp,pars,N-TerminusTruncated
1751,Q#607 - >seq606,superfamily,295487,440,520,5.2993100000000006e-05,45.3598,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3c,ORF2,hs1_chimp,pars,N-TerminusTruncated
1752,Q#609 - >seq608,non-specific,335182,41,116,1.20218e-07,47.6827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3c,ORF1,hs1_chimp,marg,CompleteHit
1753,Q#609 - >seq608,superfamily,335182,41,116,1.20218e-07,47.6827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs1_chimp.marg.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3c,ORF1,hs1_chimp,marg,CompleteHit
1754,Q#611 - >seq610,non-specific,340205,128,190,2.5913799999999997e-18,75.0652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs1_chimp,marg,CompleteHit
1755,Q#611 - >seq610,superfamily,340205,128,190,2.5913799999999997e-18,75.0652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs1_chimp,marg,CompleteHit
1756,Q#612 - >seq611,non-specific,340205,97,159,1.91204e-18,74.2948,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs1_chimp,pars,CompleteHit
1757,Q#612 - >seq611,superfamily,340205,97,159,1.91204e-18,74.2948,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs1_chimp,pars,CompleteHit
1758,Q#613 - >seq612,non-specific,335182,25,88,9.87941e-09,49.9939,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs1_chimp,pars,CompleteHit
1759,Q#613 - >seq612,superfamily,335182,25,88,9.87941e-09,49.9939,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs1_chimp,pars,CompleteHit
1760,Q#615 - >seq614,non-specific,197310,9,214,6.78545e-15,75.0805,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs0_human,marg,CompleteHit
1761,Q#615 - >seq614,superfamily,351117,9,214,6.78545e-15,75.0805,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,marg,CompleteHit
1762,Q#615 - >seq614,non-specific,197320,133,199,1.23181e-05,47.5098,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs0_human,marg,N-TerminusTruncated
1763,Q#615 - >seq614,non-specific,197306,9,214,0.000611099,42.4685,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,marg,CompleteHit
1764,Q#615 - >seq614,non-specific,223780,109,203,0.00197656,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs0_human,marg,N-TerminusTruncated
1765,Q#616 - >seq615,non-specific,238827,476,735,3.1224099999999996e-25,104.681,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs0_human,marg,CompleteHit
1766,Q#616 - >seq615,superfamily,295487,476,735,3.1224099999999996e-25,104.681,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs0_human,marg,CompleteHit
1767,Q#616 - >seq615,non-specific,197310,30,153,5.87659e-13,69.3025,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3b,ORF2,hs0_human,marg,C-TerminusTruncated
1768,Q#616 - >seq615,superfamily,351117,30,153,5.87659e-13,69.3025,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,marg,C-TerminusTruncated
1769,Q#616 - >seq615,non-specific,197306,33,177,1.982e-09,59.0321,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,marg,C-TerminusTruncated
1770,Q#616 - >seq615,non-specific,333820,490,704,1.3157099999999999e-08,55.3762,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs0_human,marg,CompleteHit
1771,Q#616 - >seq615,superfamily,333820,490,704,1.3157099999999999e-08,55.3762,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs0_human.marg.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs0_human,marg,CompleteHit
1772,Q#619 - >seq618,non-specific,197310,150,213,6.507739999999999e-13,68.9173,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs0_human.pars.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3b,ORF2,hs0_human,pars,N-TerminusTruncated
1773,Q#619 - >seq618,superfamily,351117,150,213,6.507739999999999e-13,68.9173,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.pars.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,pars,N-TerminusTruncated
1774,Q#619 - >seq618,non-specific,197320,132,198,1.03676e-05,47.5098,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs0_human.pars.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3b,ORF2,hs0_human,pars,N-TerminusTruncated
1775,Q#619 - >seq618,non-specific,197306,146,213,0.00139274,40.9277,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.pars.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,pars,N-TerminusTruncated
1776,Q#619 - >seq618,non-specific,223780,108,202,0.00280112,40.2743,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs0_human.pars.frame2,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3b,ORF2,hs0_human,pars,N-TerminusTruncated
1777,Q#620 - >seq619,non-specific,238827,466,619,6.06278e-17,80.413,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1778,Q#620 - >seq619,superfamily,295487,466,619,6.06278e-17,80.413,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1779,Q#620 - >seq619,non-specific,197310,22,144,4.96116e-11,63.1393,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1780,Q#620 - >seq619,superfamily,351117,22,144,4.96116e-11,63.1393,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1781,Q#620 - >seq619,non-specific,197306,25,168,5.2418299999999995e-09,57.4913,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1782,Q#620 - >seq619,non-specific,333820,480,620,1.6486400000000002e-05,46.1314,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1783,Q#620 - >seq619,superfamily,333820,480,620,1.6486400000000002e-05,46.1314,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs0_human.pars.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs0_human,pars,C-TerminusTruncated
1784,Q#621 - >seq620,non-specific,340205,121,186,1.57491e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,marg,CompleteHit
1785,Q#621 - >seq620,superfamily,340205,121,186,1.57491e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,marg,CompleteHit
1786,Q#621 - >seq620,non-specific,335182,19,117,0.00711894,34.5859,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,marg,CompleteHit
1787,Q#621 - >seq620,superfamily,335182,19,117,0.00711894,34.5859,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.marg.frame3,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3b,ORF1,hs0_human,marg,CompleteHit
1788,Q#623 - >seq622,non-specific,335182,59,96,0.00136806,36.5119,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.marg.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs0_human,marg,N-TerminusTruncated
1789,Q#623 - >seq622,superfamily,335182,59,96,0.00136806,36.5119,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs0_human.marg.frame1,1909122337_L1M3b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs0_human,marg,N-TerminusTruncated
1790,Q#627 - >seq626,specific,197310,145,290,2.12003e-30,120.149,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1791,Q#627 - >seq626,superfamily,351117,145,290,2.12003e-30,120.149,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1792,Q#627 - >seq626,non-specific,197306,145,307,2.52899e-18,85.2256,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1793,Q#627 - >seq626,non-specific,223780,143,282,1.26001e-06,51.0599,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1794,Q#627 - >seq626,non-specific,197320,143,282,8.169019999999999e-06,48.2802,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1795,Q#627 - >seq626,non-specific,197307,145,283,1.38557e-05,47.6677,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1796,Q#627 - >seq626,non-specific,273186,143,315,3.25385e-05,46.5032,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1797,Q#627 - >seq626,non-specific,272954,143,283,3.34395e-05,46.6073,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1798,Q#627 - >seq626,non-specific,197321,143,282,0.000296028,43.6948,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1799,Q#627 - >seq626,specific,335306,146,298,0.00039066,43.0026,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1800,Q#627 - >seq626,non-specific,197319,143,283,0.0008766630000000001,42.2637,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3b.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1801,Q#629 - >seq628,non-specific,238827,485,696,9.16851e-13,68.0866,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,pars,CompleteHit
1802,Q#629 - >seq628,superfamily,295487,485,696,9.16851e-13,68.0866,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,pars,CompleteHit
1803,Q#629 - >seq628,non-specific,197310,11,128,2.5728300000000004e-10,60.8281,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1804,Q#629 - >seq628,superfamily,351117,11,128,2.5728300000000004e-10,60.8281,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1805,Q#629 - >seq628,non-specific,197306,11,127,5.7006800000000005e-08,54.0245,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
1806,Q#629 - >seq628,non-specific,333820,572,666,1.49174e-06,48.8278,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1807,Q#629 - >seq628,superfamily,333820,572,666,1.49174e-06,48.8278,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,pars,N-TerminusTruncated
1808,Q#631 - >seq630,non-specific,340205,130,199,1.24414e-15,68.1316,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,marg,CompleteHit
1809,Q#631 - >seq630,superfamily,340205,130,199,1.24414e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,marg,CompleteHit
1810,Q#631 - >seq630,non-specific,335182,67,127,1.73763e-12,60.7795,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,marg,N-TerminusTruncated
1811,Q#631 - >seq630,superfamily,335182,67,127,1.73763e-12,60.7795,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,marg,N-TerminusTruncated
1812,Q#633 - >seq632,non-specific,335182,53,113,1.87744e-12,60.3943,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1813,Q#633 - >seq632,superfamily,335182,53,113,1.87744e-12,60.3943,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1814,Q#634 - >seq633,non-specific,340205,135,182,8.05662e-14,63.123999999999995,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1815,Q#634 - >seq633,superfamily,340205,135,182,8.05662e-14,63.123999999999995,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1816,Q#636 - >seq635,non-specific,197310,9,235,3.98033e-23,98.9628,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs1_chimp,marg,CompleteHit
1817,Q#636 - >seq635,superfamily,351117,9,235,3.98033e-23,98.9628,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs1_chimp,marg,CompleteHit
1818,Q#636 - >seq635,non-specific,197306,9,235,8.25399e-13,69.0473,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs1_chimp,marg,CompleteHit
1819,Q#637 - >seq636,non-specific,238827,647,733,0.00010944200000000001,44.2042,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs1_chimp.marg.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs1_chimp,marg,N-TerminusTruncated
1820,Q#637 - >seq636,superfamily,295487,647,733,0.00010944200000000001,44.2042,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs1_chimp.marg.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs1_chimp,marg,N-TerminusTruncated
1821,Q#638 - >seq637,non-specific,238827,493,674,3.62864e-15,75.4054,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs1_chimp,marg,C-TerminusTruncated
1822,Q#638 - >seq637,superfamily,295487,493,674,3.62864e-15,75.4054,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs1_chimp,marg,C-TerminusTruncated
1823,Q#638 - >seq637,non-specific,225087,77,405,0.00772614,39.9949,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3b.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M3b,ORF2,hs1_chimp,marg,C-TerminusTruncated
1824,Q#638 - >seq637,superfamily,225087,77,405,0.00772614,39.9949,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3b.ORF2.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M3b,ORF2,hs1_chimp,marg,C-TerminusTruncated
1825,Q#639 - >seq638,non-specific,238827,472,701,1.75301e-18,84.6502,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs1_chimp,pars,CompleteHit
1826,Q#639 - >seq638,superfamily,295487,472,701,1.75301e-18,84.6502,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs1_chimp,pars,CompleteHit
1827,Q#639 - >seq638,non-specific,333820,472,612,3.06504e-05,45.361000000000004,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1828,Q#639 - >seq638,superfamily,333820,472,612,3.06504e-05,45.361000000000004,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1829,Q#640 - >seq639,non-specific,234767,190,408,0.00568197,40.2064,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1M3b.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1830,Q#640 - >seq639,superfamily,234767,190,408,0.00568197,40.2064,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1M3b.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1831,Q#640 - >seq639,non-specific,225087,80,393,0.00817213,39.6097,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3b.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1832,Q#640 - >seq639,superfamily,225087,80,393,0.00817213,39.6097,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1M3b.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M3b,ORF2,hs1_chimp,pars,C-TerminusTruncated
1833,Q#641 - >seq640,non-specific,197310,57,192,2.70541e-12,66.9913,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs1_chimp,pars,N-TerminusTruncated
1834,Q#641 - >seq640,superfamily,351117,57,192,2.70541e-12,66.9913,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs1_chimp,pars,N-TerminusTruncated
1835,Q#641 - >seq640,non-specific,197306,70,153,3.67324e-08,54.7949,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs1_chimp,pars,BothTerminiTruncated
1836,Q#644 - >seq643,non-specific,340205,146,207,6.134810000000001e-20,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs1_chimp,marg,CompleteHit
1837,Q#644 - >seq643,superfamily,340205,146,207,6.134810000000001e-20,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs1_chimp,marg,CompleteHit
1838,Q#644 - >seq643,non-specific,335182,40,130,7.25023e-12,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs1_chimp,marg,CompleteHit
1839,Q#644 - >seq643,superfamily,335182,40,130,7.25023e-12,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs1_chimp.marg.frame1,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs1_chimp,marg,CompleteHit
1840,Q#645 - >seq644,non-specific,340205,113,172,1.06142e-20,80.458,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs1_chimp,pars,CompleteHit
1841,Q#645 - >seq644,superfamily,340205,113,172,1.06142e-20,80.458,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs1_chimp,pars,CompleteHit
1842,Q#645 - >seq644,non-specific,335182,29,98,4.05038e-09,51.1495,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs1_chimp,pars,CompleteHit
1843,Q#645 - >seq644,superfamily,335182,29,98,4.05038e-09,51.1495,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs1_chimp.pars.frame3,1909122337_L1M3b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs1_chimp,pars,CompleteHit
1844,Q#649 - >seq648,non-specific,197310,2,221,1.6836e-13,70.4581,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3b,ORF2,hs2_gorilla,pars,CompleteHit
1845,Q#649 - >seq648,superfamily,351117,2,221,1.6836e-13,70.4581,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,pars,CompleteHit
1846,Q#649 - >seq648,non-specific,197306,2,221,0.000253731,43.2389,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,pars,CompleteHit
1847,Q#650 - >seq649,non-specific,238827,697,771,4.91067e-05,45.3598,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs4_gibbon.marg.frame2,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1848,Q#650 - >seq649,superfamily,295487,697,771,4.91067e-05,45.3598,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs4_gibbon.marg.frame2,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3b,ORF2,hs4_gibbon,marg,BothTerminiTruncated
1849,Q#651 - >seq650,non-specific,238827,629,705,2.8227900000000004e-07,52.2934,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1850,Q#651 - >seq650,superfamily,295487,629,705,2.8227900000000004e-07,52.2934,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1851,Q#652 - >seq651,non-specific,197310,218,342,1.3980000000000002e-18,85.8661,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1852,Q#652 - >seq651,superfamily,351117,218,342,1.3980000000000002e-18,85.8661,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1853,Q#652 - >seq651,non-specific,333820,693,814,5.8654499999999994e-09,56.5318,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1854,Q#652 - >seq651,superfamily,333820,693,814,5.8654499999999994e-09,56.5318,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1855,Q#652 - >seq651,non-specific,238827,726,844,6.52379e-09,57.301,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1856,Q#652 - >seq651,superfamily,295487,726,844,6.52379e-09,57.301,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1857,Q#652 - >seq651,non-specific,197306,218,342,1.45051e-08,56.7209,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1858,Q#652 - >seq651,non-specific,197320,222,335,5.12488e-05,45.968999999999994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1859,Q#652 - >seq651,specific,335306,243,335,0.00178364,41.0766,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1860,Q#652 - >seq651,non-specific,197307,227,342,0.00227381,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1861,Q#652 - >seq651,non-specific,238828,658,791,0.00937786,38.7213,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3b.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs2_gorilla,marg,N-TerminusTruncated
1862,Q#653 - >seq652,non-specific,197310,164,219,1.8136800000000002e-05,46.5757,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3b,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1863,Q#653 - >seq652,superfamily,351117,164,219,1.8136800000000002e-05,46.5757,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,pars,N-TerminusTruncated
1864,Q#653 - >seq652,non-specific,238827,602,674,2.2065e-05,46.1302,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs4_gibbon,pars,BothTerminiTruncated
1865,Q#653 - >seq652,superfamily,295487,602,674,2.2065e-05,46.1302,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3b,ORF2,hs4_gibbon,pars,BothTerminiTruncated
1866,Q#655 - >seq654,non-specific,197310,38,141,4.25293e-18,83.9401,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1867,Q#655 - >seq654,superfamily,351117,38,141,4.25293e-18,83.9401,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1868,Q#655 - >seq654,non-specific,238827,482,547,7.8886e-11,62.3086,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1869,Q#655 - >seq654,superfamily,295487,482,547,7.8886e-11,62.3086,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
1870,Q#655 - >seq654,non-specific,197306,53,158,5.23082e-10,60.1877,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,pars,BothTerminiTruncated
1871,Q#658 - >seq657,non-specific,335182,64,148,5.50876e-12,60.0091,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,marg,CompleteHit
1872,Q#658 - >seq657,superfamily,335182,64,148,5.50876e-12,60.0091,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,marg,CompleteHit
1873,Q#658 - >seq657,non-specific,340205,169,231,9.09792e-12,58.5016,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,marg,CompleteHit
1874,Q#658 - >seq657,superfamily,340205,169,231,9.09792e-12,58.5016,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,marg,CompleteHit
1875,Q#659 - >seq658,non-specific,340205,117,172,1.77984e-11,56.5756,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs4_gibbon,pars,CompleteHit
1876,Q#659 - >seq658,superfamily,340205,117,172,1.77984e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs4_gibbon.pars.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs4_gibbon,pars,CompleteHit
1877,Q#661 - >seq660,non-specific,335182,19,102,2.7023500000000005e-10,54.6163,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,pars,CompleteHit
1878,Q#661 - >seq660,superfamily,335182,19,102,2.7023500000000005e-10,54.6163,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs4_gibbon.pars.frame1,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs4_gibbon,pars,CompleteHit
1879,Q#664 - >seq663,specific,197310,145,373,2.22083e-39,146.342,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1880,Q#664 - >seq663,superfamily,351117,145,373,2.22083e-39,146.342,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1881,Q#664 - >seq663,non-specific,238827,658,900,8.382289999999999e-24,100.829,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1882,Q#664 - >seq663,superfamily,295487,658,900,8.382289999999999e-24,100.829,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1883,Q#664 - >seq663,non-specific,197306,145,373,2.61015e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1884,Q#664 - >seq663,non-specific,333820,662,873,1.3319200000000002e-10,61.5394,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1885,Q#664 - >seq663,superfamily,333820,662,873,1.3319200000000002e-10,61.5394,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1886,Q#664 - >seq663,specific,335306,146,366,4.608859999999999e-10,60.7218,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1887,Q#664 - >seq663,non-specific,223780,145,283,2.9102100000000004e-09,59.1491,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1888,Q#664 - >seq663,non-specific,197307,145,373,6.40236e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,marg,CompleteHit
1889,Q#664 - >seq663,non-specific,197320,145,283,9.63239e-07,51.3618,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1890,Q#664 - >seq663,non-specific,197321,145,283,1.0282799999999998e-06,51.0136,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1891,Q#664 - >seq663,non-specific,273186,145,284,7.81203e-05,45.3476,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1892,Q#664 - >seq663,non-specific,272954,145,290,0.000168034,44.2961,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1893,Q#664 - >seq663,non-specific,197336,145,290,0.00112145,41.8291,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1894,Q#664 - >seq663,non-specific,197319,143,284,0.00497737,39.9525,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3b.ORF2.hs3_orang.marg.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,marg,C-TerminusTruncated
1895,Q#667 - >seq666,specific,197310,14,242,9.43645e-41,142.876,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,CompleteHit
1896,Q#667 - >seq666,superfamily,351117,14,242,9.43645e-41,142.876,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,pars,CompleteHit
1897,Q#667 - >seq666,non-specific,197306,14,242,1.20714e-23,97.552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,pars,CompleteHit
1898,Q#667 - >seq666,specific,335306,15,235,9.22044e-11,60.7218,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3b,ORF2,hs3_orang,pars,CompleteHit
1899,Q#667 - >seq666,non-specific,223780,14,152,3.33448e-10,59.5343,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1900,Q#667 - >seq666,non-specific,197307,14,242,7.88385e-09,55.3717,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,pars,CompleteHit
1901,Q#667 - >seq666,non-specific,197320,14,152,1.92711e-07,51.3618,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1902,Q#667 - >seq666,non-specific,197321,14,152,2.10139e-07,51.0136,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1903,Q#667 - >seq666,non-specific,273186,14,153,1.1913499999999999e-05,45.7328,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1904,Q#667 - >seq666,non-specific,272954,14,159,1.64106e-05,45.4517,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1905,Q#667 - >seq666,non-specific,197336,14,159,0.000243078,41.8291,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1906,Q#667 - >seq666,non-specific,197319,12,153,0.0006111830000000001,40.7229,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3b.ORF2.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3b,ORF2,hs3_orang,pars,C-TerminusTruncated
1907,Q#669 - >seq668,non-specific,340205,161,230,6.78492e-22,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs3_orang.marg.frame2,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs3_orang,marg,CompleteHit
1908,Q#669 - >seq668,superfamily,340205,161,230,6.78492e-22,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs3_orang.marg.frame2,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs3_orang,marg,CompleteHit
1909,Q#669 - >seq668,non-specific,335182,62,158,4.2259199999999995e-10,55.0015,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs3_orang.marg.frame2,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs3_orang,marg,CompleteHit
1910,Q#669 - >seq668,superfamily,335182,62,158,4.2259199999999995e-10,55.0015,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs3_orang.marg.frame2,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3b,ORF1,hs3_orang,marg,CompleteHit
1911,Q#671 - >seq670,non-specific,335182,55,151,1.3809299999999999e-10,56.1571,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs3_orang.pars.frame3,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs3_orang,pars,CompleteHit
1912,Q#671 - >seq670,superfamily,335182,55,151,1.3809299999999999e-10,56.1571,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3b.ORF1.hs3_orang.pars.frame3,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3b,ORF1,hs3_orang,pars,CompleteHit
1913,Q#673 - >seq672,non-specific,340205,179,223,1.60741e-14,65.8204,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs3_orang,pars,N-TerminusTruncated
1914,Q#673 - >seq672,superfamily,340205,179,223,1.60741e-14,65.8204,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3b.ORF1.hs3_orang.pars.frame1,1909122337_L1M3b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3b,ORF1,hs3_orang,pars,N-TerminusTruncated
1915,Q#674 - >seq673,non-specific,197310,134,221,1.0673700000000002e-06,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1916,Q#674 - >seq673,superfamily,351117,134,221,1.0673700000000002e-06,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1917,Q#674 - >seq673,non-specific,197306,121,224,0.000444869,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs2_gorilla.marg.frame2,1909122337_L1M3b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
1918,Q#675 - >seq674,non-specific,335182,42,92,7.73918e-08,47.6827,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1919,Q#675 - >seq674,superfamily,335182,42,92,7.73918e-08,47.6827,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1920,Q#676 - >seq675,non-specific,238827,629,694,8.41409e-11,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3b.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1921,Q#676 - >seq675,superfamily,295487,629,694,8.41409e-11,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3b.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
1922,Q#676 - >seq675,non-specific,197310,294,349,1.7203e-05,47.3461,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3b.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
1923,Q#676 - >seq675,superfamily,351117,294,349,1.7203e-05,47.3461,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3b.ORF2.hs4_gibbon.marg.frame3,1909122337_L1M3b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
1924,Q#679 - >seq678,non-specific,340205,135,168,0.00836529,33.4636,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1925,Q#679 - >seq678,superfamily,340205,135,168,0.00836529,33.4636,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame2,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,N-TerminusTruncated
1926,Q#680 - >seq679,non-specific,340205,109,160,3.48934e-05,39.6268,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,C-TerminusTruncated
1927,Q#680 - >seq679,superfamily,340205,109,160,3.48934e-05,39.6268,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,C-TerminusTruncated
1928,Q#681 - >seq680,non-specific,238827,518,626,1.05413e-24,102.755,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs1_chimp,marg,C-TerminusTruncated
1929,Q#681 - >seq680,superfamily,295487,518,626,1.05413e-24,102.755,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs1_chimp,marg,C-TerminusTruncated
1930,Q#681 - >seq680,non-specific,197310,3,223,3.2530699999999997e-19,87.4069,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs1_chimp,marg,CompleteHit
1931,Q#681 - >seq680,superfamily,351117,3,223,3.2530699999999997e-19,87.4069,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,marg,CompleteHit
1932,Q#681 - >seq680,non-specific,333820,525,641,8.45444e-12,64.2358,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs1_chimp,marg,C-TerminusTruncated
1933,Q#681 - >seq680,superfamily,333820,525,641,8.45444e-12,64.2358,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs1_chimp,marg,C-TerminusTruncated
1934,Q#681 - >seq680,non-specific,197306,3,152,1.21396e-11,65.1953,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,marg,C-TerminusTruncated
1935,Q#681 - >seq680,specific,335306,4,222,0.00016601099999999998,43.3878,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3de.ORF2.hs1_chimp.marg.frame3,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,marg,CompleteHit
1936,Q#685 - >seq684,non-specific,238827,462,542,3.6545099999999997e-16,77.3314,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3de,ORF2,hs1_chimp,pars,C-TerminusTruncated
1937,Q#685 - >seq684,superfamily,295487,462,542,3.6545099999999997e-16,77.3314,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3de,ORF2,hs1_chimp,pars,C-TerminusTruncated
1938,Q#685 - >seq684,non-specific,197310,21,198,2.04782e-05,45.8053,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3de,ORF2,hs1_chimp,pars,CompleteHit
1939,Q#685 - >seq684,superfamily,351117,21,198,2.04782e-05,45.8053,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,pars,CompleteHit
1940,Q#685 - >seq684,non-specific,333820,462,515,0.000376925,41.50899999999999,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3de,ORF2,hs1_chimp,pars,C-TerminusTruncated
1941,Q#685 - >seq684,superfamily,333820,462,515,0.000376925,41.50899999999999,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3de,ORF2,hs1_chimp,pars,C-TerminusTruncated
1942,Q#686 - >seq685,non-specific,197310,38,216,2.11021e-11,63.9097,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3de,ORF2,hs1_chimp,pars,CompleteHit
1943,Q#686 - >seq685,superfamily,351117,38,216,2.11021e-11,63.9097,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,pars,CompleteHit
1944,Q#686 - >seq685,non-specific,197306,53,148,6.575260000000001e-08,53.6393,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs1_chimp.pars.frame1,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3de,ORF2,hs1_chimp,pars,BothTerminiTruncated
1945,Q#688 - >seq687,non-specific,340205,184,248,9.47246e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs1_chimp.marg.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3de,ORF1,hs1_chimp,marg,CompleteHit
1946,Q#688 - >seq687,superfamily,340205,184,248,9.47246e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs1_chimp.marg.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3de,ORF1,hs1_chimp,marg,CompleteHit
1947,Q#691 - >seq690,non-specific,340205,144,207,1.3626199999999999e-13,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs1_chimp,pars,CompleteHit
1948,Q#691 - >seq690,superfamily,340205,144,207,1.3626199999999999e-13,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs1_chimp.pars.frame2,1909122337_L1M3de.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3de,ORF1,hs1_chimp,pars,CompleteHit
1949,Q#695 - >seq694,non-specific,197310,26,240,2.18595e-21,94.3405,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3c,ORF2,hs0_human,marg,CompleteHit
1950,Q#695 - >seq694,superfamily,351117,26,240,2.18595e-21,94.3405,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs0_human,marg,CompleteHit
1951,Q#695 - >seq694,non-specific,238827,500,735,9.923860000000001e-18,83.1094,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs0_human,marg,CompleteHit
1952,Q#695 - >seq694,superfamily,295487,500,735,9.923860000000001e-18,83.1094,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs0_human,marg,CompleteHit
1953,Q#695 - >seq694,non-specific,197306,25,202,9.480299999999999e-08,54.0245,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs0_human,marg,C-TerminusTruncated
1954,Q#695 - >seq694,non-specific,333820,515,737,0.000151969,43.8202,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs0_human,marg,CompleteHit
1955,Q#695 - >seq694,superfamily,333820,515,737,0.000151969,43.8202,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs0_human,marg,CompleteHit
1956,Q#696 - >seq695,non-specific,197310,86,212,1.123e-14,73.9249,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1957,Q#696 - >seq695,superfamily,351117,86,212,1.123e-14,73.9249,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1958,Q#696 - >seq695,non-specific,197306,44,205,9.98291e-11,62.4989,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1959,Q#696 - >seq695,non-specific,197320,89,191,2.54451e-08,55.599,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1960,Q#696 - >seq695,non-specific,223780,89,189,2.8087399999999998e-05,46.0523,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1961,Q#696 - >seq695,non-specific,315004,257,395,0.00040628699999999997,42.4359,pfam12230,PRP21_like_P,N,cl24249,"Pre-mRNA splicing factor PRP21 like protein; This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1962,Q#696 - >seq695,superfamily,315004,257,395,0.00040628699999999997,42.4359,cl24249,PRP21_like_P superfamily,N, - ,"Pre-mRNA splicing factor PRP21 like protein; This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1963,Q#696 - >seq695,non-specific,197311,86,188,0.00555325,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs0_human,pars,N-TerminusTruncated
1964,Q#697 - >seq696,non-specific,197310,24,224,0.00389477,39.6421,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs0_human.pars.frame2,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3c,ORF2,hs0_human,pars,CompleteHit
1965,Q#697 - >seq696,superfamily,351117,24,224,0.00389477,39.6421,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs0_human.pars.frame2,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs0_human,pars,CompleteHit
1966,Q#698 - >seq697,non-specific,238827,326,397,1.0747799999999999e-08,56.1454,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs0_human.pars.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs0_human,pars,C-TerminusTruncated
1967,Q#698 - >seq697,superfamily,295487,326,397,1.0747799999999999e-08,56.1454,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs0_human.pars.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs0_human,pars,C-TerminusTruncated
1968,Q#701 - >seq700,non-specific,335182,20,105,3.84722e-14,64.6315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,marg,CompleteHit
1969,Q#701 - >seq700,superfamily,335182,20,105,3.84722e-14,64.6315,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,marg,CompleteHit
1970,Q#701 - >seq700,non-specific,340205,117,164,6.264019999999999e-06,41.938,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,marg,C-TerminusTruncated
1971,Q#701 - >seq700,superfamily,340205,117,164,6.264019999999999e-06,41.938,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,marg,C-TerminusTruncated
1972,Q#703 - >seq702,non-specific,340205,136,200,1.6195e-05,41.1676,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,marg,CompleteHit
1973,Q#703 - >seq702,superfamily,340205,136,200,1.6195e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,marg,CompleteHit
1974,Q#703 - >seq702,non-specific,335182,36,109,0.00276295,35.7415,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,marg,BothTerminiTruncated
1975,Q#703 - >seq702,superfamily,335182,36,109,0.00276295,35.7415,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,marg,BothTerminiTruncated
1976,Q#704 - >seq703,non-specific,340205,102,165,3.89876e-18,73.9096,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs2_gorilla,pars,CompleteHit
1977,Q#704 - >seq703,superfamily,340205,102,165,3.89876e-18,73.9096,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs2_gorilla,pars,CompleteHit
1978,Q#707 - >seq706,non-specific,340205,135,174,0.0007759860000000001,36.5452,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs4_gibbon.pars.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1979,Q#707 - >seq706,superfamily,340205,135,174,0.0007759860000000001,36.5452,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs4_gibbon.pars.frame1,1909122337_L1M3de.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs4_gibbon,pars,C-TerminusTruncated
1980,Q#708 - >seq707,specific,197310,3,232,5.80996e-47,165.988,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1981,Q#708 - >seq707,superfamily,351117,3,232,5.80996e-47,165.988,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1982,Q#708 - >seq707,non-specific,197306,3,232,6.95502e-23,97.9372,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1983,Q#708 - >seq707,non-specific,197307,3,225,1.4080700000000002e-14,73.8613,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1984,Q#708 - >seq707,non-specific,223780,1,225,4.1829699999999994e-14,72.6311,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1985,Q#708 - >seq707,non-specific,197320,1,204,5.0958e-12,66.3846,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1986,Q#708 - >seq707,non-specific,197321,1,225,1.52637e-11,64.8808,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1987,Q#708 - >seq707,specific,335306,4,225,1.1933e-10,61.8774,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1988,Q#708 - >seq707,non-specific,272954,1,203,2.4364e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1989,Q#708 - >seq707,non-specific,273186,1,233,2.5006300000000002e-08,55.3628,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1990,Q#708 - >seq707,non-specific,197319,1,232,2.7873700000000002e-06,49.1973,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,marg,CompleteHit
1991,Q#708 - >seq707,non-specific,293682,284,460,0.00137074,41.1064,pfam17077,Msap1,C,cl25308,"Mitotic spindle associated protein SHE1; She1 seems to be related to the spindle integrity function of the Dam1 complex. She1 is a dynein regulator and limits dynein offloading by gating the recruitment of dynactin to the astral microtubule plus end. Aurora B phosphorylates She1, modulating its potency against dynein.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1992,Q#708 - >seq707,superfamily,293682,284,460,0.00137074,41.1064,cl25308,Msap1 superfamily,C, - ,"Mitotic spindle associated protein SHE1; She1 seems to be related to the spindle integrity function of the Dam1 complex. She1 is a dynein regulator and limits dynein offloading by gating the recruitment of dynactin to the astral microtubule plus end. Aurora B phosphorylates She1, modulating its potency against dynein.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1993,Q#708 - >seq707,non-specific,273727,315,439,0.00670511,39.4914,TIGR01642,U2AF_lg,C,cl36941,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1994,Q#708 - >seq707,superfamily,273727,315,439,0.00670511,39.4914,cl36941,U2AF_lg superfamily,C, - ,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1M3de.ORF2.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1995,Q#709 - >seq708,non-specific,238827,475,563,1.42949e-24,102.369,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs3_orang.marg.frame2,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1996,Q#709 - >seq708,superfamily,295487,475,563,1.42949e-24,102.369,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs3_orang.marg.frame2,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1997,Q#709 - >seq708,non-specific,333820,476,577,3.88196e-11,62.3098,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs3_orang.marg.frame2,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1998,Q#709 - >seq708,superfamily,333820,476,577,3.88196e-11,62.3098,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs3_orang.marg.frame2,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
1999,Q#710 - >seq709,non-specific,274009,268,416,0.00126109,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M3de.ORF2.hs3_orang.marg.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
2000,Q#710 - >seq709,superfamily,274009,268,416,0.00126109,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M3de.ORF2.hs3_orang.marg.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1M3de,ORF2,hs3_orang,marg,C-TerminusTruncated
2001,Q#711 - >seq710,specific,197310,2,221,2.44351e-42,152.506,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2002,Q#711 - >seq710,superfamily,351117,2,221,2.44351e-42,152.506,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2003,Q#711 - >seq710,specific,238827,489,587,2.79696e-27,109.68799999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2004,Q#711 - >seq710,superfamily,295487,489,587,2.79696e-27,109.68799999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2005,Q#711 - >seq710,non-specific,197306,2,210,6.96316e-21,91.774,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2006,Q#711 - >seq710,non-specific,223780,2,200,2.21878e-14,73.4015,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2007,Q#711 - >seq710,non-specific,197320,2,201,3.21086e-12,66.7698,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2008,Q#711 - >seq710,non-specific,197307,2,216,1.00016e-11,65.3869,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2009,Q#711 - >seq710,non-specific,197321,1,200,6.18898e-11,62.9548,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2010,Q#711 - >seq710,non-specific,333820,495,587,7.73251e-11,61.1542,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2011,Q#711 - >seq710,superfamily,333820,495,587,7.73251e-11,61.1542,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2012,Q#711 - >seq710,non-specific,272954,2,200,1.8058199999999999e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2013,Q#711 - >seq710,non-specific,273186,2,216,1.8395400000000002e-08,55.3628,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2014,Q#711 - >seq710,specific,335306,3,203,2.6924e-08,54.5586,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2015,Q#711 - >seq710,non-specific,274009,291,438,6.77221e-05,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2016,Q#711 - >seq710,superfamily,274009,291,438,6.77221e-05,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M3de,ORF2,hs3_orang,pars,C-TerminusTruncated
2017,Q#711 - >seq710,non-specific,197319,2,211,0.00010966,44.1897,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3de.ORF2.hs3_orang.pars.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs3_orang,pars,CompleteHit
2018,Q#714 - >seq713,non-specific,340205,117,179,1.62077e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs3_orang,marg,CompleteHit
2019,Q#714 - >seq713,superfamily,340205,117,179,1.62077e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs3_orang,marg,CompleteHit
2020,Q#714 - >seq713,non-specific,335182,18,90,3.3953500000000006e-10,54.2311,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs3_orang,marg,C-TerminusTruncated
2021,Q#714 - >seq713,superfamily,335182,18,90,3.3953500000000006e-10,54.2311,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs3_orang.marg.frame3,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3de,ORF1,hs3_orang,marg,C-TerminusTruncated
2022,Q#719 - >seq718,non-specific,340205,114,176,1.64762e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs3_orang.pars.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs3_orang,pars,CompleteHit
2023,Q#719 - >seq718,superfamily,340205,114,176,1.64762e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3de.ORF1.hs3_orang.pars.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs3_orang,pars,CompleteHit
2024,Q#719 - >seq718,non-specific,335182,17,87,4.6371e-09,51.1495,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs3_orang.pars.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs3_orang,pars,C-TerminusTruncated
2025,Q#719 - >seq718,superfamily,335182,17,87,4.6371e-09,51.1495,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs3_orang.pars.frame1,1909122337_L1M3de.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3de,ORF1,hs3_orang,pars,C-TerminusTruncated
2026,Q#720 - >seq719,specific,197310,3,230,7.47288e-29,115.141,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3de,ORF2,hs2_gorilla,marg,CompleteHit
2027,Q#720 - >seq719,superfamily,351117,3,230,7.47288e-29,115.141,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs2_gorilla,marg,CompleteHit
2028,Q#720 - >seq719,non-specific,238827,516,623,9.31912e-23,96.9766,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2029,Q#720 - >seq719,superfamily,295487,516,623,9.31912e-23,96.9766,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2030,Q#720 - >seq719,non-specific,197306,3,230,6.18458e-15,74.8252,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs2_gorilla,marg,CompleteHit
2031,Q#720 - >seq719,non-specific,333820,522,637,7.488219999999999e-10,58.843,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2032,Q#720 - >seq719,superfamily,333820,522,637,7.488219999999999e-10,58.843,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3de,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2033,Q#720 - >seq719,non-specific,197307,3,223,0.00019533200000000002,43.4305,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3de,ORF2,hs2_gorilla,marg,CompleteHit
2034,Q#720 - >seq719,non-specific,223780,1,139,0.00190972,40.6595,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3de,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2035,Q#723 - >seq722,specific,197310,3,229,1.72266e-29,116.682,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3de.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3de,ORF2,hs2_gorilla,pars,CompleteHit
2036,Q#723 - >seq722,superfamily,351117,3,229,1.72266e-29,116.682,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs2_gorilla,pars,CompleteHit
2037,Q#723 - >seq722,non-specific,197306,3,229,1.2144299999999999e-15,76.7512,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3de.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3de,ORF2,hs2_gorilla,pars,CompleteHit
2038,Q#723 - >seq722,non-specific,223780,1,138,0.000111006,44.1263,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3de.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2039,Q#723 - >seq722,non-specific,197307,3,222,0.000167298,43.4305,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3de.ORF2.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3de,ORF2,hs2_gorilla,pars,CompleteHit
2040,Q#724 - >seq723,non-specific,238827,460,564,3.91725e-24,100.829,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3de.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3de,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2041,Q#724 - >seq723,superfamily,295487,460,564,3.91725e-24,100.829,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3de.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3de,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2042,Q#724 - >seq723,non-specific,333820,466,578,8.73669e-11,61.1542,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3de,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2043,Q#724 - >seq723,superfamily,333820,466,578,8.73669e-11,61.1542,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3de.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3de,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2044,Q#725 - >seq724,non-specific,340205,149,213,1.9223699999999998e-13,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs0_human.marg.frame2,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs0_human,marg,CompleteHit
2045,Q#725 - >seq724,superfamily,340205,149,213,1.9223699999999998e-13,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs0_human.marg.frame2,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs0_human,marg,CompleteHit
2046,Q#726 - >seq725,non-specific,335182,20,90,6.25304e-13,61.1647,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,C-TerminusTruncated
2047,Q#726 - >seq725,superfamily,335182,20,90,6.25304e-13,61.1647,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3de.ORF1.hs2_gorilla.pars.frame3,1909122337_L1M3de.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3de,ORF1,hs2_gorilla,pars,C-TerminusTruncated
2048,Q#727 - >seq726,non-specific,197310,142,173,0.00352633,38.8717,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs3_orang.pars.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3c,ORF2,hs3_orang,pars,N-TerminusTruncated
2049,Q#727 - >seq726,superfamily,351117,142,173,0.00352633,38.8717,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs3_orang.pars.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,pars,N-TerminusTruncated
2050,Q#730 - >seq729,non-specific,340205,110,174,1.38504e-16,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs2_gorilla,marg,CompleteHit
2051,Q#730 - >seq729,superfamily,340205,110,174,1.38504e-16,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs2_gorilla.marg.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs2_gorilla,marg,CompleteHit
2052,Q#731 - >seq730,specific,197310,5,206,1.1800599999999998e-35,135.172,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2053,Q#731 - >seq730,superfamily,351117,5,206,1.1800599999999998e-35,135.172,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2054,Q#731 - >seq730,non-specific,197306,3,206,9.302e-18,83.6848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2055,Q#731 - >seq730,non-specific,197320,3,206,4.4811900000000004e-10,60.9918,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2056,Q#731 - >seq730,non-specific,223780,3,206,6.252710000000001e-10,60.6899,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2057,Q#731 - >seq730,specific,335306,5,213,1.6034799999999999e-06,49.9362,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2058,Q#731 - >seq730,non-specific,197307,3,206,2.2043000000000002e-05,46.8973,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2059,Q#731 - >seq730,non-specific,273186,3,206,2.7199e-05,46.5032,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2060,Q#731 - >seq730,non-specific,272954,3,206,0.00010828,44.6813,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2061,Q#731 - >seq730,non-specific,197311,99,203,0.00243451,40.3529,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs3_orang.marg.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,marg,N-TerminusTruncated
2062,Q#733 - >seq732,non-specific,238827,429,695,3.8849199999999996e-12,66.5458,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs3_orang.marg.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2063,Q#733 - >seq732,superfamily,295487,429,695,3.8849199999999996e-12,66.5458,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs3_orang.marg.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs3_orang,marg,CompleteHit
2064,Q#734 - >seq733,non-specific,197310,1,184,2.28719e-10,60.4429,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs3_orang.pars.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,pars,CompleteHit
2065,Q#734 - >seq733,superfamily,351117,1,184,2.28719e-10,60.4429,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs3_orang.pars.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,pars,CompleteHit
2066,Q#734 - >seq733,non-specific,197306,1,184,0.000105655,43.6241,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs3_orang.pars.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs3_orang,pars,C-TerminusTruncated
2067,Q#734 - >seq733,non-specific,197311,60,132,0.00283245,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs3_orang.pars.frame3,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs3_orang,pars,BothTerminiTruncated
2068,Q#737 - >seq736,non-specific,340205,110,174,9.72665e-17,70.4428,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs3_orang.marg.frame2,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs3_orang,marg,CompleteHit
2069,Q#737 - >seq736,superfamily,340205,110,174,9.72665e-17,70.4428,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs3_orang.marg.frame2,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs3_orang,marg,CompleteHit
2070,Q#738 - >seq737,non-specific,335182,21,101,4.2577500000000005e-09,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs4_gibbon,marg,CompleteHit
2071,Q#738 - >seq737,superfamily,335182,21,101,4.2577500000000005e-09,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs4_gibbon,marg,CompleteHit
2072,Q#739 - >seq738,non-specific,335182,50,100,2.99714e-09,51.9199,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs3_orang.marg.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs3_orang,marg,N-TerminusTruncated
2073,Q#739 - >seq738,superfamily,335182,50,100,2.99714e-09,51.9199,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs3_orang.marg.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs3_orang,marg,N-TerminusTruncated
2074,Q#740 - >seq739,non-specific,340205,104,151,2.66163e-15,65.8204,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs3_orang.pars.frame2,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs3_orang,pars,C-TerminusTruncated
2075,Q#740 - >seq739,superfamily,340205,104,151,2.66163e-15,65.8204,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs3_orang.pars.frame2,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3c,ORF1,hs3_orang,pars,C-TerminusTruncated
2076,Q#741 - >seq740,non-specific,335182,42,92,4.08804e-09,50.7643,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs3_orang.pars.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs3_orang,pars,N-TerminusTruncated
2077,Q#741 - >seq740,superfamily,335182,42,92,4.08804e-09,50.7643,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs3_orang.pars.frame1,1909122337_L1M3c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs3_orang,pars,N-TerminusTruncated
2078,Q#742 - >seq741,non-specific,197310,9,212,6.778380000000001e-08,54.2797,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3c,ORF2,hs2_gorilla,marg,CompleteHit
2079,Q#742 - >seq741,superfamily,351117,9,212,6.778380000000001e-08,54.2797,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs2_gorilla,marg,CompleteHit
2080,Q#742 - >seq741,non-specific,197306,9,230,7.20294e-05,45.1649,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs2_gorilla.marg.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs2_gorilla,marg,CompleteHit
2081,Q#743 - >seq742,non-specific,306964,719,782,0.00540227,38.3435,pfam00609,DAGK_acc,C,cl02440,Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.,L1M3c.ORF2.hs2_gorilla.marg.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M3c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2082,Q#743 - >seq742,superfamily,321935,719,782,0.00540227,38.3435,cl02440,DAGK_acc superfamily,C, - ,Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.,L1M3c.ORF2.hs2_gorilla.marg.frame2,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M3c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2083,Q#744 - >seq743,non-specific,238827,383,538,3.08502e-18,84.265,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2084,Q#744 - >seq743,superfamily,295487,383,538,3.08502e-18,84.265,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2085,Q#744 - >seq743,non-specific,333820,389,554,1.2575e-06,49.5982,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,marg,CompleteHit
2086,Q#744 - >seq743,superfamily,333820,389,554,1.2575e-06,49.5982,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs2_gorilla.marg.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,marg,CompleteHit
2087,Q#747 - >seq746,non-specific,238827,380,435,2.7979900000000003e-14,72.709,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2088,Q#747 - >seq746,superfamily,295487,380,435,2.7979900000000003e-14,72.709,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2089,Q#747 - >seq746,non-specific,197310,7,230,5.8257900000000006e-08,54.2797,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3c,ORF2,hs2_gorilla,pars,CompleteHit
2090,Q#747 - >seq746,superfamily,351117,7,230,5.8257900000000006e-08,54.2797,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs2_gorilla,pars,CompleteHit
2091,Q#747 - >seq746,non-specific,333820,386,435,4.87422e-05,44.5906,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2092,Q#747 - >seq746,superfamily,333820,386,435,4.87422e-05,44.5906,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs2_gorilla.pars.frame1,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2093,Q#748 - >seq747,non-specific,335182,72,127,4.174480000000001e-12,60.3943,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs0_human,marg,N-TerminusTruncated
2094,Q#748 - >seq747,superfamily,335182,72,127,4.174480000000001e-12,60.3943,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs0_human.marg.frame1,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs0_human,marg,N-TerminusTruncated
2095,Q#749 - >seq748,non-specific,335182,45,102,1.0258200000000002e-08,50.3791,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
2096,Q#749 - >seq748,superfamily,335182,45,102,1.0258200000000002e-08,50.3791,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs2_gorilla.marg.frame3,1909122337_L1M3c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
2097,Q#751 - >seq750,non-specific,340205,118,180,7.061589999999999e-07,44.6344,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs4_gibbon.marg.frame2,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs4_gibbon,marg,CompleteHit
2098,Q#751 - >seq750,superfamily,340205,118,180,7.061589999999999e-07,44.6344,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs4_gibbon.marg.frame2,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M3c,ORF1,hs4_gibbon,marg,CompleteHit
2099,Q#753 - >seq752,non-specific,197310,82,223,1.1357700000000002e-26,107.822,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2100,Q#753 - >seq752,superfamily,351117,82,223,1.1357700000000002e-26,107.822,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2101,Q#753 - >seq752,non-specific,197306,34,223,7.619970000000001e-13,67.8917,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,CompleteHit
2102,Q#753 - >seq752,non-specific,197320,93,212,1.35215e-10,61.7622,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2103,Q#753 - >seq752,non-specific,223780,82,212,2.75675e-09,57.6083,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2104,Q#753 - >seq752,non-specific,197307,82,223,1.73259e-06,49.2085,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2105,Q#753 - >seq752,non-specific,272954,1,194,2.37016e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,CompleteHit
2106,Q#753 - >seq752,non-specific,273186,93,224,1.05321e-05,46.8884,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2107,Q#753 - >seq752,specific,335306,3,216,3.50774e-05,44.9286,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,CompleteHit
2108,Q#753 - >seq752,non-specific,339261,95,219,0.00468799,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3c.ORF2.hs6_sqmonkey.pars.frame3,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M3c,ORF2,hs6_sqmonkey,pars,CompleteHit
2109,Q#757 - >seq756,non-specific,197310,114,259,2.00361e-25,104.741,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2110,Q#757 - >seq756,superfamily,351117,114,259,2.00361e-25,104.741,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2111,Q#757 - >seq756,non-specific,238827,535,622,1.00765e-15,76.1758,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2112,Q#757 - >seq756,superfamily,295487,535,622,1.00765e-15,76.1758,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2113,Q#757 - >seq756,non-specific,197306,66,259,2.8899e-13,69.4325,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,CompleteHit
2114,Q#757 - >seq756,non-specific,197320,129,248,4.7265e-09,57.1398,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2115,Q#757 - >seq756,non-specific,223780,130,248,2.48983e-07,52.2155,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2116,Q#757 - >seq756,non-specific,197307,130,259,1.99378e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2117,Q#757 - >seq756,non-specific,273186,129,260,5.6480699999999996e-05,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2118,Q#757 - >seq756,non-specific,235175,286,420,0.00211561,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M3c,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
2119,Q#757 - >seq756,superfamily,235175,286,420,0.00211561,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M3c,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
2120,Q#757 - >seq756,non-specific,333820,542,594,0.00325263,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2121,Q#757 - >seq756,superfamily,333820,542,594,0.00325263,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2122,Q#757 - >seq756,specific,335306,86,252,0.00471512,38.7654,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2123,Q#757 - >seq756,non-specific,272954,34,230,0.00791181,38.1329,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs6_sqmonkey.marg.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,CompleteHit
2124,Q#758 - >seq757,non-specific,197310,40,117,0.00034232699999999996,42.3385,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2125,Q#758 - >seq757,superfamily,351117,40,117,0.00034232699999999996,42.3385,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2126,Q#760 - >seq759,non-specific,197310,29,99,0.00125262,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs6_sqmonkey.pars.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2127,Q#760 - >seq759,superfamily,351117,29,99,0.00125262,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs6_sqmonkey.pars.frame2,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2128,Q#761 - >seq760,non-specific,238827,439,495,1.75405e-11,63.4642,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2129,Q#761 - >seq760,superfamily,295487,439,495,1.75405e-11,63.4642,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2130,Q#761 - >seq760,non-specific,333820,445,496,0.00183729,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2131,Q#761 - >seq760,superfamily,333820,445,496,0.00183729,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2132,Q#763 - >seq762,non-specific,340205,113,172,4.3752699999999993e-16,68.5168,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs0_human,pars,CompleteHit
2133,Q#763 - >seq762,superfamily,340205,113,172,4.3752699999999993e-16,68.5168,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs0_human,pars,CompleteHit
2134,Q#763 - >seq762,non-specific,335182,33,96,8.30189e-08,47.6827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs0_human,pars,CompleteHit
2135,Q#763 - >seq762,superfamily,335182,33,96,8.30189e-08,47.6827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs0_human.pars.frame3,1909122337_L1M3c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3c,ORF1,hs0_human,pars,CompleteHit
2136,Q#767 - >seq766,non-specific,335182,53,99,2.94983e-08,49.2235,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
2137,Q#767 - >seq766,superfamily,335182,53,99,2.94983e-08,49.2235,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
2138,Q#767 - >seq766,non-specific,340205,141,175,1.87816e-05,40.7824,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
2139,Q#767 - >seq766,superfamily,340205,141,175,1.87816e-05,40.7824,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs6_sqmonkey.pars.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
2140,Q#770 - >seq769,non-specific,197310,10,243,1.02363e-22,97.8072,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2141,Q#770 - >seq769,superfamily,351117,10,243,1.02363e-22,97.8072,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2142,Q#770 - >seq769,non-specific,238827,508,765,1.14606e-07,53.449,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2143,Q#770 - >seq769,superfamily,295487,508,765,1.14606e-07,53.449,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2144,Q#770 - >seq769,non-specific,197306,42,199,3.98071e-07,52.0985,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2145,Q#770 - >seq769,non-specific,197320,33,151,2.15025e-06,50.2062,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2146,Q#770 - >seq769,non-specific,333820,531,726,0.0010127,41.1238,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2147,Q#770 - >seq769,superfamily,333820,531,726,0.0010127,41.1238,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2148,Q#770 - >seq769,specific,335306,43,207,0.0010464,41.4618,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2149,Q#770 - >seq769,non-specific,339261,113,209,0.00202148,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M3c,ORF2,hs4_gibbon,marg,CompleteHit
2150,Q#770 - >seq769,non-specific,197321,10,151,0.0041737,39.8428,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs4_gibbon.marg.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2151,Q#771 - >seq770,non-specific,197310,68,227,2.73373e-25,103.97,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2152,Q#771 - >seq770,superfamily,351117,68,227,2.73373e-25,103.97,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2153,Q#771 - >seq770,non-specific,197306,68,201,1.3885699999999999e-09,58.2617,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2154,Q#771 - >seq770,non-specific,197320,97,199,1.0476699999999999e-07,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2155,Q#771 - >seq770,non-specific,223780,97,198,5.24861e-07,51.0599,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2156,Q#771 - >seq770,non-specific,273186,99,199,4.8621899999999996e-05,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2157,Q#771 - >seq770,specific,335306,28,201,0.000684252,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,CompleteHit
2158,Q#771 - >seq770,non-specific,339261,99,223,0.00129116,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M3c,ORF2,hs4_gibbon,pars,CompleteHit
2159,Q#771 - >seq770,non-specific,197311,91,195,0.00229704,39.1973,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2160,Q#771 - >seq770,non-specific,197307,99,227,0.0045375,38.8081,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3c.ORF2.hs4_gibbon.pars.frame3,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2161,Q#772 - >seq771,non-specific,197310,25,86,1.00557e-06,49.6573,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3c.ORF2.hs4_gibbon.pars.frame2,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2162,Q#772 - >seq771,superfamily,351117,25,86,1.00557e-06,49.6573,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3c.ORF2.hs4_gibbon.pars.frame2,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2163,Q#773 - >seq772,non-specific,238827,459,510,1.5901e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3c.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2164,Q#773 - >seq772,superfamily,295487,459,510,1.5901e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3c.ORF2.hs4_gibbon.pars.frame1,1909122337_L1M3c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2165,Q#774 - >seq773,non-specific,340205,179,222,8.437860000000001e-10,53.1088,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
2166,Q#774 - >seq773,superfamily,340205,179,222,8.437860000000001e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3c.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
2167,Q#774 - >seq773,non-specific,335182,81,135,1.23044e-06,45.3715,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
2168,Q#774 - >seq773,superfamily,335182,81,135,1.23044e-06,45.3715,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3c.ORF1.hs6_sqmonkey.marg.frame1,1909122337_L1M3c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3c,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
2169,Q#776 - >seq775,non-specific,234767,68,284,0.00380801,39.8212,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1M4a2.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M4a2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2170,Q#776 - >seq775,superfamily,234767,68,284,0.00380801,39.8212,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1M4a2.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M4a2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2171,Q#782 - >seq781,non-specific,335182,99,181,1.90642e-08,50.7643,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs7_bushaby,marg,CompleteHit
2172,Q#782 - >seq781,superfamily,335182,99,181,1.90642e-08,50.7643,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs7_bushaby,marg,CompleteHit
2173,Q#783 - >seq782,non-specific,340205,71,124,9.19842e-12,56.1904,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,pars,CompleteHit
2174,Q#783 - >seq782,superfamily,340205,71,124,9.19842e-12,56.1904,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,pars,CompleteHit
2175,Q#783 - >seq782,non-specific,335182,19,52,0.000248216,37.6675,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2176,Q#783 - >seq782,superfamily,335182,19,52,0.000248216,37.6675,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2177,Q#788 - >seq787,non-specific,340205,50,115,2.04283e-15,65.05,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a2,ORF1,hs6_sqmonkey,pars,CompleteHit
2178,Q#788 - >seq787,superfamily,340205,50,115,2.04283e-15,65.05,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a2,ORF1,hs6_sqmonkey,pars,CompleteHit
2179,Q#793 - >seq792,non-specific,197310,63,256,6.16342e-14,72.3841,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs5_gmonkey.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs5_gmonkey,marg,CompleteHit
2180,Q#793 - >seq792,superfamily,351117,63,256,6.16342e-14,72.3841,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs5_gmonkey.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs5_gmonkey,marg,CompleteHit
2181,Q#793 - >seq792,non-specific,238827,565,660,6.83784e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs5_gmonkey.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
2182,Q#793 - >seq792,superfamily,295487,565,660,6.83784e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs5_gmonkey.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
2183,Q#793 - >seq792,non-specific,197306,67,255,1.2604500000000001e-05,47.8613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs5_gmonkey.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs5_gmonkey,marg,CompleteHit
2184,Q#794 - >seq793,non-specific,340205,169,223,7.4005299999999995e-09,50.4124,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs7_bushaby.marg.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,marg,CompleteHit
2185,Q#794 - >seq793,superfamily,340205,169,223,7.4005299999999995e-09,50.4124,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs7_bushaby.marg.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs7_bushaby,marg,CompleteHit
2186,Q#795 - >seq794,non-specific,197310,67,230,2.66458e-09,57.7465,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
2187,Q#795 - >seq794,superfamily,351117,67,230,2.66458e-09,57.7465,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
2188,Q#797 - >seq796,non-specific,340205,169,217,1.6963399999999997e-09,52.7236,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
2189,Q#797 - >seq796,superfamily,340205,169,217,1.6963399999999997e-09,52.7236,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
2190,Q#803 - >seq802,non-specific,335182,85,160,1.3041e-17,75.0319,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs10_snmole,marg,CompleteHit
2191,Q#803 - >seq802,superfamily,335182,85,160,1.3041e-17,75.0319,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs10_snmole,marg,CompleteHit
2192,Q#803 - >seq802,non-specific,340205,168,233,1.3362e-15,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs10_snmole,marg,CompleteHit
2193,Q#803 - >seq802,superfamily,340205,168,233,1.3362e-15,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs10_snmole,marg,CompleteHit
2194,Q#805 - >seq804,non-specific,335182,62,137,8.19304e-18,75.0319,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs10_snmole,pars,CompleteHit
2195,Q#805 - >seq804,superfamily,335182,62,137,8.19304e-18,75.0319,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs10_snmole,pars,CompleteHit
2196,Q#805 - >seq804,non-specific,340205,145,208,1.07294e-17,73.9096,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs10_snmole,pars,CompleteHit
2197,Q#805 - >seq804,superfamily,340205,145,208,1.07294e-17,73.9096,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs10_snmole,pars,CompleteHit
2198,Q#809 - >seq808,non-specific,197310,240,455,3.71712e-13,68.9173,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs9_pika,marg,CompleteHit
2199,Q#809 - >seq808,superfamily,351117,240,455,3.71712e-13,68.9173,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs9_pika,marg,CompleteHit
2200,Q#809 - >seq808,non-specific,197306,260,455,4.07477e-05,44.7797,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs9_pika,marg,N-TerminusTruncated
2201,Q#811 - >seq810,non-specific,197310,39,126,7.82499e-08,51.5833,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs7_bushaby.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4a2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2202,Q#811 - >seq810,superfamily,351117,39,126,7.82499e-08,51.5833,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs7_bushaby.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2203,Q#815 - >seq814,non-specific,340205,231,297,3.43685e-19,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,marg,CompleteHit
2204,Q#815 - >seq814,superfamily,340205,231,297,3.43685e-19,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,marg,CompleteHit
2205,Q#815 - >seq814,non-specific,335182,123,228,1.08897e-08,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,marg,CompleteHit
2206,Q#815 - >seq814,superfamily,335182,123,228,1.08897e-08,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,marg,CompleteHit
2207,Q#818 - >seq817,non-specific,340205,153,216,4.63231e-19,77.3764,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,pars,CompleteHit
2208,Q#818 - >seq817,superfamily,340205,153,216,4.63231e-19,77.3764,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,pars,CompleteHit
2209,Q#818 - >seq817,non-specific,335182,66,150,1.33378e-13,64.2463,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,pars,CompleteHit
2210,Q#818 - >seq817,superfamily,335182,66,150,1.33378e-13,64.2463,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs9_pika,pars,CompleteHit
2211,Q#821 - >seq820,non-specific,197310,169,397,1.8448900000000002e-12,67.7617,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs7_bushaby.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs7_bushaby,marg,CompleteHit
2212,Q#821 - >seq820,superfamily,351117,169,397,1.8448900000000002e-12,67.7617,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs7_bushaby.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs7_bushaby,marg,CompleteHit
2213,Q#821 - >seq820,non-specific,197306,169,340,2.71856e-07,52.0985,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs7_bushaby.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
2214,Q#823 - >seq822,non-specific,197310,267,327,0.00146179,39.6421,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4a2,ORF2,hs9_pika,pars,N-TerminusTruncated
2215,Q#823 - >seq822,superfamily,351117,267,327,0.00146179,39.6421,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs9_pika.pars.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs9_pika,pars,N-TerminusTruncated
2216,Q#824 - >seq823,non-specific,340205,156,219,4.42161e-11,56.5756,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4a2,ORF1,hs5_gmonkey,marg,CompleteHit
2217,Q#824 - >seq823,superfamily,340205,156,219,4.42161e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M4a2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4a2,ORF1,hs5_gmonkey,marg,CompleteHit
2218,Q#827 - >seq826,non-specific,197310,25,257,1.97148e-21,94.3405,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a2,ORF2,hs2_gorilla,marg,CompleteHit
2219,Q#827 - >seq826,superfamily,351117,25,257,1.97148e-21,94.3405,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a2,ORF2,hs2_gorilla,marg,CompleteHit
2220,Q#827 - >seq826,non-specific,197306,49,202,8.25293e-11,63.2693,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a2,ORF2,hs2_gorilla,marg,CompleteHit
2221,Q#827 - >seq826,non-specific,197320,61,203,5.4231e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2222,Q#827 - >seq826,non-specific,273186,61,202,0.000114587,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2223,Q#827 - >seq826,non-specific,235175,333,466,0.000191752,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M4a2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
2224,Q#827 - >seq826,superfamily,235175,333,466,0.000191752,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M4a2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
2225,Q#827 - >seq826,non-specific,272954,61,202,0.000200243,44.2961,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2226,Q#827 - >seq826,non-specific,223780,61,202,0.000702591,42.5855,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4a2,ORF2,hs2_gorilla,marg,CompleteHit
2227,Q#827 - >seq826,non-specific,197307,61,202,0.00261437,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a2.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2228,Q#828 - >seq827,non-specific,238827,487,543,1.5918000000000002e-06,49.9822,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs2_gorilla.marg.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4a2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2229,Q#828 - >seq827,superfamily,295487,487,543,1.5918000000000002e-06,49.9822,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs2_gorilla.marg.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4a2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2230,Q#829 - >seq828,non-specific,238827,549,748,2.8293600000000003e-15,76.1758,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2231,Q#829 - >seq828,superfamily,295487,549,748,2.8293600000000003e-15,76.1758,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2232,Q#829 - >seq828,non-specific,333820,565,724,8.33489e-09,56.1466,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2233,Q#829 - >seq828,superfamily,333820,565,724,8.33489e-09,56.1466,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2234,Q#830 - >seq829,non-specific,238827,511,552,0.00485255,39.5818,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
2235,Q#830 - >seq829,superfamily,295487,511,552,0.00485255,39.5818,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
2236,Q#831 - >seq830,non-specific,197310,31,196,2.24104e-14,73.5397,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4a2,ORF2,hs2_gorilla,pars,CompleteHit
2237,Q#831 - >seq830,superfamily,351117,31,196,2.24104e-14,73.5397,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a2,ORF2,hs2_gorilla,pars,CompleteHit
2238,Q#831 - >seq830,non-specific,238827,622,708,1.64655e-06,49.9822,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4a2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2239,Q#831 - >seq830,superfamily,295487,622,708,1.64655e-06,49.9822,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4a2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2240,Q#831 - >seq830,non-specific,197306,42,199,0.00138376,41.3129,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2241,Q#832 - >seq831,non-specific,238827,449,489,2.58757e-07,52.2934,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2242,Q#832 - >seq831,superfamily,295487,449,489,2.58757e-07,52.2934,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2243,Q#832 - >seq831,non-specific,333820,452,483,0.00786178,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2244,Q#832 - >seq831,superfamily,333820,452,483,0.00786178,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2245,Q#834 - >seq833,non-specific,335182,58,124,3.72023e-07,46.5271,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs2_gorilla.marg.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs2_gorilla,marg,CompleteHit
2246,Q#834 - >seq833,superfamily,335182,58,124,3.72023e-07,46.5271,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs2_gorilla.marg.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs2_gorilla,marg,CompleteHit
2247,Q#837 - >seq836,non-specific,335182,28,85,0.00672244,34.5859,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs3_orang.pars.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,pars,C-TerminusTruncated
2248,Q#837 - >seq836,superfamily,335182,28,85,0.00672244,34.5859,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs3_orang.pars.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,pars,C-TerminusTruncated
2249,Q#838 - >seq837,non-specific,335182,37,101,2.068e-08,48.4531,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs2_gorilla,pars,CompleteHit
2250,Q#838 - >seq837,superfamily,335182,37,101,2.068e-08,48.4531,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4a2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs2_gorilla,pars,CompleteHit
2251,Q#839 - >seq838,non-specific,238827,569,779,0.00020911400000000002,43.818999999999996,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs1_chimp,marg,N-TerminusTruncated
2252,Q#839 - >seq838,superfamily,295487,569,779,0.00020911400000000002,43.818999999999996,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs1_chimp,marg,N-TerminusTruncated
2253,Q#839 - >seq838,non-specific,275209,577,770,0.00872164,39.7484,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4a2.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs1_chimp,marg,N-TerminusTruncated
2254,Q#839 - >seq838,superfamily,275209,577,770,0.00872164,39.7484,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4a2.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs1_chimp,marg,N-TerminusTruncated
2255,Q#841 - >seq840,non-specific,197310,39,243,3.56785e-07,52.3537,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs1_chimp,marg,CompleteHit
2256,Q#841 - >seq840,superfamily,351117,39,243,3.56785e-07,52.3537,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs1_chimp,marg,CompleteHit
2257,Q#841 - >seq840,non-specific,238827,586,614,3.35629e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs1_chimp,marg,C-TerminusTruncated
2258,Q#841 - >seq840,superfamily,295487,586,614,3.35629e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs1_chimp,marg,C-TerminusTruncated
2259,Q#841 - >seq840,non-specific,197306,17,247,0.00422709,40.1573,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs1_chimp,marg,CompleteHit
2260,Q#843 - >seq842,non-specific,238827,507,544,0.00682627,38.8114,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs1_chimp.pars.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4a2,ORF2,hs1_chimp,pars,BothTerminiTruncated
2261,Q#843 - >seq842,superfamily,295487,507,544,0.00682627,38.8114,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs1_chimp.pars.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4a2,ORF2,hs1_chimp,pars,BothTerminiTruncated
2262,Q#845 - >seq844,non-specific,335182,92,137,0.0095972,34.2007,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.marg.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs1_chimp,marg,N-TerminusTruncated
2263,Q#845 - >seq844,superfamily,335182,92,137,0.0095972,34.2007,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.marg.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4a2,ORF1,hs1_chimp,marg,N-TerminusTruncated
2264,Q#846 - >seq845,non-specific,335182,55,154,0.00021312799999999998,39.2083,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs1_chimp,marg,CompleteHit
2265,Q#846 - >seq845,superfamily,335182,55,154,0.00021312799999999998,39.2083,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.marg.frame1,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs1_chimp,marg,CompleteHit
2266,Q#848 - >seq847,non-specific,197310,7,128,2.5602099999999995e-06,46.9609,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4a2,ORF2,hs10_snmole,pars,C-TerminusTruncated
2267,Q#848 - >seq847,superfamily,351117,7,128,2.5602099999999995e-06,46.9609,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs10_snmole.pars.frame2,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a2,ORF2,hs10_snmole,pars,C-TerminusTruncated
2268,Q#852 - >seq851,non-specific,340205,133,198,0.00017549299999999998,38.4712,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,marg,CompleteHit
2269,Q#852 - >seq851,superfamily,340205,133,198,0.00017549299999999998,38.4712,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a2.ORF1.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,marg,CompleteHit
2270,Q#852 - >seq851,non-specific,335182,47,95,0.000590184,37.6675,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,marg,C-TerminusTruncated
2271,Q#852 - >seq851,superfamily,335182,47,95,0.000590184,37.6675,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs3_orang,marg,C-TerminusTruncated
2272,Q#858 - >seq857,non-specific,238827,536,776,8.118819999999999e-15,74.635,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2273,Q#858 - >seq857,superfamily,295487,536,776,8.118819999999999e-15,74.635,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2274,Q#858 - >seq857,non-specific,197310,11,241,7.24638e-11,63.5245,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2275,Q#858 - >seq857,superfamily,351117,11,241,7.24638e-11,63.5245,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2276,Q#858 - >seq857,non-specific,333820,539,763,1.45163e-05,46.9018,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2277,Q#858 - >seq857,superfamily,333820,539,763,1.45163e-05,46.9018,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2278,Q#858 - >seq857,non-specific,197306,11,241,0.00017590799999999998,44.3945,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs4_gibbon,marg,CompleteHit
2279,Q#859 - >seq858,non-specific,197310,5,207,1.35396e-07,53.1241,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a2,ORF2,hs4_gibbon,pars,CompleteHit
2280,Q#859 - >seq858,superfamily,351117,5,207,1.35396e-07,53.1241,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a2,ORF2,hs4_gibbon,pars,CompleteHit
2281,Q#859 - >seq858,non-specific,238827,500,710,4.72789e-07,51.523,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs4_gibbon,pars,CompleteHit
2282,Q#859 - >seq858,superfamily,295487,500,710,4.72789e-07,51.523,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs4_gibbon,pars,CompleteHit
2283,Q#861 - >seq860,non-specific,238827,446,489,6.47738e-05,44.9746,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2284,Q#861 - >seq860,superfamily,295487,446,489,6.47738e-05,44.9746,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M4a2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4a2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2285,Q#869 - >seq868,non-specific,197310,44,213,1.10473e-07,53.8945,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs3_orang.marg.frame2,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4a2,ORF2,hs3_orang,marg,N-TerminusTruncated
2286,Q#869 - >seq868,superfamily,351117,44,213,1.10473e-07,53.8945,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs3_orang.marg.frame2,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4a2,ORF2,hs3_orang,marg,N-TerminusTruncated
2287,Q#870 - >seq869,non-specific,238827,505,551,4.4269599999999996e-07,51.9082,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs3_orang,marg,C-TerminusTruncated
2288,Q#870 - >seq869,superfamily,295487,505,551,4.4269599999999996e-07,51.9082,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs3_orang.marg.frame1,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4a2,ORF2,hs3_orang,marg,C-TerminusTruncated
2289,Q#871 - >seq870,non-specific,238827,454,500,5.44176e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs3_orang.pars.frame3,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs3_orang,pars,C-TerminusTruncated
2290,Q#871 - >seq870,superfamily,295487,454,500,5.44176e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs3_orang.pars.frame3,1909122338_L1M4a2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4a2,ORF2,hs3_orang,pars,C-TerminusTruncated
2291,Q#878 - >seq877,specific,197310,9,238,4.80909e-32,124.771,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs7_bushaby.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs7_bushaby,marg,CompleteHit
2292,Q#878 - >seq877,superfamily,351117,9,238,4.80909e-32,124.771,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs7_bushaby.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,marg,CompleteHit
2293,Q#878 - >seq877,non-specific,197306,9,238,4.94195e-14,72.5141,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs7_bushaby.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,marg,CompleteHit
2294,Q#878 - >seq877,specific,335306,10,231,2.5164200000000003e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs7_bushaby.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,marg,CompleteHit
2295,Q#878 - >seq877,non-specific,197311,39,206,0.00044857,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs7_bushaby.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs7_bushaby,marg,CompleteHit
2296,Q#880 - >seq879,non-specific,340205,110,169,1.3113e-17,72.3688,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs6_sqmonkey,pars,CompleteHit
2297,Q#880 - >seq879,superfamily,340205,110,169,1.3113e-17,72.3688,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs6_sqmonkey,pars,CompleteHit
2298,Q#880 - >seq879,non-specific,311007,60,166,0.00207764,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1M4b.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M4b,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
2299,Q#880 - >seq879,superfamily,311007,60,166,0.00207764,37.3841,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1M4b.ORF1.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M4b,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
2300,Q#882 - >seq881,non-specific,335182,24,106,2.55373e-09,51.9199,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs6_sqmonkey,pars,CompleteHit
2301,Q#882 - >seq881,superfamily,335182,24,106,2.55373e-09,51.9199,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs6_sqmonkey,pars,CompleteHit
2302,Q#883 - >seq882,specific,197310,2,222,2.02936e-40,148.654,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2303,Q#883 - >seq882,superfamily,351117,2,222,2.02936e-40,148.654,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2304,Q#883 - >seq882,non-specific,197306,2,222,1.5324100000000002e-18,85.6108,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2305,Q#883 - >seq882,specific,335306,2,215,1.03502e-11,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2306,Q#883 - >seq882,non-specific,197311,21,222,2.3581099999999998e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2307,Q#883 - >seq882,non-specific,223780,2,215,2.4122e-06,49.9043,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2308,Q#883 - >seq882,non-specific,197320,21,215,1.76177e-05,47.1246,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2309,Q#883 - >seq882,non-specific,197307,4,215,8.85309e-05,44.9713,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2310,Q#883 - >seq882,non-specific,238827,574,751,9.350399999999999e-05,44.5894,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2311,Q#883 - >seq882,superfamily,295487,574,751,9.350399999999999e-05,44.5894,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2312,Q#883 - >seq882,non-specific,273186,14,223,0.00023209400000000002,43.4216,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2313,Q#883 - >seq882,non-specific,339261,98,218,0.00026727900000000004,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2314,Q#883 - >seq882,non-specific,197319,12,222,0.00131215,41.1081,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,marg,CompleteHit
2315,Q#883 - >seq882,non-specific,197321,4,67,0.00480919,39.4576,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
2316,Q#886 - >seq885,specific,197310,2,219,1.43155e-34,131.705,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,pars,CompleteHit
2317,Q#886 - >seq885,superfamily,351117,2,219,1.43155e-34,131.705,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,pars,CompleteHit
2318,Q#886 - >seq885,non-specific,197306,2,219,7.23955e-14,71.7437,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,pars,CompleteHit
2319,Q#886 - >seq885,specific,335306,2,212,1.06373e-09,59.181000000000004,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs5_gmonkey,pars,CompleteHit
2320,Q#886 - >seq885,non-specific,223780,2,136,0.00010028299999999999,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
2321,Q#886 - >seq885,non-specific,197311,21,136,0.000148685,43.4345,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
2322,Q#886 - >seq885,non-specific,197320,21,136,0.00195549,40.5762,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
2323,Q#886 - >seq885,non-specific,197321,4,67,0.00493928,39.4576,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
2324,Q#891 - >seq890,non-specific,340205,122,193,9.3771e-19,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs5_gmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs5_gmonkey,marg,CompleteHit
2325,Q#891 - >seq890,superfamily,340205,122,193,9.3771e-19,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs5_gmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs5_gmonkey,marg,CompleteHit
2326,Q#892 - >seq891,non-specific,340205,148,192,7.57641e-12,58.5016,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
2327,Q#892 - >seq891,superfamily,340205,148,192,7.57641e-12,58.5016,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
2328,Q#892 - >seq891,non-specific,335182,53,121,1.72178e-05,41.9047,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
2329,Q#892 - >seq891,superfamily,335182,53,121,1.72178e-05,41.9047,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
2330,Q#895 - >seq894,specific,197310,9,229,1.3476999999999998e-32,126.31200000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2331,Q#895 - >seq894,superfamily,351117,9,229,1.3476999999999998e-32,126.31200000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2332,Q#895 - >seq894,non-specific,238827,482,748,1.2784700000000001e-22,96.9766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2333,Q#895 - >seq894,superfamily,295487,482,748,1.2784700000000001e-22,96.9766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2334,Q#895 - >seq894,non-specific,197306,9,228,1.31128e-08,56.7209,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2335,Q#895 - >seq894,non-specific,333820,493,696,3.86544e-07,51.138999999999996,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2336,Q#895 - >seq894,superfamily,333820,493,696,3.86544e-07,51.138999999999996,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2337,Q#895 - >seq894,specific,335306,10,228,7.738580000000001e-06,48.0102,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2338,Q#896 - >seq895,non-specific,224117,222,471,0.00047028699999999995,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M4b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2339,Q#896 - >seq895,superfamily,224117,222,471,0.00047028699999999995,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1M4b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2340,Q#896 - >seq895,non-specific,274009,278,473,0.00194575,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2341,Q#896 - >seq895,superfamily,274009,278,473,0.00194575,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1M4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2342,Q#896 - >seq895,non-specific,237177,274,428,0.00447867,40.5318,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other,L1M4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2343,Q#896 - >seq895,superfamily,237177,274,428,0.00447867,40.5318,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other,L1M4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2344,Q#896 - >seq895,non-specific,235205,335,433,0.00459565,40.5704,PRK04028,PRK04028,N,cl35240,glutamyl-tRNA(Gln) amidotransferase subunit E; Validated,L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M4b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2345,Q#896 - >seq895,superfamily,235205,335,433,0.00459565,40.5704,cl35240,PRK04028 superfamily,N, - ,glutamyl-tRNA(Gln) amidotransferase subunit E; Validated,L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M4b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2346,Q#896 - >seq895,non-specific,224259,234,464,0.00609765,39.6644,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2347,Q#896 - >seq895,superfamily,224259,234,464,0.00609765,39.6644,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M4b,ORF2,hs4_gibbon,marg,CompleteHit
2348,Q#896 - >seq895,non-specific,223496,222,476,0.00785357,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1M4b,ORF2,hs4_gibbon,marg,BothTerminiTruncated
2349,Q#896 - >seq895,superfamily,223496,222,476,0.00785357,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M4b.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1M4b,ORF2,hs4_gibbon,marg,BothTerminiTruncated
2350,Q#898 - >seq897,non-specific,238827,460,542,2.1630599999999996e-16,78.1018,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2351,Q#898 - >seq897,superfamily,295487,460,542,2.1630599999999996e-16,78.1018,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2352,Q#899 - >seq898,non-specific,197310,27,173,0.00013605,43.4941,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4b,ORF2,hs4_gibbon,pars,CompleteHit
2353,Q#899 - >seq898,superfamily,351117,27,173,0.00013605,43.4941,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4b,ORF2,hs4_gibbon,pars,CompleteHit
2354,Q#900 - >seq899,non-specific,197310,4,217,4.7900299999999995e-17,80.4733,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs4_gibbon,pars,CompleteHit
2355,Q#900 - >seq899,superfamily,351117,4,217,4.7900299999999995e-17,80.4733,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs4_gibbon,pars,CompleteHit
2356,Q#902 - >seq901,non-specific,335182,57,126,0.00021931400000000002,38.8231,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs5_gmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
2357,Q#902 - >seq901,superfamily,335182,57,126,0.00021931400000000002,38.8231,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs5_gmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
2358,Q#903 - >seq902,non-specific,340205,116,182,4.8085499999999997e-20,79.3024,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs6_sqmonkey,marg,CompleteHit
2359,Q#903 - >seq902,superfamily,340205,116,182,4.8085499999999997e-20,79.3024,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs6_sqmonkey,marg,CompleteHit
2360,Q#903 - >seq902,non-specific,335182,33,113,4.444939999999999e-09,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs6_sqmonkey,marg,CompleteHit
2361,Q#903 - >seq902,superfamily,335182,33,113,4.444939999999999e-09,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs6_sqmonkey.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs6_sqmonkey,marg,CompleteHit
2362,Q#906 - >seq905,non-specific,340205,169,234,2.3193700000000003e-16,70.828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2363,Q#906 - >seq905,superfamily,340205,169,234,2.3193700000000003e-16,70.828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2364,Q#906 - >seq905,non-specific,335182,81,166,6.66517e-16,70.7947,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2365,Q#906 - >seq905,superfamily,335182,81,166,6.66517e-16,70.7947,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2366,Q#906 - >seq905,non-specific,340204,21,63,0.00928414,33.15,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2367,Q#906 - >seq905,superfamily,340204,21,63,0.00928414,33.15,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M4b.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1M4b,ORF1,hs8_ctshrew,marg,CompleteHit
2368,Q#910 - >seq909,non-specific,340205,154,218,1.6745799999999999e-18,76.2208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs8_ctshrew.pars.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs8_ctshrew,pars,CompleteHit
2369,Q#910 - >seq909,superfamily,340205,154,218,1.6745799999999999e-18,76.2208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs8_ctshrew.pars.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs8_ctshrew,pars,CompleteHit
2370,Q#910 - >seq909,non-specific,335182,73,151,2.542e-17,73.8763,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs8_ctshrew.pars.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs8_ctshrew,pars,CompleteHit
2371,Q#910 - >seq909,superfamily,335182,73,151,2.542e-17,73.8763,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs8_ctshrew.pars.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs8_ctshrew,pars,CompleteHit
2372,Q#912 - >seq911,non-specific,335182,64,125,0.00591523,34.2007,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.pars.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs1_chimp,pars,N-TerminusTruncated
2373,Q#912 - >seq911,superfamily,335182,64,125,0.00591523,34.2007,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs1_chimp.pars.frame2,1909122338_L1M4a2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a2,ORF1,hs1_chimp,pars,N-TerminusTruncated
2374,Q#915 - >seq914,specific,197310,9,228,9.97546e-32,115.52600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs7_bushaby,pars,CompleteHit
2375,Q#915 - >seq914,superfamily,351117,9,228,9.97546e-32,115.52600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,pars,CompleteHit
2376,Q#915 - >seq914,non-specific,197306,9,228,2.63628e-15,72.1289,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,pars,CompleteHit
2377,Q#915 - >seq914,specific,335306,10,228,1.97211e-09,55.7142,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs7_bushaby,pars,CompleteHit
2378,Q#915 - >seq914,non-specific,223780,9,146,4.29005e-05,42.9707,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2379,Q#915 - >seq914,non-specific,197311,7,203,0.000189445,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs7_bushaby,pars,CompleteHit
2380,Q#915 - >seq914,non-specific,197320,9,144,0.000491591,39.8058,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2381,Q#919 - >seq918,non-specific,335182,213,283,4.1894400000000003e-16,72.7207,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs7_bushaby.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs7_bushaby,marg,N-TerminusTruncated
2382,Q#919 - >seq918,superfamily,335182,213,283,4.1894400000000003e-16,72.7207,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs7_bushaby.marg.frame2,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs7_bushaby,marg,N-TerminusTruncated
2383,Q#920 - >seq919,non-specific,340205,286,351,1.04008e-19,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs7_bushaby,marg,CompleteHit
2384,Q#920 - >seq919,superfamily,340205,286,351,1.04008e-19,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs7_bushaby,marg,CompleteHit
2385,Q#921 - >seq920,non-specific,340205,103,167,5.81191e-22,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs7_bushaby,pars,CompleteHit
2386,Q#921 - >seq920,superfamily,340205,103,167,5.81191e-22,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs7_bushaby.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs7_bushaby,pars,CompleteHit
2387,Q#923 - >seq922,non-specific,335182,33,103,1.9222e-15,67.7131,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs7_bushaby.pars.frame1,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2388,Q#923 - >seq922,superfamily,335182,33,103,1.9222e-15,67.7131,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs7_bushaby.pars.frame1,1909122338_L1M4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2389,Q#926 - >seq925,specific,197310,14,246,8.117069999999999e-29,115.52600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,CompleteHit
2390,Q#926 - >seq925,superfamily,351117,14,246,8.117069999999999e-29,115.52600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,CompleteHit
2391,Q#926 - >seq925,non-specific,197306,14,246,2.3986599999999998e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,CompleteHit
2392,Q#926 - >seq925,specific,335306,15,239,3.76262e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,CompleteHit
2393,Q#926 - >seq925,non-specific,223780,14,150,4.08123e-06,49.1339,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2394,Q#926 - >seq925,non-specific,197320,14,150,5.92741e-06,48.6654,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2395,Q#926 - >seq925,non-specific,197307,14,163,5.93939e-05,45.3565,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2396,Q#926 - >seq925,non-specific,197311,42,149,0.00105285,41.1233,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2397,Q#926 - >seq925,non-specific,197321,12,150,0.00589318,39.4576,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2398,Q#927 - >seq926,specific,197310,9,229,3.2601199999999998e-28,113.6,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,CompleteHit
2399,Q#927 - >seq926,superfamily,351117,9,229,3.2601199999999998e-28,113.6,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,CompleteHit
2400,Q#927 - >seq926,non-specific,197306,9,229,6.87528e-11,62.8841,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,CompleteHit
2401,Q#927 - >seq926,specific,335306,10,222,1.17597e-07,53.0178,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,CompleteHit
2402,Q#927 - >seq926,non-specific,197320,9,144,9.64819e-06,47.895,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2403,Q#927 - >seq926,non-specific,223780,9,144,1.7750199999999998e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2404,Q#927 - >seq926,non-specific,197307,9,144,8.98392e-05,44.5861,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2405,Q#927 - >seq926,non-specific,238827,620,682,0.00322488,39.5818,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4b,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2406,Q#927 - >seq926,superfamily,295487,620,682,0.00322488,39.5818,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4b,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2407,Q#929 - >seq928,non-specific,340205,138,201,8.21097e-18,73.9096,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,marg,CompleteHit
2408,Q#929 - >seq928,superfamily,340205,138,201,8.21097e-18,73.9096,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,marg,CompleteHit
2409,Q#929 - >seq928,non-specific,335182,94,135,6.88295e-05,40.3639,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,marg,N-TerminusTruncated
2410,Q#929 - >seq928,superfamily,335182,94,135,6.88295e-05,40.3639,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs4_gibbon.marg.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,marg,N-TerminusTruncated
2411,Q#931 - >seq930,non-specific,185628,2,154,0.00954668,35.821,PTZ00449,PTZ00449,NC,cl33186,104 kDa microneme/rhoptry antigen; Provisional,L1M4b.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M4b,ORF1,hs4_gibbon,pars,BothTerminiTruncated
2412,Q#931 - >seq930,superfamily,185628,2,154,0.00954668,35.821,cl33186,PTZ00449 superfamily,NC, - ,104 kDa microneme/rhoptry antigen; Provisional,L1M4b.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M4b,ORF1,hs4_gibbon,pars,BothTerminiTruncated
2413,Q#932 - >seq931,non-specific,340205,110,173,2.55352e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,pars,CompleteHit
2414,Q#932 - >seq931,superfamily,340205,110,173,2.55352e-19,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,pars,CompleteHit
2415,Q#932 - >seq931,non-specific,335182,66,107,4.58141e-05,40.3639,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,pars,N-TerminusTruncated
2416,Q#932 - >seq931,superfamily,335182,66,107,4.58141e-05,40.3639,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs4_gibbon.pars.frame2,1909122338_L1M4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs4_gibbon,pars,N-TerminusTruncated
2417,Q#934 - >seq933,specific,197310,9,230,3.85394e-41,150.965,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,pars,CompleteHit
2418,Q#934 - >seq933,superfamily,351117,9,230,3.85394e-41,150.965,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,pars,CompleteHit
2419,Q#934 - >seq933,non-specific,197306,9,229,6.68288e-21,92.5444,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,pars,CompleteHit
2420,Q#934 - >seq933,specific,335306,10,224,4.814229999999999e-09,57.6402,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,pars,CompleteHit
2421,Q#934 - >seq933,non-specific,197307,9,224,1.1049600000000002e-06,50.7493,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,pars,CompleteHit
2422,Q#934 - >seq933,non-specific,223780,9,119,6.78902e-05,45.2819,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
2423,Q#934 - >seq933,non-specific,197320,9,145,0.000287307,43.2726,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
2424,Q#934 - >seq933,non-specific,197321,9,118,0.000402303,42.9244,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
2425,Q#934 - >seq933,non-specific,197311,7,145,0.00284606,39.9677,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
2426,Q#934 - >seq933,non-specific,272954,9,146,0.00405716,40.0589,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs1_chimp.pars.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
2427,Q#937 - >seq936,non-specific,340205,133,198,6.5862e-17,71.5984,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs1_chimp,marg,CompleteHit
2428,Q#937 - >seq936,superfamily,340205,133,198,6.5862e-17,71.5984,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs1_chimp,marg,CompleteHit
2429,Q#937 - >seq936,non-specific,335182,60,130,2.2398099999999998e-05,41.5195,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs1_chimp,marg,N-TerminusTruncated
2430,Q#937 - >seq936,superfamily,335182,60,130,2.2398099999999998e-05,41.5195,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs1_chimp,marg,N-TerminusTruncated
2431,Q#942 - >seq941,non-specific,340205,70,133,1.1904700000000001e-14,63.8944,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs1_chimp.pars.frame1,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs1_chimp,pars,CompleteHit
2432,Q#942 - >seq941,superfamily,340205,70,133,1.1904700000000001e-14,63.8944,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs1_chimp.pars.frame1,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs1_chimp,pars,CompleteHit
2433,Q#942 - >seq941,non-specific,335182,3,67,3.8542e-05,39.9787,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs1_chimp.pars.frame1,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs1_chimp,pars,N-TerminusTruncated
2434,Q#942 - >seq941,superfamily,335182,3,67,3.8542e-05,39.9787,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs1_chimp.pars.frame1,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs1_chimp,pars,N-TerminusTruncated
2435,Q#943 - >seq942,non-specific,238827,524,587,0.00272268,40.3522,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4a2.ORF2.hs0_human.marg.frame3,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs0_human,marg,C-TerminusTruncated
2436,Q#943 - >seq942,superfamily,295487,524,587,0.00272268,40.3522,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4a2.ORF2.hs0_human.marg.frame3,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4a2,ORF2,hs0_human,marg,C-TerminusTruncated
2437,Q#951 - >seq950,non-specific,335182,64,159,1.0605800000000001e-07,48.0679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs0_human.marg.frame1,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs0_human,marg,CompleteHit
2438,Q#951 - >seq950,superfamily,335182,64,159,1.0605800000000001e-07,48.0679,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs0_human.marg.frame1,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a2,ORF1,hs0_human,marg,CompleteHit
2439,Q#952 - >seq951,non-specific,335182,46,97,3.11954e-06,43.0603,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs0_human.pars.frame3,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a2,ORF1,hs0_human,pars,C-TerminusTruncated
2440,Q#952 - >seq951,superfamily,335182,46,97,3.11954e-06,43.0603,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a2.ORF1.hs0_human.pars.frame3,1909122338_L1M4a2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a2,ORF1,hs0_human,pars,C-TerminusTruncated
2441,Q#957 - >seq956,non-specific,197310,25,98,3.43613e-05,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a2.ORF2.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a2,ORF2,hs10_snmole,marg,C-TerminusTruncated
2442,Q#957 - >seq956,superfamily,351117,25,98,3.43613e-05,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a2.ORF2.hs10_snmole.marg.frame1,1909122338_L1M4a2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a2,ORF2,hs10_snmole,marg,C-TerminusTruncated
2443,Q#958 - >seq957,specific,197310,9,232,1.64047e-39,146.342,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,marg,CompleteHit
2444,Q#958 - >seq957,superfamily,351117,9,232,1.64047e-39,146.342,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,marg,CompleteHit
2445,Q#958 - >seq957,non-specific,197306,9,232,2.0159599999999998e-20,91.3888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,marg,CompleteHit
2446,Q#958 - >seq957,specific,335306,10,226,3.73569e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs1_chimp,marg,CompleteHit
2447,Q#958 - >seq957,non-specific,223780,9,119,0.000152846,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
2448,Q#958 - >seq957,non-specific,197320,9,145,0.00037025599999999996,43.2726,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
2449,Q#958 - >seq957,non-specific,197321,9,118,0.0006847110000000001,42.5392,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
2450,Q#958 - >seq957,non-specific,197307,9,226,0.000915047,41.8897,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs1_chimp,marg,CompleteHit
2451,Q#958 - >seq957,non-specific,197311,7,145,0.00313934,39.9677,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
2452,Q#958 - >seq957,non-specific,272954,9,146,0.00973816,38.9033,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs1_chimp.marg.frame3,1909122338_L1M4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
2453,Q#959 - >seq958,non-specific,340205,113,177,1.3206e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs2_gorilla,pars,CompleteHit
2454,Q#959 - >seq958,superfamily,340205,113,177,1.3206e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs2_gorilla,pars,CompleteHit
2455,Q#959 - >seq958,non-specific,335182,38,110,8.04925e-10,53.4607,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
2456,Q#959 - >seq958,superfamily,335182,38,110,8.04925e-10,53.4607,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs2_gorilla,pars,N-TerminusTruncated
2457,Q#961 - >seq960,specific,197310,9,238,7.630719999999999e-31,121.304,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2458,Q#961 - >seq960,superfamily,351117,9,238,7.630719999999999e-31,121.304,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2459,Q#961 - >seq960,non-specific,197306,9,238,2.19252e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2460,Q#961 - >seq960,specific,335306,10,231,3.2344e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2461,Q#961 - >seq960,non-specific,223780,9,239,1.2036e-08,56.8379,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2462,Q#961 - >seq960,non-specific,197321,9,81,1.70598e-05,47.1616,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,marg,C-TerminusTruncated
2463,Q#961 - >seq960,non-specific,197320,9,223,9.65018e-05,44.8134,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2464,Q#961 - >seq960,non-specific,272954,9,209,0.00030983599999999997,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2465,Q#961 - >seq960,non-specific,197307,9,238,0.00179038,40.7341,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2466,Q#961 - >seq960,non-specific,273186,9,239,0.0097351,38.414,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs3_orang.marg.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,marg,CompleteHit
2467,Q#964 - >seq963,specific,197310,5,226,6.47001e-31,117.06700000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2468,Q#964 - >seq963,superfamily,351117,5,226,6.47001e-31,117.06700000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2469,Q#964 - >seq963,non-specific,197306,5,226,6.297029999999999e-13,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2470,Q#964 - >seq963,specific,335306,6,219,7.27151e-09,55.32899999999999,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2471,Q#964 - >seq963,non-specific,223780,5,227,2.37604e-08,54.1415,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2472,Q#964 - >seq963,non-specific,197321,5,74,1.33474e-05,45.6208,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,pars,C-TerminusTruncated
2473,Q#964 - >seq963,non-specific,272954,5,197,1.99757e-05,45.4517,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2474,Q#964 - >seq963,non-specific,197307,5,226,0.00026995,41.8897,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2475,Q#964 - >seq963,non-specific,197320,5,211,0.000397601,41.3466,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2476,Q#964 - >seq963,non-specific,273186,5,227,0.00159381,39.5696,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs3_orang.pars.frame3,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs3_orang,pars,CompleteHit
2477,Q#969 - >seq968,non-specific,335182,73,147,1.0106e-20,82.7359,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs3_orang.marg.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,marg,N-TerminusTruncated
2478,Q#969 - >seq968,superfamily,335182,73,147,1.0106e-20,82.7359,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs3_orang.marg.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,marg,N-TerminusTruncated
2479,Q#969 - >seq968,non-specific,340205,150,213,2.19779e-10,54.6496,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs3_orang.marg.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,marg,CompleteHit
2480,Q#969 - >seq968,superfamily,340205,150,213,2.19779e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs3_orang.marg.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,marg,CompleteHit
2481,Q#972 - >seq971,non-specific,335182,2,73,4.15673e-21,80.8099,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs3_orang.pars.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,pars,N-TerminusTruncated
2482,Q#972 - >seq971,superfamily,335182,2,73,4.15673e-21,80.8099,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs3_orang.pars.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,pars,N-TerminusTruncated
2483,Q#972 - >seq971,non-specific,340205,76,128,8.474680000000002e-10,51.1828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs3_orang.pars.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,pars,CompleteHit
2484,Q#972 - >seq971,superfamily,340205,76,128,8.474680000000002e-10,51.1828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs3_orang.pars.frame1,1909122338_L1M4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs3_orang,pars,CompleteHit
2485,Q#975 - >seq974,specific,197310,12,256,1.1877599999999998e-40,149.809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2486,Q#975 - >seq974,superfamily,351117,12,256,1.1877599999999998e-40,149.809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2487,Q#975 - >seq974,non-specific,197306,12,256,1.5261600000000003e-18,85.99600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2488,Q#975 - >seq974,specific,335306,13,249,3.7437199999999996e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2489,Q#975 - >seq974,non-specific,197307,12,249,2.959e-07,52.6753,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2490,Q#975 - >seq974,non-specific,197320,12,249,3.59316e-07,52.5174,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2491,Q#975 - >seq974,non-specific,223780,29,249,9.170380000000001e-07,51.4451,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2492,Q#975 - >seq974,non-specific,197321,29,165,7.452850000000001e-05,45.6208,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2493,Q#975 - >seq974,non-specific,197319,29,256,0.00011784399999999999,44.9601,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2494,Q#975 - >seq974,non-specific,273186,12,257,0.00174894,41.4956,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2495,Q#975 - >seq974,non-specific,272954,29,227,0.00214727,41.2145,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,CompleteHit
2496,Q#975 - >seq974,non-specific,197311,58,165,0.00328973,39.9677,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2497,Q#976 - >seq975,non-specific,197310,7,240,1.9492e-12,67.7617,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs2_gorilla,pars,CompleteHit
2498,Q#976 - >seq975,superfamily,351117,7,240,1.9492e-12,67.7617,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,pars,CompleteHit
2499,Q#976 - >seq975,non-specific,197306,7,240,0.00601366,39.3869,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,pars,CompleteHit
2500,Q#976 - >seq975,non-specific,274009,309,458,0.00956492,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M4b.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2501,Q#976 - >seq975,superfamily,274009,309,458,0.00956492,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M4b.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2502,Q#978 - >seq977,non-specific,197310,48,193,4.05591e-15,75.8509,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs2_gorilla,pars,CompleteHit
2503,Q#978 - >seq977,superfamily,351117,48,193,4.05591e-15,75.8509,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,pars,CompleteHit
2504,Q#978 - >seq977,non-specific,197306,71,160,1.1972799999999998e-08,56.7209,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs2_gorilla,pars,BothTerminiTruncated
2505,Q#978 - >seq977,non-specific,339261,109,149,0.00406821,38.0871,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2506,Q#978 - >seq977,non-specific,197320,64,147,0.00782015,39.0354,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs2_gorilla.pars.frame1,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4b,ORF2,hs2_gorilla,pars,BothTerminiTruncated
2507,Q#979 - >seq978,non-specific,340205,160,224,9.79434e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs2_gorilla,marg,CompleteHit
2508,Q#979 - >seq978,superfamily,340205,160,224,9.79434e-24,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs2_gorilla,marg,CompleteHit
2509,Q#979 - >seq978,non-specific,335182,85,157,2.21663e-09,53.0755,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs2_gorilla,marg,N-TerminusTruncated
2510,Q#979 - >seq978,superfamily,335182,85,157,2.21663e-09,53.0755,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs2_gorilla,marg,N-TerminusTruncated
2511,Q#985 - >seq984,non-specific,197310,31,85,0.000331631,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4a1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2512,Q#985 - >seq984,superfamily,351117,31,85,0.000331631,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2513,Q#987 - >seq986,specific,238827,313,501,1.53956e-28,114.311,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2514,Q#987 - >seq986,superfamily,295487,313,501,1.53956e-28,114.311,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2515,Q#987 - >seq986,non-specific,333820,331,488,2.73243e-15,75.0214,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2516,Q#987 - >seq986,superfamily,333820,331,488,2.73243e-15,75.0214,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2517,Q#987 - >seq986,non-specific,238828,386,474,6.68276e-05,45.2697,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
2518,Q#987 - >seq986,non-specific,275209,391,474,0.00533936,40.1336,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
2519,Q#987 - >seq986,superfamily,275209,391,474,0.00533936,40.1336,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
2520,Q#993 - >seq992,specific,238827,509,712,8.88768e-36,135.111,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2521,Q#993 - >seq992,superfamily,295487,509,712,8.88768e-36,135.111,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2522,Q#993 - >seq992,non-specific,333820,513,697,7.53779e-19,85.4217,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2523,Q#993 - >seq992,superfamily,333820,513,697,7.53779e-19,85.4217,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2524,Q#993 - >seq992,non-specific,238828,539,681,3.2077599999999997e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,N-TerminusTruncated
2525,Q#993 - >seq992,non-specific,275209,544,694,5.56811e-06,49.7636,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,BothTerminiTruncated
2526,Q#993 - >seq992,superfamily,275209,544,694,5.56811e-06,49.7636,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,BothTerminiTruncated
2527,Q#993 - >seq992,non-specific,238185,613,694,0.00160362,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2528,Q#995 - >seq994,specific,197310,5,231,4.9576999999999996e-49,173.692,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2529,Q#995 - >seq994,superfamily,351117,5,231,4.9576999999999996e-49,173.692,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2530,Q#995 - >seq994,non-specific,197306,5,231,1.21532e-25,106.79700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2531,Q#995 - >seq994,non-specific,197320,3,224,2.63619e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2532,Q#995 - >seq994,non-specific,223780,3,224,9.30295e-18,84.1871,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2533,Q#995 - >seq994,specific,335306,6,224,3.3007599999999996e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2534,Q#995 - >seq994,non-specific,197307,5,231,6.0291200000000004e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2535,Q#995 - >seq994,non-specific,197321,3,231,4.91526e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2536,Q#995 - >seq994,non-specific,273186,3,232,6.17622e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2537,Q#995 - >seq994,non-specific,272954,3,231,1.3956100000000002e-10,62.7857,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2538,Q#995 - >seq994,non-specific,197319,3,231,4.61902e-10,61.1385,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2539,Q#995 - >seq994,non-specific,197318,5,231,1.2196199999999999e-05,47.6763,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2540,Q#995 - >seq994,non-specific,197336,3,224,5.0820100000000005e-05,46.0663,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,pars,CompleteHit
2541,Q#995 - >seq994,non-specific,197317,135,224,0.0017771,41.0484,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,pars,N-TerminusTruncated
2542,Q#995 - >seq994,non-specific,339261,106,227,0.00260239,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs0_human.pars.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M3f,ORF2,hs0_human,pars,CompleteHit
2543,Q#996 - >seq995,non-specific,335182,85,181,1.5679999999999998e-29,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs0_human.marg.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,marg,CompleteHit
2544,Q#996 - >seq995,superfamily,335182,85,181,1.5679999999999998e-29,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs0_human.marg.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,marg,CompleteHit
2545,Q#996 - >seq995,non-specific,340205,185,247,1.8180099999999997e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs0_human.marg.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,marg,CompleteHit
2546,Q#996 - >seq995,superfamily,340205,185,247,1.8180099999999997e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs0_human.marg.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,marg,CompleteHit
2547,Q#997 - >seq996,non-specific,238827,527,822,4.05876e-25,104.681,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3,ORF2,hs4_gibbon,marg,CompleteHit
2548,Q#997 - >seq996,superfamily,295487,527,822,4.05876e-25,104.681,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3,ORF2,hs4_gibbon,marg,CompleteHit
2549,Q#997 - >seq996,non-specific,333820,545,712,3.4401800000000005e-10,60.3838,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2550,Q#997 - >seq996,superfamily,333820,545,712,3.4401800000000005e-10,60.3838,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2551,Q#997 - >seq996,non-specific,197310,121,228,0.00109017,41.9533,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2552,Q#997 - >seq996,superfamily,351117,121,228,0.00109017,41.9533,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2553,Q#999 - >seq998,non-specific,335182,74,170,2.18067e-29,105.848,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,pars,CompleteHit
2554,Q#999 - >seq998,superfamily,335182,74,170,2.18067e-29,105.848,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,pars,CompleteHit
2555,Q#999 - >seq998,non-specific,340205,174,236,1.9803399999999997e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,pars,CompleteHit
2556,Q#999 - >seq998,superfamily,340205,174,236,1.9803399999999997e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs0_human.pars.frame3,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs0_human,pars,CompleteHit
2557,Q#1002 - >seq1001,specific,238827,517,738,1.0929899999999998e-31,123.555,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2558,Q#1002 - >seq1001,superfamily,295487,517,738,1.0929899999999998e-31,123.555,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2559,Q#1002 - >seq1001,non-specific,333820,510,738,2.6311500000000003e-10,60.3838,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2560,Q#1002 - >seq1001,superfamily,333820,510,738,2.6311500000000003e-10,60.3838,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2561,Q#1002 - >seq1001,non-specific,238828,549,690,4.19092e-05,46.0401,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2562,Q#1002 - >seq1001,non-specific,235175,192,437,0.0006212559999999999,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M3f,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2563,Q#1002 - >seq1001,superfamily,235175,192,437,0.0006212559999999999,43.513999999999996,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M3f,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
2564,Q#1002 - >seq1001,non-specific,223496,292,437,0.00476879,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
2565,Q#1002 - >seq1001,superfamily,223496,292,437,0.00476879,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M3f,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
2566,Q#1003 - >seq1002,non-specific,197310,26,216,1.2672e-17,83.1697,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2567,Q#1003 - >seq1002,superfamily,351117,26,216,1.2672e-17,83.1697,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2568,Q#1003 - >seq1002,non-specific,197306,22,218,9.37121e-11,62.8841,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2569,Q#1003 - >seq1002,non-specific,197307,28,216,0.0008956439999999999,41.8897,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2570,Q#1003 - >seq1002,non-specific,197320,28,206,0.00115339,41.7318,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2571,Q#1003 - >seq1002,non-specific,197319,20,216,0.00905026,38.7969,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs6_sqmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,marg,CompleteHit
2572,Q#1005 - >seq1004,non-specific,197310,9,214,1.5557499999999997e-26,108.978,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2573,Q#1005 - >seq1004,superfamily,351117,9,214,1.5557499999999997e-26,108.978,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2574,Q#1005 - >seq1004,non-specific,197306,9,216,3.2508099999999998e-18,84.8404,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2575,Q#1005 - >seq1004,non-specific,197307,9,214,6.31138e-09,57.6829,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2576,Q#1005 - >seq1004,non-specific,223780,7,190,5.8438099999999996e-08,54.9119,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2577,Q#1005 - >seq1004,non-specific,272954,7,203,2.36024e-07,52.7705,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2578,Q#1005 - >seq1004,non-specific,197320,7,204,2.38592e-07,52.9026,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2579,Q#1005 - >seq1004,non-specific,273186,7,204,1.17213e-05,47.6588,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2580,Q#1005 - >seq1004,non-specific,197321,7,190,1.2798e-05,47.5468,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2581,Q#1005 - >seq1004,non-specific,197319,7,214,1.53068e-05,47.2713,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2582,Q#1005 - >seq1004,specific,335306,10,206,4.03201e-05,45.699,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2583,Q#1005 - >seq1004,non-specific,197336,7,43,0.000991928,41.8291,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs6_sqmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2584,Q#1006 - >seq1005,specific,238827,520,743,9.9437e-32,123.555,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2585,Q#1006 - >seq1005,superfamily,295487,520,743,9.9437e-32,123.555,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2586,Q#1006 - >seq1005,non-specific,333820,531,743,6.157769999999999e-10,59.2282,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2587,Q#1006 - >seq1005,superfamily,333820,531,743,6.157769999999999e-10,59.2282,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs6_sqmonkey,pars,CompleteHit
2588,Q#1006 - >seq1005,non-specific,238828,554,695,5.41696e-05,45.2697,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
2589,Q#1006 - >seq1005,non-specific,223496,262,443,0.00117637,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1M3f,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
2590,Q#1006 - >seq1005,superfamily,223496,262,443,0.00117637,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1M3f,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
2591,Q#1008 - >seq1007,non-specific,340205,154,218,5.53236e-21,83.1544,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs6_sqmonkey,marg,CompleteHit
2592,Q#1008 - >seq1007,superfamily,340205,154,218,5.53236e-21,83.1544,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs6_sqmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs6_sqmonkey,marg,CompleteHit
2593,Q#1011 - >seq1010,non-specific,197310,5,109,4.69681e-05,45.8053,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2594,Q#1011 - >seq1010,superfamily,351117,5,109,4.69681e-05,45.8053,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2595,Q#1015 - >seq1014,non-specific,197310,17,193,9.33869e-14,69.6877,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs2_gorilla,pars,CompleteHit
2596,Q#1015 - >seq1014,superfamily,351117,17,193,9.33869e-14,69.6877,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs2_gorilla,pars,CompleteHit
2597,Q#1015 - >seq1014,non-specific,197319,21,147,9.72476e-05,43.0341,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2598,Q#1015 - >seq1014,non-specific,197307,29,195,0.00018801200000000002,42.2749,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4a1,ORF2,hs2_gorilla,pars,CompleteHit
2599,Q#1015 - >seq1014,non-specific,197306,17,199,0.00034679,41.3129,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs2_gorilla,pars,CompleteHit
2600,Q#1015 - >seq1014,non-specific,197321,17,193,0.000488706,40.9984,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs2_gorilla,pars,CompleteHit
2601,Q#1036 - >seq1035,non-specific,335182,60,97,0.00326004,35.7415,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs6_sqmonkey.marg.frame1,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3f,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
2602,Q#1036 - >seq1035,superfamily,335182,60,97,0.00326004,35.7415,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs6_sqmonkey.marg.frame1,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3f,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
2603,Q#1038 - >seq1037,non-specific,340205,138,202,1.67362e-20,80.8432,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs6_sqmonkey,pars,CompleteHit
2604,Q#1038 - >seq1037,superfamily,340205,138,202,1.67362e-20,80.8432,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs6_sqmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs6_sqmonkey,pars,CompleteHit
2605,Q#1039 - >seq1038,specific,238827,467,728,3.1235199999999996e-56,194.047,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2606,Q#1039 - >seq1038,superfamily,295487,467,728,3.1235199999999996e-56,194.047,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2607,Q#1039 - >seq1038,specific,333820,473,728,1.85624e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2608,Q#1039 - >seq1038,superfamily,333820,473,728,1.85624e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2609,Q#1039 - >seq1038,non-specific,238828,473,693,1.0059e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2610,Q#1039 - >seq1038,non-specific,275209,410,762,7.80532e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2611,Q#1039 - >seq1038,superfamily,275209,410,762,7.80532e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs3_orang.marg.frame1,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2612,Q#1040 - >seq1039,specific,238827,478,707,1.58072e-47,169.00900000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2613,Q#1040 - >seq1039,superfamily,295487,478,707,1.58072e-47,169.00900000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2614,Q#1040 - >seq1039,non-specific,333820,484,708,2.1778400000000002e-26,106.993,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2615,Q#1040 - >seq1039,superfamily,333820,484,708,2.1778400000000002e-26,106.993,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2616,Q#1040 - >seq1039,non-specific,197310,9,96,1.05866e-14,74.6953,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2617,Q#1040 - >seq1039,superfamily,351117,9,96,1.05866e-14,74.6953,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2618,Q#1040 - >seq1039,non-specific,238828,484,705,2.0483500000000003e-08,55.67,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2619,Q#1040 - >seq1039,non-specific,197306,9,79,6.47228e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2620,Q#1040 - >seq1039,non-specific,275209,421,705,4.3318199999999995e-05,46.681999999999995,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2621,Q#1040 - >seq1039,superfamily,275209,421,705,4.3318199999999995e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2622,Q#1040 - >seq1039,non-specific,223780,7,81,5.26583e-05,46.0523,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2623,Q#1040 - >seq1039,non-specific,273186,7,52,0.00012239,44.5772,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2624,Q#1040 - >seq1039,non-specific,197307,9,83,0.00020836099999999998,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2625,Q#1040 - >seq1039,non-specific,197321,7,42,0.00032617599999999996,43.3096,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2626,Q#1040 - >seq1039,non-specific,197336,7,75,0.000432378,42.9847,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2627,Q#1040 - >seq1039,specific,335306,10,87,0.0005222369999999999,42.6174,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2628,Q#1040 - >seq1039,non-specific,272954,7,75,0.00061737,42.7553,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,pars,C-TerminusTruncated
2629,Q#1040 - >seq1039,non-specific,223496,288,524,0.000774135,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1M3f,ORF2,hs3_orang,pars,BothTerminiTruncated
2630,Q#1040 - >seq1039,superfamily,223496,288,524,0.000774135,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M3f.ORF2.hs3_orang.pars.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1M3f,ORF2,hs3_orang,pars,BothTerminiTruncated
2631,Q#1041 - >seq1040,specific,197310,73,230,2.05326e-33,129.00799999999998,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2632,Q#1041 - >seq1040,superfamily,351117,73,230,2.05326e-33,129.00799999999998,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2633,Q#1041 - >seq1040,non-specific,197306,72,230,8.940579999999999e-18,83.6848,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2634,Q#1041 - >seq1040,non-specific,197320,100,223,1.07375e-13,72.1626,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2635,Q#1041 - >seq1040,non-specific,223780,85,223,6.3913e-12,66.8531,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2636,Q#1041 - >seq1040,non-specific,197307,79,230,1.25183e-11,65.7721,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2637,Q#1041 - >seq1040,non-specific,273186,100,231,7.472770000000001e-09,57.674,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2638,Q#1041 - >seq1040,non-specific,197319,100,230,9.55489e-09,57.2865,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2639,Q#1041 - >seq1040,non-specific,272954,85,230,5.468350000000001e-06,48.9185,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2640,Q#1041 - >seq1040,specific,335306,106,223,5.61044e-06,48.3954,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2641,Q#1041 - >seq1040,non-specific,197322,85,230,2.10637e-05,47.696999999999996,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2642,Q#1041 - >seq1040,non-specific,197321,100,230,2.5224e-05,46.7764,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2643,Q#1041 - >seq1040,non-specific,339261,102,226,0.00133819,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M3f,ORF2,hs3_orang,pars,CompleteHit
2644,Q#1041 - >seq1040,non-specific,197317,133,223,0.00158073,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,pars,N-TerminusTruncated
2645,Q#1043 - >seq1042,non-specific,335182,46,142,2.84771e-29,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs3_orang,marg,CompleteHit
2646,Q#1043 - >seq1042,superfamily,335182,46,142,2.84771e-29,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs3_orang,marg,CompleteHit
2647,Q#1043 - >seq1042,non-specific,340205,146,207,2.28132e-22,85.8508,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs3_orang,marg,CompleteHit
2648,Q#1043 - >seq1042,superfamily,340205,146,207,2.28132e-22,85.8508,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs3_orang,marg,CompleteHit
2649,Q#1047 - >seq1046,non-specific,335182,61,157,9.25136e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs3_orang,pars,CompleteHit
2650,Q#1047 - >seq1046,superfamily,335182,61,157,9.25136e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs3_orang,pars,CompleteHit
2651,Q#1047 - >seq1046,non-specific,340205,161,222,1.0415100000000002e-22,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs3_orang,pars,CompleteHit
2652,Q#1047 - >seq1046,superfamily,340205,161,222,1.0415100000000002e-22,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs3_orang.pars.frame2,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs3_orang,pars,CompleteHit
2653,Q#1050 - >seq1049,specific,197310,3,234,1.57113e-42,155.202,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2654,Q#1050 - >seq1049,superfamily,351117,3,234,1.57113e-42,155.202,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2655,Q#1050 - >seq1049,non-specific,238827,615,732,1.30349e-25,105.836,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2656,Q#1050 - >seq1049,superfamily,295487,615,732,1.30349e-25,105.836,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2657,Q#1050 - >seq1049,non-specific,197306,3,234,2.36587e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2658,Q#1050 - >seq1049,specific,335306,4,227,7.60753e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2659,Q#1050 - >seq1049,non-specific,197307,3,234,1.0943000000000001e-14,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2660,Q#1050 - >seq1049,non-specific,223780,1,227,1.3481299999999999e-14,74.9423,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2661,Q#1050 - >seq1049,non-specific,197320,1,227,9.54689e-12,66.3846,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2662,Q#1050 - >seq1049,non-specific,333820,569,732,1.5283e-11,64.2358,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2663,Q#1050 - >seq1049,superfamily,333820,569,732,1.5283e-11,64.2358,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2664,Q#1050 - >seq1049,non-specific,197321,1,234,1.98857e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2665,Q#1050 - >seq1049,non-specific,273186,1,235,9.077930000000001e-10,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2666,Q#1050 - >seq1049,non-specific,197319,1,234,9.81721e-10,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2667,Q#1050 - >seq1049,non-specific,272954,1,234,1.4704e-09,59.7041,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2668,Q#1050 - >seq1049,non-specific,238828,569,683,7.3572000000000005e-06,48.3513,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,N-TerminusTruncated
2669,Q#1050 - >seq1049,non-specific,197318,3,234,0.00013913,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2670,Q#1050 - >seq1049,non-specific,197336,1,70,0.000210278,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2671,Q#1050 - >seq1049,non-specific,238185,616,732,0.000975253,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,marg,CompleteHit
2672,Q#1051 - >seq1050,non-specific,238827,484,544,2.16235e-10,61.5382,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2673,Q#1051 - >seq1050,superfamily,295487,484,544,2.16235e-10,61.5382,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.marg.frame1,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2674,Q#1052 - >seq1051,specific,197310,3,234,6.65536e-42,153.276,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2675,Q#1052 - >seq1051,superfamily,351117,3,234,6.65536e-42,153.276,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2676,Q#1052 - >seq1051,non-specific,197306,3,234,1.91746e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2677,Q#1052 - >seq1051,specific,335306,4,227,6.99173e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2678,Q#1052 - >seq1051,non-specific,197307,3,234,1.1667200000000002e-14,74.6317,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2679,Q#1052 - >seq1051,non-specific,223780,1,227,1.56186e-14,74.5571,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2680,Q#1052 - >seq1051,non-specific,197320,1,227,1.00743e-11,65.9994,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2681,Q#1052 - >seq1051,non-specific,238827,515,575,3.66882e-10,60.7678,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2682,Q#1052 - >seq1051,superfamily,295487,515,575,3.66882e-10,60.7678,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2683,Q#1052 - >seq1051,non-specific,197321,1,234,3.86759e-10,61.413999999999994,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2684,Q#1052 - >seq1051,non-specific,273186,1,235,1.07973e-09,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2685,Q#1052 - >seq1051,non-specific,272954,1,234,1.68519e-09,59.3189,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2686,Q#1052 - >seq1051,non-specific,197319,1,234,1.83726e-09,59.2125,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2687,Q#1052 - >seq1051,non-specific,197318,3,234,0.000175735,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2688,Q#1052 - >seq1051,non-specific,197336,1,70,0.00019354099999999998,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs2_gorilla,pars,C-TerminusTruncated
2689,Q#1053 - >seq1052,non-specific,238827,591,708,4.6147300000000004e-26,106.992,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2690,Q#1053 - >seq1052,superfamily,295487,591,708,4.6147300000000004e-26,106.992,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2691,Q#1053 - >seq1052,non-specific,333820,545,708,9.405110000000001e-12,64.62100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2692,Q#1053 - >seq1052,superfamily,333820,545,708,9.405110000000001e-12,64.62100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2693,Q#1053 - >seq1052,non-specific,238828,545,659,4.33696e-06,48.7364,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,N-TerminusTruncated
2694,Q#1053 - >seq1052,non-specific,238185,592,708,0.000386294,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs2_gorilla,pars,CompleteHit
2695,Q#1055 - >seq1054,non-specific,340205,166,219,3.37121e-19,78.1468,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs2_gorilla,marg,CompleteHit
2696,Q#1055 - >seq1054,superfamily,340205,166,219,3.37121e-19,78.1468,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs2_gorilla.marg.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs2_gorilla,marg,CompleteHit
2697,Q#1057 - >seq1056,non-specific,335182,68,161,2.5574799999999996e-28,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs2_gorilla.marg.frame1,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3f,ORF1,hs2_gorilla,marg,CompleteHit
2698,Q#1057 - >seq1056,superfamily,335182,68,161,2.5574799999999996e-28,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs2_gorilla.marg.frame1,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M3f,ORF1,hs2_gorilla,marg,CompleteHit
2699,Q#1058 - >seq1057,non-specific,335182,66,159,2.4906499999999997e-28,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs2_gorilla,pars,CompleteHit
2700,Q#1058 - >seq1057,superfamily,335182,66,159,2.4906499999999997e-28,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs2_gorilla.pars.frame3,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs2_gorilla,pars,CompleteHit
2701,Q#1059 - >seq1058,non-specific,340205,169,219,9.64005e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs2_gorilla,pars,CompleteHit
2702,Q#1059 - >seq1058,superfamily,340205,169,219,9.64005e-19,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs2_gorilla.pars.frame2,1909122338_L1M3f.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M3f,ORF1,hs2_gorilla,pars,CompleteHit
2703,Q#1062 - >seq1061,specific,197310,9,235,4.54215e-55,191.02599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2704,Q#1062 - >seq1061,superfamily,351117,9,235,4.54215e-55,191.02599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2705,Q#1062 - >seq1061,non-specific,197306,9,235,2.4371999999999996e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2706,Q#1062 - >seq1061,non-specific,223780,7,228,6.27321e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2707,Q#1062 - >seq1061,non-specific,197307,9,235,1.7817500000000002e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2708,Q#1062 - >seq1061,non-specific,197320,7,228,1.12507e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2709,Q#1062 - >seq1061,non-specific,273186,7,236,5.40967e-18,84.63799999999999,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2710,Q#1062 - >seq1061,specific,335306,10,228,1.09212e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2711,Q#1062 - >seq1061,non-specific,197321,7,235,1.20586e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2712,Q#1062 - >seq1061,non-specific,272954,7,235,1.2872999999999998e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2713,Q#1062 - >seq1061,non-specific,197319,7,235,2.3531099999999997e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2714,Q#1062 - >seq1061,non-specific,197336,7,193,7.007939999999999e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2715,Q#1062 - >seq1061,non-specific,197322,8,235,3.15426e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2716,Q#1062 - >seq1061,non-specific,197318,9,235,3.31338e-07,52.6839,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2717,Q#1062 - >seq1061,non-specific,139971,7,235,4.36175e-05,46.2255,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2718,Q#1062 - >seq1061,non-specific,197311,29,235,0.000141403,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2719,Q#1062 - >seq1061,non-specific,339261,107,231,0.00125872,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M3f,ORF2,hs3_orang,marg,CompleteHit
2720,Q#1062 - >seq1061,non-specific,197317,138,228,0.00165853,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs3_orang.marg.frame3,1909122338_L1M3f.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs3_orang,marg,N-TerminusTruncated
2721,Q#1065 - >seq1064,non-specific,335182,39,117,0.00034988699999999995,38.4379,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3f,ORF1,hs6_sqmonkey,pars,CompleteHit
2722,Q#1065 - >seq1064,superfamily,335182,39,117,0.00034988699999999995,38.4379,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M3f,ORF1,hs6_sqmonkey,pars,CompleteHit
2723,Q#1066 - >seq1065,specific,197310,9,236,2.78857e-44,160.21,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2724,Q#1066 - >seq1065,superfamily,351117,9,236,2.78857e-44,160.21,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2725,Q#1066 - >seq1065,non-specific,197306,9,236,5.2268399999999994e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2726,Q#1066 - >seq1065,non-specific,197320,7,207,1.9839099999999997e-16,80.2517,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2727,Q#1066 - >seq1065,non-specific,223780,7,207,1.0982200000000001e-15,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2728,Q#1066 - >seq1065,non-specific,197307,9,236,3.8042400000000005e-15,76.1725,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2729,Q#1066 - >seq1065,non-specific,272954,7,207,4.05167e-10,61.2449,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2730,Q#1066 - >seq1065,non-specific,197319,7,236,1.1877e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2731,Q#1066 - >seq1065,non-specific,273186,7,237,1.3580300000000001e-09,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2732,Q#1066 - >seq1065,specific,335306,10,229,1.5778699999999998e-09,59.181000000000004,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2733,Q#1066 - >seq1065,non-specific,197321,7,236,3.6808900000000003e-08,55.636,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2734,Q#1066 - >seq1065,non-specific,197318,9,236,6.661e-05,45.3651,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2735,Q#1066 - >seq1065,non-specific,235175,323,464,0.0014205,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M3f,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
2736,Q#1066 - >seq1065,superfamily,235175,323,464,0.0014205,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M3f,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
2737,Q#1066 - >seq1065,non-specific,339261,108,232,0.00272139,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2738,Q#1067 - >seq1066,specific,238827,512,718,7.339149999999999e-37,138.19299999999998,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2739,Q#1067 - >seq1066,superfamily,295487,512,718,7.339149999999999e-37,138.19299999999998,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2740,Q#1067 - >seq1066,non-specific,333820,532,718,1.59016e-19,87.3477,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2741,Q#1067 - >seq1066,superfamily,333820,532,718,1.59016e-19,87.3477,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2742,Q#1067 - >seq1066,non-specific,238828,528,670,3.96413e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
2743,Q#1067 - >seq1066,non-specific,238185,602,718,4.0363e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,CompleteHit
2744,Q#1067 - >seq1066,non-specific,275209,530,683,0.000140565,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
2745,Q#1067 - >seq1066,superfamily,275209,530,683,0.000140565,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs5_gmonkey.marg.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
2746,Q#1070 - >seq1069,non-specific,235175,291,432,0.00044237599999999997,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M3f.ORF2.hs5_gmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M3f,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
2747,Q#1070 - >seq1069,superfamily,235175,291,432,0.00044237599999999997,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M3f.ORF2.hs5_gmonkey.pars.frame2,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M3f,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
2748,Q#1071 - >seq1070,specific,238827,511,731,4.887749999999999e-39,144.356,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2749,Q#1071 - >seq1070,superfamily,295487,511,731,4.887749999999999e-39,144.356,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2750,Q#1071 - >seq1070,specific,197310,10,208,1.70517e-38,143.64600000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2751,Q#1071 - >seq1070,superfamily,351117,10,208,1.70517e-38,143.64600000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2752,Q#1071 - >seq1070,non-specific,197306,10,207,5.539e-21,92.9296,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2753,Q#1071 - >seq1070,non-specific,333820,545,731,3.0889799999999996e-19,86.1921,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
2754,Q#1071 - >seq1070,superfamily,333820,545,731,3.0889799999999996e-19,86.1921,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
2755,Q#1071 - >seq1070,non-specific,197320,8,208,1.84391e-16,80.2517,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2756,Q#1071 - >seq1070,non-specific,223780,8,208,9.289210000000001e-16,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2757,Q#1071 - >seq1070,non-specific,197307,10,208,1.14543e-14,74.6317,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2758,Q#1071 - >seq1070,non-specific,238828,541,683,7.36033e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
2759,Q#1071 - >seq1070,non-specific,272954,8,208,8.55687e-11,63.1709,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2760,Q#1071 - >seq1070,non-specific,273186,8,207,5.233439999999999e-09,58.0592,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2761,Q#1071 - >seq1070,specific,335306,11,209,9.012450000000001e-09,56.8698,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2762,Q#1071 - >seq1070,non-specific,197321,8,195,1.40763e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2763,Q#1071 - >seq1070,non-specific,197319,8,195,7.8283e-07,51.5085,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2764,Q#1071 - >seq1070,non-specific,238185,615,731,0.00010321299999999999,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2765,Q#1071 - >seq1070,non-specific,275209,543,696,0.00012185100000000001,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
2766,Q#1071 - >seq1070,superfamily,275209,543,696,0.00012185100000000001,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
2767,Q#1071 - >seq1070,non-specific,197318,10,208,0.00421284,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs5_gmonkey.pars.frame1,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs5_gmonkey,pars,CompleteHit
2768,Q#1072 - >seq1071,non-specific,335182,56,152,4.4991400000000003e-29,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,marg,CompleteHit
2769,Q#1072 - >seq1071,superfamily,335182,56,152,4.4991400000000003e-29,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,marg,CompleteHit
2770,Q#1072 - >seq1071,non-specific,340205,156,218,1.09959e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,marg,CompleteHit
2771,Q#1072 - >seq1071,superfamily,340205,156,218,1.09959e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs5_gmonkey.marg.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,marg,CompleteHit
2772,Q#1075 - >seq1074,non-specific,335182,63,159,3.14111e-29,105.07700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,pars,CompleteHit
2773,Q#1075 - >seq1074,superfamily,335182,63,159,3.14111e-29,105.07700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,pars,CompleteHit
2774,Q#1075 - >seq1074,non-specific,340205,163,225,9.785010000000001e-25,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,pars,CompleteHit
2775,Q#1075 - >seq1074,superfamily,340205,163,225,9.785010000000001e-25,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs5_gmonkey.pars.frame3,1909122338_L1M3f.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs5_gmonkey,pars,CompleteHit
2776,Q#1078 - >seq1077,specific,197310,2,229,3.674409999999999e-58,199.885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2777,Q#1078 - >seq1077,superfamily,351117,2,229,3.674409999999999e-58,199.885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2778,Q#1078 - >seq1077,non-specific,197306,2,229,1.47092e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2779,Q#1078 - >seq1077,non-specific,197320,2,222,8.862579999999999e-24,101.43799999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2780,Q#1078 - >seq1077,non-specific,223780,2,222,1.07325e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2781,Q#1078 - >seq1077,non-specific,197307,2,229,1.61664e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2782,Q#1078 - >seq1077,specific,335306,3,222,2.5651999999999996e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2783,Q#1078 - >seq1077,non-specific,273186,2,230,1.3681e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2784,Q#1078 - >seq1077,non-specific,197321,1,229,2.1370100000000002e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2785,Q#1078 - >seq1077,non-specific,272954,2,229,3.94254e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2786,Q#1078 - >seq1077,non-specific,197319,2,229,1.6041699999999998e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2787,Q#1078 - >seq1077,non-specific,197336,2,187,1.56095e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2788,Q#1078 - >seq1077,non-specific,197322,1,229,1.94601e-07,53.8602,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2789,Q#1078 - >seq1077,non-specific,197318,2,229,4.83823e-07,51.9135,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2790,Q#1078 - >seq1077,non-specific,236970,2,222,3.2866900000000004e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2791,Q#1078 - >seq1077,non-specific,197311,23,229,5.8576699999999994e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2792,Q#1078 - >seq1077,non-specific,197317,1,222,0.00050406,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2793,Q#1078 - >seq1077,non-specific,339261,101,225,0.000646764,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M3f,ORF2,hs4_gibbon,marg,CompleteHit
2794,Q#1079 - >seq1078,specific,238827,481,579,2.4008099999999998e-28,113.925,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2795,Q#1079 - >seq1078,superfamily,295487,481,579,2.4008099999999998e-28,113.925,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2796,Q#1079 - >seq1078,non-specific,333820,487,598,1.3051099999999998e-09,58.4578,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2797,Q#1079 - >seq1078,superfamily,333820,487,598,1.3051099999999998e-09,58.4578,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.marg.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,marg,C-TerminusTruncated
2798,Q#1080 - >seq1079,non-specific,238827,585,665,4.66031e-14,72.3238,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2799,Q#1080 - >seq1079,superfamily,295487,585,665,4.66031e-14,72.3238,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2800,Q#1080 - >seq1079,non-specific,333820,536,663,1.7193e-06,49.213,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2801,Q#1080 - >seq1079,superfamily,333820,536,663,1.7193e-06,49.213,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2802,Q#1080 - >seq1079,non-specific,238828,536,653,0.00048214300000000004,42.5733,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs4_gibbon.marg.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,marg,N-TerminusTruncated
2803,Q#1081 - >seq1080,specific,197310,2,229,1.3366899999999996e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2804,Q#1081 - >seq1080,superfamily,351117,2,229,1.3366899999999996e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2805,Q#1081 - >seq1080,non-specific,197306,2,229,1.4033e-32,126.82700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2806,Q#1081 - >seq1080,non-specific,223780,2,222,6.68072e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2807,Q#1081 - >seq1080,non-specific,197320,2,222,9.044560000000001e-24,101.43799999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2808,Q#1081 - >seq1080,non-specific,197307,2,229,1.0659299999999999e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2809,Q#1081 - >seq1080,specific,335306,3,222,2.61611e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2810,Q#1081 - >seq1080,non-specific,197321,1,229,6.9667e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2811,Q#1081 - >seq1080,non-specific,273186,2,230,8.63126e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2812,Q#1081 - >seq1080,non-specific,272954,2,229,4.85641e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2813,Q#1081 - >seq1080,non-specific,197319,2,229,5.977059999999999e-16,78.4725,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2814,Q#1081 - >seq1080,non-specific,238827,490,535,7.66567e-11,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2815,Q#1081 - >seq1080,superfamily,295487,490,535,7.66567e-11,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M3f,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2816,Q#1081 - >seq1080,non-specific,197336,2,187,1.59221e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2817,Q#1081 - >seq1080,non-specific,197322,1,229,1.98566e-07,53.8602,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2818,Q#1081 - >seq1080,non-specific,197318,2,229,3.41909e-07,52.2987,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2819,Q#1081 - >seq1080,non-specific,236970,2,222,5.50774e-06,49.1222,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2820,Q#1081 - >seq1080,non-specific,197311,23,229,5.969990000000001e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2821,Q#1081 - >seq1080,non-specific,197317,1,222,0.00047819,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2822,Q#1081 - >seq1080,non-specific,339261,101,225,0.000527287,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M3f,ORF2,hs4_gibbon,pars,CompleteHit
2823,Q#1081 - >seq1080,non-specific,214368,436,779,0.00425361,41.0779,CHL00117,rpoC2,NC,cl33332,RNA polymerase beta'' subunit; Reviewed,L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3f,ORF2,hs4_gibbon,pars,BothTerminiTruncated
2824,Q#1081 - >seq1080,superfamily,214368,436,779,0.00425361,41.0779,cl33332,rpoC2 superfamily,NC, - ,RNA polymerase beta'' subunit; Reviewed,L1M3f.ORF2.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1M3f,ORF2,hs4_gibbon,pars,BothTerminiTruncated
2825,Q#1082 - >seq1081,non-specific,238827,507,563,8.55454e-09,56.9158,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs4_gibbon.pars.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2826,Q#1082 - >seq1081,superfamily,295487,507,563,8.55454e-09,56.9158,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs4_gibbon.pars.frame2,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M3f,ORF2,hs4_gibbon,pars,C-TerminusTruncated
2827,Q#1083 - >seq1082,non-specific,238827,566,646,1.1348e-13,71.1682,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2828,Q#1083 - >seq1082,superfamily,295487,566,646,1.1348e-13,71.1682,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2829,Q#1083 - >seq1082,non-specific,333820,517,644,7.1186800000000004e-06,47.287,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2830,Q#1083 - >seq1082,superfamily,333820,517,644,7.1186800000000004e-06,47.287,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2831,Q#1083 - >seq1082,non-specific,238828,517,634,0.00107273,41.4177,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs4_gibbon.pars.frame1,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M3f,ORF2,hs4_gibbon,pars,N-TerminusTruncated
2832,Q#1084 - >seq1083,non-specific,335182,64,160,6.66988e-29,104.307,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,marg,CompleteHit
2833,Q#1084 - >seq1083,superfamily,335182,64,160,6.66988e-29,104.307,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,marg,CompleteHit
2834,Q#1084 - >seq1083,non-specific,340205,164,226,1.1972699999999999e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,marg,CompleteHit
2835,Q#1084 - >seq1083,superfamily,340205,164,226,1.1972699999999999e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,marg,CompleteHit
2836,Q#1084 - >seq1083,non-specific,234799,1,101,0.0076565,36.7851,PRK00578,prfB,C,cl30493,peptide chain release factor 2; Validated,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3f,ORF1,hs4_gibbon,marg,C-TerminusTruncated
2837,Q#1084 - >seq1083,superfamily,234799,1,101,0.0076565,36.7851,cl30493,prfB superfamily,C, - ,peptide chain release factor 2; Validated,L1M3f.ORF1.hs4_gibbon.marg.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M3f,ORF1,hs4_gibbon,marg,C-TerminusTruncated
2838,Q#1087 - >seq1086,non-specific,335182,66,162,5.20807e-29,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,pars,CompleteHit
2839,Q#1087 - >seq1086,superfamily,335182,66,162,5.20807e-29,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M3f.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,pars,CompleteHit
2840,Q#1087 - >seq1086,non-specific,340205,166,225,4.241919999999999e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,pars,CompleteHit
2841,Q#1087 - >seq1086,superfamily,340205,166,225,4.241919999999999e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M3f.ORF1.hs4_gibbon.pars.frame3,1909122338_L1M3f.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M3f,ORF1,hs4_gibbon,pars,CompleteHit
2842,Q#1088 - >seq1087,non-specific,197310,32,174,8.63941e-05,44.6497,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2843,Q#1088 - >seq1087,superfamily,351117,32,174,8.63941e-05,44.6497,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs2_gorilla.marg.frame3,1909122338_L1M4a1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
2844,Q#1090 - >seq1089,specific,197310,5,232,7.514729999999999e-49,173.30599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2845,Q#1090 - >seq1089,superfamily,351117,5,232,7.514729999999999e-49,173.30599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2846,Q#1090 - >seq1089,specific,238827,523,726,3.8144099999999996e-35,133.571,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2847,Q#1090 - >seq1089,superfamily,295487,523,726,3.8144099999999996e-35,133.571,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2848,Q#1090 - >seq1089,non-specific,197306,5,232,1.66397e-25,106.412,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2849,Q#1090 - >seq1089,non-specific,197320,3,225,3.12499e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2850,Q#1090 - >seq1089,non-specific,333820,527,711,3.21712e-18,83.4957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2851,Q#1090 - >seq1089,superfamily,333820,527,711,3.21712e-18,83.4957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2852,Q#1090 - >seq1089,non-specific,223780,3,225,1.97833e-17,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2853,Q#1090 - >seq1089,specific,335306,6,225,1.7602900000000002e-15,76.5149,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2854,Q#1090 - >seq1089,non-specific,197307,5,232,3.66197e-15,76.1725,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2855,Q#1090 - >seq1089,non-specific,197321,3,232,5.24856e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2856,Q#1090 - >seq1089,non-specific,273186,3,233,2.09877e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2857,Q#1090 - >seq1089,non-specific,197319,3,232,3.01624e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2858,Q#1090 - >seq1089,non-specific,272954,3,232,3.06833e-10,61.6301,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2859,Q#1090 - >seq1089,non-specific,238828,553,695,8.930029999999999e-10,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,N-TerminusTruncated
2860,Q#1090 - >seq1089,non-specific,275209,558,708,8.56663e-06,48.9932,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,BothTerminiTruncated
2861,Q#1090 - >seq1089,superfamily,275209,558,708,8.56663e-06,48.9932,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,BothTerminiTruncated
2862,Q#1090 - >seq1089,non-specific,197336,3,225,2.42112e-05,46.8367,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2863,Q#1090 - >seq1089,non-specific,197318,5,232,3.46617e-05,46.5207,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,marg,CompleteHit
2864,Q#1090 - >seq1089,non-specific,339261,106,228,0.00241095,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2865,Q#1090 - >seq1089,non-specific,197317,135,225,0.00442597,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M3f,ORF2,hs0_human,marg,N-TerminusTruncated
2866,Q#1090 - >seq1089,non-specific,238185,627,708,0.00470347,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M3f.ORF2.hs0_human.marg.frame1,1909122338_L1M3f.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M3f,ORF2,hs0_human,marg,CompleteHit
2867,Q#1095 - >seq1094,non-specific,340205,159,223,5.22174e-12,59.272,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs9_pika,marg,CompleteHit
2868,Q#1095 - >seq1094,superfamily,340205,159,223,5.22174e-12,59.272,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs9_pika,marg,CompleteHit
2869,Q#1095 - >seq1094,non-specific,274330,61,116,0.000747629,39.2082,TIGR02867,spore_II_P,NC,cl02713,"stage II sporulation protein P; Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members. [Cellular processes, Sporulation and germination]",L1M4a1.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M4a1,ORF1,hs9_pika,marg,BothTerminiTruncated
2870,Q#1095 - >seq1094,superfamily,351865,61,116,0.000747629,39.2082,cl02713,MurNAc-LAA superfamily,NC, - ,"N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.",L1M4a1.ORF1.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M4a1,ORF1,hs9_pika,marg,BothTerminiTruncated
2871,Q#1097 - >seq1096,non-specific,340205,123,185,2.7270500000000003e-17,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs9_pika.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs9_pika,pars,CompleteHit
2872,Q#1097 - >seq1096,superfamily,340205,123,185,2.7270500000000003e-17,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs9_pika.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs9_pika,pars,CompleteHit
2873,Q#1099 - >seq1098,non-specific,197310,9,40,0.00121211,40.7977,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs8_ctshrew.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
2874,Q#1099 - >seq1098,superfamily,351117,9,40,0.00121211,40.7977,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
2875,Q#1101 - >seq1100,non-specific,197310,37,256,1.22195e-24,102.815,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs8_ctshrew.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,CompleteHit
2876,Q#1101 - >seq1100,superfamily,351117,37,256,1.22195e-24,102.815,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,CompleteHit
2877,Q#1101 - >seq1100,non-specific,197306,44,256,7.96241e-05,44.3945,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,CompleteHit
2878,Q#1101 - >seq1100,non-specific,197307,54,256,0.000531969,41.8897,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs8_ctshrew.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4a1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
2879,Q#1103 - >seq1102,non-specific,197310,9,104,2.1390599999999998e-13,68.9173,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs8_ctshrew.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
2880,Q#1103 - >seq1102,superfamily,351117,9,104,2.1390599999999998e-13,68.9173,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
2881,Q#1103 - >seq1102,non-specific,197306,9,132,0.00017951900000000003,42.4685,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
2882,Q#1105 - >seq1104,non-specific,340205,133,170,4.18115e-10,53.1088,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4a1,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
2883,Q#1105 - >seq1104,superfamily,340205,133,170,4.18115e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs8_ctshrew.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4a1,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
2884,Q#1108 - >seq1107,non-specific,340205,98,135,5.453669999999999e-10,51.9532,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs8_ctshrew.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
2885,Q#1108 - >seq1107,superfamily,340205,98,135,5.453669999999999e-10,51.9532,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs8_ctshrew.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
2886,Q#1112 - >seq1111,non-specific,197310,32,234,3.95969e-14,71.2285,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs7_bushaby.marg.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4a1,ORF2,hs7_bushaby,marg,CompleteHit
2887,Q#1112 - >seq1111,superfamily,351117,32,234,3.95969e-14,71.2285,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs7_bushaby.marg.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4a1,ORF2,hs7_bushaby,marg,CompleteHit
2888,Q#1112 - >seq1111,non-specific,197322,113,234,3.39622e-07,51.549,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs7_bushaby.marg.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4a1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
2889,Q#1112 - >seq1111,non-specific,197306,42,189,5.57915e-06,47.0909,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs7_bushaby.marg.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4a1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
2890,Q#1114 - >seq1113,non-specific,197310,138,220,1.4863500000000001e-08,54.6649,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs8_ctshrew.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4a1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
2891,Q#1114 - >seq1113,superfamily,351117,138,220,1.4863500000000001e-08,54.6649,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs8_ctshrew.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
2892,Q#1115 - >seq1114,non-specific,197310,8,213,1.91459e-17,81.2437,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs9_pika.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs9_pika,pars,CompleteHit
2893,Q#1115 - >seq1114,superfamily,351117,8,213,1.91459e-17,81.2437,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs9_pika.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs9_pika,pars,CompleteHit
2894,Q#1116 - >seq1115,non-specific,197310,162,226,1.3836600000000001e-06,49.6573,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a1,ORF2,hs9_pika,marg,N-TerminusTruncated
2895,Q#1116 - >seq1115,superfamily,351117,162,226,1.3836600000000001e-06,49.6573,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs9_pika.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs9_pika,marg,N-TerminusTruncated
2896,Q#1128 - >seq1127,non-specific,197310,5,111,0.000107077,43.4941,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs10_snmole.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a1,ORF2,hs10_snmole,marg,C-TerminusTruncated
2897,Q#1128 - >seq1127,superfamily,351117,5,111,0.000107077,43.4941,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs10_snmole.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs10_snmole,marg,C-TerminusTruncated
2898,Q#1130 - >seq1129,non-specific,197310,142,197,4.48942e-08,53.5093,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs10_snmole.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a1,ORF2,hs10_snmole,marg,N-TerminusTruncated
2899,Q#1130 - >seq1129,superfamily,351117,142,197,4.48942e-08,53.5093,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs10_snmole.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs10_snmole,marg,N-TerminusTruncated
2900,Q#1130 - >seq1129,non-specific,197320,140,192,0.00898779,37.8798,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs10_snmole.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4a1,ORF2,hs10_snmole,marg,N-TerminusTruncated
2901,Q#1131 - >seq1130,non-specific,197310,145,200,7.97452e-08,52.7389,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs10_snmole.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs10_snmole,pars,N-TerminusTruncated
2902,Q#1131 - >seq1130,superfamily,351117,145,200,7.97452e-08,52.7389,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs10_snmole.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs10_snmole,pars,N-TerminusTruncated
2903,Q#1131 - >seq1130,non-specific,197320,143,195,0.00962595,37.1094,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs10_snmole.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4a1,ORF2,hs10_snmole,pars,N-TerminusTruncated
2904,Q#1136 - >seq1135,non-specific,340205,127,199,7.681199999999999e-16,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs10_snmole,marg,CompleteHit
2905,Q#1136 - >seq1135,superfamily,340205,127,199,7.681199999999999e-16,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs10_snmole.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs10_snmole,marg,CompleteHit
2906,Q#1137 - >seq1136,non-specific,340205,54,121,7.05862e-18,71.5984,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs10_snmole.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs10_snmole,pars,CompleteHit
2907,Q#1137 - >seq1136,superfamily,340205,54,121,7.05862e-18,71.5984,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs10_snmole.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs10_snmole,pars,CompleteHit
2908,Q#1141 - >seq1140,non-specific,197306,1,174,1.3176000000000002e-08,54.0245,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs7_bushaby,pars,CompleteHit
2909,Q#1141 - >seq1140,superfamily,351117,1,174,1.3176000000000002e-08,54.0245,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs7_bushaby,pars,CompleteHit
2910,Q#1141 - >seq1140,non-specific,197310,62,152,1.4217600000000002e-08,53.8945,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs7_bushaby,pars,BothTerminiTruncated
2911,Q#1141 - >seq1140,non-specific,197322,74,148,0.00327357,38.0671,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4a1.ORF2.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4a1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
2912,Q#1142 - >seq1141,non-specific,197310,28,88,0.00585659,36.9457,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4a1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2913,Q#1142 - >seq1141,superfamily,351117,28,88,0.00585659,36.9457,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4a1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
2914,Q#1173 - >seq1172,non-specific,340205,157,222,4.0754900000000004e-14,64.6648,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs7_bushaby,marg,CompleteHit
2915,Q#1173 - >seq1172,superfamily,340205,157,222,4.0754900000000004e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs7_bushaby,marg,CompleteHit
2916,Q#1173 - >seq1172,non-specific,335182,88,151,7.887610000000001e-12,59.6239,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a1.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
2917,Q#1173 - >seq1172,superfamily,335182,88,151,7.887610000000001e-12,59.6239,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a1.ORF1.hs7_bushaby.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4a1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
2918,Q#1174 - >seq1173,non-specific,340205,96,123,1.0932600000000001e-06,43.864,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,C-TerminusTruncated
2919,Q#1174 - >seq1173,superfamily,340205,96,123,1.0932600000000001e-06,43.864,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame3,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,C-TerminusTruncated
2920,Q#1175 - >seq1174,non-specific,335182,37,89,6.56983e-12,58.4683,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2921,Q#1175 - >seq1174,superfamily,335182,37,89,6.56983e-12,58.4683,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2922,Q#1175 - >seq1174,non-specific,340205,121,167,7.19939e-07,44.2492,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2923,Q#1175 - >seq1174,superfamily,340205,121,167,7.19939e-07,44.2492,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs7_bushaby.pars.frame2,1909122338_L1M4a1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4a1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
2924,Q#1178 - >seq1177,non-specific,197310,37,245,0.000179136,42.7237,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4a1,ORF2,hs6_sqmonkey,marg,CompleteHit
2925,Q#1178 - >seq1177,superfamily,351117,37,245,0.000179136,42.7237,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs6_sqmonkey,marg,CompleteHit
2926,Q#1178 - >seq1177,non-specific,197306,43,230,0.00205761,39.7721,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs6_sqmonkey.marg.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4a1,ORF2,hs6_sqmonkey,marg,CompleteHit
2927,Q#1180 - >seq1179,non-specific,271035,150,277,0.00280697,38.7883,cd14133,PKc_DYRK_like,C,cl21453,"Catalytic domain of Dual-specificity tYrosine-phosphorylated and -Regulated Kinase-like protein kinases; Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of the dual-specificity DYRKs and YAK1, as well as the S/T kinases (STKs), HIPKs. DYRKs and YAK1 autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. Proteins in this subfamily play important roles in cell proliferation, differentiation, survival, growth, and development. The DYRK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.",L1M4a1.ORF2.hs6_sqmonkey.pars.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M4a1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2928,Q#1180 - >seq1179,superfamily,354810,150,277,0.00280697,38.7883,cl21453,PKc_like superfamily,C, - ,"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins.",L1M4a1.ORF2.hs6_sqmonkey.pars.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M4a1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
2929,Q#1191 - >seq1190,non-specific,197310,9,107,0.00024440700000000003,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4a1.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4a1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
2930,Q#1191 - >seq1190,superfamily,351117,9,107,0.00024440700000000003,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4a1.ORF2.hs5_gmonkey.marg.frame3,1909122338_L1M4a1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4a1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
2931,Q#1192 - >seq1191,non-specific,340205,7,65,0.00287433,32.308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a1,ORF1,hs6_sqmonkey,pars,CompleteHit
2932,Q#1192 - >seq1191,superfamily,340205,7,65,0.00287433,32.308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4a1.ORF1.hs6_sqmonkey.pars.frame1,1909122338_L1M4a1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4a1,ORF1,hs6_sqmonkey,pars,CompleteHit
2933,Q#1195 - >seq1194,non-specific,335182,67,157,1.16265e-24,93.9066,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs7_bushaby.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,marg,CompleteHit
2934,Q#1195 - >seq1194,superfamily,335182,67,157,1.16265e-24,93.9066,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs7_bushaby.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,marg,CompleteHit
2935,Q#1195 - >seq1194,non-specific,340205,176,227,1.11697e-15,69.2872,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs7_bushaby.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,marg,CompleteHit
2936,Q#1195 - >seq1194,superfamily,340205,176,227,1.11697e-15,69.2872,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs7_bushaby.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,marg,CompleteHit
2937,Q#1198 - >seq1197,specific,197310,9,235,4.627e-55,191.41099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2938,Q#1198 - >seq1197,superfamily,351117,9,235,4.627e-55,191.41099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2939,Q#1198 - >seq1197,specific,238827,503,746,1.4179999999999998e-54,189.424,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2940,Q#1198 - >seq1197,superfamily,295487,503,746,1.4179999999999998e-54,189.424,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2941,Q#1198 - >seq1197,specific,333820,509,733,1.23972e-30,119.319,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2942,Q#1198 - >seq1197,superfamily,333820,509,733,1.23972e-30,119.319,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2943,Q#1198 - >seq1197,non-specific,197306,9,235,1.43405e-25,106.412,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2944,Q#1198 - >seq1197,non-specific,223780,7,228,4.1923100000000003e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2945,Q#1198 - >seq1197,non-specific,197320,7,228,5.81421e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2946,Q#1198 - >seq1197,non-specific,197307,9,228,1.03357e-17,83.8765,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2947,Q#1198 - >seq1197,specific,335306,10,228,8.93382e-14,71.8925,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2948,Q#1198 - >seq1197,non-specific,272954,7,206,6.78335e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2949,Q#1198 - >seq1197,non-specific,273186,7,236,1.41199e-11,65.7632,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2950,Q#1198 - >seq1197,non-specific,197321,7,228,1.98885e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2951,Q#1198 - >seq1197,non-specific,238828,509,730,7.20982e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2952,Q#1198 - >seq1197,non-specific,197319,7,235,4.73101e-10,61.1385,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2953,Q#1198 - >seq1197,non-specific,275209,460,767,4.4427e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2954,Q#1198 - >seq1197,superfamily,275209,460,767,4.4427e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2955,Q#1198 - >seq1197,non-specific,197311,38,203,7.69567e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2956,Q#1198 - >seq1197,non-specific,339261,107,230,2.2169299999999998e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs6_sqmonkey,marg,CompleteHit
2957,Q#1199 - >seq1198,non-specific,335182,67,154,8.857430000000002e-24,91.2102,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,pars,CompleteHit
2958,Q#1199 - >seq1198,superfamily,335182,67,154,8.857430000000002e-24,91.2102,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,pars,CompleteHit
2959,Q#1199 - >seq1198,non-specific,340205,156,222,5.79379e-16,69.6724,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,pars,CompleteHit
2960,Q#1199 - >seq1198,superfamily,340205,156,222,5.79379e-16,69.6724,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs7_bushaby,pars,CompleteHit
2961,Q#1201 - >seq1200,specific,197310,9,238,1.6655699999999997e-57,197.959,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2962,Q#1201 - >seq1200,superfamily,351117,9,238,1.6655699999999997e-57,197.959,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2963,Q#1201 - >seq1200,non-specific,197306,9,238,1.28285e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2964,Q#1201 - >seq1200,non-specific,197320,7,231,2.0424000000000002e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2965,Q#1201 - >seq1200,non-specific,223780,7,231,1.9759299999999999e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2966,Q#1201 - >seq1200,non-specific,197307,9,231,2.0855000000000001e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2967,Q#1201 - >seq1200,specific,335306,10,231,7.844830000000001e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2968,Q#1201 - >seq1200,non-specific,197321,7,231,2.34814e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2969,Q#1201 - >seq1200,non-specific,197319,7,238,8.48873e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2970,Q#1201 - >seq1200,non-specific,272954,7,209,1.3374100000000002e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2971,Q#1201 - >seq1200,non-specific,273186,7,239,5.79143e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2972,Q#1201 - >seq1200,non-specific,197336,7,231,2.49126e-08,55.6963,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2973,Q#1201 - >seq1200,non-specific,197311,39,238,4.10829e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2974,Q#1201 - >seq1200,non-specific,339261,110,233,0.00639338,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs7_bushaby.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2975,Q#1202 - >seq1201,specific,238827,480,712,8.23203e-31,120.859,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2976,Q#1202 - >seq1201,superfamily,295487,480,712,8.23203e-31,120.859,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2977,Q#1202 - >seq1201,non-specific,333820,482,694,4.9659199999999995e-12,65.3914,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2978,Q#1202 - >seq1201,superfamily,333820,482,694,4.9659199999999995e-12,65.3914,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs7_bushaby.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs7_bushaby,pars,CompleteHit
2979,Q#1205 - >seq1204,specific,238827,553,820,5.997589999999999e-35,132.8,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs7_bushaby.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2980,Q#1205 - >seq1204,superfamily,295487,553,820,5.997589999999999e-35,132.8,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs7_bushaby.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2981,Q#1205 - >seq1204,non-specific,333820,569,802,1.82714e-13,69.6286,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs7_bushaby.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2982,Q#1205 - >seq1204,superfamily,333820,569,802,1.82714e-13,69.6286,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs7_bushaby.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2983,Q#1207 - >seq1206,specific,197310,9,238,1.55971e-57,198.34400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2984,Q#1207 - >seq1206,superfamily,351117,9,238,1.55971e-57,198.34400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2985,Q#1207 - >seq1206,non-specific,197306,9,238,3.14399e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2986,Q#1207 - >seq1206,non-specific,197320,7,231,2.34868e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2987,Q#1207 - >seq1206,non-specific,223780,7,231,1.22976e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2988,Q#1207 - >seq1206,non-specific,197307,9,231,1.672e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2989,Q#1207 - >seq1206,specific,335306,10,231,8.981219999999999e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2990,Q#1207 - >seq1206,non-specific,197321,7,231,2.72298e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2991,Q#1207 - >seq1206,non-specific,197319,7,238,6.890299999999999e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2992,Q#1207 - >seq1206,non-specific,272954,7,209,9.7078e-14,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2993,Q#1207 - >seq1206,non-specific,273186,7,239,3.17738e-13,70.7708,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2994,Q#1207 - >seq1206,non-specific,197336,7,231,2.8540900000000002e-08,55.6963,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2995,Q#1207 - >seq1206,non-specific,197311,39,238,2.39526e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2996,Q#1207 - >seq1206,non-specific,339261,110,233,0.00262718,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs7_bushaby,marg,CompleteHit
2997,Q#1207 - >seq1206,non-specific,197317,126,231,0.00856108,39.1224,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M4c.ORF2.hs7_bushaby.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs7_bushaby,marg,N-TerminusTruncated
2998,Q#1209 - >seq1208,non-specific,335555,286,360,0.00143585,42.2476,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1M4c.ORF2.hs6_sqmonkey.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1M4c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
2999,Q#1209 - >seq1208,superfamily,354396,286,360,0.00143585,42.2476,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1M4c.ORF2.hs6_sqmonkey.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1M4c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
3000,Q#1210 - >seq1209,non-specific,335555,300,374,0.000972165,42.6328,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1M4c.ORF2.hs6_sqmonkey.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1M4c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3001,Q#1210 - >seq1209,superfamily,354396,300,374,0.000972165,42.6328,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1M4c.ORF2.hs6_sqmonkey.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Flagellar,L1M4c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3002,Q#1212 - >seq1211,non-specific,340205,234,299,1.2151399999999999e-26,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs5_gmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,pars,CompleteHit
3003,Q#1212 - >seq1211,superfamily,340205,234,299,1.2151399999999999e-26,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs5_gmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,pars,CompleteHit
3004,Q#1212 - >seq1211,non-specific,335182,156,231,6.07377e-20,82.7359,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs5_gmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
3005,Q#1212 - >seq1211,superfamily,335182,156,231,6.07377e-20,82.7359,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs5_gmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
3006,Q#1215 - >seq1214,non-specific,340205,244,309,1.46895e-26,99.3327,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs5_gmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,marg,CompleteHit
3007,Q#1215 - >seq1214,superfamily,340205,244,309,1.46895e-26,99.3327,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs5_gmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,marg,CompleteHit
3008,Q#1215 - >seq1214,non-specific,335182,166,241,2.6174800000000004e-19,81.1951,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs5_gmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
3009,Q#1215 - >seq1214,superfamily,335182,166,241,2.6174800000000004e-19,81.1951,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs5_gmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
3010,Q#1216 - >seq1215,specific,197310,9,235,1.5795999999999997e-53,186.78799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3011,Q#1216 - >seq1215,superfamily,351117,9,235,1.5795999999999997e-53,186.78799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3012,Q#1216 - >seq1215,non-specific,197306,9,235,4.68995e-26,107.95200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3013,Q#1216 - >seq1215,non-specific,223780,7,228,6.075749999999999e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3014,Q#1216 - >seq1215,non-specific,197320,7,228,3.51582e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3015,Q#1216 - >seq1215,non-specific,197307,9,228,2.6204000000000003e-18,85.4173,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3016,Q#1216 - >seq1215,specific,335306,10,228,7.84903e-14,71.8925,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3017,Q#1216 - >seq1215,non-specific,272954,7,206,2.23331e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3018,Q#1216 - >seq1215,non-specific,273186,7,236,5.55462e-12,66.9188,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3019,Q#1216 - >seq1215,non-specific,197321,7,228,1.01569e-11,66.0364,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3020,Q#1216 - >seq1215,non-specific,197319,7,235,1.70366e-10,62.2941,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3021,Q#1216 - >seq1215,non-specific,197311,38,203,1.30025e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3022,Q#1216 - >seq1215,non-specific,339261,107,230,9.248620000000001e-05,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3023,Q#1218 - >seq1217,non-specific,340205,167,229,2.24027e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,pars,CompleteHit
3024,Q#1218 - >seq1217,superfamily,340205,167,229,2.24027e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,pars,CompleteHit
3025,Q#1218 - >seq1217,non-specific,335182,86,155,1.2513299999999999e-10,56.5423,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
3026,Q#1218 - >seq1217,superfamily,335182,86,155,1.2513299999999999e-10,56.5423,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs6_sqmonkey.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
3027,Q#1221 - >seq1220,non-specific,340205,170,233,2.9618500000000004e-20,81.2284,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,marg,CompleteHit
3028,Q#1221 - >seq1220,superfamily,340205,170,233,2.9618500000000004e-20,81.2284,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,marg,CompleteHit
3029,Q#1221 - >seq1220,non-specific,335182,89,158,1.9893599999999998e-10,55.7719,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
3030,Q#1221 - >seq1220,superfamily,335182,89,158,1.9893599999999998e-10,55.7719,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs6_sqmonkey.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
3031,Q#1222 - >seq1221,specific,238827,472,714,1.1702699999999998e-54,189.424,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3032,Q#1222 - >seq1221,superfamily,295487,472,714,1.1702699999999998e-54,189.424,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3033,Q#1222 - >seq1221,specific,333820,478,701,6.740269999999999e-31,120.09,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3034,Q#1222 - >seq1221,superfamily,333820,478,701,6.740269999999999e-31,120.09,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3035,Q#1222 - >seq1221,non-specific,238828,478,698,7.29703e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3036,Q#1222 - >seq1221,non-specific,275209,429,735,1.2556600000000002e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3037,Q#1222 - >seq1221,superfamily,275209,429,735,1.2556600000000002e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs6_sqmonkey.pars.frame1,1909122339_L1M4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4c,ORF2,hs6_sqmonkey,pars,CompleteHit
3038,Q#1224 - >seq1223,non-specific,335182,50,122,6.7551000000000004e-15,66.9427,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
3039,Q#1224 - >seq1223,superfamily,335182,50,122,6.7551000000000004e-15,66.9427,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
3040,Q#1224 - >seq1223,non-specific,340205,142,196,3.2897799999999997e-10,53.8792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,pars,CompleteHit
3041,Q#1224 - >seq1223,superfamily,340205,142,196,3.2897799999999997e-10,53.8792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,pars,CompleteHit
3042,Q#1227 - >seq1226,non-specific,340205,111,163,1.8608900000000002e-10,53.8792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs1_chimp.marg.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,marg,CompleteHit
3043,Q#1227 - >seq1226,superfamily,340205,111,163,1.8608900000000002e-10,53.8792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs1_chimp.marg.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,marg,CompleteHit
3044,Q#1227 - >seq1226,non-specific,335182,18,108,9.312260000000002e-10,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs1_chimp.marg.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,marg,CompleteHit
3045,Q#1227 - >seq1226,superfamily,335182,18,108,9.312260000000002e-10,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs1_chimp.marg.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,marg,CompleteHit
3046,Q#1229 - >seq1228,non-specific,197310,31,256,4.7011800000000006e-18,83.9401,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4,ORF2,hs1_chimp,pars,CompleteHit
3047,Q#1229 - >seq1228,superfamily,351117,31,256,4.7011800000000006e-18,83.9401,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs1_chimp,pars,CompleteHit
3048,Q#1229 - >seq1228,non-specific,238827,536,631,7.94864e-05,44.5894,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs1_chimp,pars,C-TerminusTruncated
3049,Q#1229 - >seq1228,superfamily,295487,536,631,7.94864e-05,44.5894,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs1_chimp,pars,C-TerminusTruncated
3050,Q#1229 - >seq1228,non-specific,197320,189,241,0.000389714,42.8874,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4,ORF2,hs1_chimp,pars,N-TerminusTruncated
3051,Q#1229 - >seq1228,non-specific,197306,31,256,0.000915597,41.6981,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs1_chimp.pars.frame1,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs1_chimp,pars,CompleteHit
3052,Q#1234 - >seq1233,non-specific,197310,33,258,3.3119e-18,84.7105,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs1_chimp,marg,CompleteHit
3053,Q#1234 - >seq1233,superfamily,351117,33,258,3.3119e-18,84.7105,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs1_chimp,marg,CompleteHit
3054,Q#1234 - >seq1233,non-specific,238827,539,633,9.46768e-08,53.8342,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs1_chimp,marg,C-TerminusTruncated
3055,Q#1234 - >seq1233,superfamily,295487,539,633,9.46768e-08,53.8342,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs1_chimp,marg,C-TerminusTruncated
3056,Q#1234 - >seq1233,non-specific,197320,191,243,0.0005225259999999999,42.8874,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs1_chimp,marg,N-TerminusTruncated
3057,Q#1234 - >seq1233,non-specific,197306,33,258,0.00111882,41.6981,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs1_chimp.marg.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs1_chimp,marg,CompleteHit
3058,Q#1237 - >seq1236,non-specific,340205,108,179,0.00023766,37.7008,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs2_gorilla.marg.frame1,1909122339_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs2_gorilla,marg,CompleteHit
3059,Q#1237 - >seq1236,superfamily,340205,108,179,0.00023766,37.7008,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs2_gorilla.marg.frame1,1909122339_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs2_gorilla,marg,CompleteHit
3060,Q#1243 - >seq1242,non-specific,335182,40,97,4.0965e-06,43.0603,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs1_chimp.pars.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs1_chimp,pars,N-TerminusTruncated
3061,Q#1243 - >seq1242,superfamily,335182,40,97,4.0965e-06,43.0603,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs1_chimp.pars.frame3,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs1_chimp,pars,N-TerminusTruncated
3062,Q#1245 - >seq1244,non-specific,340205,184,222,3.77736e-09,51.568000000000005,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs8_ctshrew.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
3063,Q#1245 - >seq1244,superfamily,340205,184,222,3.77736e-09,51.568000000000005,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs8_ctshrew.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4c,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
3064,Q#1246 - >seq1245,non-specific,335182,80,145,7.460630000000001e-09,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs8_ctshrew.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs8_ctshrew,marg,CompleteHit
3065,Q#1246 - >seq1245,superfamily,335182,80,145,7.460630000000001e-09,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs8_ctshrew.marg.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs8_ctshrew,marg,CompleteHit
3066,Q#1248 - >seq1247,non-specific,197310,67,157,1.1295400000000001e-07,51.5833,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
3067,Q#1248 - >seq1247,superfamily,351117,67,157,1.1295400000000001e-07,51.5833,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.pars.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
3068,Q#1249 - >seq1248,non-specific,197310,2,195,1.01436e-18,82.7845,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,CompleteHit
3069,Q#1249 - >seq1248,superfamily,351117,2,195,1.01436e-18,82.7845,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,CompleteHit
3070,Q#1249 - >seq1248,non-specific,197306,2,198,4.808600000000001e-07,49.4021,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,CompleteHit
3071,Q#1249 - >seq1248,non-specific,223780,2,37,9.0905e-05,42.9707,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3072,Q#1249 - >seq1248,non-specific,197307,2,67,0.000244339,41.5045,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3073,Q#1249 - >seq1248,specific,335306,3,181,0.000300428,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,CompleteHit
3074,Q#1249 - >seq1248,non-specific,197321,1,37,0.00046313400000000003,40.6132,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3075,Q#1249 - >seq1248,non-specific,197336,2,43,0.00053775,40.2883,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3076,Q#1249 - >seq1248,non-specific,197318,2,129,0.000607352,40.3575,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3077,Q#1249 - >seq1248,non-specific,273186,2,37,0.00122448,39.1844,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3078,Q#1249 - >seq1248,non-specific,197320,2,37,0.00258632,38.265,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3079,Q#1249 - >seq1248,non-specific,197319,2,37,0.00381799,38.0265,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3080,Q#1249 - >seq1248,non-specific,272954,2,39,0.00546869,37.3625,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs8_ctshrew.pars.frame3,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3081,Q#1250 - >seq1249,non-specific,197310,74,225,1.24691e-15,76.6213,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3082,Q#1250 - >seq1249,superfamily,351117,74,225,1.24691e-15,76.6213,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3083,Q#1250 - >seq1249,non-specific,197306,74,225,4.610619999999999e-10,60.1877,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3084,Q#1250 - >seq1249,non-specific,223780,72,218,0.00243878,39.8891,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3085,Q#1250 - >seq1249,non-specific,197321,72,187,0.00654111,38.6872,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3086,Q#1250 - >seq1249,non-specific,197307,74,187,0.006814199999999999,38.4229,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4c,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3087,Q#1251 - >seq1250,non-specific,340205,114,150,3.11163e-05,40.012,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,pars,N-TerminusTruncated
3088,Q#1251 - >seq1250,superfamily,340205,114,150,3.11163e-05,40.012,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs1_chimp,pars,N-TerminusTruncated
3089,Q#1252 - >seq1251,non-specific,197310,239,285,1.21736e-06,49.6573,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs8_ctshrew.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4c,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3090,Q#1252 - >seq1251,superfamily,351117,239,285,1.21736e-06,49.6573,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs8_ctshrew.marg.frame2,1909122339_L1M4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4c,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3091,Q#1253 - >seq1252,non-specific,340205,166,227,8.79401e-27,97.792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs0_human.pars.frame1,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs0_human,pars,CompleteHit
3092,Q#1253 - >seq1252,superfamily,340205,166,227,8.79401e-27,97.792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs0_human.pars.frame1,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs0_human,pars,CompleteHit
3093,Q#1253 - >seq1252,non-specific,335182,86,163,1.25547e-24,93.5214,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs0_human.pars.frame1,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs0_human,pars,N-TerminusTruncated
3094,Q#1253 - >seq1252,superfamily,335182,86,163,1.25547e-24,93.5214,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs0_human.pars.frame1,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs0_human,pars,N-TerminusTruncated
3095,Q#1258 - >seq1257,non-specific,340205,158,219,1.65675e-26,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs0_human.marg.frame3,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs0_human,marg,CompleteHit
3096,Q#1258 - >seq1257,superfamily,340205,158,219,1.65675e-26,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs0_human.marg.frame3,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs0_human,marg,CompleteHit
3097,Q#1258 - >seq1257,non-specific,335182,79,155,1.2264299999999998e-22,88.1286,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs0_human.marg.frame3,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs0_human,marg,N-TerminusTruncated
3098,Q#1258 - >seq1257,superfamily,335182,79,155,1.2264299999999998e-22,88.1286,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs0_human.marg.frame3,1909122339_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs0_human,marg,N-TerminusTruncated
3099,Q#1261 - >seq1260,non-specific,340205,161,225,6.27566e-13,61.5832,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs0_human,marg,CompleteHit
3100,Q#1261 - >seq1260,superfamily,340205,161,225,6.27566e-13,61.5832,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs0_human,marg,CompleteHit
3101,Q#1261 - >seq1260,non-specific,335182,87,158,1.35548e-07,48.0679,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs0_human,marg,N-TerminusTruncated
3102,Q#1261 - >seq1260,superfamily,335182,87,158,1.35548e-07,48.0679,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4b,ORF1,hs0_human,marg,N-TerminusTruncated
3103,Q#1263 - >seq1262,non-specific,340205,119,180,1.31937e-11,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs0_human,pars,CompleteHit
3104,Q#1263 - >seq1262,superfamily,340205,119,180,1.31937e-11,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs0_human,pars,CompleteHit
3105,Q#1263 - >seq1262,non-specific,335182,52,116,7.4426e-06,42.6751,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs0_human,pars,N-TerminusTruncated
3106,Q#1263 - >seq1262,superfamily,335182,52,116,7.4426e-06,42.6751,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs0_human,pars,N-TerminusTruncated
3107,Q#1264 - >seq1263,specific,197310,23,231,2.57354e-37,139.79399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3108,Q#1264 - >seq1263,superfamily,351117,23,231,2.57354e-37,139.79399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3109,Q#1264 - >seq1263,non-specific,197306,23,231,8.6226e-14,71.7437,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3110,Q#1264 - >seq1263,non-specific,197320,53,203,5.828599999999999e-11,63.6882,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs10_snmole,marg,N-TerminusTruncated
3111,Q#1264 - >seq1263,non-specific,223780,53,189,2.9668400000000003e-08,55.6823,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs10_snmole,marg,C-TerminusTruncated
3112,Q#1264 - >seq1263,non-specific,197307,44,224,2.13493e-07,52.6753,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3113,Q#1264 - >seq1263,non-specific,197321,23,189,1.00234e-05,47.931999999999995,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3114,Q#1264 - >seq1263,specific,335306,23,224,1.60106e-05,46.8546,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3115,Q#1264 - >seq1263,non-specific,272954,53,197,0.000167049,43.9109,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs10_snmole,marg,N-TerminusTruncated
3116,Q#1264 - >seq1263,non-specific,339261,102,226,0.00207501,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs10_snmole.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3117,Q#1265 - >seq1264,non-specific,238827,497,761,1.53024e-23,99.67299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs10_snmole.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3118,Q#1265 - >seq1264,superfamily,295487,497,761,1.53024e-23,99.67299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs10_snmole.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,marg,CompleteHit
3119,Q#1265 - >seq1264,non-specific,333820,503,707,6.464800000000001e-05,44.5906,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs10_snmole.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,marg,C-TerminusTruncated
3120,Q#1265 - >seq1264,superfamily,333820,503,707,6.464800000000001e-05,44.5906,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs10_snmole.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,marg,C-TerminusTruncated
3121,Q#1268 - >seq1267,specific,197310,1,199,6.198680000000001e-34,129.779,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4b,ORF2,hs10_snmole,pars,CompleteHit
3122,Q#1268 - >seq1267,superfamily,351117,1,199,6.198680000000001e-34,129.779,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,pars,CompleteHit
3123,Q#1268 - >seq1267,non-specific,197306,17,203,4.54944e-13,69.4325,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,pars,CompleteHit
3124,Q#1268 - >seq1267,non-specific,197320,46,187,3.2232e-08,54.8286,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4b,ORF2,hs10_snmole,pars,N-TerminusTruncated
3125,Q#1268 - >seq1267,non-specific,223780,46,173,6.40022e-07,51.0599,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
3126,Q#1268 - >seq1267,non-specific,197307,37,181,2.0707399999999998e-05,46.5121,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4b,ORF2,hs10_snmole,pars,CompleteHit
3127,Q#1268 - >seq1267,specific,335306,26,189,0.00012842,43.773,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4b,ORF2,hs10_snmole,pars,CompleteHit
3128,Q#1268 - >seq1267,non-specific,339261,92,179,0.00345243,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
3129,Q#1268 - >seq1267,non-specific,272954,46,181,0.00637515,38.9033,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4b,ORF2,hs10_snmole,pars,N-TerminusTruncated
3130,Q#1268 - >seq1267,non-specific,238827,469,509,0.00677109,38.4262,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
3131,Q#1268 - >seq1267,superfamily,295487,469,509,0.00677109,38.4262,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs10_snmole.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
3132,Q#1272 - >seq1271,non-specific,335182,121,207,8.198840000000001e-19,79.2691,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs10_snmole.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,marg,CompleteHit
3133,Q#1272 - >seq1271,superfamily,335182,121,207,8.198840000000001e-19,79.2691,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs10_snmole.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,marg,CompleteHit
3134,Q#1272 - >seq1271,non-specific,340205,210,274,2.43404e-18,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs10_snmole.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,marg,CompleteHit
3135,Q#1272 - >seq1271,superfamily,340205,210,274,2.43404e-18,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs10_snmole.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,marg,CompleteHit
3136,Q#1273 - >seq1272,non-specific,335182,52,126,7.66859e-11,56.1571,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs10_snmole.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs10_snmole,pars,CompleteHit
3137,Q#1273 - >seq1272,superfamily,335182,52,126,7.66859e-11,56.1571,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs10_snmole.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4b,ORF1,hs10_snmole,pars,CompleteHit
3138,Q#1275 - >seq1274,non-specific,340205,127,178,2.48055e-16,69.2872,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs10_snmole.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,pars,CompleteHit
3139,Q#1275 - >seq1274,superfamily,340205,127,178,2.48055e-16,69.2872,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs10_snmole.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4b,ORF1,hs10_snmole,pars,CompleteHit
3140,Q#1276 - >seq1275,non-specific,197310,27,198,4.14576e-08,54.2797,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs9_pika.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs9_pika,marg,CompleteHit
3141,Q#1276 - >seq1275,superfamily,351117,27,198,4.14576e-08,54.2797,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs9_pika.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs9_pika,marg,CompleteHit
3142,Q#1277 - >seq1276,non-specific,238827,513,763,5.36395e-26,106.60700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs9_pika.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs9_pika,marg,CompleteHit
3143,Q#1277 - >seq1276,superfamily,295487,513,763,5.36395e-26,106.60700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs9_pika.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs9_pika,marg,CompleteHit
3144,Q#1277 - >seq1276,non-specific,333820,525,704,4.9189e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs9_pika.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs9_pika,marg,C-TerminusTruncated
3145,Q#1277 - >seq1276,superfamily,333820,525,704,4.9189e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs9_pika.marg.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4b,ORF2,hs9_pika,marg,C-TerminusTruncated
3146,Q#1278 - >seq1277,non-specific,197310,113,210,1.12357e-12,66.9913,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs9_pika.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs9_pika,pars,N-TerminusTruncated
3147,Q#1278 - >seq1277,superfamily,351117,113,210,1.12357e-12,66.9913,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs9_pika.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs9_pika,pars,N-TerminusTruncated
3148,Q#1278 - >seq1277,non-specific,197306,88,210,1.86924e-05,45.5501,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs9_pika.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs9_pika,pars,N-TerminusTruncated
3149,Q#1278 - >seq1277,non-specific,197320,95,182,0.00150961,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs9_pika.pars.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs9_pika,pars,N-TerminusTruncated
3150,Q#1279 - >seq1278,non-specific,197310,38,199,4.47948e-27,108.59299999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs8_ctshrew,pars,CompleteHit
3151,Q#1279 - >seq1278,superfamily,351117,38,199,4.47948e-27,108.59299999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,CompleteHit
3152,Q#1279 - >seq1278,non-specific,197306,47,202,1.7259e-11,63.6545,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3153,Q#1279 - >seq1278,non-specific,197320,42,189,1.6221200000000002e-10,60.9918,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3154,Q#1279 - >seq1278,non-specific,223780,48,188,4.67176e-07,50.6747,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3155,Q#1279 - >seq1278,non-specific,197307,36,199,4.4495699999999995e-05,44.5861,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,CompleteHit
3156,Q#1279 - >seq1278,non-specific,339261,89,188,6.42433e-05,42.3243,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M4b,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3157,Q#1279 - >seq1278,non-specific,197322,87,198,9.3942e-05,44.2302,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3158,Q#1279 - >seq1278,non-specific,335306,47,191,0.000205163,42.6174,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3159,Q#1279 - >seq1278,non-specific,273186,88,189,0.000355299,41.8808,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3160,Q#1279 - >seq1278,non-specific,272954,32,188,0.00235224,39.2885,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs8_ctshrew.pars.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4b,ORF2,hs8_ctshrew,pars,CompleteHit
3161,Q#1282 - >seq1281,non-specific,238827,469,682,3.47986e-18,83.8798,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4b.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3162,Q#1282 - >seq1281,superfamily,295487,469,682,3.47986e-18,83.8798,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4b.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3163,Q#1282 - >seq1281,non-specific,333820,475,690,3.2893e-07,50.7538,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3164,Q#1282 - >seq1281,superfamily,333820,475,690,3.2893e-07,50.7538,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4b.ORF2.hs8_ctshrew.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3165,Q#1284 - >seq1283,specific,197310,9,237,5.150999999999999e-39,144.031,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3166,Q#1284 - >seq1283,superfamily,351117,9,237,5.150999999999999e-39,144.031,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3167,Q#1284 - >seq1283,non-specific,197306,9,237,4.64387e-19,86.7664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3168,Q#1284 - >seq1283,non-specific,197320,106,222,6.1208e-11,63.303000000000004,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3169,Q#1284 - >seq1283,non-specific,223780,9,222,2.30461e-10,61.4603,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3170,Q#1284 - >seq1283,non-specific,197307,9,229,6.39989e-09,56.9125,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3171,Q#1284 - >seq1283,specific,335306,12,229,8.204080000000002e-08,53.403,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3172,Q#1284 - >seq1283,non-specific,273186,9,238,8.5837e-06,47.6588,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3173,Q#1284 - >seq1283,non-specific,197319,9,237,1.7659100000000002e-05,46.5009,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3174,Q#1284 - >seq1283,non-specific,339261,108,229,2.07529e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3175,Q#1284 - >seq1283,non-specific,197321,7,229,2.45169e-05,46.3912,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3176,Q#1284 - >seq1283,non-specific,197322,106,223,0.00018340200000000002,43.845,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3177,Q#1284 - >seq1283,non-specific,272954,9,208,0.000741845,41.5997,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,CompleteHit
3178,Q#1284 - >seq1283,non-specific,197311,73,208,0.004425999999999999,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs8_ctshrew.marg.frame3,1909122339_L1M4b.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3179,Q#1288 - >seq1287,non-specific,335182,219,302,4.2984199999999997e-23,91.9806,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3180,Q#1288 - >seq1287,superfamily,335182,219,302,4.2984199999999997e-23,91.9806,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3181,Q#1288 - >seq1287,non-specific,340205,305,370,2.42438e-21,86.236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3182,Q#1288 - >seq1287,superfamily,340205,305,370,2.42438e-21,86.236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3183,Q#1288 - >seq1287,non-specific,340204,159,204,0.00692926,33.9204,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3184,Q#1288 - >seq1287,superfamily,340204,159,204,0.00692926,33.9204,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1M4b.ORF1.hs9_pika.marg.frame1,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1M4b,ORF1,hs9_pika,marg,CompleteHit
3185,Q#1292 - >seq1291,non-specific,197310,21,104,1.29846e-06,48.8869,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4b,ORF2,hs9_pika,pars,C-TerminusTruncated
3186,Q#1292 - >seq1291,superfamily,351117,21,104,1.29846e-06,48.8869,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4b,ORF2,hs9_pika,pars,C-TerminusTruncated
3187,Q#1293 - >seq1292,non-specific,335182,49,127,2.23942e-23,88.899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs9_pika,pars,CompleteHit
3188,Q#1293 - >seq1292,superfamily,335182,49,127,2.23942e-23,88.899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4b.ORF1.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs9_pika,pars,CompleteHit
3189,Q#1293 - >seq1292,non-specific,340205,130,182,3.6764e-17,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs9_pika,pars,CompleteHit
3190,Q#1293 - >seq1292,superfamily,340205,130,182,3.6764e-17,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4b.ORF1.hs9_pika.pars.frame2,1909122339_L1M4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4b,ORF1,hs9_pika,pars,CompleteHit
3191,Q#1297 - >seq1296,non-specific,340205,197,260,5.87614e-26,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs4_gibbon.marg.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,marg,CompleteHit
3192,Q#1297 - >seq1296,superfamily,340205,197,260,5.87614e-26,96.6364,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs4_gibbon.marg.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,marg,CompleteHit
3193,Q#1297 - >seq1296,non-specific,335182,107,194,1.26225e-25,96.603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs4_gibbon.marg.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,marg,CompleteHit
3194,Q#1297 - >seq1296,superfamily,335182,107,194,1.26225e-25,96.603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs4_gibbon.marg.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,marg,CompleteHit
3195,Q#1300 - >seq1299,non-specific,335182,87,174,1.17973e-25,96.603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs4_gibbon.pars.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,pars,CompleteHit
3196,Q#1300 - >seq1299,superfamily,335182,87,174,1.17973e-25,96.603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs4_gibbon.pars.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,pars,CompleteHit
3197,Q#1300 - >seq1299,non-specific,340205,177,240,2.5754699999999995e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs4_gibbon.pars.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,pars,CompleteHit
3198,Q#1300 - >seq1299,superfamily,340205,177,240,2.5754699999999995e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs4_gibbon.pars.frame3,1909122339_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4c,ORF1,hs4_gibbon,pars,CompleteHit
3199,Q#1304 - >seq1303,non-specific,340205,78,140,1.5153700000000002e-23,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,CompleteHit
3200,Q#1304 - >seq1303,superfamily,340205,78,140,1.5153700000000002e-23,86.6212,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,CompleteHit
3201,Q#1304 - >seq1303,non-specific,340205,78,140,1.5153700000000002e-23,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,CompleteHit
3202,Q#1304 - >seq1303,non-specific,335182,1,75,3.1082799999999995e-20,79.2691,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,N-TerminusTruncated
3203,Q#1304 - >seq1303,superfamily,335182,1,75,3.1082799999999995e-20,79.2691,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,N-TerminusTruncated
3204,Q#1304 - >seq1303,non-specific,335182,1,75,3.1082799999999995e-20,79.2691,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.marg.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,marg,N-TerminusTruncated
3205,Q#1307 - >seq1306,non-specific,340205,78,140,1.5153700000000002e-23,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,CompleteHit
3206,Q#1307 - >seq1306,superfamily,340205,78,140,1.5153700000000002e-23,86.6212,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,CompleteHit
3207,Q#1307 - >seq1306,non-specific,340205,78,140,1.5153700000000002e-23,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,CompleteHit
3208,Q#1307 - >seq1306,non-specific,335182,1,75,3.1082799999999995e-20,79.2691,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,N-TerminusTruncated
3209,Q#1307 - >seq1306,superfamily,335182,1,75,3.1082799999999995e-20,79.2691,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,N-TerminusTruncated
3210,Q#1307 - >seq1306,non-specific,335182,1,75,3.1082799999999995e-20,79.2691,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs3_orang.pars.frame1,1909122339_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs3_orang,pars,N-TerminusTruncated
3211,Q#1308 - >seq1307,non-specific,340205,212,275,4.4680799999999995e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs2_gorilla.marg.frame3,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs2_gorilla,marg,CompleteHit
3212,Q#1308 - >seq1307,superfamily,340205,212,275,4.4680799999999995e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs2_gorilla.marg.frame3,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs2_gorilla,marg,CompleteHit
3213,Q#1308 - >seq1307,non-specific,335182,130,209,6.8723e-21,84.6618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs2_gorilla.marg.frame3,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs2_gorilla,marg,CompleteHit
3214,Q#1308 - >seq1307,superfamily,335182,130,209,6.8723e-21,84.6618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs2_gorilla.marg.frame3,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4c,ORF1,hs2_gorilla,marg,CompleteHit
3215,Q#1311 - >seq1310,specific,197310,5,217,5.9921e-30,118.993,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3216,Q#1311 - >seq1310,superfamily,351117,5,217,5.9921e-30,118.993,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3217,Q#1311 - >seq1310,non-specific,197306,1,217,6.06648e-13,69.4325,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3218,Q#1311 - >seq1310,non-specific,197307,4,210,4.7605900000000004e-05,46.1269,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3219,Q#1311 - >seq1310,non-specific,339261,91,212,5.895479999999999e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4b,ORF2,hs0_human,marg,CompleteHit
3220,Q#1311 - >seq1310,non-specific,197320,4,210,0.000341311,43.2726,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3221,Q#1311 - >seq1310,non-specific,223780,4,210,0.000993413,41.8151,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3222,Q#1311 - >seq1310,non-specific,335306,6,210,0.00218648,40.6914,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs0_human.marg.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,marg,CompleteHit
3223,Q#1314 - >seq1313,specific,197310,3,211,5.75981e-29,115.912,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3224,Q#1314 - >seq1313,superfamily,351117,3,211,5.75981e-29,115.912,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3225,Q#1314 - >seq1313,non-specific,197306,5,211,5.11123e-13,69.4325,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3226,Q#1314 - >seq1313,specific,335306,4,204,0.00034516099999999997,43.0026,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3227,Q#1314 - >seq1313,non-specific,197307,2,204,0.000576391,42.2749,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3228,Q#1314 - >seq1313,non-specific,223780,2,204,0.00116123,41.4299,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3229,Q#1314 - >seq1313,non-specific,197320,2,204,0.00740347,39.0354,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4b,ORF2,hs0_human,pars,CompleteHit
3230,Q#1314 - >seq1313,non-specific,339261,86,206,0.00745618,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4b.ORF2.hs0_human.pars.frame3,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4b,ORF2,hs0_human,pars,CompleteHit
3231,Q#1318 - >seq1317,non-specific,340205,180,243,2.2654400000000002e-28,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs1_chimp,pars,CompleteHit
3232,Q#1318 - >seq1317,superfamily,340205,180,243,2.2654400000000002e-28,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs1_chimp,pars,CompleteHit
3233,Q#1318 - >seq1317,non-specific,335182,105,152,6.1279e-12,60.0091,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs1_chimp,pars,BothTerminiTruncated
3234,Q#1318 - >seq1317,superfamily,335182,105,152,6.1279e-12,60.0091,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs1_chimp.pars.frame2,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4c,ORF1,hs1_chimp,pars,BothTerminiTruncated
3235,Q#1319 - >seq1318,non-specific,340205,208,270,2.8754699999999996e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs1_chimp.marg.frame1,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs1_chimp,marg,CompleteHit
3236,Q#1319 - >seq1318,superfamily,340205,208,270,2.8754699999999996e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs1_chimp.marg.frame1,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs1_chimp,marg,CompleteHit
3237,Q#1319 - >seq1318,non-specific,335182,133,180,1.0829000000000001e-11,60.0091,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs1_chimp.marg.frame1,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs1_chimp,marg,BothTerminiTruncated
3238,Q#1319 - >seq1318,superfamily,335182,133,180,1.0829000000000001e-11,60.0091,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs1_chimp.marg.frame1,1909122339_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4c,ORF1,hs1_chimp,marg,BothTerminiTruncated
3239,Q#1322 - >seq1321,non-specific,340205,207,270,1.5528599999999998e-25,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs2_gorilla.pars.frame1,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs2_gorilla,pars,CompleteHit
3240,Q#1322 - >seq1321,superfamily,340205,207,270,1.5528599999999998e-25,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4c.ORF1.hs2_gorilla.pars.frame1,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs2_gorilla,pars,CompleteHit
3241,Q#1322 - >seq1321,non-specific,335182,125,204,1.01233e-20,84.2766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs2_gorilla.pars.frame1,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs2_gorilla,pars,CompleteHit
3242,Q#1322 - >seq1321,superfamily,335182,125,204,1.01233e-20,84.2766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4c.ORF1.hs2_gorilla.pars.frame1,1909122339_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4c,ORF1,hs2_gorilla,pars,CompleteHit
3243,Q#1326 - >seq1325,non-specific,311332,670,788,0.0006357180000000001,40.7609,pfam07316,DUF1463, - ,cl06376,Protein of unknown function (DUF1463); This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.,L1M4b.ORF2.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M4b,ORF2,hs0_human,pars,CompleteHit
3244,Q#1326 - >seq1325,superfamily,311332,670,788,0.0006357180000000001,40.7609,cl06376,DUF1463 superfamily, - , - ,Protein of unknown function (DUF1463); This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.,L1M4b.ORF2.hs0_human.pars.frame1,1909122339_L1M4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1M4b,ORF2,hs0_human,pars,CompleteHit
3245,Q#1329 - >seq1328,non-specific,340205,99,162,1.83059e-25,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs7_bushaby,pars,CompleteHit
3246,Q#1329 - >seq1328,superfamily,340205,99,162,1.83059e-25,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs7_bushaby,pars,CompleteHit
3247,Q#1329 - >seq1328,non-specific,335182,41,96,7.1355e-10,53.0755,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs7_bushaby,pars,N-TerminusTruncated
3248,Q#1329 - >seq1328,superfamily,335182,41,96,7.1355e-10,53.0755,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs7_bushaby,pars,N-TerminusTruncated
3249,Q#1330 - >seq1329,non-specific,238827,576,832,2.96086e-25,105.066,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs5_gmonkey,marg,CompleteHit
3250,Q#1330 - >seq1329,superfamily,295487,576,832,2.96086e-25,105.066,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs5_gmonkey,marg,CompleteHit
3251,Q#1330 - >seq1329,non-specific,333820,594,832,1.18418e-14,73.0954,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs5_gmonkey,marg,CompleteHit
3252,Q#1330 - >seq1329,superfamily,333820,594,832,1.18418e-14,73.0954,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs5_gmonkey,marg,CompleteHit
3253,Q#1330 - >seq1329,non-specific,238828,661,789,1.12869e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4.ORF2.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3254,Q#1331 - >seq1330,specific,197310,9,237,1.3776999999999999e-45,161.365,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3255,Q#1331 - >seq1330,superfamily,351117,9,237,1.3776999999999999e-45,161.365,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3256,Q#1331 - >seq1330,non-specific,197306,9,237,1.50332e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3257,Q#1331 - >seq1330,non-specific,223780,7,230,1.7917700000000002e-14,73.4015,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3258,Q#1331 - >seq1330,non-specific,197307,9,230,6.25807e-13,68.8537,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3259,Q#1331 - >seq1330,specific,335306,10,230,3.4249699999999997e-12,66.1146,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3260,Q#1331 - >seq1330,non-specific,197320,7,230,1.24263e-11,64.8438,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3261,Q#1331 - >seq1330,non-specific,197321,7,230,2.6143799999999996e-10,61.0288,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3262,Q#1331 - >seq1330,non-specific,273186,7,238,6.718260000000001e-10,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3263,Q#1331 - >seq1330,non-specific,272954,7,208,7.63089e-09,56.6225,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3264,Q#1331 - >seq1330,non-specific,197319,7,237,2.1807800000000002e-06,49.1973,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3265,Q#1331 - >seq1330,non-specific,339261,109,232,0.00102472,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3266,Q#1331 - >seq1330,non-specific,197322,8,230,0.00253021,39.993,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3267,Q#1331 - >seq1330,non-specific,197336,7,230,0.00653277,38.3623,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4.ORF2.hs6_sqmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,marg,CompleteHit
3268,Q#1339 - >seq1338,non-specific,340205,150,214,1.3135e-21,84.31,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs6_sqmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs6_sqmonkey,marg,CompleteHit
3269,Q#1339 - >seq1338,superfamily,340205,150,214,1.3135e-21,84.31,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs6_sqmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs6_sqmonkey,marg,CompleteHit
3270,Q#1339 - >seq1338,non-specific,335182,101,147,2.9444899999999996e-09,52.6903,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs6_sqmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
3271,Q#1339 - >seq1338,superfamily,335182,101,147,2.9444899999999996e-09,52.6903,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs6_sqmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
3272,Q#1340 - >seq1339,non-specific,340205,31,95,1.77077e-23,85.4656,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs6_sqmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs6_sqmonkey,pars,CompleteHit
3273,Q#1340 - >seq1339,superfamily,340205,31,95,1.77077e-23,85.4656,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs6_sqmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs6_sqmonkey,pars,CompleteHit
3274,Q#1340 - >seq1339,non-specific,335182,2,28,0.00803163,33.0451,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs6_sqmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
3275,Q#1340 - >seq1339,superfamily,335182,2,28,0.00803163,33.0451,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs6_sqmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
3276,Q#1344 - >seq1343,non-specific,340205,226,289,1.54081e-25,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs7_bushaby,marg,CompleteHit
3277,Q#1344 - >seq1343,superfamily,340205,226,289,1.54081e-25,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs7_bushaby,marg,CompleteHit
3278,Q#1344 - >seq1343,non-specific,335182,128,223,2.20465e-18,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs7_bushaby,marg,CompleteHit
3279,Q#1344 - >seq1343,superfamily,335182,128,223,2.20465e-18,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs7_bushaby,marg,CompleteHit
3280,Q#1346 - >seq1345,non-specific,197310,101,220,5.12516e-18,82.7845,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3281,Q#1346 - >seq1345,superfamily,351117,101,220,5.12516e-18,82.7845,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3282,Q#1346 - >seq1345,non-specific,197306,111,220,2.6646999999999997e-08,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3283,Q#1346 - >seq1345,non-specific,197320,112,213,8.67112e-08,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3284,Q#1346 - >seq1345,specific,335306,107,213,1.03743e-06,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3285,Q#1346 - >seq1345,non-specific,197322,108,213,3.38017e-05,45.3858,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3286,Q#1346 - >seq1345,non-specific,223780,110,213,5.59748e-05,44.5115,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3287,Q#1346 - >seq1345,non-specific,197307,124,213,0.00010331899999999999,43.4305,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3288,Q#1346 - >seq1345,non-specific,197317,113,213,0.00301514,39.1224,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M4.ORF2.hs7_bushaby.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,N-TerminusTruncated
3289,Q#1347 - >seq1346,non-specific,197310,145,258,2.1238000000000004e-19,88.5625,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3290,Q#1347 - >seq1346,superfamily,351117,145,258,2.1238000000000004e-19,88.5625,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3291,Q#1347 - >seq1346,non-specific,197306,145,258,9.120450000000001e-09,57.1061,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3292,Q#1347 - >seq1346,non-specific,223780,145,260,2.8982499999999997e-06,49.9043,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3293,Q#1347 - >seq1346,non-specific,197307,145,253,2.5376599999999997e-05,46.8973,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3294,Q#1347 - >seq1346,non-specific,197321,145,217,0.0032671999999999996,40.228,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3295,Q#1347 - >seq1346,non-specific,197320,168,259,0.00581124,39.8058,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3296,Q#1347 - >seq1346,non-specific,272954,145,253,0.00654518,39.6737,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs5_gmonkey.marg.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3297,Q#1348 - >seq1347,specific,197310,9,230,1.07761e-46,164.832,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3298,Q#1348 - >seq1347,superfamily,351117,9,230,1.07761e-46,164.832,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3299,Q#1348 - >seq1347,non-specific,197306,9,230,2.3668800000000002e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3300,Q#1348 - >seq1347,non-specific,223780,7,223,9.77628e-16,77.2535,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3301,Q#1348 - >seq1347,specific,335306,10,223,3.2397900000000003e-12,66.1146,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3302,Q#1348 - >seq1347,non-specific,197320,100,223,3.58682e-12,66.7698,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3303,Q#1348 - >seq1347,non-specific,197307,9,223,3.6126599999999997e-12,66.5425,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3304,Q#1348 - >seq1347,non-specific,197319,7,230,3.39504e-09,57.6717,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3305,Q#1348 - >seq1347,non-specific,197321,7,223,1.03095e-08,56.4064,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3306,Q#1348 - >seq1347,non-specific,273186,7,231,2.6522799999999998e-08,54.9776,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3307,Q#1348 - >seq1347,non-specific,272954,7,201,7.56334e-08,53.9261,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3308,Q#1348 - >seq1347,non-specific,339261,102,225,4.15616e-07,48.8727,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3309,Q#1348 - >seq1347,non-specific,197322,85,223,5.7015299999999996e-05,45.3858,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3310,Q#1348 - >seq1347,non-specific,197336,7,223,0.00013513700000000002,43.7551,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,CompleteHit
3311,Q#1348 - >seq1347,non-specific,197311,66,230,0.000211215,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3312,Q#1349 - >seq1348,non-specific,238827,493,649,1.41288e-11,64.2346,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs8_ctshrew.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3313,Q#1349 - >seq1348,superfamily,295487,493,649,1.41288e-11,64.2346,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs8_ctshrew.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3314,Q#1349 - >seq1348,non-specific,333820,494,649,3.36028e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs8_ctshrew.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3315,Q#1349 - >seq1348,superfamily,333820,494,649,3.36028e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs8_ctshrew.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3316,Q#1349 - >seq1348,non-specific,238828,541,636,0.000422958,42.1881,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4.ORF2.hs8_ctshrew.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
3317,Q#1350 - >seq1349,specific,197310,9,228,7.93545e-47,164.832,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3318,Q#1350 - >seq1349,superfamily,351117,9,228,7.93545e-47,164.832,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3319,Q#1350 - >seq1349,non-specific,197306,9,228,2.40765e-22,96.3964,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3320,Q#1350 - >seq1349,non-specific,223780,7,221,9.08209e-16,77.2535,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3321,Q#1350 - >seq1349,non-specific,197307,9,221,1.04578e-12,68.0833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3322,Q#1350 - >seq1349,non-specific,197320,7,221,1.88892e-12,67.5402,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3323,Q#1350 - >seq1349,specific,335306,10,221,1.66246e-11,64.1886,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3324,Q#1350 - >seq1349,non-specific,197321,7,221,2.49795e-09,57.9472,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3325,Q#1350 - >seq1349,non-specific,272954,7,199,1.33663e-08,55.8521,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3326,Q#1350 - >seq1349,non-specific,273186,7,229,1.49045e-08,55.748000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3327,Q#1350 - >seq1349,non-specific,197319,7,228,3.31629e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3328,Q#1350 - >seq1349,non-specific,339261,100,223,2.6807e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3329,Q#1350 - >seq1349,non-specific,197336,7,221,3.46552e-05,45.6811,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,CompleteHit
3330,Q#1350 - >seq1349,non-specific,197322,83,221,5.41362e-05,45.3858,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3331,Q#1350 - >seq1349,non-specific,197311,64,228,0.00044485900000000003,41.8937,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
3332,Q#1350 - >seq1349,non-specific,238827,502,565,0.00289188,39.5818,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3333,Q#1350 - >seq1349,superfamily,295487,502,565,0.00289188,39.5818,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3334,Q#1351 - >seq1350,non-specific,238828,523,618,0.00048014900000000003,41.8029,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4.ORF2.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
3335,Q#1351 - >seq1350,superfamily,295487,523,618,0.00048014900000000003,41.8029,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
3336,Q#1351 - >seq1350,non-specific,333820,494,621,0.00194577,39.583,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3337,Q#1351 - >seq1350,superfamily,333820,494,621,0.00194577,39.583,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3338,Q#1353 - >seq1352,non-specific,340205,113,177,5.5010799999999996e-27,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,marg,CompleteHit
3339,Q#1353 - >seq1352,superfamily,340205,113,177,5.5010799999999996e-27,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,marg,CompleteHit
3340,Q#1353 - >seq1352,non-specific,335182,20,110,1.09803e-18,76.5727,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,marg,CompleteHit
3341,Q#1353 - >seq1352,superfamily,335182,20,110,1.09803e-18,76.5727,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs8_ctshrew.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,marg,CompleteHit
3342,Q#1354 - >seq1353,non-specific,197310,9,83,3.91976e-07,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
3343,Q#1354 - >seq1353,superfamily,351117,9,83,3.91976e-07,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.pars.frame1,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
3344,Q#1356 - >seq1355,non-specific,335182,20,78,1.0887499999999999e-07,47.2975,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
3345,Q#1356 - >seq1355,superfamily,335182,20,78,1.0887499999999999e-07,47.2975,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs8_ctshrew.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
3346,Q#1357 - >seq1356,non-specific,340205,111,174,5.61359e-28,99.3327,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs8_ctshrew,pars,CompleteHit
3347,Q#1357 - >seq1356,superfamily,340205,111,174,5.61359e-28,99.3327,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs8_ctshrew.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs8_ctshrew,pars,CompleteHit
3348,Q#1359 - >seq1358,non-specific,197310,10,130,7.29619e-18,82.7845,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3349,Q#1359 - >seq1358,superfamily,351117,10,130,7.29619e-18,82.7845,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3350,Q#1359 - >seq1358,non-specific,238827,483,543,2.64407e-12,66.1606,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3351,Q#1359 - >seq1358,superfamily,295487,483,543,2.64407e-12,66.1606,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3352,Q#1359 - >seq1358,non-specific,197306,10,138,4.84109e-07,50.9429,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3353,Q#1359 - >seq1358,non-specific,333820,488,529,0.000125299,43.0498,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3354,Q#1359 - >seq1358,superfamily,333820,488,529,0.000125299,43.0498,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3355,Q#1359 - >seq1358,non-specific,223780,8,118,0.00039674400000000004,42.2003,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3356,Q#1359 - >seq1358,non-specific,197307,10,116,0.000634744,41.5045,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.marg.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
3357,Q#1360 - >seq1359,non-specific,197310,107,226,3.3215100000000005e-18,83.9401,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3358,Q#1360 - >seq1359,superfamily,351117,107,226,3.3215100000000005e-18,83.9401,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3359,Q#1360 - >seq1359,non-specific,197306,117,226,5.05521e-08,54.0245,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3360,Q#1360 - >seq1359,non-specific,197320,118,219,1.18467e-07,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3361,Q#1360 - >seq1359,specific,335306,58,219,2.4630400000000003e-07,51.477,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3362,Q#1360 - >seq1359,non-specific,197322,114,219,4.61929e-05,45.3858,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3363,Q#1360 - >seq1359,non-specific,223780,116,219,0.000116524,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3364,Q#1360 - >seq1359,non-specific,197307,130,219,0.000208715,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3365,Q#1360 - >seq1359,non-specific,197317,119,219,0.00409702,39.1224,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M4.ORF2.hs7_bushaby.marg.frame2,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,marg,N-TerminusTruncated
3366,Q#1362 - >seq1361,non-specific,197310,24,121,1.3785499999999999e-05,46.1905,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs7_bushaby.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
3367,Q#1362 - >seq1361,superfamily,351117,24,121,1.3785499999999999e-05,46.1905,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs7_bushaby.pars.frame3,1909122340_L1M4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
3368,Q#1364 - >seq1363,non-specific,197310,292,357,1.96796e-12,68.1469,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs5_gmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3369,Q#1364 - >seq1363,superfamily,351117,292,357,1.96796e-12,68.1469,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs5_gmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3370,Q#1364 - >seq1363,non-specific,197320,290,350,0.00532277,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.marg.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3371,Q#1365 - >seq1364,specific,197310,9,235,1.4130099999999999e-42,153.276,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3372,Q#1365 - >seq1364,superfamily,351117,9,235,1.4130099999999999e-42,153.276,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3373,Q#1365 - >seq1364,non-specific,197306,9,235,2.2246300000000002e-20,90.6184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3374,Q#1365 - >seq1364,non-specific,223780,7,228,1.94601e-11,64.5419,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3375,Q#1365 - >seq1364,specific,335306,10,228,2.67865e-11,63.4182,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3376,Q#1365 - >seq1364,non-specific,197307,9,228,1.62862e-10,61.5349,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3377,Q#1365 - >seq1364,non-specific,197320,7,228,7.29153e-10,59.8362,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3378,Q#1365 - >seq1364,non-specific,197321,7,228,4.61306e-07,51.3988,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3379,Q#1365 - >seq1364,non-specific,273186,7,236,6.61598e-07,50.7404,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3380,Q#1365 - >seq1364,non-specific,272954,7,206,2.43872e-06,49.3037,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3381,Q#1365 - >seq1364,non-specific,197319,7,235,0.00019865,43.4193,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3382,Q#1365 - >seq1364,non-specific,197322,139,228,0.00510069,39.2227,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3383,Q#1365 - >seq1364,non-specific,227355,409,625,0.00513328,40.0612,COG5022,COG5022,N,cl34868,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3384,Q#1365 - >seq1364,superfamily,227355,409,625,0.00513328,40.0612,cl34868,COG5022 superfamily,N, - ,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3385,Q#1365 - >seq1364,non-specific,339261,109,230,0.00736577,36.5463,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs6_sqmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M4,ORF2,hs6_sqmonkey,pars,CompleteHit
3386,Q#1371 - >seq1370,non-specific,197310,23,223,3.61898e-20,89.7181,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M4,ORF2,hs3_orang,pars,CompleteHit
3387,Q#1371 - >seq1370,superfamily,351117,23,223,3.61898e-20,89.7181,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,pars,CompleteHit
3388,Q#1371 - >seq1370,non-specific,197306,58,223,1.4840899999999999e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,pars,N-TerminusTruncated
3389,Q#1371 - >seq1370,non-specific,197320,58,216,1.68351e-05,46.7394,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4,ORF2,hs3_orang,pars,N-TerminusTruncated
3390,Q#1371 - >seq1370,specific,335306,23,216,0.0007202939999999999,41.4618,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,pars,CompleteHit
3391,Q#1371 - >seq1370,non-specific,223780,54,216,0.00440276,39.1187,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M4,ORF2,hs3_orang,pars,N-TerminusTruncated
3392,Q#1372 - >seq1371,non-specific,340205,158,219,1.16298e-17,73.9096,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs3_orang,marg,CompleteHit
3393,Q#1372 - >seq1371,superfamily,340205,158,219,1.16298e-17,73.9096,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs3_orang,marg,CompleteHit
3394,Q#1372 - >seq1371,non-specific,335182,75,155,5.83266e-13,62.3203,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs3_orang,marg,CompleteHit
3395,Q#1372 - >seq1371,superfamily,335182,75,155,5.83266e-13,62.3203,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs3_orang,marg,CompleteHit
3396,Q#1375 - >seq1374,non-specific,335182,59,139,3.67971e-13,62.7055,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs3_orang.pars.frame2,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs3_orang,pars,CompleteHit
3397,Q#1375 - >seq1374,superfamily,335182,59,139,3.67971e-13,62.7055,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs3_orang.pars.frame2,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs3_orang,pars,CompleteHit
3398,Q#1375 - >seq1374,non-specific,340205,142,176,0.00349396,34.6192,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.pars.frame2,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs3_orang,pars,C-TerminusTruncated
3399,Q#1375 - >seq1374,superfamily,340205,142,176,0.00349396,34.6192,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.pars.frame2,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs3_orang,pars,C-TerminusTruncated
3400,Q#1376 - >seq1375,non-specific,340205,150,192,2.44277e-08,48.8716,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs3_orang,pars,N-TerminusTruncated
3401,Q#1376 - >seq1375,superfamily,340205,150,192,2.44277e-08,48.8716,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs3_orang.pars.frame1,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs3_orang,pars,N-TerminusTruncated
3402,Q#1377 - >seq1376,specific,197310,32,257,8.658059999999999e-29,115.52600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs2_gorilla.marg.frame3,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs2_gorilla,marg,CompleteHit
3403,Q#1377 - >seq1376,superfamily,351117,32,257,8.658059999999999e-29,115.52600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs2_gorilla.marg.frame3,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs2_gorilla,marg,CompleteHit
3404,Q#1377 - >seq1376,non-specific,238827,534,654,3.31994e-12,66.931,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs2_gorilla.marg.frame3,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
3405,Q#1377 - >seq1376,superfamily,295487,534,654,3.31994e-12,66.931,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs2_gorilla.marg.frame3,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
3406,Q#1377 - >seq1376,non-specific,197306,32,257,3.4546800000000004e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs2_gorilla.marg.frame3,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs2_gorilla,marg,CompleteHit
3407,Q#1381 - >seq1380,non-specific,197310,62,252,2.67755e-20,90.4885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs2_gorilla.pars.frame2,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs2_gorilla,pars,CompleteHit
3408,Q#1381 - >seq1380,superfamily,351117,62,252,2.67755e-20,90.4885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs2_gorilla.pars.frame2,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs2_gorilla,pars,CompleteHit
3409,Q#1381 - >seq1380,non-specific,238827,519,641,9.9966e-14,70.783,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs2_gorilla.pars.frame2,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
3410,Q#1381 - >seq1380,superfamily,295487,519,641,9.9966e-14,70.783,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs2_gorilla.pars.frame2,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
3411,Q#1381 - >seq1380,non-specific,197306,61,252,1.24418e-07,53.2541,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs2_gorilla.pars.frame2,1909122340_L1M4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs2_gorilla,pars,CompleteHit
3412,Q#1383 - >seq1382,non-specific,197310,8,232,1.6196100000000001e-24,102.815,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs5_gmonkey,pars,CompleteHit
3413,Q#1383 - >seq1382,superfamily,351117,8,232,1.6196100000000001e-24,102.815,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs5_gmonkey,pars,CompleteHit
3414,Q#1383 - >seq1382,non-specific,197306,8,232,2.0125599999999998e-06,49.7873,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs5_gmonkey,pars,CompleteHit
3415,Q#1383 - >seq1382,non-specific,197307,8,76,4.40312e-05,45.7417,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3416,Q#1383 - >seq1382,non-specific,197321,8,77,0.00301391,40.228,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3417,Q#1383 - >seq1382,non-specific,197320,165,225,0.00388721,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs5_gmonkey.pars.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3418,Q#1384 - >seq1383,specific,197310,2,232,7.97833e-32,124.001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3419,Q#1384 - >seq1383,superfamily,351117,2,232,7.97833e-32,124.001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3420,Q#1384 - >seq1383,non-specific,197306,2,232,1.1676700000000002e-09,59.4173,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3421,Q#1384 - >seq1383,specific,335306,3,225,7.64803e-07,50.7066,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3422,Q#1384 - >seq1383,non-specific,223780,2,225,1.7561500000000001e-06,50.2895,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3423,Q#1384 - >seq1383,non-specific,197320,109,225,1.8261900000000002e-05,47.1246,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs3_orang,marg,N-TerminusTruncated
3424,Q#1384 - >seq1383,non-specific,197307,2,225,9.95006e-05,44.5861,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs3_orang.marg.frame3,1909122340_L1M4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs3_orang,marg,CompleteHit
3425,Q#1385 - >seq1384,non-specific,340205,151,212,2.36063e-24,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs4_gibbon.pars.frame1,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs4_gibbon,pars,CompleteHit
3426,Q#1385 - >seq1384,superfamily,340205,151,212,2.36063e-24,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs4_gibbon.pars.frame1,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs4_gibbon,pars,CompleteHit
3427,Q#1385 - >seq1384,non-specific,335182,69,148,1.79822e-13,63.8611,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs4_gibbon.pars.frame1,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs4_gibbon,pars,CompleteHit
3428,Q#1385 - >seq1384,superfamily,335182,69,148,1.79822e-13,63.8611,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs4_gibbon.pars.frame1,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs4_gibbon,pars,CompleteHit
3429,Q#1388 - >seq1387,non-specific,238827,471,714,8.12359e-20,88.8874,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs5_gmonkey.pars.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs5_gmonkey,pars,CompleteHit
3430,Q#1388 - >seq1387,superfamily,295487,471,714,8.12359e-20,88.8874,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs5_gmonkey.pars.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs5_gmonkey,pars,CompleteHit
3431,Q#1388 - >seq1387,non-specific,333820,491,666,5.47273e-11,62.3098,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs5_gmonkey.pars.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3432,Q#1388 - >seq1387,superfamily,333820,491,666,5.47273e-11,62.3098,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs5_gmonkey.pars.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3433,Q#1388 - >seq1387,non-specific,238828,557,677,6.98169e-06,47.9661,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4.ORF2.hs5_gmonkey.pars.frame1,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3434,Q#1390 - >seq1389,non-specific,340205,161,225,7.8493e-22,85.4656,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs5_gmonkey,marg,CompleteHit
3435,Q#1390 - >seq1389,superfamily,340205,161,225,7.8493e-22,85.4656,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs5_gmonkey,marg,CompleteHit
3436,Q#1390 - >seq1389,non-specific,335182,87,158,2.14742e-11,58.4683,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
3437,Q#1390 - >seq1389,superfamily,335182,87,158,2.14742e-11,58.4683,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs5_gmonkey.marg.frame3,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
3438,Q#1394 - >seq1393,non-specific,340205,152,195,6.642739999999999e-13,60.8128,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs5_gmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
3439,Q#1394 - >seq1393,superfamily,340205,152,195,6.642739999999999e-13,60.8128,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs5_gmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
3440,Q#1394 - >seq1393,non-specific,335182,78,149,6.5329900000000004e-12,59.2387,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs5_gmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
3441,Q#1394 - >seq1393,superfamily,335182,78,149,6.5329900000000004e-12,59.2387,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs5_gmonkey.pars.frame2,1909122340_L1M4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
3442,Q#1395 - >seq1394,non-specific,197310,5,55,1.52974e-05,46.5757,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
3443,Q#1395 - >seq1394,superfamily,351117,5,55,1.52974e-05,46.5757,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
3444,Q#1396 - >seq1395,non-specific,197310,51,229,7.3275e-25,103.585,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3445,Q#1396 - >seq1395,superfamily,351117,51,229,7.3275e-25,103.585,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3446,Q#1396 - >seq1395,non-specific,197320,99,222,2.73393e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3447,Q#1396 - >seq1395,non-specific,223780,54,222,1.8366700000000003e-07,52.6007,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,marg,CompleteHit
3448,Q#1396 - >seq1395,non-specific,197306,55,229,2.96224e-07,51.7133,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3449,Q#1396 - >seq1395,specific,335306,54,222,2.19856e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3450,Q#1396 - >seq1395,non-specific,197307,99,222,0.00219877,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3451,Q#1396 - >seq1395,non-specific,273186,100,230,0.00220697,39.9548,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3452,Q#1396 - >seq1395,non-specific,339261,101,224,0.00496028,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs4_gibbon.marg.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1M4,ORF2,hs4_gibbon,marg,CompleteHit
3453,Q#1399 - >seq1398,non-specific,197310,5,55,1.53284e-05,46.5757,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs4_gibbon.pars.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3454,Q#1399 - >seq1398,superfamily,351117,5,55,1.53284e-05,46.5757,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.pars.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3455,Q#1400 - >seq1399,non-specific,197310,51,228,4.7719999999999995e-26,107.052,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3456,Q#1400 - >seq1399,superfamily,351117,51,228,4.7719999999999995e-26,107.052,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3457,Q#1400 - >seq1399,non-specific,197320,98,221,2.64033e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3458,Q#1400 - >seq1399,non-specific,223780,54,221,1.42509e-07,52.9859,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,pars,CompleteHit
3459,Q#1400 - >seq1399,non-specific,197306,92,228,4.65634e-07,51.3281,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3460,Q#1400 - >seq1399,specific,335306,54,221,8.00597e-06,47.2398,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3461,Q#1400 - >seq1399,non-specific,273186,99,229,0.00207661,40.34,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3462,Q#1400 - >seq1399,non-specific,197307,98,221,0.00218312,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3463,Q#1400 - >seq1399,non-specific,339261,100,223,0.00421734,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs4_gibbon.pars.frame2,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M4,ORF2,hs4_gibbon,pars,CompleteHit
3464,Q#1402 - >seq1401,non-specific,340205,179,240,6.76148e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs4_gibbon,marg,CompleteHit
3465,Q#1402 - >seq1401,superfamily,340205,179,240,6.76148e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs4_gibbon,marg,CompleteHit
3466,Q#1402 - >seq1401,non-specific,335182,99,176,3.09733e-17,74.2615,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs4_gibbon,marg,N-TerminusTruncated
3467,Q#1402 - >seq1401,superfamily,335182,99,176,3.09733e-17,74.2615,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs4_gibbon.marg.frame3,1909122340_L1M4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs4_gibbon,marg,N-TerminusTruncated
3468,Q#1440 - >seq1439,non-specific,238827,36,69,0.000939817,41.1226,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M6.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M6.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M6,ORF2,hs11_armadillo,marg,C-TerminusTruncated
3469,Q#1440 - >seq1439,superfamily,295487,36,69,0.000939817,41.1226,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M6.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M6.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M6,ORF2,hs11_armadillo,marg,C-TerminusTruncated
3470,Q#1448 - >seq1447,non-specific,197310,3,235,1.5068900000000002e-13,70.8433,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,CompleteHit
3471,Q#1448 - >seq1447,superfamily,351117,3,235,1.5068900000000002e-13,70.8433,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs9_pika,marg,CompleteHit
3472,Q#1448 - >seq1447,non-specific,197306,3,149,4.0231199999999996e-08,54.7949,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3473,Q#1448 - >seq1447,non-specific,197307,3,147,3.85749e-07,51.9049,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3474,Q#1448 - >seq1447,non-specific,197336,3,36,5.4561e-06,48.3775,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3475,Q#1448 - >seq1447,non-specific,197319,3,141,6.10316e-06,48.4269,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3476,Q#1448 - >seq1447,non-specific,273186,3,147,0.000145486,44.192,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3477,Q#1448 - >seq1447,non-specific,197321,3,128,0.00028052299999999997,43.3096,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3478,Q#1448 - >seq1447,non-specific,272954,3,147,0.000901963,41.5997,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M8.ORF2.hs9_pika.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,marg,C-TerminusTruncated
3479,Q#1451 - >seq1450,non-specific,197310,54,199,2.1647199999999998e-13,66.6061,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs10_snmole.pars.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M8,ORF2,hs10_snmole,pars,N-TerminusTruncated
3480,Q#1451 - >seq1450,superfamily,351117,54,199,2.1647199999999998e-13,66.6061,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs10_snmole.pars.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M8,ORF2,hs10_snmole,pars,N-TerminusTruncated
3481,Q#1451 - >seq1450,non-specific,225036,48,102,0.00659495,34.991,COG2125,RPS6A,N,cl00931,"Ribosomal protein S6E (S10)  [Translation, ribosomal structure and biogenesis]; Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis].",L1M8.ORF2.hs10_snmole.pars.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,pars,N-TerminusTruncated
3482,Q#1451 - >seq1450,superfamily,351315,48,102,0.00659495,34.991,cl00931,Ribosomal_S6e superfamily,N, - ,Ribosomal protein S6e; Ribosomal protein S6e.  ,L1M8.ORF2.hs10_snmole.pars.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,pars,N-TerminusTruncated
3483,Q#1451 - >seq1450,non-specific,235271,48,101,0.00715251,34.8232,PRK04290,PRK04290,N,cl00931,30S ribosomal protein S6e; Validated,L1M8.ORF2.hs10_snmole.pars.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,pars,N-TerminusTruncated
3484,Q#1452 - >seq1451,non-specific,197310,2,64,2.39642e-07,49.2721,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3485,Q#1452 - >seq1451,superfamily,351117,2,64,2.39642e-07,49.2721,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3486,Q#1452 - >seq1451,non-specific,197336,2,36,1.96945e-06,46.4515,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3487,Q#1452 - >seq1451,non-specific,197319,2,36,7.837310000000001e-06,44.9601,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3488,Q#1452 - >seq1451,non-specific,197307,2,36,2.66192e-05,43.4305,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3489,Q#1452 - >seq1451,non-specific,273186,2,36,0.000123636,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3490,Q#1452 - >seq1451,non-specific,197321,2,42,0.000131941,41.3836,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3491,Q#1452 - >seq1451,non-specific,223780,2,36,0.00147271,38.3483,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3492,Q#1452 - >seq1451,non-specific,197306,2,120,0.00263961,37.4609,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs10_snmole.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs10_snmole,pars,C-TerminusTruncated
3493,Q#1454 - >seq1453,non-specific,197310,54,203,3.1611100000000002e-15,75.4657,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs10_snmole.marg.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M8,ORF2,hs10_snmole,marg,N-TerminusTruncated
3494,Q#1454 - >seq1453,superfamily,351117,54,203,3.1611100000000002e-15,75.4657,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs10_snmole.marg.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M8,ORF2,hs10_snmole,marg,N-TerminusTruncated
3495,Q#1454 - >seq1453,non-specific,235271,48,101,0.00702761,36.7492,PRK04290,PRK04290,N,cl00931,30S ribosomal protein S6e; Validated,L1M8.ORF2.hs10_snmole.marg.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,marg,N-TerminusTruncated
3496,Q#1454 - >seq1453,superfamily,351315,48,101,0.00702761,36.7492,cl00931,Ribosomal_S6e superfamily,N, - ,Ribosomal protein S6e; Ribosomal protein S6e.  ,L1M8.ORF2.hs10_snmole.marg.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,marg,N-TerminusTruncated
3497,Q#1454 - >seq1453,non-specific,225036,48,102,0.00763276,36.917,COG2125,RPS6A,N,cl00931,"Ribosomal protein S6E (S10)  [Translation, ribosomal structure and biogenesis]; Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis].",L1M8.ORF2.hs10_snmole.marg.frame2,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M8,ORF2,hs10_snmole,marg,N-TerminusTruncated
3498,Q#1455 - >seq1454,non-specific,197310,2,64,2.0101400000000003e-06,49.2721,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3499,Q#1455 - >seq1454,superfamily,351117,2,64,2.0101400000000003e-06,49.2721,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3500,Q#1455 - >seq1454,non-specific,197336,2,36,1.8330999999999998e-05,46.4515,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3501,Q#1455 - >seq1454,non-specific,197319,2,36,0.000144677,43.8045,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3502,Q#1455 - >seq1454,non-specific,197307,2,36,0.000444067,42.2749,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3503,Q#1455 - >seq1454,non-specific,273186,2,36,0.000967097,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3504,Q#1455 - >seq1454,non-specific,197321,2,42,0.0017024000000000002,40.6132,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs10_snmole.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs10_snmole,marg,C-TerminusTruncated
3505,Q#1456 - >seq1455,non-specific,340205,217,245,0.000167293,38.8564,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,pars,N-TerminusTruncated
3506,Q#1456 - >seq1455,superfamily,340205,217,245,0.000167293,38.8564,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,pars,N-TerminusTruncated
3507,Q#1457 - >seq1456,non-specific,335182,119,194,7.81349e-08,48.8383,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs1_chimp,pars,N-TerminusTruncated
3508,Q#1457 - >seq1456,superfamily,335182,119,194,7.81349e-08,48.8383,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs1_chimp,pars,N-TerminusTruncated
3509,Q#1457 - >seq1456,non-specific,340205,197,227,9.696950000000001e-05,39.2416,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs1_chimp,pars,C-TerminusTruncated
3510,Q#1457 - >seq1456,superfamily,340205,197,227,9.696950000000001e-05,39.2416,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs1_chimp,pars,C-TerminusTruncated
3511,Q#1458 - >seq1457,non-specific,340205,195,237,0.000752736,36.9304,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs1_chimp,pars,C-TerminusTruncated
3512,Q#1458 - >seq1457,superfamily,340205,195,237,0.000752736,36.9304,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs1_chimp,pars,C-TerminusTruncated
3513,Q#1459 - >seq1458,non-specific,340205,258,321,1.36689e-15,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,marg,CompleteHit
3514,Q#1459 - >seq1458,superfamily,340205,258,321,1.36689e-15,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,marg,CompleteHit
3515,Q#1459 - >seq1458,non-specific,335182,171,255,4.82516e-12,61.1647,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,marg,CompleteHit
3516,Q#1459 - >seq1458,superfamily,335182,171,255,4.82516e-12,61.1647,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs1_chimp,marg,CompleteHit
3517,Q#1462 - >seq1461,specific,238827,483,717,3.15588e-33,127.79299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3518,Q#1462 - >seq1461,superfamily,295487,483,717,3.15588e-33,127.79299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3519,Q#1462 - >seq1461,non-specific,333820,483,717,1.0056e-16,79.2586,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3520,Q#1462 - >seq1461,superfamily,333820,483,717,1.0056e-16,79.2586,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs1_chimp.pars.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3521,Q#1463 - >seq1462,non-specific,197310,141,228,2.0746599999999997e-14,73.9249,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3522,Q#1463 - >seq1462,superfamily,351117,141,228,2.0746599999999997e-14,73.9249,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3523,Q#1463 - >seq1462,non-specific,197320,165,221,5.383399999999999e-05,45.968999999999994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3524,Q#1463 - >seq1462,non-specific,223780,168,221,0.00062439,42.5855,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3525,Q#1463 - >seq1462,non-specific,273186,168,229,0.00219368,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3526,Q#1463 - >seq1462,non-specific,197307,168,221,0.00251832,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3527,Q#1463 - >seq1462,non-specific,197306,126,228,0.00841303,39.0017,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.pars.frame2,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
3528,Q#1464 - >seq1463,non-specific,197310,9,154,6.288009999999999e-23,98.5776,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
3529,Q#1464 - >seq1463,superfamily,351117,9,154,6.288009999999999e-23,98.5776,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
3530,Q#1464 - >seq1463,non-specific,197306,9,169,9.536130000000001e-10,60.1877,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
3531,Q#1464 - >seq1463,non-specific,223780,7,143,0.000141037,44.8967,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
3532,Q#1464 - >seq1463,specific,311990,1119,1137,0.000479926,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3533,Q#1464 - >seq1463,superfamily,311990,1119,1137,0.000479926,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs1_chimp.pars.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA10,ORF2,hs1_chimp,pars,CompleteHit
3534,Q#1465 - >seq1464,specific,197310,25,228,6.272219999999999e-42,153.661,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3535,Q#1465 - >seq1464,superfamily,351117,25,228,6.272219999999999e-42,153.661,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3536,Q#1465 - >seq1464,non-specific,197306,3,228,9.06406e-21,92.5444,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3537,Q#1465 - >seq1464,non-specific,197320,55,221,4.33303e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3538,Q#1465 - >seq1464,non-specific,223780,54,221,2.2201300000000003e-09,59.5343,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3539,Q#1465 - >seq1464,non-specific,197307,52,221,1.24579e-07,53.8309,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3540,Q#1465 - >seq1464,specific,335306,25,221,3.3147899999999997e-07,52.2474,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3541,Q#1465 - >seq1464,non-specific,197319,98,228,3.76157e-05,46.5009,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3542,Q#1465 - >seq1464,non-specific,273186,14,229,5.18369e-05,46.118,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3543,Q#1465 - >seq1464,non-specific,272954,15,199,8.8281e-05,45.4517,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3544,Q#1465 - >seq1464,non-specific,339261,100,223,0.00277663,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3545,Q#1465 - >seq1464,non-specific,238827,620,723,0.00301567,40.3522,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3546,Q#1465 - >seq1464,superfamily,295487,620,723,0.00301567,40.3522,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs1_chimp.marg.frame1,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
3547,Q#1467 - >seq1466,specific,238827,503,713,1.66078e-31,123.17,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3548,Q#1467 - >seq1466,superfamily,295487,503,713,1.66078e-31,123.17,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3549,Q#1467 - >seq1466,non-specific,333820,503,712,1.96495e-16,78.4882,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3550,Q#1467 - >seq1466,superfamily,333820,503,712,1.96495e-16,78.4882,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3551,Q#1467 - >seq1466,specific,311990,1172,1190,0.000904431,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3552,Q#1467 - >seq1466,superfamily,311990,1172,1190,0.000904431,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs1_chimp.marg.frame3,1909122341_L1MA10.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA10,ORF2,hs1_chimp,marg,CompleteHit
3553,Q#1476 - >seq1475,non-specific,197310,3,111,1.5654300000000002e-09,56.9761,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs8_ctshrew.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3554,Q#1476 - >seq1475,superfamily,351117,3,111,1.5654300000000002e-09,56.9761,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs8_ctshrew.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3555,Q#1476 - >seq1475,non-specific,197336,3,45,0.00136675,39.5179,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs8_ctshrew.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3556,Q#1476 - >seq1475,non-specific,197306,3,114,0.00363775,37.8461,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs8_ctshrew.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3557,Q#1476 - >seq1475,non-specific,197319,3,110,0.00818113,36.871,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs8_ctshrew.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
3558,Q#1477 - >seq1476,non-specific,188708,396,546,0.00132482,40.7495,cd08754,RGS_LARG,N,cl02565,"Regulator of G protein signaling (RGS) domain found in the leukemia-associated Rho guanine nucleotide exchange factor (RhoGEF) protein (LARG); The RGS domain is an essential part of the leukemia-associated RhoGEF protein (LARG), a member of the RhoGEF (Rho guanine nucleotide exchange factor) subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, cell cycle progression of cells, and gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. The RhoGEF subfamily includes p115RhoGEF, LARG, PDZ-RhoGEF, and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. In addition to being a G-alpha13 effector, the LARG protein also functions as a GTPase-activating protein (GAP) for G-alpha13. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development.",L1M8.ORF2.hs8_ctshrew.marg.frame1,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3559,Q#1477 - >seq1476,superfamily,321993,396,546,0.00132482,40.7495,cl02565,RGS superfamily,N, - ,"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision.",L1M8.ORF2.hs8_ctshrew.marg.frame1,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1M8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
3560,Q#1479 - >seq1478,non-specific,197310,12,212,3.1507e-14,72.7693,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,marg,CompleteHit
3561,Q#1479 - >seq1478,superfamily,351117,12,212,3.1507e-14,72.7693,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs8_ctshrew,marg,CompleteHit
3562,Q#1479 - >seq1478,non-specific,197306,12,207,1.2769e-06,50.1725,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs8_ctshrew,marg,CompleteHit
3563,Q#1479 - >seq1478,non-specific,197307,12,155,7.18812e-05,44.9713,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M8,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3564,Q#1479 - >seq1478,non-specific,197336,12,155,0.00117287,41.0587,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3565,Q#1479 - >seq1478,non-specific,197319,12,149,0.00131282,41.1081,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs8_ctshrew.marg.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M8,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3566,Q#1483 - >seq1482,non-specific,335182,25,110,0.00063193,36.8971,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M8.ORF1.hs9_pika.marg.frame1,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M8,ORF1,hs9_pika,marg,CompleteHit
3567,Q#1483 - >seq1482,superfamily,335182,25,110,0.00063193,36.8971,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M8.ORF1.hs9_pika.marg.frame1,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M8,ORF1,hs9_pika,marg,CompleteHit
3568,Q#1488 - >seq1487,non-specific,197310,2,200,3.4848499999999996e-08,54.2797,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,pars,CompleteHit
3569,Q#1488 - >seq1487,superfamily,351117,2,200,3.4848499999999996e-08,54.2797,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M8,ORF2,hs9_pika,pars,CompleteHit
3570,Q#1488 - >seq1487,non-specific,197336,2,35,2.9922900000000003e-06,48.3775,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,pars,C-TerminusTruncated
3571,Q#1488 - >seq1487,non-specific,197319,2,35,0.000140966,43.4193,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,pars,C-TerminusTruncated
3572,Q#1488 - >seq1487,non-specific,273186,2,43,0.000591857,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,pars,C-TerminusTruncated
3573,Q#1488 - >seq1487,non-specific,197321,2,44,0.00172638,40.228,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M8,ORF2,hs9_pika,pars,C-TerminusTruncated
3574,Q#1488 - >seq1487,non-specific,197307,2,35,0.00311064,39.1933,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M8.ORF2.hs9_pika.pars.frame3,1909122341_L1M8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M8,ORF2,hs9_pika,pars,C-TerminusTruncated
3575,Q#1496 - >seq1495,non-specific,238827,536,618,9.27915e-18,82.7242,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs10_snmole,marg,C-TerminusTruncated
3576,Q#1496 - >seq1495,superfamily,295487,536,618,9.27915e-18,82.7242,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs10_snmole,marg,C-TerminusTruncated
3577,Q#1496 - >seq1495,non-specific,333820,546,593,1.83859e-05,46.1314,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs10_snmole,marg,C-TerminusTruncated
3578,Q#1496 - >seq1495,superfamily,333820,546,593,1.83859e-05,46.1314,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs10_snmole,marg,C-TerminusTruncated
3579,Q#1497 - >seq1496,non-specific,340205,114,162,4.45879e-10,52.7236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs11_armadillo,pars,CompleteHit
3580,Q#1497 - >seq1496,superfamily,340205,114,162,4.45879e-10,52.7236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs11_armadillo,pars,CompleteHit
3581,Q#1498 - >seq1497,non-specific,335182,16,95,1.64222e-16,70.7947,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs11_armadillo,pars,CompleteHit
3582,Q#1498 - >seq1497,superfamily,335182,16,95,1.64222e-16,70.7947,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs11_armadillo,pars,CompleteHit
3583,Q#1498 - >seq1497,non-specific,340205,113,147,0.00679843,33.4636,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs11_armadillo,pars,C-TerminusTruncated
3584,Q#1498 - >seq1497,superfamily,340205,113,147,0.00679843,33.4636,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs11_armadillo,pars,C-TerminusTruncated
3585,Q#1498 - >seq1497,non-specific,235878,77,153,0.00981742,35.3242,PRK06851,PRK06851,NC,cl20200,hypothetical protein; Provisional,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF1,hs11_armadillo,pars,BothTerminiTruncated
3586,Q#1498 - >seq1497,superfamily,235878,77,153,0.00981742,35.3242,cl20200,PRK06851 superfamily,NC, - ,hypothetical protein; Provisional,L1M4.ORF1.hs11_armadillo.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF1,hs11_armadillo,pars,BothTerminiTruncated
3587,Q#1500 - >seq1499,non-specific,340205,105,140,0.00504973,33.8488,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs11_armadillo,marg,C-TerminusTruncated
3588,Q#1500 - >seq1499,superfamily,340205,105,140,0.00504973,33.8488,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs11_armadillo,marg,C-TerminusTruncated
3589,Q#1502 - >seq1501,non-specific,335182,17,95,1.0836700000000001e-16,71.1799,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs11_armadillo,marg,CompleteHit
3590,Q#1502 - >seq1501,superfamily,335182,17,95,1.0836700000000001e-16,71.1799,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs11_armadillo,marg,CompleteHit
3591,Q#1502 - >seq1501,non-specific,340205,125,162,6.640310000000001e-08,47.3308,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs11_armadillo,marg,C-TerminusTruncated
3592,Q#1502 - >seq1501,superfamily,340205,125,162,6.640310000000001e-08,47.3308,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs11_armadillo.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs11_armadillo,marg,C-TerminusTruncated
3593,Q#1505 - >seq1504,non-specific,197310,9,104,9.0028e-08,51.1981,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs11_armadillo.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs11_armadillo,pars,C-TerminusTruncated
3594,Q#1505 - >seq1504,superfamily,351117,9,104,9.0028e-08,51.1981,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs11_armadillo.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs11_armadillo,pars,C-TerminusTruncated
3595,Q#1505 - >seq1504,non-specific,197320,7,107,4.87388e-05,43.2726,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs11_armadillo.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs11_armadillo,pars,C-TerminusTruncated
3596,Q#1506 - >seq1505,specific,197310,10,246,3.5704e-29,115.141,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3597,Q#1506 - >seq1505,superfamily,351117,10,246,3.5704e-29,115.141,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3598,Q#1506 - >seq1505,non-specific,197306,10,246,7.0203e-08,53.2541,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3599,Q#1506 - >seq1505,non-specific,223780,8,239,2.07032e-06,49.1339,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3600,Q#1506 - >seq1505,non-specific,197307,14,239,1.57528e-05,46.5121,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3601,Q#1506 - >seq1505,specific,335306,12,239,0.00139702,40.3062,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs11_armadillo.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs11_armadillo,marg,CompleteHit
3602,Q#1510 - >seq1509,non-specific,340205,108,154,3.57502e-07,45.0196,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs0_human.pars.frame2,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs0_human,pars,C-TerminusTruncated
3603,Q#1510 - >seq1509,superfamily,340205,108,154,3.57502e-07,45.0196,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs0_human.pars.frame2,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs0_human,pars,C-TerminusTruncated
3604,Q#1514 - >seq1513,non-specific,340205,159,222,1.24981e-07,47.3308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs0_human,marg,CompleteHit
3605,Q#1514 - >seq1513,superfamily,340205,159,222,1.24981e-07,47.3308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs0_human,marg,CompleteHit
3606,Q#1515 - >seq1514,non-specific,238827,648,716,1.99773e-08,55.375,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs10_snmole.marg.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3607,Q#1515 - >seq1514,superfamily,295487,648,716,1.99773e-08,55.375,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs10_snmole.marg.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3608,Q#1517 - >seq1516,specific,197310,8,248,2.62434e-40,148.268,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3609,Q#1517 - >seq1516,superfamily,351117,8,248,2.62434e-40,148.268,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3610,Q#1517 - >seq1516,non-specific,197306,8,248,7.30152e-20,89.4628,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3611,Q#1517 - >seq1516,non-specific,197320,80,241,8.720120000000001e-13,69.081,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3612,Q#1517 - >seq1516,non-specific,223780,6,241,5.7519300000000005e-12,66.4679,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3613,Q#1517 - >seq1516,specific,335306,9,241,1.7647599999999999e-10,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3614,Q#1517 - >seq1516,non-specific,197307,8,241,5.2471e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3615,Q#1517 - >seq1516,non-specific,339261,120,243,3.2334500000000004e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M4,ORF2,hs10_snmole,marg,CompleteHit
3616,Q#1517 - >seq1516,non-specific,197311,84,248,7.466119999999999e-06,47.2865,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3617,Q#1517 - >seq1516,non-specific,273186,118,249,7.72173e-06,48.044,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3618,Q#1517 - >seq1516,non-specific,197319,118,248,9.04562e-06,47.6565,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3619,Q#1517 - >seq1516,non-specific,197321,80,241,2.69079e-05,46.3912,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3620,Q#1517 - >seq1516,non-specific,272954,80,219,4.51548e-05,45.8369,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3621,Q#1517 - >seq1516,non-specific,197322,119,241,0.00033438300000000005,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs10_snmole,marg,N-TerminusTruncated
3622,Q#1520 - >seq1519,non-specific,340205,75,138,9.92107e-27,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs9_pika.pars.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs9_pika,pars,CompleteHit
3623,Q#1520 - >seq1519,superfamily,340205,75,138,9.92107e-27,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs9_pika.pars.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1M4,ORF1,hs9_pika,pars,CompleteHit
3624,Q#1522 - >seq1521,non-specific,335182,2,62,3.86461e-16,68.8687,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs9_pika,pars,N-TerminusTruncated
3625,Q#1522 - >seq1521,superfamily,335182,2,62,3.86461e-16,68.8687,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs9_pika,pars,N-TerminusTruncated
3626,Q#1523 - >seq1522,non-specific,335182,92,148,6.8052e-14,65.0167,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs9_pika,marg,N-TerminusTruncated
3627,Q#1523 - >seq1522,superfamily,335182,92,148,6.8052e-14,65.0167,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1M4,ORF1,hs9_pika,marg,N-TerminusTruncated
3628,Q#1524 - >seq1523,non-specific,340205,156,219,1.2710799999999998e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs9_pika.marg.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs9_pika,marg,CompleteHit
3629,Q#1524 - >seq1523,superfamily,340205,156,219,1.2710799999999998e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs9_pika.marg.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1M4,ORF1,hs9_pika,marg,CompleteHit
3630,Q#1528 - >seq1527,specific,197310,9,227,4.4813800000000004e-48,165.217,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3631,Q#1528 - >seq1527,superfamily,351117,9,227,4.4813800000000004e-48,165.217,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3632,Q#1528 - >seq1527,non-specific,197306,9,227,1.6559e-18,84.4552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3633,Q#1528 - >seq1527,non-specific,223780,7,220,6.99594e-15,74.1719,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3634,Q#1528 - >seq1527,non-specific,197320,97,220,7.42071e-12,65.229,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs9_pika,pars,N-TerminusTruncated
3635,Q#1528 - >seq1527,specific,335306,10,220,4.05663e-11,62.6478,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3636,Q#1528 - >seq1527,non-specific,197307,9,220,6.22329e-11,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3637,Q#1528 - >seq1527,non-specific,197321,7,220,9.568270000000002e-09,56.0212,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3638,Q#1528 - >seq1527,non-specific,273186,7,228,1.008e-08,55.748000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3639,Q#1528 - >seq1527,non-specific,272954,7,198,8.07371e-08,53.1557,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3640,Q#1528 - >seq1527,non-specific,339261,99,222,1.05305e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4,ORF2,hs9_pika,pars,CompleteHit
3641,Q#1528 - >seq1527,non-specific,197319,7,227,4.3706300000000005e-06,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3642,Q#1528 - >seq1527,non-specific,197311,63,227,1.68023e-05,45.3605,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,N-TerminusTruncated
3643,Q#1528 - >seq1527,non-specific,197322,98,220,0.000163654,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,N-TerminusTruncated
3644,Q#1528 - >seq1527,non-specific,197336,7,220,0.00405351,38.7475,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4.ORF2.hs9_pika.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs9_pika,pars,CompleteHit
3645,Q#1529 - >seq1528,specific,197310,13,233,5.2740699999999996e-49,169.84,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3646,Q#1529 - >seq1528,superfamily,351117,13,233,5.2740699999999996e-49,169.84,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3647,Q#1529 - >seq1528,non-specific,197306,13,233,8.865510000000001e-20,88.6924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3648,Q#1529 - >seq1528,non-specific,223780,11,226,2.83825e-15,75.7127,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3649,Q#1529 - >seq1528,non-specific,197320,11,226,4.44468e-12,65.9994,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3650,Q#1529 - >seq1528,non-specific,197307,13,226,4.74038e-12,66.1573,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3651,Q#1529 - >seq1528,specific,335306,14,226,8.48709e-12,64.959,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3652,Q#1529 - >seq1528,non-specific,273186,11,234,1.88756e-09,58.4444,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3653,Q#1529 - >seq1528,non-specific,272954,11,204,4.54439e-09,57.3929,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3654,Q#1529 - >seq1528,non-specific,197321,11,226,7.62297e-09,56.4064,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3655,Q#1529 - >seq1528,non-specific,339261,105,228,8.87655e-07,47.7171,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M4,ORF2,hs9_pika,marg,CompleteHit
3656,Q#1529 - >seq1528,non-specific,197319,11,233,5.51995e-06,48.0417,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3657,Q#1529 - >seq1528,non-specific,197311,13,233,8.55946e-06,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3658,Q#1529 - >seq1528,non-specific,197322,104,226,0.00021292099999999998,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,N-TerminusTruncated
3659,Q#1529 - >seq1528,non-specific,197336,11,226,0.00572631,38.7475,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4.ORF2.hs9_pika.marg.frame1,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M4,ORF2,hs9_pika,marg,CompleteHit
3660,Q#1531 - >seq1530,non-specific,238827,474,560,1.72123e-13,69.6274,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs9_pika,marg,C-TerminusTruncated
3661,Q#1531 - >seq1530,superfamily,295487,474,560,1.72123e-13,69.6274,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs9_pika,marg,C-TerminusTruncated
3662,Q#1531 - >seq1530,non-specific,333820,486,529,5.3504899999999997e-05,43.8202,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs9_pika,marg,C-TerminusTruncated
3663,Q#1531 - >seq1530,superfamily,333820,486,529,5.3504899999999997e-05,43.8202,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1M4,ORF2,hs9_pika,marg,C-TerminusTruncated
3664,Q#1531 - >seq1530,non-specific,311769,283,529,0.00099112,41.6947,pfam07964,Red1,N,cl25852,Rec10 / Red1; Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localizes to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe. This family is currently only found in fungi.,L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M4,ORF2,hs9_pika,marg,N-TerminusTruncated
3665,Q#1531 - >seq1530,superfamily,311769,283,529,0.00099112,41.6947,cl25852,Red1 superfamily,N, - ,Rec10 / Red1; Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localizes to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe. This family is currently only found in fungi.,L1M4.ORF2.hs9_pika.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1M4,ORF2,hs9_pika,marg,N-TerminusTruncated
3666,Q#1533 - >seq1532,non-specific,340205,151,214,7.1641999999999995e-28,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs10_snmole,pars,CompleteHit
3667,Q#1533 - >seq1532,superfamily,340205,151,214,7.1641999999999995e-28,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs10_snmole,pars,CompleteHit
3668,Q#1533 - >seq1532,non-specific,335182,96,148,4.71519e-11,57.3127,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs10_snmole,pars,N-TerminusTruncated
3669,Q#1533 - >seq1532,superfamily,335182,96,148,4.71519e-11,57.3127,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1M4,ORF1,hs10_snmole,pars,N-TerminusTruncated
3670,Q#1534 - >seq1533,non-specific,335182,65,107,0.00624923,34.9711,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,pars,C-TerminusTruncated
3671,Q#1534 - >seq1533,superfamily,335182,65,107,0.00624923,34.9711,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,pars,C-TerminusTruncated
3672,Q#1537 - >seq1536,non-specific,340205,160,223,1.2042699999999999e-26,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,marg,CompleteHit
3673,Q#1537 - >seq1536,superfamily,340205,160,223,1.2042699999999999e-26,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1M4.ORF1.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,marg,CompleteHit
3674,Q#1537 - >seq1536,non-specific,335182,65,157,1.18062e-20,83.1211,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,marg,CompleteHit
3675,Q#1537 - >seq1536,superfamily,335182,65,157,1.18062e-20,83.1211,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1M4.ORF1.hs10_snmole.marg.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1M4,ORF1,hs10_snmole,marg,CompleteHit
3676,Q#1538 - >seq1537,specific,197310,21,227,7.275660000000001e-39,141.72,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3677,Q#1538 - >seq1537,superfamily,351117,21,227,7.275660000000001e-39,141.72,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3678,Q#1538 - >seq1537,non-specific,197306,20,227,1.82357e-20,90.6184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3679,Q#1538 - >seq1537,non-specific,197320,59,220,5.69477e-13,68.6958,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3680,Q#1538 - >seq1537,specific,335306,21,220,4.67122e-12,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3681,Q#1538 - >seq1537,non-specific,223780,17,220,2.05025e-11,64.1567,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3682,Q#1538 - >seq1537,non-specific,197307,16,220,2.82134e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3683,Q#1538 - >seq1537,non-specific,197321,20,220,2.51004e-07,51.784,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3684,Q#1538 - >seq1537,non-specific,339261,99,222,2.84757e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3685,Q#1538 - >seq1537,non-specific,197311,63,227,6.12689e-06,46.9013,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3686,Q#1538 - >seq1537,non-specific,273186,97,228,1.0994500000000001e-05,46.8884,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3687,Q#1538 - >seq1537,non-specific,197319,97,227,2.2045e-05,45.7305,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3688,Q#1538 - >seq1537,non-specific,272954,14,198,3.06534e-05,45.4517,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,CompleteHit
3689,Q#1538 - >seq1537,non-specific,197322,98,220,0.000194873,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3690,Q#1538 - >seq1537,non-specific,335313,77,142,0.00530652,38.961999999999996,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3691,Q#1538 - >seq1537,superfamily,354836,77,142,0.00530652,38.961999999999996,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1M4.ORF2.hs10_snmole.pars.frame2,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M4,ORF2,hs10_snmole,pars,N-TerminusTruncated
3692,Q#1540 - >seq1539,non-specific,238827,430,494,6.68729e-15,73.4794,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4.ORF2.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs10_snmole,pars,C-TerminusTruncated
3693,Q#1540 - >seq1539,superfamily,295487,430,494,6.68729e-15,73.4794,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4.ORF2.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs10_snmole,pars,C-TerminusTruncated
3694,Q#1540 - >seq1539,non-specific,333820,440,487,1.0721700000000001e-05,45.7462,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs10_snmole,pars,C-TerminusTruncated
3695,Q#1540 - >seq1539,superfamily,333820,440,487,1.0721700000000001e-05,45.7462,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4.ORF2.hs10_snmole.pars.frame3,1909122341_L1M4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4,ORF2,hs10_snmole,pars,C-TerminusTruncated
3696,Q#1543 - >seq1542,non-specific,183703,80,215,0.00739532,39.5621,PRK12724,PRK12724,C,cl32815,flagellar biosynthesis regulator FlhF; Provisional,L1M6.ORF2.hs8_ctshrew.marg.frame2,1909122341_L1M6.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M6,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3697,Q#1543 - >seq1542,superfamily,183703,80,215,0.00739532,39.5621,cl32815,PRK12724 superfamily,C, - ,flagellar biosynthesis regulator FlhF; Provisional,L1M6.ORF2.hs8_ctshrew.marg.frame2,1909122341_L1M6.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1M6,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
3698,Q#1559 - >seq1558,specific,197310,3,227,6.67942e-49,171.38,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3699,Q#1559 - >seq1558,superfamily,351117,3,227,6.67942e-49,171.38,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3700,Q#1559 - >seq1558,non-specific,197306,3,227,1.6238600000000002e-24,102.56,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3701,Q#1559 - >seq1558,specific,335306,3,220,3.55394e-13,69.1962,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3702,Q#1559 - >seq1558,non-specific,223780,4,220,4.07017e-13,69.5495,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3703,Q#1559 - >seq1558,non-specific,197320,4,220,2.8479099999999997e-12,67.155,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3704,Q#1559 - >seq1558,non-specific,197307,4,220,7.61173e-11,62.6905,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3705,Q#1559 - >seq1558,non-specific,197321,4,220,5.41782e-09,57.1768,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3706,Q#1559 - >seq1558,non-specific,273186,4,228,5.36394e-07,51.1256,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3707,Q#1559 - >seq1558,non-specific,272954,1,198,9.71635e-07,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3708,Q#1559 - >seq1558,non-specific,339261,99,222,1.30123e-06,47.7171,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4,ORF2,hs0_human,pars,CompleteHit
3709,Q#1559 - >seq1558,non-specific,197319,4,227,7.90657e-06,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3710,Q#1559 - >seq1558,non-specific,197311,28,195,1.93409e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs0_human.pars.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,pars,CompleteHit
3711,Q#1569 - >seq1568,non-specific,238827,562,783,3.5148199999999998e-12,66.931,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M5.ORF2.hs10_snmole.marg.frame1,1909122341_L1M5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M5,ORF2,hs10_snmole,marg,CompleteHit
3712,Q#1569 - >seq1568,superfamily,295487,562,783,3.5148199999999998e-12,66.931,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M5.ORF2.hs10_snmole.marg.frame1,1909122341_L1M5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M5,ORF2,hs10_snmole,marg,CompleteHit
3713,Q#1569 - >seq1568,non-specific,333820,599,750,0.00965694,38.4274,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M5.ORF2.hs10_snmole.marg.frame1,1909122341_L1M5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M5,ORF2,hs10_snmole,marg,N-TerminusTruncated
3714,Q#1569 - >seq1568,superfamily,333820,599,750,0.00965694,38.4274,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M5.ORF2.hs10_snmole.marg.frame1,1909122341_L1M5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1M5,ORF2,hs10_snmole,marg,N-TerminusTruncated
3715,Q#1574 - >seq1573,specific,197310,3,228,4.81188e-48,169.454,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3716,Q#1574 - >seq1573,superfamily,351117,3,228,4.81188e-48,169.454,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3717,Q#1574 - >seq1573,non-specific,197306,3,228,7.631230000000001e-24,101.01899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3718,Q#1574 - >seq1573,non-specific,223780,4,221,7.797230000000001e-14,71.8607,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3719,Q#1574 - >seq1573,specific,335306,3,221,3.66744e-13,69.1962,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3720,Q#1574 - >seq1573,non-specific,197320,4,221,1.8008099999999999e-12,67.9254,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3721,Q#1574 - >seq1573,non-specific,197307,4,221,2.44278e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3722,Q#1574 - >seq1573,non-specific,197321,4,221,1.9412000000000003e-09,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3723,Q#1574 - >seq1573,non-specific,273186,4,229,7.76185e-08,53.821999999999996,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3724,Q#1574 - >seq1573,non-specific,272954,1,199,2.79995e-07,52.3853,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3725,Q#1574 - >seq1573,non-specific,339261,100,223,1.17913e-06,47.7171,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4,ORF2,hs0_human,marg,CompleteHit
3726,Q#1574 - >seq1573,non-specific,197319,4,228,1.01651e-05,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3727,Q#1574 - >seq1573,non-specific,197311,29,196,2.1227600000000003e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4.ORF2.hs0_human.marg.frame3,1909122341_L1M4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4,ORF2,hs0_human,marg,CompleteHit
3728,Q#1585 - >seq1584,non-specific,225177,22,159,0.00286368,39.0454,COG2268,YqiK,NC,cl34451,"Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].",L1MA10.ORF1.hs0_human.marg.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA10,ORF1,hs0_human,marg,BothTerminiTruncated
3729,Q#1585 - >seq1584,superfamily,225177,22,159,0.00286368,39.0454,cl34451,YqiK superfamily,NC, - ,"Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].",L1MA10.ORF1.hs0_human.marg.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA10,ORF1,hs0_human,marg,BothTerminiTruncated
3730,Q#1587 - >seq1586,non-specific,197310,3,210,1.2005899999999999e-26,109.363,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA10,ORF2,hs0_human,pars,CompleteHit
3731,Q#1587 - >seq1586,superfamily,351117,3,210,1.2005899999999999e-26,109.363,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,pars,CompleteHit
3732,Q#1587 - >seq1586,non-specific,197306,55,210,1.04024e-11,65.9657,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,pars,N-TerminusTruncated
3733,Q#1587 - >seq1586,non-specific,223780,33,203,6.600599999999999e-06,48.7487,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA10,ORF2,hs0_human,pars,N-TerminusTruncated
3734,Q#1587 - >seq1586,non-specific,197307,65,203,0.000173757,44.2009,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA10,ORF2,hs0_human,pars,N-TerminusTruncated
3735,Q#1587 - >seq1586,specific,335306,2,203,0.0008671989999999999,41.847,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA10.ORF2.hs0_human.pars.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,pars,CompleteHit
3736,Q#1590 - >seq1589,non-specific,197310,63,187,1.52356e-10,62.3689,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3737,Q#1590 - >seq1589,superfamily,351117,63,187,1.52356e-10,62.3689,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3738,Q#1590 - >seq1589,non-specific,197306,55,197,0.000541859,42.8537,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3739,Q#1591 - >seq1590,non-specific,340205,263,327,8.36807e-06,42.7084,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs0_human,marg,CompleteHit
3740,Q#1591 - >seq1590,superfamily,340205,263,327,8.36807e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs0_human,marg,CompleteHit
3741,Q#1591 - >seq1590,non-specific,223327,17,150,0.00104082,40.7307,COG0249,MutS,NC,cl33816,"DNA mismatch repair ATPase MutS [Replication, recombination and repair]; Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].",L1MA10.ORF1.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF1,hs0_human,marg,BothTerminiTruncated
3742,Q#1591 - >seq1590,superfamily,223327,17,150,0.00104082,40.7307,cl33816,MutS superfamily,NC, - ,"DNA mismatch repair ATPase MutS [Replication, recombination and repair]; Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].",L1MA10.ORF1.hs0_human.marg.frame1,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF1,hs0_human,marg,BothTerminiTruncated
3743,Q#1592 - >seq1591,specific,238827,459,697,1.7265099999999998e-35,134.341,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs0_human,marg,CompleteHit
3744,Q#1592 - >seq1591,superfamily,295487,459,697,1.7265099999999998e-35,134.341,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs0_human,marg,CompleteHit
3745,Q#1592 - >seq1591,non-specific,333820,459,672,6.11116e-17,80.029,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs0_human,marg,CompleteHit
3746,Q#1592 - >seq1591,superfamily,333820,459,672,6.11116e-17,80.029,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs0_human,marg,CompleteHit
3747,Q#1592 - >seq1591,non-specific,197310,127,190,6.74524e-08,54.6649,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3748,Q#1592 - >seq1591,superfamily,351117,127,190,6.74524e-08,54.6649,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3749,Q#1592 - >seq1591,non-specific,238828,506,648,0.00266647,40.6473,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs0_human.marg.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs0_human,marg,N-TerminusTruncated
3750,Q#1593 - >seq1592,non-specific,197310,1,65,0.00123577,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs0_human.marg.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA10,ORF2,hs0_human,marg,C-TerminusTruncated
3751,Q#1593 - >seq1592,superfamily,351117,1,65,0.00123577,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs0_human.marg.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs0_human,marg,C-TerminusTruncated
3752,Q#1594 - >seq1593,specific,238827,464,700,4.85837e-37,138.963,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs0_human.pars.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs0_human,pars,CompleteHit
3753,Q#1594 - >seq1593,superfamily,295487,464,700,4.85837e-37,138.963,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs0_human.pars.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs0_human,pars,CompleteHit
3754,Q#1594 - >seq1593,non-specific,333820,464,700,4.3826599999999995e-16,77.3326,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs0_human.pars.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs0_human,pars,CompleteHit
3755,Q#1594 - >seq1593,superfamily,333820,464,700,4.3826599999999995e-16,77.3326,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs0_human.pars.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs0_human,pars,CompleteHit
3756,Q#1594 - >seq1593,non-specific,238828,511,652,0.00703873,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs0_human.pars.frame3,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs0_human,pars,N-TerminusTruncated
3757,Q#1598 - >seq1597,non-specific,197310,1,239,2.62177e-20,91.2589,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs6_sqmonkey.marg.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA10,ORF2,hs6_sqmonkey,marg,CompleteHit
3758,Q#1598 - >seq1597,superfamily,351117,1,239,2.62177e-20,91.2589,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs6_sqmonkey.marg.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs6_sqmonkey,marg,CompleteHit
3759,Q#1598 - >seq1597,non-specific,197306,1,239,0.00027448,43.6241,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs6_sqmonkey.marg.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs6_sqmonkey,marg,CompleteHit
3760,Q#1599 - >seq1598,non-specific,238827,478,728,1.06608e-15,77.3314,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs6_sqmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs6_sqmonkey,marg,CompleteHit
3761,Q#1599 - >seq1598,superfamily,295487,478,728,1.06608e-15,77.3314,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs6_sqmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs6_sqmonkey,marg,CompleteHit
3762,Q#1599 - >seq1598,non-specific,333820,644,728,0.00144057,40.7386,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
3763,Q#1599 - >seq1598,superfamily,333820,644,728,0.00144057,40.7386,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
3764,Q#1600 - >seq1599,non-specific,238827,489,616,2.0504400000000003e-12,67.7014,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
3765,Q#1600 - >seq1599,superfamily,295487,489,616,2.0504400000000003e-12,67.7014,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
3766,Q#1600 - >seq1599,non-specific,333820,525,621,4.40244e-07,51.138999999999996,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
3767,Q#1600 - >seq1599,superfamily,333820,525,621,4.40244e-07,51.138999999999996,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
3768,Q#1600 - >seq1599,non-specific,238828,521,640,5.65912e-05,45.6549,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
3769,Q#1600 - >seq1599,non-specific,240317,265,342,0.00470884,40.7617,PTZ00217,PTZ00217,N,cl36527,flap endonuclease-1; Provisional,L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
3770,Q#1600 - >seq1599,superfamily,240317,265,342,0.00470884,40.7617,cl36527,PTZ00217 superfamily,N, - ,flap endonuclease-1; Provisional,L1MA10.ORF2.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
3771,Q#1601 - >seq1600,non-specific,238827,371,605,2.14604e-14,73.0942,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs6_sqmonkey,pars,CompleteHit
3772,Q#1601 - >seq1600,superfamily,295487,371,605,2.14604e-14,73.0942,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs6_sqmonkey,pars,CompleteHit
3773,Q#1601 - >seq1600,non-specific,333820,386,592,9.58746e-08,53.065,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs6_sqmonkey,pars,CompleteHit
3774,Q#1601 - >seq1600,superfamily,333820,386,592,9.58746e-08,53.065,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs6_sqmonkey,pars,CompleteHit
3775,Q#1601 - >seq1600,non-specific,238828,461,554,0.00017244099999999998,44.1141,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
3776,Q#1602 - >seq1601,non-specific,197310,41,161,4.1647699999999996e-14,72.7693,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs6_sqmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3777,Q#1602 - >seq1601,superfamily,351117,41,161,4.1647699999999996e-14,72.7693,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs6_sqmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3778,Q#1602 - >seq1601,non-specific,197307,23,154,0.00396344,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs6_sqmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
3779,Q#1605 - >seq1604,non-specific,335182,31,120,5.810529999999999e-13,61.9351,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs6_sqmonkey,marg,CompleteHit
3780,Q#1605 - >seq1604,superfamily,335182,31,120,5.810529999999999e-13,61.9351,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs6_sqmonkey,marg,CompleteHit
3781,Q#1605 - >seq1604,non-specific,340205,124,164,3.26135e-09,50.7976,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
3782,Q#1605 - >seq1604,superfamily,340205,124,164,3.26135e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs6_sqmonkey.marg.frame1,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
3783,Q#1606 - >seq1605,non-specific,340205,156,217,5.66755e-09,50.7976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs0_human.pars.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs0_human,pars,CompleteHit
3784,Q#1606 - >seq1605,superfamily,340205,156,217,5.66755e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs0_human.pars.frame2,1909122342_L1MA10.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs0_human,pars,CompleteHit
3785,Q#1608 - >seq1607,non-specific,335182,20,116,1.9288799999999998e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3786,Q#1608 - >seq1607,superfamily,335182,20,116,1.9288799999999998e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3787,Q#1608 - >seq1607,non-specific,335182,20,116,1.9288799999999998e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3788,Q#1608 - >seq1607,non-specific,340205,120,182,3.39471e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3789,Q#1608 - >seq1607,superfamily,340205,120,182,3.39471e-24,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3790,Q#1608 - >seq1607,non-specific,340205,120,182,3.39471e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,pars,CompleteHit
3791,Q#1610 - >seq1609,non-specific,335182,20,116,1.9288799999999998e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3792,Q#1610 - >seq1609,superfamily,335182,20,116,1.9288799999999998e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3793,Q#1610 - >seq1609,non-specific,335182,20,116,1.9288799999999998e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3794,Q#1610 - >seq1609,non-specific,340205,120,182,3.39471e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3795,Q#1610 - >seq1609,superfamily,340205,120,182,3.39471e-24,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3796,Q#1610 - >seq1609,non-specific,340205,120,182,3.39471e-24,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs4_gibbon.marg.frame3,1909122342_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs4_gibbon,marg,CompleteHit
3797,Q#1611 - >seq1610,non-specific,335182,7,79,2.62418e-06,43.4455,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
3798,Q#1611 - >seq1610,superfamily,335182,7,79,2.62418e-06,43.4455,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs6_sqmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
3799,Q#1616 - >seq1615,non-specific,335182,66,162,2.53255e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs3_orang.marg.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,marg,CompleteHit
3800,Q#1616 - >seq1615,superfamily,335182,66,162,2.53255e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs3_orang.marg.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,marg,CompleteHit
3801,Q#1616 - >seq1615,non-specific,340205,166,228,1.1519299999999999e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs3_orang.marg.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,marg,CompleteHit
3802,Q#1616 - >seq1615,superfamily,340205,166,228,1.1519299999999999e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs3_orang.marg.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,marg,CompleteHit
3803,Q#1618 - >seq1617,non-specific,335182,65,161,2.02799e-29,106.23299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs1_chimp.pars.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,pars,CompleteHit
3804,Q#1618 - >seq1617,superfamily,335182,65,161,2.02799e-29,106.23299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs1_chimp.pars.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,pars,CompleteHit
3805,Q#1618 - >seq1617,non-specific,340205,165,220,1.0162100000000001e-13,63.8944,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs1_chimp.pars.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,pars,CompleteHit
3806,Q#1618 - >seq1617,superfamily,340205,165,220,1.0162100000000001e-13,63.8944,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs1_chimp.pars.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,pars,CompleteHit
3807,Q#1622 - >seq1621,non-specific,335182,66,162,3.762899999999999e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3808,Q#1622 - >seq1621,superfamily,335182,66,162,3.762899999999999e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3809,Q#1622 - >seq1621,non-specific,335182,66,162,3.762899999999999e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3810,Q#1622 - >seq1621,non-specific,340205,166,228,1.67238e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3811,Q#1622 - >seq1621,superfamily,340205,166,228,1.67238e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3812,Q#1622 - >seq1621,non-specific,340205,166,228,1.67238e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.marg.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,marg,CompleteHit
3813,Q#1625 - >seq1624,non-specific,335182,66,162,3.762899999999999e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3814,Q#1625 - >seq1624,superfamily,335182,66,162,3.762899999999999e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3815,Q#1625 - >seq1624,non-specific,335182,66,162,3.762899999999999e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3816,Q#1625 - >seq1624,non-specific,340205,166,228,1.67238e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3817,Q#1625 - >seq1624,superfamily,340205,166,228,1.67238e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3818,Q#1625 - >seq1624,non-specific,340205,166,228,1.67238e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs2_gorilla,pars,CompleteHit
3819,Q#1628 - >seq1627,non-specific,335182,66,162,2.1955999999999998e-29,105.848,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs1_chimp.marg.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,marg,CompleteHit
3820,Q#1628 - >seq1627,superfamily,335182,66,162,2.1955999999999998e-29,105.848,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs1_chimp.marg.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,marg,CompleteHit
3821,Q#1628 - >seq1627,non-specific,340205,166,221,1.0413499999999999e-13,63.8944,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs1_chimp.marg.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,marg,CompleteHit
3822,Q#1628 - >seq1627,superfamily,340205,166,221,1.0413499999999999e-13,63.8944,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs1_chimp.marg.frame3,1909122342_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs1_chimp,marg,CompleteHit
3823,Q#1630 - >seq1629,non-specific,335182,66,162,2.53255e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs3_orang.pars.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,pars,CompleteHit
3824,Q#1630 - >seq1629,superfamily,335182,66,162,2.53255e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs3_orang.pars.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,pars,CompleteHit
3825,Q#1630 - >seq1629,non-specific,340205,166,228,1.1519299999999999e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs3_orang.pars.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,pars,CompleteHit
3826,Q#1630 - >seq1629,superfamily,340205,166,228,1.1519299999999999e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs3_orang.pars.frame3,1909122342_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs3_orang,pars,CompleteHit
3827,Q#1631 - >seq1630,non-specific,340205,93,133,4.88041e-09,50.0272,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs6_sqmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
3828,Q#1631 - >seq1630,superfamily,340205,93,133,4.88041e-09,50.0272,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs6_sqmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA10,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
3829,Q#1634 - >seq1633,specific,238827,521,742,3.72954e-39,145.127,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3830,Q#1634 - >seq1633,superfamily,295487,521,742,3.72954e-39,145.127,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3831,Q#1634 - >seq1633,non-specific,333820,509,742,2.65607e-19,86.5773,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3832,Q#1634 - >seq1633,superfamily,333820,509,742,2.65607e-19,86.5773,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3833,Q#1634 - >seq1633,non-specific,197310,115,203,1.0888e-13,71.6137,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3834,Q#1634 - >seq1633,superfamily,351117,115,203,1.0888e-13,71.6137,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3835,Q#1634 - >seq1633,non-specific,238828,553,742,8.15168e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3836,Q#1634 - >seq1633,non-specific,235175,247,435,4.351e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA10,ORF2,hs3_orang,pars,BothTerminiTruncated
3837,Q#1634 - >seq1633,superfamily,235175,247,435,4.351e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA10,ORF2,hs3_orang,pars,BothTerminiTruncated
3838,Q#1634 - >seq1633,non-specific,197320,125,202,0.00061198,42.8874,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3839,Q#1634 - >seq1633,non-specific,197307,149,202,0.00101823,41.8897,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3840,Q#1634 - >seq1633,non-specific,275209,558,766,0.00116363,42.4448,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3841,Q#1634 - >seq1633,superfamily,275209,558,766,0.00116363,42.4448,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3842,Q#1634 - >seq1633,non-specific,223780,149,202,0.00176026,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3843,Q#1634 - >seq1633,non-specific,235175,247,401,0.00865599,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA10.ORF2.hs3_orang.pars.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA10,ORF2,hs3_orang,pars,BothTerminiTruncated
3844,Q#1635 - >seq1634,non-specific,197310,19,202,5.530689999999999e-25,104.741,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3845,Q#1635 - >seq1634,superfamily,351117,19,202,5.530689999999999e-25,104.741,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3846,Q#1635 - >seq1634,non-specific,197306,21,147,2.03382e-13,70.9733,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,pars,C-TerminusTruncated
3847,Q#1635 - >seq1634,specific,311990,1152,1170,0.00035433,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3848,Q#1635 - >seq1634,superfamily,311990,1152,1170,0.00035433,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3849,Q#1635 - >seq1634,non-specific,197320,15,134,0.00052443,42.8874,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA10,ORF2,hs3_orang,pars,C-TerminusTruncated
3850,Q#1635 - >seq1634,specific,335306,20,188,0.000609354,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,pars,CompleteHit
3851,Q#1635 - >seq1634,non-specific,197311,61,134,0.00159574,41.1233,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA10,ORF2,hs3_orang,pars,BothTerminiTruncated
3852,Q#1635 - >seq1634,non-specific,223780,20,134,0.00686565,39.5039,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA10,ORF2,hs3_orang,pars,C-TerminusTruncated
3853,Q#1635 - >seq1634,non-specific,335313,73,158,0.0071076,40.1176,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3854,Q#1635 - >seq1634,superfamily,354836,73,158,0.0071076,40.1176,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1MA10.ORF2.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA10,ORF2,hs3_orang,pars,N-TerminusTruncated
3855,Q#1638 - >seq1637,non-specific,340205,134,201,6.09558e-14,63.8944,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,marg,CompleteHit
3856,Q#1638 - >seq1637,superfamily,340205,134,201,6.09558e-14,63.8944,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,marg,CompleteHit
3857,Q#1638 - >seq1637,non-specific,335182,35,94,0.00021622400000000002,38.8231,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,marg,C-TerminusTruncated
3858,Q#1638 - >seq1637,superfamily,335182,35,94,0.00021622400000000002,38.8231,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,marg,C-TerminusTruncated
3859,Q#1641 - >seq1640,non-specific,340205,117,178,1.60111e-12,59.6572,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,pars,CompleteHit
3860,Q#1641 - >seq1640,superfamily,340205,117,178,1.60111e-12,59.6572,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,pars,CompleteHit
3861,Q#1641 - >seq1640,non-specific,335182,34,78,0.00193723,36.1267,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,pars,C-TerminusTruncated
3862,Q#1641 - >seq1640,superfamily,335182,34,78,0.00193723,36.1267,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs3_orang.pars.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs3_orang,pars,C-TerminusTruncated
3863,Q#1643 - >seq1642,specific,238827,302,544,4.3529e-42,153.216,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3864,Q#1643 - >seq1642,superfamily,295487,302,544,4.3529e-42,153.216,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3865,Q#1643 - >seq1642,non-specific,333820,302,544,1.06521e-21,93.5109,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3866,Q#1643 - >seq1642,superfamily,333820,302,544,1.06521e-21,93.5109,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3867,Q#1643 - >seq1642,non-specific,238828,358,484,6.954e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,N-TerminusTruncated
3868,Q#1643 - >seq1642,non-specific,197310,7,146,5.71086e-06,48.5017,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3869,Q#1643 - >seq1642,superfamily,351117,7,146,5.71086e-06,48.5017,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3870,Q#1643 - >seq1642,non-specific,238185,428,544,9.58889e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,CompleteHit
3871,Q#1643 - >seq1642,non-specific,275209,359,568,0.00014113100000000001,45.1412,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,N-TerminusTruncated
3872,Q#1643 - >seq1642,superfamily,275209,359,568,0.00014113100000000001,45.1412,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs2_gorilla.marg.frame1,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs2_gorilla,marg,N-TerminusTruncated
3873,Q#1645 - >seq1644,specific,238827,229,471,2.4039099999999997e-42,153.986,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,CompleteHit
3874,Q#1645 - >seq1644,superfamily,295487,229,471,2.4039099999999997e-42,153.986,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,CompleteHit
3875,Q#1645 - >seq1644,non-specific,333820,229,471,1.1865799999999998e-21,93.1257,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,CompleteHit
3876,Q#1645 - >seq1644,superfamily,333820,229,471,1.1865799999999998e-21,93.1257,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,CompleteHit
3877,Q#1645 - >seq1644,non-specific,238828,285,411,5.13052e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,N-TerminusTruncated
3878,Q#1645 - >seq1644,non-specific,275209,286,498,3.03569e-05,47.0672,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,N-TerminusTruncated
3879,Q#1645 - >seq1644,superfamily,275209,286,498,3.03569e-05,47.0672,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,N-TerminusTruncated
3880,Q#1645 - >seq1644,non-specific,238185,355,471,7.04552e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs2_gorilla.pars.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs2_gorilla,pars,CompleteHit
3881,Q#1648 - >seq1647,non-specific,340205,266,336,8.030700000000001e-06,42.7084,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs2_gorilla.marg.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA10,ORF1,hs2_gorilla,marg,CompleteHit
3882,Q#1648 - >seq1647,superfamily,340205,266,336,8.030700000000001e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs2_gorilla.marg.frame2,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA10,ORF1,hs2_gorilla,marg,CompleteHit
3883,Q#1650 - >seq1649,non-specific,340205,128,186,2.03271e-06,43.4788,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs2_gorilla,pars,CompleteHit
3884,Q#1650 - >seq1649,superfamily,340205,128,186,2.03271e-06,43.4788,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs2_gorilla.pars.frame3,1909122342_L1MA10.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs2_gorilla,pars,CompleteHit
3885,Q#1654 - >seq1653,non-specific,197310,23,206,2.1528400000000003e-24,102.815,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3886,Q#1654 - >seq1653,superfamily,351117,23,206,2.1528400000000003e-24,102.815,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3887,Q#1654 - >seq1653,non-specific,197306,25,151,3.5773000000000003e-13,70.2029,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,marg,C-TerminusTruncated
3888,Q#1654 - >seq1653,non-specific,197320,19,138,0.0005792869999999999,42.8874,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA10,ORF2,hs3_orang,marg,C-TerminusTruncated
3889,Q#1654 - >seq1653,specific,335306,24,192,0.000599082,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3890,Q#1654 - >seq1653,non-specific,197311,65,138,0.00228556,40.3529,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA10,ORF2,hs3_orang,marg,BothTerminiTruncated
3891,Q#1654 - >seq1653,non-specific,335313,77,162,0.00680627,40.1176,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3892,Q#1654 - >seq1653,superfamily,354836,77,162,0.00680627,40.1176,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1MA10.ORF2.hs3_orang.marg.frame1,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3893,Q#1655 - >seq1654,specific,238827,528,750,2.0408199999999998e-41,151.675,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3894,Q#1655 - >seq1654,superfamily,295487,528,750,2.0408199999999998e-41,151.675,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3895,Q#1655 - >seq1654,non-specific,333820,516,750,7.377100000000001e-20,88.5033,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3896,Q#1655 - >seq1654,superfamily,333820,516,750,7.377100000000001e-20,88.5033,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3897,Q#1655 - >seq1654,non-specific,197310,122,210,9.00193e-14,71.9989,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3898,Q#1655 - >seq1654,superfamily,351117,122,210,9.00193e-14,71.9989,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3899,Q#1655 - >seq1654,non-specific,238828,560,750,2.9212e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3900,Q#1655 - >seq1654,non-specific,275209,565,774,1.60186e-05,48.2228,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3901,Q#1655 - >seq1654,superfamily,275209,565,774,1.60186e-05,48.2228,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3902,Q#1655 - >seq1654,non-specific,235175,254,442,7.4206e-05,46.9808,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA10,ORF2,hs3_orang,marg,BothTerminiTruncated
3903,Q#1655 - >seq1654,superfamily,235175,254,442,7.4206e-05,46.9808,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA10,ORF2,hs3_orang,marg,BothTerminiTruncated
3904,Q#1655 - >seq1654,non-specific,197320,132,209,0.0005437230000000001,42.8874,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3905,Q#1655 - >seq1654,non-specific,197307,156,209,0.000872771,42.2749,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3906,Q#1655 - >seq1654,non-specific,223780,156,209,0.00140608,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs3_orang.marg.frame2,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs3_orang,marg,N-TerminusTruncated
3907,Q#1659 - >seq1658,specific,238827,437,686,6.888449999999999e-36,135.497,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,CompleteHit
3908,Q#1659 - >seq1658,superfamily,295487,437,686,6.888449999999999e-36,135.497,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,CompleteHit
3909,Q#1659 - >seq1658,non-specific,333820,440,652,9.523719999999999e-22,93.8961,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,CompleteHit
3910,Q#1659 - >seq1658,superfamily,333820,440,652,9.523719999999999e-22,93.8961,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,CompleteHit
3911,Q#1659 - >seq1658,non-specific,238828,503,640,2.4875e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3912,Q#1659 - >seq1658,non-specific,275209,504,636,1.6985299999999998e-07,54.386,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
3913,Q#1659 - >seq1658,superfamily,275209,504,636,1.6985299999999998e-07,54.386,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
3914,Q#1659 - >seq1658,non-specific,197310,4,92,4.7126300000000003e-07,51.9685,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3915,Q#1659 - >seq1658,superfamily,351117,4,92,4.7126300000000003e-07,51.9685,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3916,Q#1659 - >seq1658,non-specific,238185,573,650,0.00180517,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs5_gmonkey.pars.frame3,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
3917,Q#1660 - >seq1659,non-specific,197310,88,200,2.8138499999999997e-13,70.4581,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3918,Q#1660 - >seq1659,superfamily,351117,88,200,2.8138499999999997e-13,70.4581,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3919,Q#1660 - >seq1659,non-specific,197306,73,193,0.000103139,44.7797,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3920,Q#1660 - >seq1659,non-specific,197320,105,190,0.000235456,44.043,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3921,Q#1660 - >seq1659,non-specific,197307,90,199,0.00030462,43.4305,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3922,Q#1660 - >seq1659,non-specific,223780,79,199,0.00166383,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs5_gmonkey.pars.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
3923,Q#1663 - >seq1662,non-specific,340205,235,298,0.00373746,35.0044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA10,ORF1,hs5_gmonkey,marg,CompleteHit
3924,Q#1663 - >seq1662,superfamily,340205,235,298,0.00373746,35.0044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA10,ORF1,hs5_gmonkey,marg,CompleteHit
3925,Q#1667 - >seq1666,non-specific,340205,64,127,4.56042e-05,38.8564,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs5_gmonkey.pars.frame1,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs5_gmonkey,pars,CompleteHit
3926,Q#1667 - >seq1666,superfamily,340205,64,127,4.56042e-05,38.8564,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs5_gmonkey.pars.frame1,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA10,ORF1,hs5_gmonkey,pars,CompleteHit
3927,Q#1668 - >seq1667,specific,238827,483,738,4.86653e-41,150.519,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,CompleteHit
3928,Q#1668 - >seq1667,superfamily,295487,483,738,4.86653e-41,150.519,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,CompleteHit
3929,Q#1668 - >seq1667,non-specific,333820,489,704,2.18874e-22,95.4369,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,CompleteHit
3930,Q#1668 - >seq1667,superfamily,333820,489,704,2.18874e-22,95.4369,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,CompleteHit
3931,Q#1668 - >seq1667,non-specific,197310,73,209,6.53897e-20,90.1033,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3932,Q#1668 - >seq1667,superfamily,351117,73,209,6.53897e-20,90.1033,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3933,Q#1668 - >seq1667,non-specific,238828,555,692,2.3359e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3934,Q#1668 - >seq1667,non-specific,197306,73,202,2.9314e-08,55.9505,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3935,Q#1668 - >seq1667,non-specific,275209,556,688,9.44458e-08,55.1564,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
3936,Q#1668 - >seq1667,superfamily,275209,556,688,9.44458e-08,55.1564,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
3937,Q#1668 - >seq1667,non-specific,197320,83,199,1.0736099999999999e-05,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3938,Q#1668 - >seq1667,non-specific,197307,83,208,0.000291558,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3939,Q#1668 - >seq1667,non-specific,223780,83,208,0.0020096,41.0447,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
3940,Q#1668 - >seq1667,non-specific,274009,295,431,0.0027445,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3941,Q#1668 - >seq1667,superfamily,274009,295,431,0.0027445,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3942,Q#1668 - >seq1667,non-specific,238185,625,702,0.00306009,38.1008,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs5_gmonkey.marg.frame2,1909122342_L1MA10.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
3943,Q#1669 - >seq1668,specific,197310,10,240,6.7448e-32,124.771,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3944,Q#1669 - >seq1668,superfamily,351117,10,240,6.7448e-32,124.771,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3945,Q#1669 - >seq1668,non-specific,197306,10,240,7.1402e-10,60.5729,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3946,Q#1669 - >seq1668,non-specific,197307,14,233,6.41785e-05,45.7417,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3947,Q#1669 - >seq1668,specific,335306,13,233,0.000512813,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3948,Q#1669 - >seq1668,non-specific,272954,10,150,0.00141474,41.5997,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA10.ORF2.hs4_gibbon.marg.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
3949,Q#1671 - >seq1670,specific,238827,461,723,1.0097100000000002e-40,149.364,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3950,Q#1671 - >seq1670,superfamily,295487,461,723,1.0097100000000002e-40,149.364,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3951,Q#1671 - >seq1670,non-specific,333820,482,698,1.33445e-17,81.9549,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3952,Q#1671 - >seq1670,superfamily,333820,482,698,1.33445e-17,81.9549,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs4_gibbon,marg,CompleteHit
3953,Q#1671 - >seq1670,non-specific,238828,532,698,2.54153e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA10,ORF2,hs4_gibbon,marg,N-TerminusTruncated
3954,Q#1672 - >seq1671,non-specific,197310,164,215,3.27023e-05,46.5757,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs4_gibbon.pars.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3955,Q#1672 - >seq1671,superfamily,351117,164,215,3.27023e-05,46.5757,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs4_gibbon.pars.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3956,Q#1673 - >seq1672,specific,238827,463,725,9.84452e-41,149.364,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs4_gibbon,pars,CompleteHit
3957,Q#1673 - >seq1672,superfamily,295487,463,725,9.84452e-41,149.364,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs4_gibbon,pars,CompleteHit
3958,Q#1673 - >seq1672,non-specific,197310,30,153,2.1480700000000003e-19,88.5625,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3959,Q#1673 - >seq1672,superfamily,351117,30,153,2.1480700000000003e-19,88.5625,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3960,Q#1673 - >seq1672,non-specific,333820,484,700,1.1940099999999999e-17,81.9549,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs4_gibbon,pars,CompleteHit
3961,Q#1673 - >seq1672,superfamily,333820,484,700,1.1940099999999999e-17,81.9549,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs4_gibbon,pars,CompleteHit
3962,Q#1673 - >seq1672,non-specific,197306,30,166,1.51322e-09,59.4173,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3963,Q#1673 - >seq1672,non-specific,238828,534,700,3.48187e-05,46.0401,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
3964,Q#1673 - >seq1672,non-specific,197320,30,145,0.00942884,39.0354,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA10.ORF2.hs4_gibbon.pars.frame2,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
3965,Q#1677 - >seq1676,non-specific,335182,168,248,2.3771e-06,45.3715,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs4_gibbon,marg,CompleteHit
3966,Q#1677 - >seq1676,superfamily,335182,168,248,2.3771e-06,45.3715,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA10.ORF1.hs4_gibbon.marg.frame1,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA10,ORF1,hs4_gibbon,marg,CompleteHit
3967,Q#1678 - >seq1677,non-specific,340205,169,223,0.000508124,37.3156,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs4_gibbon,pars,CompleteHit
3968,Q#1678 - >seq1677,superfamily,340205,169,223,0.000508124,37.3156,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA10.ORF1.hs4_gibbon.pars.frame3,1909122342_L1MA10.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA10,ORF1,hs4_gibbon,pars,CompleteHit
3969,Q#1680 - >seq1679,specific,311990,1139,1157,0.000961112,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs3_orang.marg.frame3,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3970,Q#1680 - >seq1679,superfamily,311990,1139,1157,0.000961112,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA10.ORF2.hs3_orang.marg.frame3,1909122342_L1MA10.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA10,ORF2,hs3_orang,marg,CompleteHit
3971,Q#1683 - >seq1682,non-specific,335182,66,162,1.3834099999999998e-26,98.9142,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs5_gmonkey.pars.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,pars,CompleteHit
3972,Q#1683 - >seq1682,superfamily,335182,66,162,1.3834099999999998e-26,98.9142,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs5_gmonkey.pars.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,pars,CompleteHit
3973,Q#1683 - >seq1682,non-specific,340205,166,228,7.657439999999999e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs5_gmonkey.pars.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,pars,CompleteHit
3974,Q#1683 - >seq1682,superfamily,340205,166,228,7.657439999999999e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs5_gmonkey.pars.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,pars,CompleteHit
3975,Q#1686 - >seq1685,non-specific,335182,66,162,1.27377e-26,98.9142,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs5_gmonkey.marg.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,marg,CompleteHit
3976,Q#1686 - >seq1685,superfamily,335182,66,162,1.27377e-26,98.9142,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs5_gmonkey.marg.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,marg,CompleteHit
3977,Q#1686 - >seq1685,non-specific,340205,166,228,5.74908e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs5_gmonkey.marg.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,marg,CompleteHit
3978,Q#1686 - >seq1685,superfamily,340205,166,228,5.74908e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs5_gmonkey.marg.frame3,1909122344_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs5_gmonkey,marg,CompleteHit
3979,Q#1689 - >seq1688,non-specific,335182,101,197,1.01444e-27,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,marg,CompleteHit
3980,Q#1689 - >seq1688,superfamily,335182,101,197,1.01444e-27,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,marg,CompleteHit
3981,Q#1689 - >seq1688,non-specific,340205,201,256,1.91915e-15,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,marg,CompleteHit
3982,Q#1689 - >seq1688,superfamily,340205,201,256,1.91915e-15,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,marg,CompleteHit
3983,Q#1689 - >seq1688,non-specific,224117,27,144,0.0023575,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF1,hs0_human,marg,N-TerminusTruncated
3984,Q#1689 - >seq1688,superfamily,224117,27,144,0.0023575,38.9272,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA1,ORF1,hs0_human,marg,N-TerminusTruncated
3985,Q#1689 - >seq1688,non-specific,224117,29,115,0.00663377,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF1,hs0_human,marg,BothTerminiTruncated
3986,Q#1689 - >seq1688,non-specific,340204,56,97,0.00674979,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MA1,ORF1,hs0_human,marg,CompleteHit
3987,Q#1689 - >seq1688,superfamily,340204,56,97,0.00674979,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA1.ORF1.hs0_human.marg.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MA1,ORF1,hs0_human,marg,CompleteHit
3988,Q#1692 - >seq1691,non-specific,335182,66,162,3.35778e-28,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs1_chimp.pars.frame3,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs1_chimp,pars,CompleteHit
3989,Q#1692 - >seq1691,superfamily,335182,66,162,3.35778e-28,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs1_chimp.pars.frame3,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs1_chimp,pars,CompleteHit
3990,Q#1692 - >seq1691,non-specific,340205,166,228,7.860160000000001e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs1_chimp.pars.frame3,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs1_chimp,pars,CompleteHit
3991,Q#1692 - >seq1691,superfamily,340205,166,228,7.860160000000001e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs1_chimp.pars.frame3,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs1_chimp,pars,CompleteHit
3992,Q#1693 - >seq1692,non-specific,335182,77,173,1.29959e-27,101.225,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs1_chimp.marg.frame1,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs1_chimp,marg,CompleteHit
3993,Q#1693 - >seq1692,superfamily,335182,77,173,1.29959e-27,101.225,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs1_chimp.marg.frame1,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs1_chimp,marg,CompleteHit
3994,Q#1693 - >seq1692,non-specific,340205,177,239,1.8585100000000002e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs1_chimp.marg.frame1,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs1_chimp,marg,CompleteHit
3995,Q#1693 - >seq1692,superfamily,340205,177,239,1.8585100000000002e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs1_chimp.marg.frame1,1909122345_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs1_chimp,marg,CompleteHit
3996,Q#1696 - >seq1695,non-specific,335182,97,193,2.8026799999999997e-27,101.225,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,pars,CompleteHit
3997,Q#1696 - >seq1695,superfamily,335182,97,193,2.8026799999999997e-27,101.225,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,pars,CompleteHit
3998,Q#1696 - >seq1695,non-specific,340205,197,259,9.03673e-22,85.8508,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,pars,CompleteHit
3999,Q#1696 - >seq1695,superfamily,340205,197,259,9.03673e-22,85.8508,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs0_human,pars,CompleteHit
4000,Q#1696 - >seq1695,non-specific,224117,23,140,0.00371786,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF1,hs0_human,pars,N-TerminusTruncated
4001,Q#1696 - >seq1695,superfamily,224117,23,140,0.00371786,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA1,ORF1,hs0_human,pars,N-TerminusTruncated
4002,Q#1696 - >seq1695,non-specific,340204,52,93,0.00939165,33.15,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MA1,ORF1,hs0_human,pars,CompleteHit
4003,Q#1696 - >seq1695,superfamily,340204,52,93,0.00939165,33.15,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MA1,ORF1,hs0_human,pars,CompleteHit
4004,Q#1696 - >seq1695,non-specific,224117,25,111,0.00975102,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF1.hs0_human.pars.frame3,1909122345_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF1,hs0_human,pars,BothTerminiTruncated
4005,Q#1697 - >seq1696,non-specific,197310,139,200,0.00021993,43.8793,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs6_sqmonkey.pars.frame1,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4006,Q#1697 - >seq1696,superfamily,351117,139,200,0.00021993,43.8793,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs6_sqmonkey.pars.frame1,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4007,Q#1703 - >seq1702,non-specific,335182,66,162,5.3285499999999995e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,pars,CompleteHit
4008,Q#1703 - >seq1702,superfamily,335182,66,162,5.3285499999999995e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,pars,CompleteHit
4009,Q#1703 - >seq1702,non-specific,340205,166,228,5.0708400000000004e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,pars,CompleteHit
4010,Q#1703 - >seq1702,superfamily,340205,166,228,5.0708400000000004e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,pars,CompleteHit
4011,Q#1705 - >seq1704,non-specific,197310,1,129,1.28191e-11,65.4505,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs6_sqmonkey.pars.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4012,Q#1705 - >seq1704,superfamily,351117,1,129,1.28191e-11,65.4505,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs6_sqmonkey.pars.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4013,Q#1705 - >seq1704,specific,311990,1133,1151,0.000578815,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs6_sqmonkey.pars.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4014,Q#1705 - >seq1704,superfamily,311990,1133,1151,0.000578815,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs6_sqmonkey.pars.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4015,Q#1706 - >seq1705,specific,238827,463,703,7.90672e-58,198.669,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4016,Q#1706 - >seq1705,superfamily,295487,463,703,7.90672e-58,198.669,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4017,Q#1706 - >seq1705,specific,333820,469,693,6.427349999999999e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4018,Q#1706 - >seq1705,superfamily,333820,469,693,6.427349999999999e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4019,Q#1706 - >seq1705,non-specific,238828,469,690,2.1276900000000001e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4020,Q#1706 - >seq1705,non-specific,275209,421,690,1.3223200000000001e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4021,Q#1706 - >seq1705,superfamily,275209,421,690,1.3223200000000001e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4022,Q#1706 - >seq1705,non-specific,235175,260,418,0.00139076,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4023,Q#1706 - >seq1705,superfamily,235175,260,418,0.00139076,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4024,Q#1706 - >seq1705,non-specific,238185,611,694,0.00998329,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs6_sqmonkey.pars.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,pars,CompleteHit
4025,Q#1708 - >seq1707,specific,311990,1164,1182,0.000256531,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs6_sqmonkey.marg.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4026,Q#1708 - >seq1707,superfamily,311990,1164,1182,0.000256531,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs6_sqmonkey.marg.frame2,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4027,Q#1709 - >seq1708,specific,238827,507,769,1.9468499999999997e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4028,Q#1709 - >seq1708,superfamily,295487,507,769,1.9468499999999997e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4029,Q#1709 - >seq1708,specific,197310,9,234,3.07984e-41,151.735,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4030,Q#1709 - >seq1708,superfamily,351117,9,234,3.07984e-41,151.735,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4031,Q#1709 - >seq1708,specific,333820,513,769,3.0057299999999997e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4032,Q#1709 - >seq1708,superfamily,333820,513,769,3.0057299999999997e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4033,Q#1709 - >seq1708,non-specific,197306,9,234,5.67641e-26,107.95200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4034,Q#1709 - >seq1708,non-specific,238828,513,734,1.5981e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4035,Q#1709 - >seq1708,specific,335306,10,227,4.01964e-12,66.885,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4036,Q#1709 - >seq1708,non-specific,223780,7,146,6.33397e-12,67.2383,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4037,Q#1709 - >seq1708,non-specific,197307,9,160,9.323999999999999e-11,63.4609,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4038,Q#1709 - >seq1708,non-specific,272954,7,162,1.72445e-10,62.7857,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4039,Q#1709 - >seq1708,non-specific,197336,7,161,3.69256e-09,58.7779,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4040,Q#1709 - >seq1708,non-specific,197320,7,152,7.21159e-09,57.9102,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4041,Q#1709 - >seq1708,non-specific,275209,465,807,3.00462e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4042,Q#1709 - >seq1708,superfamily,275209,465,807,3.00462e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4043,Q#1709 - >seq1708,non-specific,273186,7,159,1.18527e-07,54.2072,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4044,Q#1709 - >seq1708,non-specific,197319,7,234,2.85273e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4045,Q#1709 - >seq1708,non-specific,197321,7,120,1.2122200000000001e-06,51.0136,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4046,Q#1709 - >seq1708,non-specific,238185,655,769,0.000319234,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs6_sqmonkey,marg,CompleteHit
4047,Q#1709 - >seq1708,non-specific,236970,9,165,0.000802211,42.5738,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4048,Q#1709 - >seq1708,non-specific,235175,304,462,0.0015501,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
4049,Q#1709 - >seq1708,superfamily,235175,304,462,0.0015501,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
4050,Q#1710 - >seq1709,non-specific,335182,66,162,5.3285499999999995e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,marg,CompleteHit
4051,Q#1710 - >seq1709,superfamily,335182,66,162,5.3285499999999995e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA1.ORF1.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,marg,CompleteHit
4052,Q#1710 - >seq1709,non-specific,340205,166,228,5.0708400000000004e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,marg,CompleteHit
4053,Q#1710 - >seq1709,superfamily,340205,166,228,5.0708400000000004e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA1.ORF1.hs6_sqmonkey.marg.frame3,1909122345_L1MA1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA1,ORF1,hs6_sqmonkey,marg,CompleteHit
4054,Q#1714 - >seq1713,non-specific,335182,64,160,5.87803e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4055,Q#1714 - >seq1713,superfamily,335182,64,160,5.87803e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4056,Q#1714 - >seq1713,non-specific,340205,164,226,4.787939999999999e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4057,Q#1714 - >seq1713,superfamily,340205,164,226,4.787939999999999e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4058,Q#1714 - >seq1713,non-specific,340204,19,60,0.00298657,34.3056,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4059,Q#1714 - >seq1713,superfamily,340204,19,60,0.00298657,34.3056,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MA2,ORF1,hs3_orang,marg,CompleteHit
4060,Q#1714 - >seq1713,non-specific,224117,1,107,0.00566537,37.3864,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA2,ORF1,hs3_orang,marg,N-TerminusTruncated
4061,Q#1714 - >seq1713,superfamily,224117,1,107,0.00566537,37.3864,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MA2,ORF1,hs3_orang,marg,N-TerminusTruncated
4062,Q#1714 - >seq1713,non-specific,274008,1,79,0.00948104,36.5731,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA2,ORF1,hs3_orang,marg,BothTerminiTruncated
4063,Q#1714 - >seq1713,superfamily,274008,1,79,0.00948104,36.5731,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs3_orang.marg.frame1,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA2,ORF1,hs3_orang,marg,BothTerminiTruncated
4064,Q#1715 - >seq1714,non-specific,335182,66,162,4.889899999999999e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4065,Q#1715 - >seq1714,superfamily,335182,66,162,4.889899999999999e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4066,Q#1715 - >seq1714,non-specific,340205,166,228,4.7141499999999995e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4067,Q#1715 - >seq1714,superfamily,340205,166,228,4.7141499999999995e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4068,Q#1715 - >seq1714,non-specific,340204,21,62,0.00244922,34.6908,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4069,Q#1715 - >seq1714,superfamily,340204,21,62,0.00244922,34.6908,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MA2,ORF1,hs3_orang,pars,CompleteHit
4070,Q#1715 - >seq1714,non-specific,224117,1,109,0.00562448,37.3864,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs3_orang,pars,N-TerminusTruncated
4071,Q#1715 - >seq1714,superfamily,224117,1,109,0.00562448,37.3864,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA2,ORF1,hs3_orang,pars,N-TerminusTruncated
4072,Q#1715 - >seq1714,non-specific,274008,1,81,0.00601423,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs3_orang,pars,BothTerminiTruncated
4073,Q#1715 - >seq1714,superfamily,274008,1,81,0.00601423,37.3435,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs3_orang.pars.frame3,1909122347_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs3_orang,pars,BothTerminiTruncated
4074,Q#1717 - >seq1716,non-specific,335182,65,161,4.05501e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4075,Q#1717 - >seq1716,superfamily,335182,65,161,4.05501e-28,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4076,Q#1717 - >seq1716,non-specific,335182,65,161,4.05501e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4077,Q#1717 - >seq1716,non-specific,340205,165,227,6.4696300000000004e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4078,Q#1717 - >seq1716,superfamily,340205,165,227,6.4696300000000004e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4079,Q#1717 - >seq1716,non-specific,340205,165,227,6.4696300000000004e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.marg.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,marg,CompleteHit
4080,Q#1720 - >seq1719,non-specific,335182,65,161,4.05501e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4081,Q#1720 - >seq1719,superfamily,335182,65,161,4.05501e-28,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4082,Q#1720 - >seq1719,non-specific,335182,65,161,4.05501e-28,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4083,Q#1720 - >seq1719,non-specific,340205,165,227,6.4696300000000004e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4084,Q#1720 - >seq1719,superfamily,340205,165,227,6.4696300000000004e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4085,Q#1720 - >seq1719,non-specific,340205,165,227,6.4696300000000004e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs2_gorilla.pars.frame3,1909122347_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs2_gorilla,pars,CompleteHit
4086,Q#1723 - >seq1722,non-specific,335182,66,162,8.83787e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,pars,CompleteHit
4087,Q#1723 - >seq1722,superfamily,335182,66,162,8.83787e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,pars,CompleteHit
4088,Q#1723 - >seq1722,non-specific,340205,166,228,5.9286000000000005e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,pars,CompleteHit
4089,Q#1723 - >seq1722,superfamily,340205,166,228,5.9286000000000005e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,pars,CompleteHit
4090,Q#1723 - >seq1722,non-specific,224117,1,109,0.00211642,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs3_orang,pars,N-TerminusTruncated
4091,Q#1723 - >seq1722,superfamily,224117,1,109,0.00211642,38.9272,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs3_orang,pars,N-TerminusTruncated
4092,Q#1723 - >seq1722,non-specific,224117,1,79,0.00947081,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.pars.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs3_orang,pars,BothTerminiTruncated
4093,Q#1726 - >seq1725,non-specific,335182,66,162,5.9423e-27,99.6846,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,marg,CompleteHit
4094,Q#1726 - >seq1725,superfamily,335182,66,162,5.9423e-27,99.6846,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,marg,CompleteHit
4095,Q#1726 - >seq1725,non-specific,340205,166,228,3.90876e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,marg,CompleteHit
4096,Q#1726 - >seq1725,superfamily,340205,166,228,3.90876e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,marg,CompleteHit
4097,Q#1726 - >seq1725,non-specific,224117,1,109,0.00142801,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
4098,Q#1726 - >seq1725,superfamily,224117,1,109,0.00142801,39.3124,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
4099,Q#1726 - >seq1725,non-specific,224117,1,79,0.00751341,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
4100,Q#1726 - >seq1725,non-specific,274008,1,81,0.00854934,36.9583,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
4101,Q#1726 - >seq1725,superfamily,274008,1,81,0.00854934,36.9583,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA3.ORF1.hs2_gorilla.marg.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
4102,Q#1732 - >seq1731,non-specific,335182,66,162,3.79829e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4103,Q#1732 - >seq1731,superfamily,335182,66,162,3.79829e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4104,Q#1732 - >seq1731,non-specific,335182,66,162,3.79829e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4105,Q#1732 - >seq1731,non-specific,340205,166,228,6.43079e-25,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4106,Q#1732 - >seq1731,superfamily,340205,166,228,6.43079e-25,93.1696,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4107,Q#1732 - >seq1731,non-specific,340205,166,228,6.43079e-25,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,marg,CompleteHit
4108,Q#1732 - >seq1731,non-specific,224117,1,109,0.00225319,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs1_chimp,marg,N-TerminusTruncated
4109,Q#1732 - >seq1731,superfamily,224117,1,109,0.00225319,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs1_chimp,marg,N-TerminusTruncated
4110,Q#1732 - >seq1731,non-specific,224117,1,109,0.00225319,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.marg.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs1_chimp,marg,N-TerminusTruncated
4111,Q#1733 - >seq1732,non-specific,335182,66,162,3.79829e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4112,Q#1733 - >seq1732,superfamily,335182,66,162,3.79829e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4113,Q#1733 - >seq1732,non-specific,335182,66,162,3.79829e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4114,Q#1733 - >seq1732,non-specific,340205,166,228,6.43079e-25,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4115,Q#1733 - >seq1732,superfamily,340205,166,228,6.43079e-25,93.1696,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4116,Q#1733 - >seq1732,non-specific,340205,166,228,6.43079e-25,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs1_chimp,pars,CompleteHit
4117,Q#1733 - >seq1732,non-specific,224117,1,109,0.00225319,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs1_chimp,pars,N-TerminusTruncated
4118,Q#1733 - >seq1732,superfamily,224117,1,109,0.00225319,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs1_chimp,pars,N-TerminusTruncated
4119,Q#1733 - >seq1732,non-specific,224117,1,109,0.00225319,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs1_chimp.pars.frame3,1909122350_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs1_chimp,pars,N-TerminusTruncated
4120,Q#1736 - >seq1735,non-specific,335182,66,162,1.1236700000000002e-26,98.9142,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,pars,CompleteHit
4121,Q#1736 - >seq1735,superfamily,335182,66,162,1.1236700000000002e-26,98.9142,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,pars,CompleteHit
4122,Q#1736 - >seq1735,non-specific,340205,166,228,6.41143e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,pars,CompleteHit
4123,Q#1736 - >seq1735,superfamily,340205,166,228,6.41143e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs2_gorilla,pars,CompleteHit
4124,Q#1736 - >seq1735,non-specific,224117,1,109,0.00240002,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs2_gorilla,pars,N-TerminusTruncated
4125,Q#1736 - >seq1735,superfamily,224117,1,109,0.00240002,38.9272,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs2_gorilla.pars.frame3,1909122350_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs2_gorilla,pars,N-TerminusTruncated
4126,Q#1742 - >seq1741,non-specific,335182,65,161,2.92236e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4127,Q#1742 - >seq1741,superfamily,335182,65,161,2.92236e-27,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4128,Q#1742 - >seq1741,non-specific,335182,65,161,2.92236e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4129,Q#1742 - >seq1741,non-specific,340205,165,227,5.98081e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4130,Q#1742 - >seq1741,superfamily,340205,165,227,5.98081e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4131,Q#1742 - >seq1741,non-specific,340205,165,227,5.98081e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA3,ORF1,hs5_gmonkey,marg,CompleteHit
4132,Q#1742 - >seq1741,non-specific,224117,1,80,0.009903499999999999,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4133,Q#1742 - >seq1741,superfamily,224117,1,80,0.009903499999999999,37.0012,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MA3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4134,Q#1742 - >seq1741,non-specific,224117,1,80,0.009903499999999999,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.marg.frame1,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4135,Q#1743 - >seq1742,non-specific,335182,65,161,2.92236e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4136,Q#1743 - >seq1742,superfamily,335182,65,161,2.92236e-27,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4137,Q#1743 - >seq1742,non-specific,335182,65,161,2.92236e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4138,Q#1743 - >seq1742,non-specific,340205,165,227,5.98081e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4139,Q#1743 - >seq1742,superfamily,340205,165,227,5.98081e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4140,Q#1743 - >seq1742,non-specific,340205,165,227,5.98081e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs5_gmonkey,pars,CompleteHit
4141,Q#1743 - >seq1742,non-specific,224117,1,80,0.009903499999999999,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4142,Q#1743 - >seq1742,superfamily,224117,1,80,0.009903499999999999,37.0012,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4143,Q#1743 - >seq1742,non-specific,224117,1,80,0.009903499999999999,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4144,Q#1744 - >seq1743,non-specific,335182,66,162,8.83787e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,marg,CompleteHit
4145,Q#1744 - >seq1743,superfamily,335182,66,162,8.83787e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,marg,CompleteHit
4146,Q#1744 - >seq1743,non-specific,340205,166,228,5.9286000000000005e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,marg,CompleteHit
4147,Q#1744 - >seq1743,superfamily,340205,166,228,5.9286000000000005e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs3_orang,marg,CompleteHit
4148,Q#1744 - >seq1743,non-specific,224117,1,109,0.00211642,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs3_orang,marg,N-TerminusTruncated
4149,Q#1744 - >seq1743,superfamily,224117,1,109,0.00211642,38.9272,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs3_orang,marg,N-TerminusTruncated
4150,Q#1744 - >seq1743,non-specific,224117,1,79,0.00947081,37.0012,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs3_orang.marg.frame3,1909122350_L1MA3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs3_orang,marg,BothTerminiTruncated
4151,Q#1746 - >seq1745,non-specific,335182,66,162,3.71767e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4152,Q#1746 - >seq1745,superfamily,335182,66,162,3.71767e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4153,Q#1746 - >seq1745,non-specific,335182,66,162,3.71767e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4154,Q#1746 - >seq1745,non-specific,340205,166,228,1.2622500000000001e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4155,Q#1746 - >seq1745,superfamily,340205,166,228,1.2622500000000001e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4156,Q#1746 - >seq1745,non-specific,340205,166,228,1.2622500000000001e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,marg,CompleteHit
4157,Q#1746 - >seq1745,non-specific,224117,1,109,0.00229402,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
4158,Q#1746 - >seq1745,superfamily,224117,1,109,0.00229402,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
4159,Q#1746 - >seq1745,non-specific,224117,1,109,0.00229402,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.marg.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
4160,Q#1749 - >seq1748,non-specific,335182,66,162,3.71767e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4161,Q#1749 - >seq1748,superfamily,335182,66,162,3.71767e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4162,Q#1749 - >seq1748,non-specific,335182,66,162,3.71767e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4163,Q#1749 - >seq1748,non-specific,340205,166,228,1.2622500000000001e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4164,Q#1749 - >seq1748,superfamily,340205,166,228,1.2622500000000001e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4165,Q#1749 - >seq1748,non-specific,340205,166,228,1.2622500000000001e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs4_gibbon,pars,CompleteHit
4166,Q#1749 - >seq1748,non-specific,224117,1,109,0.00229402,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
4167,Q#1749 - >seq1748,superfamily,224117,1,109,0.00229402,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
4168,Q#1749 - >seq1748,non-specific,224117,1,109,0.00229402,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF1.hs4_gibbon.pars.frame3,1909122350_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
4169,Q#1753 - >seq1752,non-specific,335182,66,162,1.60998e-27,101.225,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs4_gibbon.pars.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,pars,CompleteHit
4170,Q#1753 - >seq1752,superfamily,335182,66,162,1.60998e-27,101.225,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs4_gibbon.pars.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,pars,CompleteHit
4171,Q#1753 - >seq1752,non-specific,340205,166,228,4.16749e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs4_gibbon.pars.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,pars,CompleteHit
4172,Q#1753 - >seq1752,superfamily,340205,166,228,4.16749e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs4_gibbon.pars.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,pars,CompleteHit
4173,Q#1756 - >seq1755,non-specific,335182,66,162,4.49993e-28,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs4_gibbon.marg.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,marg,CompleteHit
4174,Q#1756 - >seq1755,superfamily,335182,66,162,4.49993e-28,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs4_gibbon.marg.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,marg,CompleteHit
4175,Q#1756 - >seq1755,non-specific,340205,166,228,1.5100400000000002e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs4_gibbon.marg.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,marg,CompleteHit
4176,Q#1756 - >seq1755,superfamily,340205,166,228,1.5100400000000002e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs4_gibbon.marg.frame1,1909122350_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs4_gibbon,marg,CompleteHit
4177,Q#1760 - >seq1759,non-specific,335182,66,162,2.52414e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4178,Q#1760 - >seq1759,superfamily,335182,66,162,2.52414e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4179,Q#1760 - >seq1759,non-specific,335182,66,162,2.52414e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4180,Q#1760 - >seq1759,non-specific,340205,166,228,3.95074e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4181,Q#1760 - >seq1759,superfamily,340205,166,228,3.95074e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4182,Q#1760 - >seq1759,non-specific,340205,166,228,3.95074e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,pars,CompleteHit
4183,Q#1760 - >seq1759,non-specific,224117,1,80,0.00545147,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4184,Q#1760 - >seq1759,superfamily,224117,1,80,0.00545147,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4185,Q#1760 - >seq1759,non-specific,224117,1,80,0.00545147,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4186,Q#1760 - >seq1759,non-specific,274008,1,81,0.00625926,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4187,Q#1760 - >seq1759,superfamily,274008,1,81,0.00625926,37.3435,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4188,Q#1760 - >seq1759,non-specific,274008,1,81,0.00625926,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.pars.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
4189,Q#1763 - >seq1762,non-specific,335182,66,162,2.52414e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4190,Q#1763 - >seq1762,superfamily,335182,66,162,2.52414e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4191,Q#1763 - >seq1762,non-specific,335182,66,162,2.52414e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4192,Q#1763 - >seq1762,non-specific,340205,166,228,3.95074e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4193,Q#1763 - >seq1762,superfamily,340205,166,228,3.95074e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4194,Q#1763 - >seq1762,non-specific,340205,166,228,3.95074e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs5_gmonkey,marg,CompleteHit
4195,Q#1763 - >seq1762,non-specific,224117,1,80,0.00545147,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4196,Q#1763 - >seq1762,superfamily,224117,1,80,0.00545147,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4197,Q#1763 - >seq1762,non-specific,224117,1,80,0.00545147,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4198,Q#1763 - >seq1762,non-specific,274008,1,81,0.00625926,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4199,Q#1763 - >seq1762,superfamily,274008,1,81,0.00625926,37.3435,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4200,Q#1763 - >seq1762,non-specific,274008,1,81,0.00625926,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs5_gmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
4201,Q#1767 - >seq1766,non-specific,335182,65,161,2.18821e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs0_human.pars.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,pars,CompleteHit
4202,Q#1767 - >seq1766,superfamily,335182,65,161,2.18821e-27,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs0_human.pars.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,pars,CompleteHit
4203,Q#1767 - >seq1766,non-specific,340205,165,227,2.0303e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs0_human.pars.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,pars,CompleteHit
4204,Q#1767 - >seq1766,superfamily,340205,165,227,2.0303e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs0_human.pars.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,pars,CompleteHit
4205,Q#1770 - >seq1769,non-specific,335182,66,162,2.60929e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,marg,CompleteHit
4206,Q#1770 - >seq1769,superfamily,335182,66,162,2.60929e-27,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,marg,CompleteHit
4207,Q#1770 - >seq1769,non-specific,340205,166,228,2.6287400000000004e-23,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,marg,CompleteHit
4208,Q#1770 - >seq1769,superfamily,340205,166,228,2.6287400000000004e-23,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs0_human,marg,CompleteHit
4209,Q#1770 - >seq1769,non-specific,274008,1,81,0.00793786,36.9583,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs0_human,marg,BothTerminiTruncated
4210,Q#1770 - >seq1769,superfamily,274008,1,81,0.00793786,36.9583,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF1.hs0_human.marg.frame3,1909122350_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF1,hs0_human,marg,BothTerminiTruncated
4211,Q#1772 - >seq1771,non-specific,335182,67,163,7.11612e-27,99.6846,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,CompleteHit
4212,Q#1772 - >seq1771,superfamily,335182,67,163,7.11612e-27,99.6846,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,CompleteHit
4213,Q#1772 - >seq1771,non-specific,340205,167,217,5.580930000000001e-14,64.6648,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
4214,Q#1772 - >seq1771,superfamily,340205,167,217,5.580930000000001e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame3,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
4215,Q#1774 - >seq1773,non-specific,335182,57,153,2.12314e-27,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs6_sqmonkey.pars.frame2,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA2,ORF1,hs6_sqmonkey,pars,CompleteHit
4216,Q#1774 - >seq1773,superfamily,335182,57,153,2.12314e-27,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA2.ORF1.hs6_sqmonkey.pars.frame2,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA2,ORF1,hs6_sqmonkey,pars,CompleteHit
4217,Q#1774 - >seq1773,non-specific,340205,157,219,6.306880000000001e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.pars.frame2,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA2,ORF1,hs6_sqmonkey,pars,CompleteHit
4218,Q#1774 - >seq1773,superfamily,340205,157,219,6.306880000000001e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.pars.frame2,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA2,ORF1,hs6_sqmonkey,pars,CompleteHit
4219,Q#1775 - >seq1774,non-specific,340205,189,212,0.0044653,34.6192,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame1,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
4220,Q#1775 - >seq1774,superfamily,340205,189,212,0.0044653,34.6192,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA2.ORF1.hs6_sqmonkey.marg.frame1,1909122350_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
4221,Q#1777 - >seq1776,non-specific,340205,243,306,4.4391099999999995e-27,100.488,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs1_chimp.marg.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,marg,CompleteHit
4222,Q#1777 - >seq1776,superfamily,340205,243,306,4.4391099999999995e-27,100.488,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs1_chimp.marg.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,marg,CompleteHit
4223,Q#1777 - >seq1776,non-specific,335182,148,240,1.4663299999999997e-25,97.7586,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs1_chimp.marg.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,marg,CompleteHit
4224,Q#1777 - >seq1776,superfamily,335182,148,240,1.4663299999999997e-25,97.7586,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs1_chimp.marg.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,marg,CompleteHit
4225,Q#1779 - >seq1778,non-specific,234767,83,290,0.00414928,38.6656,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MA4A.ORF1.hs1_chimp.marg.frame1,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA4A,ORF1,hs1_chimp,marg,C-TerminusTruncated
4226,Q#1779 - >seq1778,superfamily,234767,83,290,0.00414928,38.6656,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MA4A.ORF1.hs1_chimp.marg.frame1,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA4A,ORF1,hs1_chimp,marg,C-TerminusTruncated
4227,Q#1783 - >seq1782,non-specific,335182,66,162,1.6448899999999998e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs0_human.marg.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,marg,CompleteHit
4228,Q#1783 - >seq1782,superfamily,335182,66,162,1.6448899999999998e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs0_human.marg.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,marg,CompleteHit
4229,Q#1783 - >seq1782,non-specific,340205,166,228,1.64994e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs0_human.marg.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,marg,CompleteHit
4230,Q#1783 - >seq1782,superfamily,340205,166,228,1.64994e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs0_human.marg.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,marg,CompleteHit
4231,Q#1785 - >seq1784,non-specific,340205,243,306,2.74715e-27,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs1_chimp.pars.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,pars,CompleteHit
4232,Q#1785 - >seq1784,superfamily,340205,243,306,2.74715e-27,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs1_chimp.pars.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,pars,CompleteHit
4233,Q#1785 - >seq1784,non-specific,335182,148,240,9.322069999999999e-24,93.1362,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs1_chimp.pars.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,pars,CompleteHit
4234,Q#1785 - >seq1784,superfamily,335182,148,240,9.322069999999999e-24,93.1362,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs1_chimp.pars.frame3,1909122351_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4A,ORF1,hs1_chimp,pars,CompleteHit
4235,Q#1786 - >seq1785,non-specific,335182,66,162,1.6448899999999998e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs0_human.pars.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,pars,CompleteHit
4236,Q#1786 - >seq1785,superfamily,335182,66,162,1.6448899999999998e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs0_human.pars.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,pars,CompleteHit
4237,Q#1786 - >seq1785,non-specific,340205,166,228,1.64994e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs0_human.pars.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,pars,CompleteHit
4238,Q#1786 - >seq1785,superfamily,340205,166,228,1.64994e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs0_human.pars.frame3,1909122351_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA3,ORF1,hs0_human,pars,CompleteHit
4239,Q#1792 - >seq1791,non-specific,340205,177,239,1.11466e-24,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs6_sqmonkey.pars.frame1,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA3,ORF1,hs6_sqmonkey,pars,CompleteHit
4240,Q#1792 - >seq1791,superfamily,340205,177,239,1.11466e-24,93.1696,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs6_sqmonkey.pars.frame1,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA3,ORF1,hs6_sqmonkey,pars,CompleteHit
4241,Q#1792 - >seq1791,non-specific,335182,86,173,3.68027e-24,92.751,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs6_sqmonkey.pars.frame1,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA3,ORF1,hs6_sqmonkey,pars,CompleteHit
4242,Q#1792 - >seq1791,superfamily,335182,86,173,3.68027e-24,92.751,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs6_sqmonkey.pars.frame1,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA3,ORF1,hs6_sqmonkey,pars,CompleteHit
4243,Q#1793 - >seq1792,non-specific,340205,194,256,9.05507e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs6_sqmonkey.marg.frame3,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs6_sqmonkey,marg,CompleteHit
4244,Q#1793 - >seq1792,superfamily,340205,194,256,9.05507e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA3.ORF1.hs6_sqmonkey.marg.frame3,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs6_sqmonkey,marg,CompleteHit
4245,Q#1793 - >seq1792,non-specific,335182,103,190,2.3019000000000001e-23,90.825,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs6_sqmonkey.marg.frame3,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs6_sqmonkey,marg,CompleteHit
4246,Q#1793 - >seq1792,superfamily,335182,103,190,2.3019000000000001e-23,90.825,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA3.ORF1.hs6_sqmonkey.marg.frame3,1909122351_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA3,ORF1,hs6_sqmonkey,marg,CompleteHit
4247,Q#1797 - >seq1796,non-specific,335182,63,156,4.82609e-33,114.70700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs4_gibbon.marg.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,marg,CompleteHit
4248,Q#1797 - >seq1796,superfamily,335182,63,156,4.82609e-33,114.70700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs4_gibbon.marg.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,marg,CompleteHit
4249,Q#1797 - >seq1796,non-specific,340205,159,222,2.6274299999999998e-28,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs4_gibbon.marg.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,marg,CompleteHit
4250,Q#1797 - >seq1796,superfamily,340205,159,222,2.6274299999999998e-28,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs4_gibbon.marg.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,marg,CompleteHit
4251,Q#1800 - >seq1799,non-specific,335182,167,260,1.39062e-31,113.93700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs4_gibbon.pars.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,pars,CompleteHit
4252,Q#1800 - >seq1799,superfamily,335182,167,260,1.39062e-31,113.93700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs4_gibbon.pars.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,pars,CompleteHit
4253,Q#1800 - >seq1799,non-specific,340205,263,326,5.0134799999999994e-27,100.874,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs4_gibbon.pars.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,pars,CompleteHit
4254,Q#1800 - >seq1799,superfamily,340205,263,326,5.0134799999999994e-27,100.874,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs4_gibbon.pars.frame2,1909122358_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs4_gibbon,pars,CompleteHit
4255,Q#1802 - >seq1801,non-specific,317979,2,172,0.00145735,39.0465,pfam15676,S6OS1,NC,cl25858,Six6 opposite strand transcript 1 family; This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 587 amino acids in length. The function is not known.,L1MA4A.ORF1.hs3_orang.marg.frame3,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4A,ORF1,hs3_orang,marg,BothTerminiTruncated
4256,Q#1802 - >seq1801,superfamily,317979,2,172,0.00145735,39.0465,cl25858,S6OS1 superfamily,NC, - ,Six6 opposite strand transcript 1 family; This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 587 amino acids in length. The function is not known.,L1MA4A.ORF1.hs3_orang.marg.frame3,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4A,ORF1,hs3_orang,marg,BothTerminiTruncated
4257,Q#1803 - >seq1802,non-specific,335182,59,152,2.01718e-33,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs3_orang.marg.frame1,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs3_orang,marg,CompleteHit
4258,Q#1803 - >seq1802,superfamily,335182,59,152,2.01718e-33,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs3_orang.marg.frame1,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs3_orang,marg,CompleteHit
4259,Q#1803 - >seq1802,non-specific,340205,155,218,9.54593e-29,102.8,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs3_orang.marg.frame1,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs3_orang,marg,CompleteHit
4260,Q#1803 - >seq1802,superfamily,340205,155,218,9.54593e-29,102.8,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs3_orang.marg.frame1,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs3_orang,marg,CompleteHit
4261,Q#1804 - >seq1803,non-specific,335182,61,154,2.84656e-31,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs3_orang.pars.frame2,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs3_orang,pars,CompleteHit
4262,Q#1804 - >seq1803,superfamily,335182,61,154,2.84656e-31,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs3_orang.pars.frame2,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs3_orang,pars,CompleteHit
4263,Q#1804 - >seq1803,non-specific,340205,157,220,1.8687e-28,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs3_orang.pars.frame2,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs3_orang,pars,CompleteHit
4264,Q#1804 - >seq1803,superfamily,340205,157,220,1.8687e-28,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs3_orang.pars.frame2,1909122358_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs3_orang,pars,CompleteHit
4265,Q#1808 - >seq1807,non-specific,335182,160,255,1.5040799999999997e-30,111.626,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs2_gorilla.marg.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,marg,CompleteHit
4266,Q#1808 - >seq1807,superfamily,335182,160,255,1.5040799999999997e-30,111.626,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs2_gorilla.marg.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,marg,CompleteHit
4267,Q#1808 - >seq1807,non-specific,340205,258,323,5.24603e-22,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs2_gorilla.marg.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,marg,CompleteHit
4268,Q#1808 - >seq1807,superfamily,340205,258,323,5.24603e-22,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs2_gorilla.marg.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,marg,CompleteHit
4269,Q#1811 - >seq1810,non-specific,335182,157,252,1.75356e-30,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs2_gorilla.pars.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,pars,CompleteHit
4270,Q#1811 - >seq1810,superfamily,335182,157,252,1.75356e-30,111.241,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs2_gorilla.pars.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,pars,CompleteHit
4271,Q#1811 - >seq1810,non-specific,340205,255,320,5.09813e-22,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs2_gorilla.pars.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,pars,CompleteHit
4272,Q#1811 - >seq1810,superfamily,340205,255,320,5.09813e-22,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs2_gorilla.pars.frame1,1909122358_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs2_gorilla,pars,CompleteHit
4273,Q#1813 - >seq1812,non-specific,335182,192,268,8.8053e-26,98.9142,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
4274,Q#1813 - >seq1812,superfamily,335182,192,268,8.8053e-26,98.9142,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
4275,Q#1813 - >seq1812,non-specific,340205,271,334,1.0570600000000001e-24,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs5_gmonkey,marg,CompleteHit
4276,Q#1813 - >seq1812,superfamily,340205,271,334,1.0570600000000001e-24,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs5_gmonkey,marg,CompleteHit
4277,Q#1813 - >seq1812,non-specific,227278,66,141,0.00563212,38.1645,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4278,Q#1813 - >seq1812,superfamily,227278,66,141,0.00563212,38.1645,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4279,Q#1813 - >seq1812,non-specific,237177,49,140,0.00867606,37.8354,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MA4A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4280,Q#1813 - >seq1812,superfamily,237177,49,140,0.00867606,37.8354,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MA4A.ORF1.hs5_gmonkey.marg.frame3,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MA4A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4281,Q#1817 - >seq1816,non-specific,335182,81,157,1.09127e-28,103.92200000000001,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs5_gmonkey.pars.frame1,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
4282,Q#1817 - >seq1816,superfamily,335182,81,157,1.09127e-28,103.92200000000001,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs5_gmonkey.pars.frame1,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
4283,Q#1817 - >seq1816,non-specific,340205,160,223,4.474919999999999e-26,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs5_gmonkey.pars.frame1,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs5_gmonkey,pars,CompleteHit
4284,Q#1817 - >seq1816,superfamily,340205,160,223,4.474919999999999e-26,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs5_gmonkey.pars.frame1,1909130018_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs5_gmonkey,pars,CompleteHit
4285,Q#1823 - >seq1822,non-specific,340205,148,193,1.99166e-06,43.864,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs7_bushaby.pars.frame1,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs7_bushaby,pars,C-TerminusTruncated
4286,Q#1823 - >seq1822,superfamily,340205,148,193,1.99166e-06,43.864,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs7_bushaby.pars.frame1,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4A,ORF1,hs7_bushaby,pars,C-TerminusTruncated
4287,Q#1824 - >seq1823,non-specific,335182,72,177,8.4045399999999995e-16,70.7947,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs7_bushaby.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs7_bushaby,marg,CompleteHit
4288,Q#1824 - >seq1823,superfamily,335182,72,177,8.4045399999999995e-16,70.7947,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs7_bushaby.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs7_bushaby,marg,CompleteHit
4289,Q#1824 - >seq1823,non-specific,340205,181,245,1.67836e-11,58.1164,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs7_bushaby.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs7_bushaby,marg,CompleteHit
4290,Q#1824 - >seq1823,superfamily,340205,181,245,1.67836e-11,58.1164,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs7_bushaby.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs7_bushaby,marg,CompleteHit
4291,Q#1825 - >seq1824,non-specific,340205,166,229,5.149389999999999e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs6_sqmonkey.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,marg,CompleteHit
4292,Q#1825 - >seq1824,superfamily,340205,166,229,5.149389999999999e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs6_sqmonkey.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,marg,CompleteHit
4293,Q#1825 - >seq1824,non-specific,335182,70,163,9.55309e-31,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs6_sqmonkey.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,marg,CompleteHit
4294,Q#1825 - >seq1824,superfamily,335182,70,163,9.55309e-31,109.315,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs6_sqmonkey.marg.frame3,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,marg,CompleteHit
4295,Q#1829 - >seq1828,non-specific,340205,161,224,2.44351e-30,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs6_sqmonkey.pars.frame2,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,pars,CompleteHit
4296,Q#1829 - >seq1828,superfamily,340205,161,224,2.44351e-30,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs6_sqmonkey.pars.frame2,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,pars,CompleteHit
4297,Q#1829 - >seq1828,non-specific,335182,65,158,4.72793e-29,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs6_sqmonkey.pars.frame2,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,pars,CompleteHit
4298,Q#1829 - >seq1828,superfamily,335182,65,158,4.72793e-29,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs6_sqmonkey.pars.frame2,1909130019_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs6_sqmonkey,pars,CompleteHit
4299,Q#1834 - >seq1833,non-specific,335182,66,162,7.2689e-30,107.00299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs1_chimp.marg.frame3,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs1_chimp,marg,CompleteHit
4300,Q#1834 - >seq1833,superfamily,335182,66,162,7.2689e-30,107.00299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs1_chimp.marg.frame3,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs1_chimp,marg,CompleteHit
4301,Q#1834 - >seq1833,non-specific,340205,166,229,6.95558e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs1_chimp.marg.frame3,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs1_chimp,marg,CompleteHit
4302,Q#1834 - >seq1833,superfamily,340205,166,229,6.95558e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs1_chimp.marg.frame3,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs1_chimp,marg,CompleteHit
4303,Q#1837 - >seq1836,non-specific,335182,67,163,9.45938e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4304,Q#1837 - >seq1836,superfamily,335182,67,163,9.45938e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4305,Q#1837 - >seq1836,non-specific,335182,67,163,9.45938e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4306,Q#1837 - >seq1836,non-specific,340205,167,230,1.25225e-22,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4307,Q#1837 - >seq1836,superfamily,340205,167,230,1.25225e-22,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4308,Q#1837 - >seq1836,non-specific,340205,167,230,1.25225e-22,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.pars.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,pars,CompleteHit
4309,Q#1840 - >seq1839,non-specific,335182,67,163,9.45938e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4310,Q#1840 - >seq1839,superfamily,335182,67,163,9.45938e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4311,Q#1840 - >seq1839,non-specific,335182,67,163,9.45938e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4312,Q#1840 - >seq1839,non-specific,340205,167,230,1.25225e-22,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4313,Q#1840 - >seq1839,superfamily,340205,167,230,1.25225e-22,87.3916,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4314,Q#1840 - >seq1839,non-specific,340205,167,230,1.25225e-22,87.3916,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs2_gorilla.marg.frame3,1909130020_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs2_gorilla,marg,CompleteHit
4315,Q#1842 - >seq1841,non-specific,335182,65,161,6.92568e-30,107.00299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs1_chimp.pars.frame1,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs1_chimp,pars,CompleteHit
4316,Q#1842 - >seq1841,superfamily,335182,65,161,6.92568e-30,107.00299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs1_chimp.pars.frame1,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs1_chimp,pars,CompleteHit
4317,Q#1842 - >seq1841,non-specific,340205,165,228,7.247350000000001e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs1_chimp.pars.frame1,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs1_chimp,pars,CompleteHit
4318,Q#1842 - >seq1841,superfamily,340205,165,228,7.247350000000001e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs1_chimp.pars.frame1,1909130020_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs1_chimp,pars,CompleteHit
4319,Q#1846 - >seq1845,non-specific,335182,148,244,6.960300000000001e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs0_human.pars.frame2,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs0_human,pars,CompleteHit
4320,Q#1846 - >seq1845,superfamily,335182,148,244,6.960300000000001e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs0_human.pars.frame2,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs0_human,pars,CompleteHit
4321,Q#1846 - >seq1845,non-specific,340205,247,310,4.97369e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs0_human.pars.frame2,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs0_human,pars,CompleteHit
4322,Q#1846 - >seq1845,superfamily,340205,247,310,4.97369e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs0_human.pars.frame2,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA4A,ORF1,hs0_human,pars,CompleteHit
4323,Q#1849 - >seq1848,non-specific,238827,610,649,2.11365e-05,46.9006,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs7_bushaby.marg.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,marg,BothTerminiTruncated
4324,Q#1849 - >seq1848,superfamily,295487,610,649,2.11365e-05,46.9006,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs7_bushaby.marg.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,marg,BothTerminiTruncated
4325,Q#1850 - >seq1849,non-specific,197310,4,231,2.86886e-24,102.815,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4A,ORF2,hs7_bushaby,marg,CompleteHit
4326,Q#1850 - >seq1849,superfamily,351117,4,231,2.86886e-24,102.815,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4A,ORF2,hs7_bushaby,marg,CompleteHit
4327,Q#1850 - >seq1849,non-specific,238827,534,652,3.67251e-18,84.6502,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4328,Q#1850 - >seq1849,superfamily,295487,534,652,3.67251e-18,84.6502,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4329,Q#1850 - >seq1849,non-specific,333820,555,658,4.6073100000000004e-05,45.361000000000004,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4330,Q#1850 - >seq1849,superfamily,333820,555,658,4.6073100000000004e-05,45.361000000000004,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4331,Q#1850 - >seq1849,non-specific,197306,4,235,0.000157257,44.7797,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs7_bushaby.marg.frame1,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4A,ORF2,hs7_bushaby,marg,CompleteHit
4332,Q#1852 - >seq1851,non-specific,238827,265,420,1.4993099999999998e-17,82.339,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs7_bushaby.pars.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,pars,C-TerminusTruncated
4333,Q#1852 - >seq1851,superfamily,295487,265,420,1.4993099999999998e-17,82.339,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs7_bushaby.pars.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,pars,C-TerminusTruncated
4334,Q#1852 - >seq1851,non-specific,333820,265,420,3.355e-08,54.2206,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs7_bushaby.pars.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,pars,C-TerminusTruncated
4335,Q#1852 - >seq1851,superfamily,333820,265,420,3.355e-08,54.2206,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs7_bushaby.pars.frame2,1909130020_L1MA4A.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs7_bushaby,pars,C-TerminusTruncated
4336,Q#1854 - >seq1853,non-specific,335182,154,250,4.655e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs0_human.marg.frame3,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs0_human,marg,CompleteHit
4337,Q#1854 - >seq1853,superfamily,335182,154,250,4.655e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4A.ORF1.hs0_human.marg.frame3,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs0_human,marg,CompleteHit
4338,Q#1854 - >seq1853,non-specific,340205,253,316,4.05477e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs0_human.marg.frame3,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs0_human,marg,CompleteHit
4339,Q#1854 - >seq1853,superfamily,340205,253,316,4.05477e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4A.ORF1.hs0_human.marg.frame3,1909130020_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4A,ORF1,hs0_human,marg,CompleteHit
4340,Q#1856 - >seq1855,non-specific,335182,67,163,1.40638e-27,100.84,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs3_orang.marg.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,marg,CompleteHit
4341,Q#1856 - >seq1855,superfamily,335182,67,163,1.40638e-27,100.84,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs3_orang.marg.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,marg,CompleteHit
4342,Q#1856 - >seq1855,non-specific,340205,167,229,2.11741e-25,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs3_orang.marg.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,marg,CompleteHit
4343,Q#1856 - >seq1855,superfamily,340205,167,229,2.11741e-25,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs3_orang.marg.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,marg,CompleteHit
4344,Q#1860 - >seq1859,non-specific,335182,68,164,7.156089999999999e-28,101.99600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs3_orang.pars.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,pars,CompleteHit
4345,Q#1860 - >seq1859,superfamily,335182,68,164,7.156089999999999e-28,101.99600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs3_orang.pars.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,pars,CompleteHit
4346,Q#1860 - >seq1859,non-specific,340205,168,230,1.6230899999999998e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs3_orang.pars.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,pars,CompleteHit
4347,Q#1860 - >seq1859,superfamily,340205,168,230,1.6230899999999998e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs3_orang.pars.frame3,1909130023_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs3_orang,pars,CompleteHit
4348,Q#1861 - >seq1860,non-specific,335182,21,117,2.4638899999999998e-29,104.307,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs4_gibbon.pars.frame1,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs4_gibbon,pars,CompleteHit
4349,Q#1861 - >seq1860,superfamily,335182,21,117,2.4638899999999998e-29,104.307,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs4_gibbon.pars.frame1,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs4_gibbon,pars,CompleteHit
4350,Q#1861 - >seq1860,non-specific,340205,121,184,2.13606e-21,82.7692,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs4_gibbon.pars.frame1,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs4_gibbon,pars,CompleteHit
4351,Q#1861 - >seq1860,superfamily,340205,121,184,2.13606e-21,82.7692,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs4_gibbon.pars.frame1,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA4,ORF1,hs4_gibbon,pars,CompleteHit
4352,Q#1866 - >seq1865,non-specific,335182,62,158,1.43934e-28,103.537,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs4_gibbon,marg,CompleteHit
4353,Q#1866 - >seq1865,superfamily,335182,62,158,1.43934e-28,103.537,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs4_gibbon,marg,CompleteHit
4354,Q#1866 - >seq1865,non-specific,340205,162,224,2.06485e-24,91.6288,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs4_gibbon,marg,CompleteHit
4355,Q#1866 - >seq1865,superfamily,340205,162,224,2.06485e-24,91.6288,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs4_gibbon,marg,CompleteHit
4356,Q#1866 - >seq1865,non-specific,234799,1,99,0.00398619,37.5555,PRK00578,prfB,C,cl30493,peptide chain release factor 2; Validated,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4,ORF1,hs4_gibbon,marg,C-TerminusTruncated
4357,Q#1866 - >seq1865,superfamily,234799,1,99,0.00398619,37.5555,cl30493,prfB superfamily,C, - ,peptide chain release factor 2; Validated,L1MA4.ORF1.hs4_gibbon.marg.frame3,1909130026_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4,ORF1,hs4_gibbon,marg,C-TerminusTruncated
4358,Q#1867 - >seq1866,non-specific,335182,63,159,3.97324e-30,107.389,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs5_gmonkey.marg.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,marg,CompleteHit
4359,Q#1867 - >seq1866,superfamily,335182,63,159,3.97324e-30,107.389,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs5_gmonkey.marg.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,marg,CompleteHit
4360,Q#1867 - >seq1866,non-specific,340205,163,208,1.35825e-13,63.5092,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs5_gmonkey.marg.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4361,Q#1867 - >seq1866,superfamily,340205,163,208,1.35825e-13,63.5092,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs5_gmonkey.marg.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
4362,Q#1872 - >seq1871,non-specific,335182,63,159,4.54782e-30,107.389,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs5_gmonkey.pars.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,pars,CompleteHit
4363,Q#1872 - >seq1871,superfamily,335182,63,159,4.54782e-30,107.389,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs5_gmonkey.pars.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,pars,CompleteHit
4364,Q#1872 - >seq1871,non-specific,340205,163,223,2.97651e-22,86.236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs5_gmonkey.pars.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,pars,CompleteHit
4365,Q#1872 - >seq1871,superfamily,340205,163,223,2.97651e-22,86.236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs5_gmonkey.pars.frame3,1909130027_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs5_gmonkey,pars,CompleteHit
4366,Q#1875 - >seq1874,non-specific,197310,4,229,1.7637500000000002e-17,83.1697,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs7_bushaby,marg,CompleteHit
4367,Q#1875 - >seq1874,superfamily,351117,4,229,1.7637500000000002e-17,83.1697,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs7_bushaby,marg,CompleteHit
4368,Q#1875 - >seq1874,non-specific,197306,4,213,4.13674e-05,46.3205,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs7_bushaby,marg,CompleteHit
4369,Q#1875 - >seq1874,non-specific,234767,449,702,0.000148064,46.3696,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4370,Q#1875 - >seq1874,superfamily,234767,449,702,0.000148064,46.3696,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
4371,Q#1875 - >seq1874,non-specific,227889,395,652,0.00386343,41.441,COG5602,Sin3,NC,cl35027,"Histone deacetylase complex, regulatory component SIN3  [Chromatin structure and dynamics]; Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics].",L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA4,ORF2,hs7_bushaby,marg,BothTerminiTruncated
4372,Q#1875 - >seq1874,superfamily,227889,395,652,0.00386343,41.441,cl35027,Sin3 superfamily,NC, - ,"Histone deacetylase complex, regulatory component SIN3  [Chromatin structure and dynamics]; Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics].",L1MA4.ORF2.hs7_bushaby.marg.frame1,1909130028_L1MA4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA4,ORF2,hs7_bushaby,marg,BothTerminiTruncated
4373,Q#1881 - >seq1880,non-specific,335182,62,158,1.72849e-29,105.848,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs6_sqmonkey.pars.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,pars,CompleteHit
4374,Q#1881 - >seq1880,superfamily,335182,62,158,1.72849e-29,105.848,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs6_sqmonkey.pars.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,pars,CompleteHit
4375,Q#1881 - >seq1880,non-specific,340205,162,224,4.213320000000001e-26,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs6_sqmonkey.pars.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,pars,CompleteHit
4376,Q#1881 - >seq1880,superfamily,340205,162,224,4.213320000000001e-26,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs6_sqmonkey.pars.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,pars,CompleteHit
4377,Q#1884 - >seq1883,non-specific,335182,58,154,8.94862e-30,106.23299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs6_sqmonkey.marg.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,marg,CompleteHit
4378,Q#1884 - >seq1883,superfamily,335182,58,154,8.94862e-30,106.23299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs6_sqmonkey.marg.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,marg,CompleteHit
4379,Q#1884 - >seq1883,non-specific,340205,158,220,4.33002e-26,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs6_sqmonkey.marg.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,marg,CompleteHit
4380,Q#1884 - >seq1883,superfamily,340205,158,220,4.33002e-26,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs6_sqmonkey.marg.frame3,1909130028_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs6_sqmonkey,marg,CompleteHit
4381,Q#1885 - >seq1884,non-specific,335182,131,227,1.1455000000000001e-27,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs1_chimp.marg.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,marg,CompleteHit
4382,Q#1885 - >seq1884,superfamily,335182,131,227,1.1455000000000001e-27,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs1_chimp.marg.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,marg,CompleteHit
4383,Q#1885 - >seq1884,non-specific,340205,254,295,2.03286e-12,61.198,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs1_chimp.marg.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,marg,N-TerminusTruncated
4384,Q#1885 - >seq1884,superfamily,340205,254,295,2.03286e-12,61.198,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs1_chimp.marg.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,marg,N-TerminusTruncated
4385,Q#1889 - >seq1888,non-specific,335182,133,229,6.88408e-28,103.537,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs1_chimp.pars.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,pars,CompleteHit
4386,Q#1889 - >seq1888,superfamily,335182,133,229,6.88408e-28,103.537,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs1_chimp.pars.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,pars,CompleteHit
4387,Q#1889 - >seq1888,non-specific,340205,256,297,4.04215e-12,60.4276,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs1_chimp.pars.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,pars,N-TerminusTruncated
4388,Q#1889 - >seq1888,superfamily,340205,256,297,4.04215e-12,60.4276,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs1_chimp.pars.frame1,1909130029_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs1_chimp,pars,N-TerminusTruncated
4389,Q#1892 - >seq1891,non-specific,335182,62,158,9.72036e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs0_human.marg.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,marg,CompleteHit
4390,Q#1892 - >seq1891,superfamily,335182,62,158,9.72036e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs0_human.marg.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,marg,CompleteHit
4391,Q#1892 - >seq1891,non-specific,340205,162,227,4.920149999999999e-21,83.1544,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs0_human.marg.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,marg,CompleteHit
4392,Q#1892 - >seq1891,superfamily,340205,162,227,4.920149999999999e-21,83.1544,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs0_human.marg.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,marg,CompleteHit
4393,Q#1894 - >seq1893,non-specific,335182,62,158,1.34896e-29,106.23299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs0_human.pars.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,pars,CompleteHit
4394,Q#1894 - >seq1893,superfamily,335182,62,158,1.34896e-29,106.23299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA4.ORF1.hs0_human.pars.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,pars,CompleteHit
4395,Q#1894 - >seq1893,non-specific,340205,162,230,2.89243e-19,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs0_human.pars.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,pars,CompleteHit
4396,Q#1894 - >seq1893,superfamily,340205,162,230,2.89243e-19,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA4.ORF1.hs0_human.pars.frame3,1909130029_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA4,ORF1,hs0_human,pars,CompleteHit
4397,Q#1897 - >seq1896,specific,238827,518,761,2.0458999999999997e-55,191.736,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4398,Q#1897 - >seq1896,superfamily,295487,518,761,2.0458999999999997e-55,191.736,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4399,Q#1897 - >seq1896,specific,197310,9,230,1.6278299999999998e-34,132.475,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4400,Q#1897 - >seq1896,superfamily,351117,9,230,1.6278299999999998e-34,132.475,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4401,Q#1897 - >seq1896,specific,333820,518,730,3.78578e-30,118.164,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4402,Q#1897 - >seq1896,superfamily,333820,518,730,3.78578e-30,118.164,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4403,Q#1897 - >seq1896,non-specific,197306,9,230,9.00286e-21,92.5444,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4404,Q#1897 - >seq1896,non-specific,238828,572,730,4.81493e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
4405,Q#1897 - >seq1896,specific,335306,10,223,7.71811e-11,63.033,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4406,Q#1897 - >seq1896,non-specific,275209,577,729,4.42903e-06,50.1488,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
4407,Q#1897 - >seq1896,superfamily,275209,577,729,4.42903e-06,50.1488,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
4408,Q#1897 - >seq1896,non-specific,197320,7,201,4.32406e-05,46.3542,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4409,Q#1897 - >seq1896,non-specific,272954,7,230,0.00014819,44.6813,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4410,Q#1897 - >seq1896,non-specific,223780,7,201,0.000220482,44.1263,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4411,Q#1897 - >seq1896,non-specific,274009,300,491,0.000221793,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
4412,Q#1897 - >seq1896,superfamily,274009,300,491,0.000221793,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
4413,Q#1897 - >seq1896,non-specific,197321,7,49,0.000420376,43.3096,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
4414,Q#1897 - >seq1896,non-specific,197336,7,43,0.00105343,42.2143,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
4415,Q#1897 - >seq1896,non-specific,197307,9,230,0.00172425,41.5045,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4416,Q#1897 - >seq1896,specific,311990,1229,1247,0.00215724,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4417,Q#1897 - >seq1896,superfamily,311990,1229,1247,0.00215724,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4418,Q#1897 - >seq1896,non-specific,235175,284,462,0.00249364,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
4419,Q#1897 - >seq1896,superfamily,235175,284,462,0.00249364,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
4420,Q#1897 - >seq1896,non-specific,197318,9,230,0.00317239,40.7427,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,marg,CompleteHit
4421,Q#1897 - >seq1896,non-specific,273186,7,43,0.00698661,39.5696,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
4422,Q#1900 - >seq1899,specific,238827,509,730,7.50091e-44,158.608,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4423,Q#1900 - >seq1899,superfamily,295487,509,730,7.50091e-44,158.608,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4424,Q#1900 - >seq1899,specific,197310,9,232,2.92601e-34,131.705,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4425,Q#1900 - >seq1899,superfamily,351117,9,232,2.92601e-34,131.705,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4426,Q#1900 - >seq1899,non-specific,333820,507,699,1.95966e-22,95.8221,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4427,Q#1900 - >seq1899,superfamily,333820,507,699,1.95966e-22,95.8221,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4428,Q#1900 - >seq1899,non-specific,197306,9,232,7.37058e-21,92.9296,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4429,Q#1900 - >seq1899,non-specific,238828,541,699,1.93563e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
4430,Q#1900 - >seq1899,specific,335306,10,226,5.50366e-11,63.4182,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4431,Q#1900 - >seq1899,non-specific,275209,546,698,3.54767e-06,50.534,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4432,Q#1900 - >seq1899,superfamily,275209,546,698,3.54767e-06,50.534,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4433,Q#1900 - >seq1899,non-specific,197320,7,204,0.00011978700000000001,44.8134,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4434,Q#1900 - >seq1899,non-specific,223780,7,43,0.00016528900000000002,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4435,Q#1900 - >seq1899,non-specific,197321,7,49,0.00033248,43.6948,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4436,Q#1900 - >seq1899,non-specific,197318,9,229,0.000502183,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4437,Q#1900 - >seq1899,non-specific,272954,7,232,0.000511951,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4438,Q#1900 - >seq1899,specific,311990,1198,1216,0.0007096,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4439,Q#1900 - >seq1899,superfamily,311990,1198,1216,0.0007096,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4440,Q#1900 - >seq1899,non-specific,197336,7,43,0.00102464,42.2143,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4441,Q#1900 - >seq1899,non-specific,197307,9,232,0.00142733,41.5045,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,CompleteHit
4442,Q#1900 - >seq1899,non-specific,273186,7,43,0.00563584,39.9548,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs2_gorilla.pars.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4443,Q#1902 - >seq1901,non-specific,274009,270,461,6.88174e-05,46.9847,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4444,Q#1902 - >seq1901,superfamily,274009,270,461,6.88174e-05,46.9847,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4445,Q#1902 - >seq1901,non-specific,235175,229,432,0.000209244,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4446,Q#1902 - >seq1901,superfamily,235175,229,432,0.000209244,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4447,Q#1902 - >seq1901,non-specific,238827,488,508,0.000251073,43.4338,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4448,Q#1902 - >seq1901,superfamily,295487,488,508,0.000251073,43.4338,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
4449,Q#1902 - >seq1901,non-specific,223496,283,460,0.006026300000000001,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4450,Q#1902 - >seq1901,superfamily,223496,283,460,0.006026300000000001,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MA5A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
4451,Q#1902 - >seq1901,non-specific,224117,228,449,0.00958281,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
4452,Q#1902 - >seq1901,superfamily,224117,228,449,0.00958281,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA5A.ORF2.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1MA5A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
4453,Q#1903 - >seq1902,non-specific,335182,155,245,9.894590000000001e-21,85.04700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs2_gorilla,marg,CompleteHit
4454,Q#1903 - >seq1902,superfamily,335182,155,245,9.894590000000001e-21,85.04700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs2_gorilla,marg,CompleteHit
4455,Q#1903 - >seq1902,non-specific,340205,248,310,3.11327e-15,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs2_gorilla,marg,CompleteHit
4456,Q#1903 - >seq1902,superfamily,340205,248,310,3.11327e-15,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs2_gorilla.marg.frame3,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs2_gorilla,marg,CompleteHit
4457,Q#1908 - >seq1907,non-specific,335182,58,144,1.7421400000000003e-22,87.3582,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs2_gorilla,pars,CompleteHit
4458,Q#1908 - >seq1907,superfamily,335182,58,144,1.7421400000000003e-22,87.3582,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs2_gorilla,pars,CompleteHit
4459,Q#1908 - >seq1907,non-specific,340205,147,209,3.39534e-16,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs2_gorilla,pars,CompleteHit
4460,Q#1908 - >seq1907,superfamily,340205,147,209,3.39534e-16,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs2_gorilla.pars.frame1,1909130031_L1MA5A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs2_gorilla,pars,CompleteHit
4461,Q#1909 - >seq1908,specific,238827,529,773,5.697449999999999e-59,202.136,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4462,Q#1909 - >seq1908,superfamily,295487,529,773,5.697449999999999e-59,202.136,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4463,Q#1909 - >seq1908,specific,197310,9,240,1.7889499999999999e-56,195.648,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4464,Q#1909 - >seq1908,superfamily,351117,9,240,1.7889499999999999e-56,195.648,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4465,Q#1909 - >seq1908,specific,333820,529,773,5.739699999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4466,Q#1909 - >seq1908,superfamily,333820,529,773,5.739699999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4467,Q#1909 - >seq1908,non-specific,197306,9,240,7.1537999999999994e-31,122.205,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4468,Q#1909 - >seq1908,specific,335306,10,233,3.3400599999999995e-14,73.0481,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4469,Q#1909 - >seq1908,non-specific,197307,9,240,8.112100000000001e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4470,Q#1909 - >seq1908,non-specific,197320,7,233,2.6620500000000003e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4471,Q#1909 - >seq1908,non-specific,197321,7,240,8.16214e-12,66.8068,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4472,Q#1909 - >seq1908,non-specific,223780,7,233,2.55316e-11,65.3123,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4473,Q#1909 - >seq1908,non-specific,238828,583,738,4.55704e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,N-TerminusTruncated
4474,Q#1909 - >seq1908,non-specific,273186,7,241,2.21348e-10,62.2964,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4475,Q#1909 - >seq1908,non-specific,197319,7,240,3.8716899999999995e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4476,Q#1909 - >seq1908,non-specific,275209,588,797,8.10683e-08,55.5416,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,N-TerminusTruncated
4477,Q#1909 - >seq1908,superfamily,275209,588,797,8.10683e-08,55.5416,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,N-TerminusTruncated
4478,Q#1909 - >seq1908,non-specific,197336,7,198,7.114e-07,51.8443,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4479,Q#1909 - >seq1908,non-specific,197311,41,240,2.7393400000000004e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4480,Q#1909 - >seq1908,non-specific,272954,7,240,2.31235e-05,47.3777,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4481,Q#1909 - >seq1908,non-specific,274009,310,459,0.00016538599999999998,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4482,Q#1909 - >seq1908,superfamily,274009,310,459,0.00016538599999999998,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4483,Q#1909 - >seq1908,non-specific,238185,657,773,0.00019203799999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4484,Q#1909 - >seq1908,non-specific,339261,112,236,0.000674755,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4485,Q#1909 - >seq1908,specific,311990,1242,1260,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4486,Q#1909 - >seq1908,superfamily,311990,1242,1260,0.00205315,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs1_chimp,marg,CompleteHit
4487,Q#1909 - >seq1908,non-specific,235175,245,465,0.0021824,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4488,Q#1909 - >seq1908,superfamily,235175,245,465,0.0021824,42.3584,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4489,Q#1909 - >seq1908,non-specific,308206,254,447,0.0035378,41.4961,pfam02463,SMC_N,C,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4490,Q#1909 - >seq1908,superfamily,308206,254,447,0.0035378,41.4961,cl37666,SMC_N superfamily,C, - ,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MA5A,ORF2,hs1_chimp,marg,C-TerminusTruncated
4491,Q#1909 - >seq1908,non-specific,223496,323,503,0.00559669,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs1_chimp,marg,BothTerminiTruncated
4492,Q#1909 - >seq1908,superfamily,223496,323,503,0.00559669,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.marg.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA5A,ORF2,hs1_chimp,marg,BothTerminiTruncated
4493,Q#1912 - >seq1911,specific,197310,9,240,8.159130000000001e-57,196.418,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4494,Q#1912 - >seq1911,superfamily,351117,9,240,8.159130000000001e-57,196.418,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4495,Q#1912 - >seq1911,non-specific,197306,9,240,1.81404e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4496,Q#1912 - >seq1911,non-specific,197307,9,240,6.41913e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4497,Q#1912 - >seq1911,specific,335306,10,233,3.0393400000000004e-14,73.0481,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4498,Q#1912 - >seq1911,non-specific,197320,7,233,1.22187e-13,72.1626,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4499,Q#1912 - >seq1911,non-specific,197321,7,240,1.71602e-12,68.7328,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4500,Q#1912 - >seq1911,non-specific,223780,7,233,1.90664e-12,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4501,Q#1912 - >seq1911,non-specific,273186,7,241,3.89579e-11,64.6076,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4502,Q#1912 - >seq1911,non-specific,197319,7,240,2.4534400000000004e-10,62.2941,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4503,Q#1912 - >seq1911,non-specific,197336,7,198,6.022930000000001e-07,51.8443,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4504,Q#1912 - >seq1911,non-specific,197311,41,240,1.6116299999999997e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4505,Q#1912 - >seq1911,non-specific,272954,7,240,2.89124e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4506,Q#1912 - >seq1911,non-specific,274009,310,459,5.79121e-05,47.3699,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4507,Q#1912 - >seq1911,superfamily,274009,310,459,5.79121e-05,47.3699,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4508,Q#1912 - >seq1911,non-specific,235175,245,465,0.00033239,44.6696,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4509,Q#1912 - >seq1911,superfamily,235175,245,465,0.00033239,44.6696,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4510,Q#1912 - >seq1911,specific,311990,1170,1188,0.000569831,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4511,Q#1912 - >seq1911,superfamily,311990,1170,1188,0.000569831,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4512,Q#1912 - >seq1911,non-specific,339261,112,236,0.000628643,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4513,Q#1912 - >seq1911,non-specific,308206,254,447,0.00114992,43.0369,pfam02463,SMC_N,C,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4514,Q#1912 - >seq1911,superfamily,308206,254,447,0.00114992,43.0369,cl37666,SMC_N superfamily,C, - ,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA5A,ORF2,hs1_chimp,pars,C-TerminusTruncated
4515,Q#1912 - >seq1911,non-specific,334125,214,413,0.00134051,42.5216,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA5A,ORF2,hs1_chimp,pars,N-TerminusTruncated
4516,Q#1912 - >seq1911,superfamily,334125,214,413,0.00134051,42.5216,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA5A,ORF2,hs1_chimp,pars,N-TerminusTruncated
4517,Q#1912 - >seq1911,non-specific,274009,324,465,0.00397882,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs1_chimp,pars,BothTerminiTruncated
4518,Q#1912 - >seq1911,non-specific,223496,323,502,0.00551107,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs1_chimp,pars,BothTerminiTruncated
4519,Q#1912 - >seq1911,superfamily,223496,323,502,0.00551107,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs1_chimp.pars.frame3,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA5A,ORF2,hs1_chimp,pars,BothTerminiTruncated
4520,Q#1913 - >seq1912,specific,238827,471,733,8.842299999999998e-61,207.144,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4521,Q#1913 - >seq1912,superfamily,295487,471,733,8.842299999999998e-61,207.144,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4522,Q#1913 - >seq1912,specific,333820,489,733,3.25598e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4523,Q#1913 - >seq1912,superfamily,333820,489,733,3.25598e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4524,Q#1913 - >seq1912,non-specific,238828,543,698,9.012589999999999e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,N-TerminusTruncated
4525,Q#1913 - >seq1912,non-specific,275209,548,757,6.38597e-08,55.9268,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,N-TerminusTruncated
4526,Q#1913 - >seq1912,superfamily,275209,548,757,6.38597e-08,55.9268,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,N-TerminusTruncated
4527,Q#1913 - >seq1912,non-specific,238185,617,733,1.4120899999999999e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs1_chimp.pars.frame2,1909130031_L1MA5A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs1_chimp,pars,CompleteHit
4528,Q#1917 - >seq1916,non-specific,335182,1,78,2.628e-29,102.766,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs3_orang.pars.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,pars,N-TerminusTruncated
4529,Q#1917 - >seq1916,superfamily,335182,1,78,2.628e-29,102.766,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs3_orang.pars.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,pars,N-TerminusTruncated
4530,Q#1917 - >seq1916,non-specific,340205,93,144,5.732430000000001e-18,72.75399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs3_orang.pars.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,pars,CompleteHit
4531,Q#1917 - >seq1916,superfamily,340205,93,144,5.732430000000001e-18,72.75399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs3_orang.pars.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,pars,CompleteHit
4532,Q#1920 - >seq1919,non-specific,335182,165,248,4.2969699999999995e-28,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs3_orang.marg.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,marg,CompleteHit
4533,Q#1920 - >seq1919,superfamily,335182,165,248,4.2969699999999995e-28,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs3_orang.marg.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,marg,CompleteHit
4534,Q#1920 - >seq1919,non-specific,340205,271,322,8.43215e-12,59.6572,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs3_orang.marg.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,marg,CompleteHit
4535,Q#1920 - >seq1919,superfamily,340205,271,322,8.43215e-12,59.6572,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs3_orang.marg.frame3,1909130033_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs3_orang,marg,CompleteHit
4536,Q#1921 - >seq1920,specific,238827,490,711,1.0745499999999999e-42,155.142,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4537,Q#1921 - >seq1920,superfamily,295487,490,711,1.0745499999999999e-42,155.142,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4538,Q#1921 - >seq1920,non-specific,333820,493,679,1.06929e-22,96.5925,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4539,Q#1921 - >seq1920,superfamily,333820,493,679,1.06929e-22,96.5925,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4540,Q#1921 - >seq1920,non-specific,238828,521,676,2.43922e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,N-TerminusTruncated
4541,Q#1921 - >seq1920,non-specific,275209,526,735,3.0089e-08,57.0824,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,N-TerminusTruncated
4542,Q#1921 - >seq1920,superfamily,275209,526,735,3.0089e-08,57.0824,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,N-TerminusTruncated
4543,Q#1921 - >seq1920,non-specific,238185,595,680,0.00229882,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4544,Q#1921 - >seq1920,non-specific,240420,206,401,0.00651872,40.3325,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,marg,N-TerminusTruncated
4545,Q#1921 - >seq1920,superfamily,240420,206,401,0.00651872,40.3325,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1MA5A.ORF2.hs3_orang.marg.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,marg,N-TerminusTruncated
4546,Q#1922 - >seq1921,non-specific,197310,47,120,1.13096e-06,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs3_orang.marg.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4547,Q#1922 - >seq1921,superfamily,351117,47,120,1.13096e-06,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.marg.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4548,Q#1922 - >seq1921,non-specific,197306,38,122,0.00183806,41.3129,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.marg.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4549,Q#1923 - >seq1922,specific,197310,9,234,3.78283e-32,125.542,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4550,Q#1923 - >seq1922,superfamily,351117,9,234,3.78283e-32,125.542,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4551,Q#1923 - >seq1922,non-specific,197306,9,234,7.358369999999999e-17,81.3736,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4552,Q#1923 - >seq1922,specific,335306,10,227,2.23746e-13,70.7369,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4553,Q#1923 - >seq1922,non-specific,197307,9,234,3.49179e-05,46.5121,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4554,Q#1923 - >seq1922,non-specific,238827,506,554,0.000139744,44.5894,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4555,Q#1923 - >seq1922,superfamily,295487,506,554,0.000139744,44.5894,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4556,Q#1923 - >seq1922,non-specific,197321,7,63,0.00024953700000000003,44.08,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4557,Q#1923 - >seq1922,non-specific,273186,7,235,0.00102255,42.266000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4558,Q#1923 - >seq1922,specific,311990,1200,1218,0.00109278,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4559,Q#1923 - >seq1922,superfamily,311990,1200,1218,0.00109278,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs3_orang,marg,CompleteHit
4560,Q#1923 - >seq1922,non-specific,223780,7,43,0.00159248,41.4299,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5A,ORF2,hs3_orang,marg,C-TerminusTruncated
4561,Q#1923 - >seq1922,non-specific,223496,318,552,0.00170111,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs3_orang,marg,BothTerminiTruncated
4562,Q#1923 - >seq1922,superfamily,223496,318,552,0.00170111,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.marg.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA5A,ORF2,hs3_orang,marg,BothTerminiTruncated
4563,Q#1924 - >seq1923,specific,238827,492,704,6.0784699999999995e-40,147.438,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4564,Q#1924 - >seq1923,superfamily,295487,492,704,6.0784699999999995e-40,147.438,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4565,Q#1924 - >seq1923,non-specific,333820,495,681,6.551069999999999e-22,94.2813,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4566,Q#1924 - >seq1923,superfamily,333820,495,681,6.551069999999999e-22,94.2813,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4567,Q#1924 - >seq1923,non-specific,238828,523,678,8.24212e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,N-TerminusTruncated
4568,Q#1924 - >seq1923,non-specific,275209,528,750,7.77819e-08,55.5416,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,N-TerminusTruncated
4569,Q#1924 - >seq1923,superfamily,275209,528,750,7.77819e-08,55.5416,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,N-TerminusTruncated
4570,Q#1924 - >seq1923,specific,311990,1171,1189,0.000616777,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4571,Q#1924 - >seq1923,superfamily,311990,1171,1189,0.000616777,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4572,Q#1924 - >seq1923,non-specific,240420,208,403,0.00184956,42.2585,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,pars,N-TerminusTruncated
4573,Q#1924 - >seq1923,superfamily,240420,208,403,0.00184956,42.2585,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,pars,N-TerminusTruncated
4574,Q#1924 - >seq1923,non-specific,238185,597,682,0.00516863,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4575,Q#1924 - >seq1923,non-specific,273727,299,477,0.00622776,40.2618,TIGR01642,U2AF_lg,C,cl36941,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4576,Q#1924 - >seq1923,superfamily,273727,299,477,0.00622776,40.2618,cl36941,U2AF_lg superfamily,C, - ,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA5A.ORF2.hs3_orang.pars.frame2,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4577,Q#1925 - >seq1924,specific,197310,12,237,3.13155e-32,125.542,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4578,Q#1925 - >seq1924,superfamily,351117,12,237,3.13155e-32,125.542,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4579,Q#1925 - >seq1924,non-specific,197306,12,237,3.8040999999999997e-17,82.14399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4580,Q#1925 - >seq1924,specific,335306,13,230,2.1207399999999999e-13,70.7369,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4581,Q#1925 - >seq1924,non-specific,197307,12,237,7.8397e-06,48.4381,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4582,Q#1925 - >seq1924,non-specific,238827,509,557,6.54694e-05,45.3598,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4583,Q#1925 - >seq1924,superfamily,295487,509,557,6.54694e-05,45.3598,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4584,Q#1925 - >seq1924,non-specific,197321,10,66,0.000149711,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4585,Q#1925 - >seq1924,non-specific,273186,10,238,0.000445054,43.0364,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4586,Q#1925 - >seq1924,non-specific,223496,321,555,0.00048966,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,BothTerminiTruncated
4587,Q#1925 - >seq1924,superfamily,223496,321,555,0.00048966,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA5A,ORF2,hs3_orang,pars,BothTerminiTruncated
4588,Q#1925 - >seq1924,non-specific,223780,10,230,0.00103976,42.2003,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4589,Q#1925 - >seq1924,non-specific,197319,10,237,0.00378276,40.3377,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs3_orang.pars.frame3,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs3_orang,pars,CompleteHit
4590,Q#1926 - >seq1925,non-specific,197310,50,123,1.2565799999999998e-06,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs3_orang.pars.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4591,Q#1926 - >seq1925,superfamily,351117,50,123,1.2565799999999998e-06,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.pars.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4592,Q#1926 - >seq1925,non-specific,197306,41,125,0.00176464,41.3129,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs3_orang.pars.frame1,1909130034_L1MA5A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs3_orang,pars,C-TerminusTruncated
4593,Q#1929 - >seq1928,non-specific,335182,32,123,8.75734e-31,108.15899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,pars,CompleteHit
4594,Q#1929 - >seq1928,superfamily,335182,32,123,8.75734e-31,108.15899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,pars,CompleteHit
4595,Q#1929 - >seq1928,non-specific,340205,126,190,2.67395e-15,66.976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,pars,CompleteHit
4596,Q#1929 - >seq1928,superfamily,340205,126,190,2.67395e-15,66.976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,pars,CompleteHit
4597,Q#1932 - >seq1931,non-specific,197310,135,212,3.43106e-06,49.2721,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.pars.frame1,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
4598,Q#1932 - >seq1931,superfamily,351117,135,212,3.43106e-06,49.2721,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.pars.frame1,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
4599,Q#1933 - >seq1932,non-specific,197310,84,170,1.66424e-11,65.4505,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
4600,Q#1933 - >seq1932,superfamily,351117,84,170,1.66424e-11,65.4505,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
4601,Q#1933 - >seq1932,non-specific,197306,90,178,3.4749300000000004e-06,49.4021,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
4602,Q#1933 - >seq1932,non-specific,197320,91,169,8.95854e-05,45.1986,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
4603,Q#1933 - >seq1932,non-specific,238827,655,710,0.0038207999999999996,39.967,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
4604,Q#1933 - >seq1932,superfamily,295487,655,710,0.0038207999999999996,39.967,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
4605,Q#1933 - >seq1932,non-specific,197311,78,130,0.00733214,39.1973,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.pars.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
4606,Q#1934 - >seq1933,specific,238827,472,669,5.21816e-52,182.106,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4607,Q#1934 - >seq1933,superfamily,295487,472,669,5.21816e-52,182.106,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4608,Q#1934 - >seq1933,non-specific,333820,478,669,3.94179e-28,112.001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4609,Q#1934 - >seq1933,superfamily,333820,478,669,3.94179e-28,112.001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4610,Q#1934 - >seq1933,non-specific,238828,478,669,2.1222000000000002e-10,61.8332,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4611,Q#1934 - >seq1933,non-specific,197310,1,103,5.59932e-10,60.8281,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4612,Q#1934 - >seq1933,superfamily,351117,1,103,5.59932e-10,60.8281,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4613,Q#1934 - >seq1933,non-specific,275209,429,633,3.35897e-07,53.6156,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4614,Q#1934 - >seq1933,superfamily,275209,429,633,3.35897e-07,53.6156,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
4615,Q#1934 - >seq1933,non-specific,197306,1,167,0.000670197,42.4685,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.pars.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,pars,CompleteHit
4616,Q#1935 - >seq1934,non-specific,197310,147,224,4.1869699999999995e-06,49.2721,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.marg.frame1,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
4617,Q#1935 - >seq1934,superfamily,351117,147,224,4.1869699999999995e-06,49.2721,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.marg.frame1,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
4618,Q#1936 - >seq1935,specific,197310,9,188,8.964069999999999e-31,121.304,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
4619,Q#1936 - >seq1935,superfamily,351117,9,188,8.964069999999999e-31,121.304,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
4620,Q#1936 - >seq1935,non-specific,197306,9,196,3.49258e-19,87.92200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4621,Q#1936 - >seq1935,specific,335306,10,190,6.894780000000001e-07,51.477,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4622,Q#1936 - >seq1935,non-specific,197320,108,187,7.277890000000001e-05,45.5838,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
4623,Q#1936 - >seq1935,non-specific,223780,7,187,0.00019381099999999998,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
4624,Q#1936 - >seq1935,specific,311990,1176,1194,0.00024688900000000003,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4625,Q#1936 - >seq1935,superfamily,311990,1176,1194,0.00024688900000000003,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4626,Q#1936 - >seq1935,non-specific,197307,9,195,0.00348715,40.3489,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4627,Q#1936 - >seq1935,non-specific,197311,104,148,0.00833377,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs4_gibbon.marg.frame2,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
4628,Q#1937 - >seq1936,specific,238827,467,728,2.8878999999999994e-63,214.077,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4629,Q#1937 - >seq1936,superfamily,295487,467,728,2.8878999999999994e-63,214.077,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4630,Q#1937 - >seq1936,specific,333820,473,696,7.033510000000001e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4631,Q#1937 - >seq1936,superfamily,333820,473,696,7.033510000000001e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4632,Q#1937 - >seq1936,non-specific,238828,473,693,8.58148e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4633,Q#1937 - >seq1936,non-specific,275209,424,752,6.32941e-11,65.1716,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4634,Q#1937 - >seq1936,superfamily,275209,424,752,6.32941e-11,65.1716,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4635,Q#1937 - >seq1936,non-specific,238185,612,697,0.00874808,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5A,ORF2,hs4_gibbon,marg,CompleteHit
4636,Q#1938 - >seq1937,non-specific,335182,144,235,1.67959e-28,105.463,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,marg,CompleteHit
4637,Q#1938 - >seq1937,superfamily,335182,144,235,1.67959e-28,105.463,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,marg,CompleteHit
4638,Q#1938 - >seq1937,non-specific,340205,238,302,2.45088e-14,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,marg,CompleteHit
4639,Q#1938 - >seq1937,superfamily,340205,238,302,2.45088e-14,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs4_gibbon.marg.frame3,1909130036_L1MA5A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5A,ORF1,hs4_gibbon,marg,CompleteHit
4640,Q#1940 - >seq1939,non-specific,335182,162,254,1.36956e-27,103.15100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs5_gmonkey.marg.frame2,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs5_gmonkey,marg,CompleteHit
4641,Q#1940 - >seq1939,superfamily,335182,162,254,1.36956e-27,103.15100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs5_gmonkey.marg.frame2,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs5_gmonkey,marg,CompleteHit
4642,Q#1940 - >seq1939,non-specific,340205,257,320,2.67771e-22,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs5_gmonkey.marg.frame2,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs5_gmonkey,marg,CompleteHit
4643,Q#1940 - >seq1939,superfamily,340205,257,320,2.67771e-22,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs5_gmonkey.marg.frame2,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs5_gmonkey,marg,CompleteHit
4644,Q#1943 - >seq1942,non-specific,335182,22,96,6.0412899999999994e-27,97.3734,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs5_gmonkey.pars.frame1,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
4645,Q#1943 - >seq1942,superfamily,335182,22,96,6.0412899999999994e-27,97.3734,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs5_gmonkey.pars.frame1,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
4646,Q#1943 - >seq1942,non-specific,340205,99,161,4.17725e-25,91.6288,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs5_gmonkey.pars.frame1,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs5_gmonkey,pars,CompleteHit
4647,Q#1943 - >seq1942,superfamily,340205,99,161,4.17725e-25,91.6288,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs5_gmonkey.pars.frame1,1909130037_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs5_gmonkey,pars,CompleteHit
4648,Q#1947 - >seq1946,non-specific,340205,132,195,1.9517899999999999e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs0_human,marg,CompleteHit
4649,Q#1947 - >seq1946,superfamily,340205,132,195,1.9517899999999999e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs0_human,marg,CompleteHit
4650,Q#1947 - >seq1946,non-specific,335182,52,129,4.25261e-24,90.825,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs0_human,marg,N-TerminusTruncated
4651,Q#1947 - >seq1946,superfamily,335182,52,129,4.25261e-24,90.825,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs0_human,marg,N-TerminusTruncated
4652,Q#1949 - >seq1948,specific,238827,609,721,1.6022399999999999e-26,108.53299999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,N-TerminusTruncated
4653,Q#1949 - >seq1948,superfamily,295487,609,721,1.6022399999999999e-26,108.53299999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,N-TerminusTruncated
4654,Q#1949 - >seq1948,non-specific,333820,564,721,2.40026e-11,63.8506,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,N-TerminusTruncated
4655,Q#1949 - >seq1948,superfamily,333820,564,721,2.40026e-11,63.8506,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,N-TerminusTruncated
4656,Q#1949 - >seq1948,non-specific,238185,609,721,0.000168457,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4657,Q#1949 - >seq1948,non-specific,238828,609,721,0.00159617,41.0325,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs0_human,pars,N-TerminusTruncated
4658,Q#1949 - >seq1948,non-specific,236995,650,742,0.00991673,40.0327,PRK11824,PRK11824,NC,cl36064,polynucleotide phosphorylase/polyadenylase; Provisional,L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA5A,ORF2,hs0_human,pars,BothTerminiTruncated
4659,Q#1949 - >seq1948,superfamily,236995,650,742,0.00991673,40.0327,cl36064,PRK11824 superfamily,NC, - ,polynucleotide phosphorylase/polyadenylase; Provisional,L1MA5A.ORF2.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA5A,ORF2,hs0_human,pars,BothTerminiTruncated
4660,Q#1950 - >seq1949,specific,197310,9,237,3.1637499999999996e-36,137.09799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4661,Q#1950 - >seq1949,superfamily,351117,9,237,3.1637499999999996e-36,137.09799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4662,Q#1950 - >seq1949,specific,238827,511,617,3.25978e-28,113.54,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4663,Q#1950 - >seq1949,superfamily,295487,511,617,3.25978e-28,113.54,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4664,Q#1950 - >seq1949,non-specific,197306,9,237,7.44332e-20,89.848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4665,Q#1950 - >seq1949,non-specific,333820,529,628,2.48468e-13,69.6286,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4666,Q#1950 - >seq1949,superfamily,333820,529,628,2.48468e-13,69.6286,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4667,Q#1950 - >seq1949,specific,335306,10,230,4.0997e-12,66.885,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4668,Q#1950 - >seq1949,non-specific,197320,7,230,3.25942e-08,55.9842,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4669,Q#1950 - >seq1949,non-specific,197321,7,237,3.5082499999999997e-08,55.636,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4670,Q#1950 - >seq1949,non-specific,197307,9,237,5.57871e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4671,Q#1950 - >seq1949,non-specific,197319,7,237,6.49426e-07,51.8937,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4672,Q#1950 - >seq1949,non-specific,223780,7,230,2.02224e-06,50.2895,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs0_human.pars.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4673,Q#1951 - >seq1950,specific,311990,1139,1157,0.000194787,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs0_human.pars.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4674,Q#1951 - >seq1950,superfamily,311990,1139,1157,0.000194787,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs0_human.pars.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5A,ORF2,hs0_human,pars,CompleteHit
4675,Q#1951 - >seq1950,non-specific,197310,43,113,0.00216439,40.7977,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs0_human.pars.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4676,Q#1951 - >seq1950,superfamily,351117,43,113,0.00216439,40.7977,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.pars.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,pars,C-TerminusTruncated
4677,Q#1952 - >seq1951,specific,238827,532,776,1.65e-60,206.373,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4678,Q#1952 - >seq1951,superfamily,295487,532,776,1.65e-60,206.373,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4679,Q#1952 - >seq1951,specific,197310,9,239,9.80736e-35,132.86,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4680,Q#1952 - >seq1951,superfamily,351117,9,239,9.80736e-35,132.86,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4681,Q#1952 - >seq1951,specific,333820,532,776,2.0862199999999998e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4682,Q#1952 - >seq1951,superfamily,333820,532,776,2.0862199999999998e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4683,Q#1952 - >seq1951,non-specific,197306,9,239,4.62227e-19,87.92200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4684,Q#1952 - >seq1951,specific,335306,10,232,4.72882e-12,66.885,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4685,Q#1952 - >seq1951,non-specific,238828,586,776,5.71313e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,N-TerminusTruncated
4686,Q#1952 - >seq1951,non-specific,275209,591,804,4.40874e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,N-TerminusTruncated
4687,Q#1952 - >seq1951,superfamily,275209,591,804,4.40874e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,N-TerminusTruncated
4688,Q#1952 - >seq1951,non-specific,197320,116,232,5.9356e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,marg,N-TerminusTruncated
4689,Q#1952 - >seq1951,non-specific,197321,7,239,1.6418400000000004e-06,50.6284,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4690,Q#1952 - >seq1951,non-specific,197307,9,239,2.70471e-06,49.9789,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4691,Q#1952 - >seq1951,non-specific,197319,7,239,2.63745e-05,46.8861,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4692,Q#1952 - >seq1951,non-specific,223780,7,232,3.97112e-05,46.4375,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4693,Q#1952 - >seq1951,non-specific,238185,660,776,4.8234399999999993e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4694,Q#1952 - >seq1951,non-specific,239569,544,789,0.00507187,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MA5A.ORF2.hs0_human.marg.frame2,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4695,Q#1953 - >seq1952,non-specific,197310,45,115,0.00211028,40.7977,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs0_human.marg.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5A,ORF2,hs0_human,marg,C-TerminusTruncated
4696,Q#1953 - >seq1952,superfamily,351117,45,115,0.00211028,40.7977,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs0_human.marg.frame3,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs0_human,marg,C-TerminusTruncated
4697,Q#1955 - >seq1954,non-specific,340205,242,305,1.0596199999999999e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs1_chimp.pars.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,pars,CompleteHit
4698,Q#1955 - >seq1954,superfamily,340205,242,305,1.0596199999999999e-27,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs1_chimp.pars.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,pars,CompleteHit
4699,Q#1955 - >seq1954,non-specific,335182,145,239,1.47032e-19,81.9655,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs1_chimp.pars.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,pars,CompleteHit
4700,Q#1955 - >seq1954,superfamily,335182,145,239,1.47032e-19,81.9655,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs1_chimp.pars.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,pars,CompleteHit
4701,Q#1960 - >seq1959,specific,311990,1161,1179,4.2673e-05,41.1184,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs0_human.marg.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4702,Q#1960 - >seq1959,superfamily,311990,1161,1179,4.2673e-05,41.1184,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs0_human.marg.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5A,ORF2,hs0_human,marg,CompleteHit
4703,Q#1961 - >seq1960,non-specific,340205,141,204,1.8433399999999999e-25,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs0_human,pars,CompleteHit
4704,Q#1961 - >seq1960,superfamily,340205,141,204,1.8433399999999999e-25,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs0_human,pars,CompleteHit
4705,Q#1961 - >seq1960,non-specific,335182,44,138,2.5561699999999997e-25,94.2918,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs0_human,pars,CompleteHit
4706,Q#1961 - >seq1960,superfamily,335182,44,138,2.5561699999999997e-25,94.2918,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs0_human.pars.frame1,1909130038_L1MA5A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs0_human,pars,CompleteHit
4707,Q#1962 - >seq1961,non-specific,340205,249,312,2.23635e-28,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs1_chimp.marg.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,marg,CompleteHit
4708,Q#1962 - >seq1961,superfamily,340205,249,312,2.23635e-28,104.34,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs1_chimp.marg.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,marg,CompleteHit
4709,Q#1962 - >seq1961,non-specific,335182,152,246,1.0640999999999999e-19,82.3507,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs1_chimp.marg.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,marg,CompleteHit
4710,Q#1962 - >seq1961,superfamily,335182,152,246,1.0640999999999999e-19,82.3507,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs1_chimp.marg.frame2,1909130038_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs1_chimp,marg,CompleteHit
4711,Q#1963 - >seq1962,specific,197310,21,231,1.02884e-36,138.638,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4712,Q#1963 - >seq1962,superfamily,351117,21,231,1.02884e-36,138.638,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4713,Q#1963 - >seq1962,non-specific,197306,21,231,2.42225e-19,88.3072,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4714,Q#1963 - >seq1962,specific,335306,27,224,1.78914e-07,53.0178,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4715,Q#1963 - >seq1962,non-specific,197307,27,231,1.6965400000000002e-06,50.7493,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4716,Q#1963 - >seq1962,non-specific,197320,27,202,1.11327e-05,48.2802,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4717,Q#1963 - >seq1962,non-specific,273186,27,232,1.45579e-05,47.6588,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4718,Q#1963 - >seq1962,specific,311990,1164,1182,0.00021056400000000003,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4719,Q#1963 - >seq1962,superfamily,311990,1164,1182,0.00021056400000000003,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4720,Q#1963 - >seq1962,non-specific,272954,14,231,0.000256781,43.9109,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4721,Q#1963 - >seq1962,non-specific,197311,33,141,0.000319071,43.0493,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
4722,Q#1963 - >seq1962,non-specific,197319,27,231,0.000511921,43.0341,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4723,Q#1963 - >seq1962,non-specific,223780,27,202,0.00313832,40.6595,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4724,Q#1964 - >seq1963,specific,238827,489,714,1.0051600000000001e-47,169.77900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4725,Q#1964 - >seq1963,superfamily,295487,489,714,1.0051600000000001e-47,169.77900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4726,Q#1964 - >seq1963,non-specific,333820,498,714,2.40068e-23,98.5185,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4727,Q#1964 - >seq1963,superfamily,333820,498,714,2.40068e-23,98.5185,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4728,Q#1964 - >seq1963,non-specific,238828,524,679,1.6559099999999998e-12,67.9964,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4729,Q#1964 - >seq1963,non-specific,197310,22,124,2.77501e-12,67.7617,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4730,Q#1964 - >seq1963,superfamily,351117,22,124,2.77501e-12,67.7617,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4731,Q#1964 - >seq1963,non-specific,275209,529,738,5.53205e-08,55.9268,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4732,Q#1964 - >seq1963,superfamily,275209,529,738,5.53205e-08,55.9268,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4733,Q#1964 - >seq1963,non-specific,197306,10,168,5.55665e-07,52.0985,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4734,Q#1964 - >seq1963,non-specific,238185,598,714,2.1987600000000003e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs5_gmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4735,Q#1966 - >seq1965,specific,311990,1148,1166,0.00021857599999999998,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs5_gmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4736,Q#1966 - >seq1965,superfamily,311990,1148,1166,0.00021857599999999998,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs5_gmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs5_gmonkey,pars,CompleteHit
4737,Q#1967 - >seq1966,non-specific,197310,126,231,8.535680000000001e-20,89.7181,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4738,Q#1967 - >seq1966,superfamily,351117,126,231,8.535680000000001e-20,89.7181,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4739,Q#1967 - >seq1966,non-specific,197306,120,231,1.32985e-09,59.8025,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4740,Q#1967 - >seq1966,non-specific,197320,128,203,5.28665e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4741,Q#1967 - >seq1966,non-specific,238827,503,538,1.22862e-06,50.7526,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4742,Q#1967 - >seq1966,superfamily,295487,503,538,1.22862e-06,50.7526,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4743,Q#1967 - >seq1966,specific,335306,123,224,3.82797e-06,49.1658,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4744,Q#1967 - >seq1966,non-specific,197307,128,231,4.75216e-06,49.2085,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4745,Q#1967 - >seq1966,non-specific,235175,286,457,1.191e-05,49.6772,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4746,Q#1967 - >seq1966,superfamily,235175,286,457,1.191e-05,49.6772,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4747,Q#1967 - >seq1966,non-specific,274009,302,451,0.000112654,46.5995,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4748,Q#1967 - >seq1966,superfamily,274009,302,451,0.000112654,46.5995,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4749,Q#1967 - >seq1966,non-specific,333820,509,567,0.000518269,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4750,Q#1967 - >seq1966,superfamily,333820,509,567,0.000518269,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4751,Q#1967 - >seq1966,non-specific,223780,128,224,0.00255957,41.0447,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4752,Q#1967 - >seq1966,non-specific,223496,315,493,0.00495869,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4753,Q#1967 - >seq1966,superfamily,223496,315,493,0.00495869,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA5A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4754,Q#1967 - >seq1966,non-specific,197319,128,231,0.00807546,39.1821,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4755,Q#1967 - >seq1966,non-specific,334125,205,405,0.008729700000000002,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4756,Q#1967 - >seq1966,superfamily,334125,205,405,0.008729700000000002,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA5A.ORF2.hs5_gmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA5A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4757,Q#1968 - >seq1967,specific,238827,500,761,2.7899299999999995e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4758,Q#1968 - >seq1967,superfamily,295487,500,761,2.7899299999999995e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4759,Q#1968 - >seq1967,specific,333820,506,761,2.0053999999999998e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4760,Q#1968 - >seq1967,superfamily,333820,506,761,2.0053999999999998e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4761,Q#1968 - >seq1967,non-specific,197310,122,227,3.94244e-20,90.8737,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4762,Q#1968 - >seq1967,superfamily,351117,122,227,3.94244e-20,90.8737,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4763,Q#1968 - >seq1967,non-specific,238828,506,727,1.8953e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4764,Q#1968 - >seq1967,non-specific,197306,116,227,9.16029e-10,60.1877,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4765,Q#1968 - >seq1967,non-specific,275209,577,785,3.65403e-07,53.6156,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4766,Q#1968 - >seq1967,superfamily,275209,577,785,3.65403e-07,53.6156,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4767,Q#1968 - >seq1967,non-specific,197320,124,199,5.37921e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4768,Q#1968 - >seq1967,specific,335306,119,220,3.893680000000001e-06,49.1658,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4769,Q#1968 - >seq1967,non-specific,197307,124,227,5.85217e-06,48.8233,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4770,Q#1968 - >seq1967,non-specific,235175,282,453,8.67989e-05,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
4771,Q#1968 - >seq1967,superfamily,235175,282,453,8.67989e-05,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
4772,Q#1968 - >seq1967,non-specific,274009,298,477,0.00021264,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4773,Q#1968 - >seq1967,superfamily,274009,298,477,0.00021264,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MA5A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4774,Q#1968 - >seq1967,non-specific,223780,124,220,0.00267404,41.0447,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4775,Q#1968 - >seq1967,non-specific,223496,311,490,0.00290861,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
4776,Q#1968 - >seq1967,superfamily,223496,311,490,0.00290861,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1MA5A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
4777,Q#1968 - >seq1967,non-specific,238185,646,761,0.00948652,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4778,Q#1968 - >seq1967,non-specific,197319,124,227,0.00981687,39.1821,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5A.ORF2.hs5_gmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4779,Q#1969 - >seq1968,non-specific,197310,12,132,2.3521500000000002e-18,85.4809,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs5_gmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4780,Q#1969 - >seq1968,superfamily,351117,12,132,2.3521500000000002e-18,85.4809,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4781,Q#1969 - >seq1968,non-specific,197306,9,176,2.20961e-09,59.0321,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs5_gmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4782,Q#1970 - >seq1969,specific,311990,1162,1180,0.00010014799999999999,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs5_gmonkey.marg.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4783,Q#1970 - >seq1969,superfamily,311990,1162,1180,0.00010014799999999999,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs5_gmonkey.marg.frame3,1909130038_L1MA5A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5A,ORF2,hs5_gmonkey,marg,CompleteHit
4784,Q#1971 - >seq1970,non-specific,335182,1,46,1.8803000000000002e-09,51.9199,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
4785,Q#1971 - >seq1970,superfamily,335182,1,46,1.8803000000000002e-09,51.9199,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
4786,Q#1972 - >seq1971,non-specific,340205,92,157,4.53589e-26,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,CompleteHit
4787,Q#1972 - >seq1971,superfamily,340205,92,157,4.53589e-26,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,CompleteHit
4788,Q#1972 - >seq1971,non-specific,335182,50,89,6.299099999999999e-10,53.0755,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
4789,Q#1972 - >seq1971,superfamily,335182,50,89,6.299099999999999e-10,53.0755,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
4790,Q#1973 - >seq1972,non-specific,340205,174,240,4.549199999999999e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,CompleteHit
4791,Q#1973 - >seq1972,superfamily,340205,174,240,4.549199999999999e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,CompleteHit
4792,Q#1973 - >seq1972,non-specific,335182,77,171,1.85652e-13,64.2463,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,CompleteHit
4793,Q#1973 - >seq1972,superfamily,335182,77,171,1.85652e-13,64.2463,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,CompleteHit
4794,Q#1974 - >seq1973,non-specific,335182,90,111,0.00792544,34.5859,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
4795,Q#1974 - >seq1973,superfamily,335182,90,111,0.00792544,34.5859,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5A.ORF1.hs6_sqmonkey.marg.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
4796,Q#1976 - >seq1975,non-specific,197310,63,224,4.7639099999999995e-18,84.3253,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4797,Q#1976 - >seq1975,superfamily,351117,63,224,4.7639099999999995e-18,84.3253,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4798,Q#1976 - >seq1975,non-specific,197306,63,224,6.20798e-10,60.5729,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4799,Q#1976 - >seq1975,non-specific,197311,63,135,0.00571092,39.1973,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4800,Q#1977 - >seq1976,specific,238827,460,716,1.22042e-39,146.282,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4801,Q#1977 - >seq1976,superfamily,295487,460,716,1.22042e-39,146.282,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4802,Q#1977 - >seq1976,non-specific,333820,466,684,1.13027e-19,87.7329,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4803,Q#1977 - >seq1976,superfamily,333820,466,684,1.13027e-19,87.7329,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4804,Q#1977 - >seq1976,non-specific,238828,526,681,6.23768e-07,51.4328,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
4805,Q#1977 - >seq1976,specific,311990,1166,1184,0.0006377430000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4806,Q#1977 - >seq1976,superfamily,311990,1166,1184,0.0006377430000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4807,Q#1977 - >seq1976,non-specific,238185,602,716,0.00247398,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,CompleteHit
4808,Q#1977 - >seq1976,non-specific,275209,531,681,0.00444042,40.5188,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4809,Q#1977 - >seq1976,superfamily,275209,531,681,0.00444042,40.5188,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs6_sqmonkey.pars.frame2,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4810,Q#1978 - >seq1977,non-specific,197310,9,68,1.68678e-05,47.3461,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4811,Q#1978 - >seq1977,superfamily,351117,9,68,1.68678e-05,47.3461,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5A.ORF2.hs6_sqmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
4812,Q#1978 - >seq1977,non-specific,340095,204,378,0.00658592,40.5812,pfam17380,DUF5401,NC,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA5A.ORF2.hs6_sqmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA5A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4813,Q#1978 - >seq1977,superfamily,340095,204,378,0.00658592,40.5812,cl38662,DUF5401 superfamily,NC, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA5A.ORF2.hs6_sqmonkey.pars.frame3,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA5A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
4814,Q#1979 - >seq1978,specific,238827,481,744,3.7135300000000005e-40,147.82299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4815,Q#1979 - >seq1978,superfamily,295487,481,744,3.7135300000000005e-40,147.82299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4816,Q#1979 - >seq1978,non-specific,333820,487,712,1.33076e-18,84.6513,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4817,Q#1979 - >seq1978,superfamily,333820,487,712,1.33076e-18,84.6513,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4818,Q#1979 - >seq1978,non-specific,238828,554,709,1.0051799999999998e-06,51.0476,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
4819,Q#1979 - >seq1978,non-specific,238185,630,744,0.00125583,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,CompleteHit
4820,Q#1979 - >seq1978,non-specific,275209,559,709,0.00627048,40.1336,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
4821,Q#1979 - >seq1978,superfamily,275209,559,709,0.00627048,40.1336,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5A.ORF2.hs6_sqmonkey.marg.frame1,1909130038_L1MA5A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
4822,Q#1981 - >seq1980,non-specific,340205,257,320,1.7874099999999997e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs2_gorilla.marg.frame3,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5,ORF1,hs2_gorilla,marg,CompleteHit
4823,Q#1981 - >seq1980,superfamily,340205,257,320,1.7874099999999997e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs2_gorilla.marg.frame3,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5,ORF1,hs2_gorilla,marg,CompleteHit
4824,Q#1981 - >seq1980,non-specific,335182,160,254,4.4361099999999995e-22,88.899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs2_gorilla.marg.frame3,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5,ORF1,hs2_gorilla,marg,CompleteHit
4825,Q#1981 - >seq1980,superfamily,335182,160,254,4.4361099999999995e-22,88.899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs2_gorilla.marg.frame3,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA5,ORF1,hs2_gorilla,marg,CompleteHit
4826,Q#1982 - >seq1981,non-specific,340205,253,316,3.54674e-28,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs2_gorilla.pars.frame1,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs2_gorilla,pars,CompleteHit
4827,Q#1982 - >seq1981,superfamily,340205,253,316,3.54674e-28,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs2_gorilla.pars.frame1,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs2_gorilla,pars,CompleteHit
4828,Q#1982 - >seq1981,non-specific,335182,156,250,1.4939300000000001e-21,87.3582,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs2_gorilla.pars.frame1,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs2_gorilla,pars,CompleteHit
4829,Q#1982 - >seq1981,superfamily,335182,156,250,1.4939300000000001e-21,87.3582,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs2_gorilla.pars.frame1,1909130039_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs2_gorilla,pars,CompleteHit
4830,Q#1988 - >seq1987,non-specific,335182,152,248,7.272169999999999e-29,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs3_orang.pars.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,pars,CompleteHit
4831,Q#1988 - >seq1987,superfamily,335182,152,248,7.272169999999999e-29,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs3_orang.pars.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,pars,CompleteHit
4832,Q#1988 - >seq1987,non-specific,340205,251,314,9.3792e-29,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs3_orang.pars.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,pars,CompleteHit
4833,Q#1988 - >seq1987,superfamily,340205,251,314,9.3792e-29,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs3_orang.pars.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,pars,CompleteHit
4834,Q#1991 - >seq1990,non-specific,340205,257,320,1.03167e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,marg,CompleteHit
4835,Q#1991 - >seq1990,superfamily,340205,257,320,1.03167e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,marg,CompleteHit
4836,Q#1991 - >seq1990,non-specific,335182,158,254,1.27673e-29,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,marg,CompleteHit
4837,Q#1991 - >seq1990,superfamily,335182,158,254,1.27673e-29,108.544,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs3_orang,marg,CompleteHit
4838,Q#1991 - >seq1990,non-specific,235461,56,117,0.00401378,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_tRNAsynthetase,L1MA5,ORF1,hs3_orang,marg,C-TerminusTruncated
4839,Q#1991 - >seq1990,superfamily,235461,56,117,0.00401378,38.5106,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_tRNAsynthetase,L1MA5,ORF1,hs3_orang,marg,C-TerminusTruncated
4840,Q#1991 - >seq1990,non-specific,337033,43,123,0.00565971,37.9437,pfam08385,DHC_N1,NC,cl20356,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA5,ORF1,hs3_orang,marg,BothTerminiTruncated
4841,Q#1991 - >seq1990,superfamily,337033,43,123,0.00565971,37.9437,cl20356,DHC_N1 superfamily,NC, - ,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA5,ORF1,hs3_orang,marg,BothTerminiTruncated
4842,Q#1991 - >seq1990,non-specific,275316,56,120,0.0092029,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Mycoplasma,L1MA5,ORF1,hs3_orang,marg,BothTerminiTruncated
4843,Q#1991 - >seq1990,superfamily,275316,56,120,0.0092029,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1MA5.ORF1.hs3_orang.marg.frame2,1909130043_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Mycoplasma,L1MA5,ORF1,hs3_orang,marg,BothTerminiTruncated
4844,Q#1996 - >seq1995,non-specific,335182,63,154,1.4233299999999999e-30,108.929,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs4_gibbon.pars.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,pars,CompleteHit
4845,Q#1996 - >seq1995,superfamily,335182,63,154,1.4233299999999999e-30,108.929,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs4_gibbon.pars.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,pars,CompleteHit
4846,Q#1996 - >seq1995,non-specific,340205,157,221,1.67339e-27,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs4_gibbon.pars.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,pars,CompleteHit
4847,Q#1996 - >seq1995,superfamily,340205,157,221,1.67339e-27,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs4_gibbon.pars.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,pars,CompleteHit
4848,Q#1998 - >seq1997,non-specific,335182,63,154,1.72003e-30,108.15899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs4_gibbon.marg.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,marg,CompleteHit
4849,Q#1998 - >seq1997,superfamily,335182,63,154,1.72003e-30,108.15899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs4_gibbon.marg.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,marg,CompleteHit
4850,Q#1998 - >seq1997,non-specific,340205,157,221,8.09779e-28,100.488,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs4_gibbon.marg.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,marg,CompleteHit
4851,Q#1998 - >seq1997,superfamily,340205,157,221,8.09779e-28,100.488,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs4_gibbon.marg.frame2,1909130044_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs4_gibbon,marg,CompleteHit
4852,Q#2000 - >seq1999,non-specific,335182,168,264,4.44438e-22,88.899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs5_gmonkey.pars.frame2,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs5_gmonkey,pars,CompleteHit
4853,Q#2000 - >seq1999,superfamily,335182,168,264,4.44438e-22,88.899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs5_gmonkey.pars.frame2,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs5_gmonkey,pars,CompleteHit
4854,Q#2001 - >seq2000,non-specific,340205,255,306,8.34169e-16,70.828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs5_gmonkey.pars.frame3,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5,ORF1,hs5_gmonkey,pars,CompleteHit
4855,Q#2001 - >seq2000,superfamily,340205,255,306,8.34169e-16,70.828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs5_gmonkey.pars.frame3,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA5,ORF1,hs5_gmonkey,pars,CompleteHit
4856,Q#2002 - >seq2001,non-specific,335182,183,279,4.0740499999999993e-22,89.2842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs5_gmonkey.marg.frame1,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs5_gmonkey,marg,CompleteHit
4857,Q#2002 - >seq2001,superfamily,335182,183,279,4.0740499999999993e-22,89.2842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs5_gmonkey.marg.frame1,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs5_gmonkey,marg,CompleteHit
4858,Q#2003 - >seq2002,non-specific,340205,262,313,2.53433e-15,69.2872,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs5_gmonkey.marg.frame2,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs5_gmonkey,marg,CompleteHit
4859,Q#2003 - >seq2002,superfamily,340205,262,313,2.53433e-15,69.2872,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs5_gmonkey.marg.frame2,1909130046_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs5_gmonkey,marg,CompleteHit
4860,Q#2005 - >seq2004,non-specific,335182,138,235,1.0855999999999998e-17,76.5727,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,CompleteHit
4861,Q#2005 - >seq2004,superfamily,335182,138,235,1.0855999999999998e-17,76.5727,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,CompleteHit
4862,Q#2005 - >seq2004,non-specific,340205,238,271,1.48553e-06,44.6344,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
4863,Q#2005 - >seq2004,superfamily,340205,238,271,1.48553e-06,44.6344,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
4864,Q#2007 - >seq2006,non-specific,335182,145,242,9.09409e-18,76.9579,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs6_sqmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,marg,CompleteHit
4865,Q#2007 - >seq2006,superfamily,335182,145,242,9.09409e-18,76.9579,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs6_sqmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,marg,CompleteHit
4866,Q#2007 - >seq2006,non-specific,340205,245,300,6.00139e-11,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,marg,CompleteHit
4867,Q#2007 - >seq2006,superfamily,340205,245,300,6.00139e-11,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA5,ORF1,hs6_sqmonkey,marg,CompleteHit
4868,Q#2010 - >seq2009,non-specific,340205,255,307,0.00043096300000000003,37.7008,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,CompleteHit
4869,Q#2010 - >seq2009,superfamily,340205,255,307,0.00043096300000000003,37.7008,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs6_sqmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA5,ORF1,hs6_sqmonkey,pars,CompleteHit
4870,Q#2011 - >seq2010,non-specific,178578,283,450,0.00030486099999999997,45.011,PLN03000,PLN03000,N,cl31963,amine oxidase,L1MA5.ORF2.hs5_gmonkey.marg.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4871,Q#2011 - >seq2010,superfamily,178578,283,450,0.00030486099999999997,45.011,cl31963,PLN03000 superfamily,N, - ,amine oxidase,L1MA5.ORF2.hs5_gmonkey.marg.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4872,Q#2012 - >seq2011,non-specific,238827,480,514,5.43975e-08,54.6046,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs5_gmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4873,Q#2012 - >seq2011,superfamily,295487,480,514,5.43975e-08,54.6046,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs5_gmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4874,Q#2012 - >seq2011,non-specific,333820,486,535,0.000271246,43.0498,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4875,Q#2012 - >seq2011,superfamily,333820,486,535,0.000271246,43.0498,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.marg.frame2,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
4876,Q#2013 - >seq2012,specific,197310,9,236,8.74757e-51,179.084,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4877,Q#2013 - >seq2012,superfamily,351117,9,236,8.74757e-51,179.084,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4878,Q#2013 - >seq2012,non-specific,197306,9,236,1.43997e-21,94.8556,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4879,Q#2013 - >seq2012,non-specific,223780,7,229,4.90002e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4880,Q#2013 - >seq2012,non-specific,197320,7,229,1.87897e-11,65.6142,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4881,Q#2013 - >seq2012,non-specific,197307,9,236,1.94345e-11,65.3869,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4882,Q#2013 - >seq2012,specific,335306,10,229,3.48865e-11,64.1886,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4883,Q#2013 - >seq2012,non-specific,238827,508,542,1.0130900000000001e-07,53.8342,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4884,Q#2013 - >seq2012,superfamily,295487,508,542,1.0130900000000001e-07,53.8342,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4885,Q#2013 - >seq2012,non-specific,197321,7,236,1.23892e-06,51.0136,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4886,Q#2013 - >seq2012,non-specific,197319,7,236,1.9478099999999997e-06,50.3529,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4887,Q#2013 - >seq2012,non-specific,272954,7,236,2.1165700000000003e-05,47.3777,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4888,Q#2013 - >seq2012,non-specific,235175,263,467,5.12941e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4889,Q#2013 - >seq2012,superfamily,235175,263,467,5.12941e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4890,Q#2013 - >seq2012,non-specific,223496,320,498,0.000158851,45.9067,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4891,Q#2013 - >seq2012,superfamily,223496,320,498,0.000158851,45.9067,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4892,Q#2013 - >seq2012,non-specific,197311,54,236,0.000205241,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4893,Q#2013 - >seq2012,non-specific,333820,514,563,0.000364545,42.6646,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4894,Q#2013 - >seq2012,superfamily,333820,514,563,0.000364545,42.6646,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4895,Q#2013 - >seq2012,non-specific,235175,263,428,0.00217901,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
4896,Q#2013 - >seq2012,non-specific,339261,108,232,0.00429647,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4897,Q#2013 - >seq2012,non-specific,274009,307,456,0.00741915,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4898,Q#2013 - >seq2012,superfamily,274009,307,456,0.00741915,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA5.ORF2.hs5_gmonkey.pars.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
4899,Q#2015 - >seq2014,specific,238827,477,705,2.80999e-45,162.846,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4900,Q#2015 - >seq2014,superfamily,295487,477,705,2.80999e-45,162.846,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4901,Q#2015 - >seq2014,non-specific,333820,462,673,2.27806e-22,95.4369,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4902,Q#2015 - >seq2014,superfamily,333820,462,673,2.27806e-22,95.4369,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,CompleteHit
4903,Q#2015 - >seq2014,non-specific,238828,515,670,3.61649e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4904,Q#2015 - >seq2014,non-specific,275209,520,724,6.0821e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4905,Q#2015 - >seq2014,superfamily,275209,520,724,6.0821e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs5_gmonkey.pars.frame1,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
4906,Q#2016 - >seq2015,specific,197310,9,236,2.8090699999999994e-51,180.625,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4907,Q#2016 - >seq2015,superfamily,351117,9,236,2.8090699999999994e-51,180.625,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4908,Q#2016 - >seq2015,specific,238827,529,757,2.44162e-44,160.149,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4909,Q#2016 - >seq2015,superfamily,295487,529,757,2.44162e-44,160.149,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4910,Q#2016 - >seq2015,non-specific,333820,514,725,5.16159e-22,94.6665,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4911,Q#2016 - >seq2015,superfamily,333820,514,725,5.16159e-22,94.6665,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4912,Q#2016 - >seq2015,non-specific,197306,9,236,7.062789999999999e-22,96.0112,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4913,Q#2016 - >seq2015,non-specific,223780,7,229,1.62852e-11,66.0827,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4914,Q#2016 - >seq2015,non-specific,197320,7,229,1.93739e-11,65.6142,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4915,Q#2016 - >seq2015,specific,335306,10,229,3.59477e-11,64.1886,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4916,Q#2016 - >seq2015,non-specific,197307,9,236,6.41075e-11,63.8461,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4917,Q#2016 - >seq2015,non-specific,238828,567,722,1.0865000000000002e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4918,Q#2016 - >seq2015,non-specific,275209,572,776,1.0376e-06,52.0748,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4919,Q#2016 - >seq2015,superfamily,275209,572,776,1.0376e-06,52.0748,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
4920,Q#2016 - >seq2015,non-specific,197321,7,236,3.44515e-06,49.858000000000004,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4921,Q#2016 - >seq2015,non-specific,197319,7,236,6.316119999999999e-06,48.8121,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4922,Q#2016 - >seq2015,non-specific,272954,7,236,2.8606900000000002e-05,46.9925,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4923,Q#2016 - >seq2015,non-specific,197311,54,236,0.00017090400000000002,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4924,Q#2016 - >seq2015,non-specific,339261,108,232,0.000792936,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs5_gmonkey.marg.frame3,1909130049_L1MA5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs5_gmonkey,marg,CompleteHit
4925,Q#2020 - >seq2019,non-specific,335182,148,244,2.7166500000000003e-26,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs1_chimp.pars.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,pars,CompleteHit
4926,Q#2020 - >seq2019,superfamily,335182,148,244,2.7166500000000003e-26,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs1_chimp.pars.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,pars,CompleteHit
4927,Q#2020 - >seq2019,non-specific,340205,247,311,3.82985e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs1_chimp.pars.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,pars,CompleteHit
4928,Q#2020 - >seq2019,superfamily,340205,247,311,3.82985e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs1_chimp.pars.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,pars,CompleteHit
4929,Q#2022 - >seq2021,non-specific,335182,161,257,4.71437e-27,102.381,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs1_chimp.marg.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,marg,CompleteHit
4930,Q#2022 - >seq2021,superfamily,335182,161,257,4.71437e-27,102.381,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs1_chimp.marg.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,marg,CompleteHit
4931,Q#2022 - >seq2021,non-specific,340205,260,323,3.3191800000000003e-25,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs1_chimp.marg.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,marg,CompleteHit
4932,Q#2022 - >seq2021,superfamily,340205,260,323,3.3191800000000003e-25,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs1_chimp.marg.frame2,1909130050_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs1_chimp,marg,CompleteHit
4933,Q#2024 - >seq2023,non-specific,335182,110,207,6.50338e-24,92.751,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs2_gorilla.pars.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,pars,CompleteHit
4934,Q#2024 - >seq2023,superfamily,335182,110,207,6.50338e-24,92.751,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs2_gorilla.pars.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,pars,CompleteHit
4935,Q#2024 - >seq2023,non-specific,340205,210,273,9.14749e-19,78.1468,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs2_gorilla.pars.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,pars,CompleteHit
4936,Q#2024 - >seq2023,superfamily,340205,210,273,9.14749e-19,78.1468,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs2_gorilla.pars.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,pars,CompleteHit
4937,Q#2027 - >seq2026,non-specific,335182,18,114,5.19513e-26,95.4474,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs2_gorilla.marg.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,marg,CompleteHit
4938,Q#2027 - >seq2026,superfamily,335182,18,114,5.19513e-26,95.4474,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs2_gorilla.marg.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,marg,CompleteHit
4939,Q#2027 - >seq2026,non-specific,340205,117,180,1.12845e-19,78.1468,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs2_gorilla.marg.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,marg,CompleteHit
4940,Q#2027 - >seq2026,superfamily,340205,117,180,1.12845e-19,78.1468,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs2_gorilla.marg.frame1,1909130050_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA6,ORF1,hs2_gorilla,marg,CompleteHit
4941,Q#2030 - >seq2029,non-specific,340205,252,315,6.61307e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs0_human,marg,CompleteHit
4942,Q#2030 - >seq2029,superfamily,340205,252,315,6.61307e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs0_human,marg,CompleteHit
4943,Q#2030 - >seq2029,non-specific,335182,154,249,1.9681099999999996e-22,89.6694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs0_human,marg,CompleteHit
4944,Q#2030 - >seq2029,superfamily,335182,154,249,1.9681099999999996e-22,89.6694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA5,ORF1,hs0_human,marg,CompleteHit
4945,Q#2030 - >seq2029,non-specific,340016,51,121,0.000641435,40.5165,pfam17300,FIN1,N,cl38584,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA5,ORF1,hs0_human,marg,N-TerminusTruncated
4946,Q#2030 - >seq2029,superfamily,340016,51,121,0.000641435,40.5165,cl38584,FIN1 superfamily,N, - ,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1MA5.ORF1.hs0_human.marg.frame1,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA5,ORF1,hs0_human,marg,N-TerminusTruncated
4947,Q#2032 - >seq2031,non-specific,340205,247,310,2.37073e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs0_human.pars.frame2,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs0_human,pars,CompleteHit
4948,Q#2032 - >seq2031,superfamily,340205,247,310,2.37073e-27,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA5.ORF1.hs0_human.pars.frame2,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs0_human,pars,CompleteHit
4949,Q#2032 - >seq2031,non-specific,335182,149,244,1.63423e-22,90.0546,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs0_human.pars.frame2,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs0_human,pars,CompleteHit
4950,Q#2032 - >seq2031,superfamily,335182,149,244,1.63423e-22,90.0546,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA5.ORF1.hs0_human.pars.frame2,1909130050_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA5,ORF1,hs0_human,pars,CompleteHit
4951,Q#2035 - >seq2034,specific,197310,9,236,1.3521999999999998e-63,215.678,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4952,Q#2035 - >seq2034,superfamily,351117,9,236,1.3521999999999998e-63,215.678,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4953,Q#2035 - >seq2034,specific,238827,501,753,1.5582699999999997e-58,200.595,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4954,Q#2035 - >seq2034,superfamily,295487,501,753,1.5582699999999997e-58,200.595,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4955,Q#2035 - >seq2034,non-specific,197306,9,236,4.660349999999999e-34,131.064,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4956,Q#2035 - >seq2034,specific,333820,507,730,1.0175799999999999e-30,119.705,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4957,Q#2035 - >seq2034,superfamily,333820,507,730,1.0175799999999999e-30,119.705,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4958,Q#2035 - >seq2034,non-specific,197320,7,229,1.3050100000000001e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4959,Q#2035 - >seq2034,non-specific,223780,7,229,4.54122e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4960,Q#2035 - >seq2034,non-specific,197307,9,236,5.33327e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4961,Q#2035 - >seq2034,specific,335306,10,229,6.080069999999999e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4962,Q#2035 - >seq2034,non-specific,197321,7,236,1.9538500000000002e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4963,Q#2035 - >seq2034,non-specific,273186,7,237,9.60102e-16,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4964,Q#2035 - >seq2034,non-specific,272954,7,236,1.9152400000000001e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4965,Q#2035 - >seq2034,non-specific,197319,7,236,3.88112e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4966,Q#2035 - >seq2034,non-specific,238828,507,737,9.10311e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4967,Q#2035 - >seq2034,non-specific,275209,458,785,1.0467e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4968,Q#2035 - >seq2034,superfamily,275209,458,785,1.0467e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4969,Q#2035 - >seq2034,non-specific,197336,7,229,1.24299e-08,57.2371,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4970,Q#2035 - >seq2034,non-specific,197311,37,236,3.89143e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4971,Q#2035 - >seq2034,non-specific,339261,108,232,0.000128014,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4972,Q#2035 - >seq2034,non-specific,239569,531,737,0.000976846,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MA5.ORF2.hs6_sqmonkey.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs6_sqmonkey,pars,CompleteHit
4973,Q#2036 - >seq2035,specific,311990,1154,1172,0.00524969,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs6_sqmonkey.marg.frame1,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4974,Q#2036 - >seq2035,superfamily,311990,1154,1172,0.00524969,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs6_sqmonkey.marg.frame1,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4975,Q#2037 - >seq2036,specific,238827,488,750,5.00639e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4976,Q#2037 - >seq2036,superfamily,295487,488,750,5.00639e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4977,Q#2037 - >seq2036,specific,333820,494,718,2.51627e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4978,Q#2037 - >seq2036,superfamily,333820,494,718,2.51627e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4979,Q#2037 - >seq2036,non-specific,238828,494,725,3.0180400000000003e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4980,Q#2037 - >seq2036,non-specific,275209,445,769,3.67724e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4981,Q#2037 - >seq2036,superfamily,275209,445,769,3.67724e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4982,Q#2037 - >seq2036,non-specific,238185,634,750,0.000379581,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs6_sqmonkey.marg.frame2,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4983,Q#2038 - >seq2037,specific,197310,9,236,2.1767299999999995e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4984,Q#2038 - >seq2037,superfamily,351117,9,236,2.1767299999999995e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4985,Q#2038 - >seq2037,non-specific,197306,9,236,1.2559299999999998e-34,132.605,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4986,Q#2038 - >seq2037,non-specific,197320,7,229,1.23729e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4987,Q#2038 - >seq2037,non-specific,223780,7,229,1.4059900000000001e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4988,Q#2038 - >seq2037,non-specific,197307,9,236,4.5797299999999994e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4989,Q#2038 - >seq2037,specific,335306,10,229,5.77288e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4990,Q#2038 - >seq2037,non-specific,197321,7,236,5.67589e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4991,Q#2038 - >seq2037,non-specific,273186,7,237,4.4109099999999995e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4992,Q#2038 - >seq2037,non-specific,272954,7,236,2.14595e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4993,Q#2038 - >seq2037,non-specific,197319,7,236,3.2519400000000004e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4994,Q#2038 - >seq2037,non-specific,197336,7,229,1.17991e-08,57.2371,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4995,Q#2038 - >seq2037,non-specific,197311,37,236,3.7003199999999997e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4996,Q#2038 - >seq2037,non-specific,339261,108,232,9.13149e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs6_sqmonkey.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs6_sqmonkey,marg,CompleteHit
4997,Q#2040 - >seq2039,specific,197310,43,211,2.34007e-27,111.67399999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
4998,Q#2040 - >seq2039,superfamily,351117,43,211,2.34007e-27,111.67399999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
4999,Q#2040 - >seq2039,non-specific,238827,517,743,3.0638500000000006e-25,105.066,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5000,Q#2040 - >seq2039,superfamily,295487,517,743,3.0638500000000006e-25,105.066,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5001,Q#2040 - >seq2039,non-specific,197306,59,211,4.91965e-14,72.8993,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5002,Q#2040 - >seq2039,non-specific,333820,508,725,2.05655e-12,66.9322,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5003,Q#2040 - >seq2039,superfamily,333820,508,725,2.05655e-12,66.9322,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5004,Q#2040 - >seq2039,non-specific,197320,101,202,1.0269200000000001e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5005,Q#2040 - >seq2039,non-specific,223780,101,201,8.17453e-06,48.7487,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5006,Q#2040 - >seq2039,non-specific,197311,55,198,2.6276700000000002e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5007,Q#2040 - >seq2039,specific,335306,43,204,5.4113800000000004e-05,45.699,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,CompleteHit
5008,Q#2040 - >seq2039,non-specific,197307,59,210,0.000136882,44.5861,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5009,Q#2040 - >seq2039,non-specific,197319,101,210,0.000885997,42.2637,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5010,Q#2040 - >seq2039,non-specific,339261,102,142,0.00123547,39.6279,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs7_bushaby.pars.frame2,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MA5,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5011,Q#2041 - >seq2040,non-specific,197310,11,57,1.0064e-05,48.1165,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5012,Q#2041 - >seq2040,superfamily,351117,11,57,1.0064e-05,48.1165,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5013,Q#2041 - >seq2040,non-specific,238827,621,647,3.2005300000000003e-05,46.5154,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5014,Q#2041 - >seq2040,superfamily,295487,621,647,3.2005300000000003e-05,46.5154,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5015,Q#2041 - >seq2040,non-specific,197306,9,72,0.000517872,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5016,Q#2041 - >seq2040,non-specific,333820,602,646,0.00327193,39.9682,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5017,Q#2041 - >seq2040,superfamily,333820,602,646,0.00327193,39.9682,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5018,Q#2041 - >seq2040,non-specific,197321,7,49,0.00753786,39.4576,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5019,Q#2041 - >seq2040,non-specific,238828,611,661,0.00866272,39.1065,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs7_bushaby.pars.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5020,Q#2042 - >seq2041,non-specific,238827,555,621,3.7203300000000003e-10,61.153,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs7_bushaby.marg.frame1,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5021,Q#2042 - >seq2041,superfamily,295487,555,621,3.7203300000000003e-10,61.153,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs7_bushaby.marg.frame1,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5022,Q#2044 - >seq2043,specific,197310,11,249,4.0268199999999994e-32,125.542,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs7_bushaby,marg,CompleteHit
5023,Q#2044 - >seq2043,superfamily,351117,11,249,4.0268199999999994e-32,125.542,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,marg,CompleteHit
5024,Q#2044 - >seq2043,non-specific,238827,728,853,2.06709e-14,73.8646,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5025,Q#2044 - >seq2043,superfamily,295487,728,853,2.06709e-14,73.8646,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5026,Q#2044 - >seq2043,non-specific,197306,9,249,3.6810300000000005e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,marg,CompleteHit
5027,Q#2044 - >seq2043,non-specific,333820,679,817,3.5130100000000005e-09,57.6874,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5028,Q#2044 - >seq2043,superfamily,333820,679,817,3.5130100000000005e-09,57.6874,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5029,Q#2044 - >seq2043,non-specific,238828,679,825,1.5611799999999998e-06,50.6624,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5030,Q#2044 - >seq2043,specific,335306,11,242,6.0381100000000005e-06,48.7806,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs7_bushaby,marg,CompleteHit
5031,Q#2044 - >seq2043,non-specific,197321,7,242,0.0005317259999999999,43.3096,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs7_bushaby,marg,CompleteHit
5032,Q#2044 - >seq2043,non-specific,238185,729,815,0.00884457,36.9452,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5033,Q#2044 - >seq2043,non-specific,310273,344,509,0.00955714,40.1138,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MA5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5034,Q#2044 - >seq2043,superfamily,310273,344,509,0.00955714,40.1138,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1MA5.ORF2.hs7_bushaby.marg.frame3,1909130050_L1MA5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MA5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5035,Q#2047 - >seq2046,non-specific,335182,145,234,3.19081e-25,96.603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs3_orang.marg.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,marg,CompleteHit
5036,Q#2047 - >seq2046,superfamily,335182,145,234,3.19081e-25,96.603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs3_orang.marg.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,marg,CompleteHit
5037,Q#2047 - >seq2046,non-specific,340205,237,302,9.9652e-23,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs3_orang.marg.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,marg,CompleteHit
5038,Q#2047 - >seq2046,superfamily,340205,237,302,9.9652e-23,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs3_orang.marg.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,marg,CompleteHit
5039,Q#2050 - >seq2049,non-specific,335182,144,233,5.432709999999999e-25,95.8326,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs3_orang.pars.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,pars,CompleteHit
5040,Q#2050 - >seq2049,superfamily,335182,144,233,5.432709999999999e-25,95.8326,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs3_orang.pars.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,pars,CompleteHit
5041,Q#2050 - >seq2049,non-specific,340205,236,301,1.57773e-22,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs3_orang.pars.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,pars,CompleteHit
5042,Q#2050 - >seq2049,superfamily,340205,236,301,1.57773e-22,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs3_orang.pars.frame3,1909130053_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs3_orang,pars,CompleteHit
5043,Q#2054 - >seq2053,non-specific,340205,233,292,1.17533e-15,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs5_gmonkey.marg.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,marg,CompleteHit
5044,Q#2054 - >seq2053,superfamily,340205,233,292,1.17533e-15,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs5_gmonkey.marg.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,marg,CompleteHit
5045,Q#2055 - >seq2054,non-specific,335182,129,223,5.1769100000000006e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs5_gmonkey.marg.frame2,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs5_gmonkey,marg,CompleteHit
5046,Q#2055 - >seq2054,superfamily,335182,129,223,5.1769100000000006e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs5_gmonkey.marg.frame2,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs5_gmonkey,marg,CompleteHit
5047,Q#2057 - >seq2056,non-specific,335182,141,235,6.2961199999999996e-21,85.4322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs5_gmonkey.pars.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,pars,CompleteHit
5048,Q#2057 - >seq2056,superfamily,335182,141,235,6.2961199999999996e-21,85.4322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs5_gmonkey.pars.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,pars,CompleteHit
5049,Q#2057 - >seq2056,non-specific,340205,243,305,3.3236e-17,74.2948,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs5_gmonkey.pars.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,pars,CompleteHit
5050,Q#2057 - >seq2056,superfamily,340205,243,305,3.3236e-17,74.2948,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs5_gmonkey.pars.frame3,1909130055_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs5_gmonkey,pars,CompleteHit
5051,Q#2059 - >seq2058,non-specific,335182,51,142,2.03288e-28,102.766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs4_gibbon.marg.frame2,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs4_gibbon,marg,CompleteHit
5052,Q#2059 - >seq2058,superfamily,335182,51,142,2.03288e-28,102.766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs4_gibbon.marg.frame2,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs4_gibbon,marg,CompleteHit
5053,Q#2059 - >seq2058,non-specific,340205,145,210,5.01759e-22,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs4_gibbon.marg.frame2,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs4_gibbon,marg,CompleteHit
5054,Q#2059 - >seq2058,superfamily,340205,145,210,5.01759e-22,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs4_gibbon.marg.frame2,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA6,ORF1,hs4_gibbon,marg,CompleteHit
5055,Q#2061 - >seq2060,non-specific,335182,67,158,6.81491e-29,104.307,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs4_gibbon.pars.frame3,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs4_gibbon,pars,CompleteHit
5056,Q#2061 - >seq2060,superfamily,335182,67,158,6.81491e-29,104.307,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs4_gibbon.pars.frame3,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs4_gibbon,pars,CompleteHit
5057,Q#2061 - >seq2060,non-specific,340205,161,226,7.301380000000001e-22,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs4_gibbon.pars.frame3,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs4_gibbon,pars,CompleteHit
5058,Q#2061 - >seq2060,superfamily,340205,161,226,7.301380000000001e-22,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs4_gibbon.pars.frame3,1909130055_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs4_gibbon,pars,CompleteHit
5059,Q#2066 - >seq2065,specific,311990,1137,1155,0.00115577,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA6.ORF2.hs5_gmonkey.pars.frame2,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5060,Q#2066 - >seq2065,superfamily,311990,1137,1155,0.00115577,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA6.ORF2.hs5_gmonkey.pars.frame2,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5061,Q#2067 - >seq2066,specific,238827,496,758,3.919449999999999e-61,208.299,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5062,Q#2067 - >seq2066,superfamily,295487,496,758,3.919449999999999e-61,208.299,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5063,Q#2067 - >seq2066,specific,197310,9,225,4.12339e-54,188.71400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5064,Q#2067 - >seq2066,superfamily,351117,9,225,4.12339e-54,188.71400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5065,Q#2067 - >seq2066,specific,333820,502,758,4.306819999999999e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5066,Q#2067 - >seq2066,superfamily,333820,502,758,4.306819999999999e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5067,Q#2067 - >seq2066,non-specific,197306,9,225,1.4084399999999999e-30,121.04899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5068,Q#2067 - >seq2066,non-specific,197320,7,218,1.2404499999999999e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5069,Q#2067 - >seq2066,non-specific,223780,7,218,5.61507e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5070,Q#2067 - >seq2066,specific,335306,10,218,1.32936e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5071,Q#2067 - >seq2066,non-specific,273186,7,226,4.24177e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5072,Q#2067 - >seq2066,non-specific,197321,7,225,4.99642e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5073,Q#2067 - >seq2066,non-specific,197307,9,225,7.51344e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5074,Q#2067 - >seq2066,non-specific,272954,7,225,2.63245e-13,71.2601,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5075,Q#2067 - >seq2066,non-specific,197319,7,225,5.71807e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5076,Q#2067 - >seq2066,non-specific,238828,502,724,8.12837e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5077,Q#2067 - >seq2066,non-specific,275209,453,835,2.3296300000000003e-05,47.8376,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5078,Q#2067 - >seq2066,superfamily,275209,453,835,2.3296300000000003e-05,47.8376,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5079,Q#2067 - >seq2066,non-specific,339261,104,221,0.000192119,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5080,Q#2067 - >seq2066,non-specific,197318,9,225,0.000203375,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5081,Q#2067 - >seq2066,non-specific,238185,643,758,0.00036196199999999996,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,pars,CompleteHit
5082,Q#2067 - >seq2066,non-specific,197322,134,225,0.000631582,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.pars.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5083,Q#2069 - >seq2068,specific,311990,1140,1158,0.00115674,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA6.ORF2.hs5_gmonkey.marg.frame2,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5084,Q#2069 - >seq2068,superfamily,311990,1140,1158,0.00115674,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA6.ORF2.hs5_gmonkey.marg.frame2,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5085,Q#2070 - >seq2069,specific,238827,498,760,4.3242599999999996e-61,207.91400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5086,Q#2070 - >seq2069,superfamily,295487,498,760,4.3242599999999996e-61,207.91400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5087,Q#2070 - >seq2069,specific,197310,9,227,2.6587300000000003e-55,192.18099999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5088,Q#2070 - >seq2069,superfamily,351117,9,227,2.6587300000000003e-55,192.18099999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5089,Q#2070 - >seq2069,specific,333820,504,760,4.39474e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5090,Q#2070 - >seq2069,superfamily,333820,504,760,4.39474e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5091,Q#2070 - >seq2069,non-specific,197306,9,227,1.34444e-31,124.131,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5092,Q#2070 - >seq2069,non-specific,223780,7,220,2.5407099999999996e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5093,Q#2070 - >seq2069,non-specific,197320,7,220,5.18913e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5094,Q#2070 - >seq2069,specific,335306,10,220,1.6092600000000001e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5095,Q#2070 - >seq2069,non-specific,197307,9,227,2.15264e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5096,Q#2070 - >seq2069,non-specific,197321,7,227,9.29769e-15,75.2812,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5097,Q#2070 - >seq2069,non-specific,273186,7,228,2.45685e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5098,Q#2070 - >seq2069,non-specific,272954,7,227,1.91703e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5099,Q#2070 - >seq2069,non-specific,197319,7,227,1.06869e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5100,Q#2070 - >seq2069,non-specific,238828,504,726,7.98453e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5101,Q#2070 - >seq2069,non-specific,275209,455,837,2.3114899999999998e-05,47.8376,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5102,Q#2070 - >seq2069,superfamily,275209,455,837,2.3114899999999998e-05,47.8376,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5103,Q#2070 - >seq2069,non-specific,197318,9,227,2.6293600000000002e-05,46.9059,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5104,Q#2070 - >seq2069,non-specific,238185,645,760,0.000362265,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs5_gmonkey,marg,CompleteHit
5105,Q#2070 - >seq2069,non-specific,197322,136,227,0.0006321580000000001,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs5_gmonkey.marg.frame3,1909130057_L1MA6.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5106,Q#2071 - >seq2070,non-specific,340205,160,208,0.00025403,38.086,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs7_bushaby,pars,CompleteHit
5107,Q#2071 - >seq2070,superfamily,340205,160,208,0.00025403,38.086,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA6,ORF1,hs7_bushaby,pars,CompleteHit
5108,Q#2072 - >seq2071,non-specific,238827,606,733,2.43094e-13,70.3978,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5109,Q#2072 - >seq2071,superfamily,295487,606,733,2.43094e-13,70.3978,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5110,Q#2072 - >seq2071,non-specific,333820,591,685,2.76985e-05,46.1314,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5111,Q#2072 - >seq2071,superfamily,333820,591,685,2.76985e-05,46.1314,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5112,Q#2073 - >seq2072,non-specific,335182,67,151,4.74409e-13,62.7055,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,pars,CompleteHit
5113,Q#2073 - >seq2072,superfamily,335182,67,151,4.74409e-13,62.7055,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,pars,CompleteHit
5114,Q#2076 - >seq2075,non-specific,238827,504,613,3.83382e-09,58.0714,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5115,Q#2076 - >seq2075,superfamily,295487,504,613,3.83382e-09,58.0714,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5116,Q#2076 - >seq2075,non-specific,197310,154,223,0.000118093,44.6497,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5117,Q#2076 - >seq2075,superfamily,351117,154,223,0.000118093,44.6497,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5118,Q#2076 - >seq2075,non-specific,235175,306,458,0.0007174039999999999,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA6,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5119,Q#2076 - >seq2075,superfamily,235175,306,458,0.0007174039999999999,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA6,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5120,Q#2076 - >seq2075,non-specific,114219,294,426,0.00163178,42.4013,pfam05483,SCP-1,NC,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5121,Q#2076 - >seq2075,superfamily,114219,294,426,0.00163178,42.4013,cl30946,SCP-1 superfamily,NC, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5122,Q#2076 - >seq2075,non-specific,274009,310,452,0.00386872,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5123,Q#2076 - >seq2075,superfamily,274009,310,452,0.00386872,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5124,Q#2076 - >seq2075,non-specific,224259,325,498,0.00550683,40.0496,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5125,Q#2076 - >seq2075,superfamily,224259,325,498,0.00550683,40.0496,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5126,Q#2076 - >seq2075,non-specific,240274,834,999,0.00589511,40.7437,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5127,Q#2076 - >seq2075,superfamily,240274,834,999,0.00589511,40.7437,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5128,Q#2076 - >seq2075,non-specific,240271,301,542,0.00777714,40.4148,PTZ00108,PTZ00108,N,cl36510,DNA topoisomerase 2-like protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5129,Q#2076 - >seq2075,superfamily,240271,301,542,0.00777714,40.4148,cl36510,PTZ00108 superfamily,N, - ,DNA topoisomerase 2-like protein; Provisional,L1MA6.ORF2.hs7_bushaby.marg.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA6,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5130,Q#2078 - >seq2077,non-specific,238827,354,462,3.9399999999999997e-17,81.1834,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5131,Q#2078 - >seq2077,superfamily,295487,354,462,3.9399999999999997e-17,81.1834,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5132,Q#2078 - >seq2077,non-specific,333820,360,474,1.41266e-06,49.5982,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5133,Q#2078 - >seq2077,superfamily,333820,360,474,1.41266e-06,49.5982,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5134,Q#2079 - >seq2078,non-specific,238827,461,584,7.87098e-13,68.4718,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5135,Q#2079 - >seq2078,superfamily,295487,461,584,7.87098e-13,68.4718,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5136,Q#2079 - >seq2078,non-specific,197310,22,116,9.117939999999999e-10,60.0577,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5137,Q#2079 - >seq2078,superfamily,351117,22,116,9.117939999999999e-10,60.0577,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5138,Q#2079 - >seq2078,non-specific,333820,446,517,5.806479999999999e-05,44.5906,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5139,Q#2079 - >seq2078,superfamily,333820,446,517,5.806479999999999e-05,44.5906,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5140,Q#2079 - >seq2078,non-specific,238828,464,528,0.00915474,38.7213,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs7_bushaby.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5141,Q#2080 - >seq2079,non-specific,197310,33,171,0.00805874,39.2569,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs7_bushaby.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5142,Q#2080 - >seq2079,superfamily,351117,33,171,0.00805874,39.2569,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs7_bushaby.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5143,Q#2081 - >seq2080,non-specific,340205,129,189,1.19955e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,marg,CompleteHit
5144,Q#2081 - >seq2080,superfamily,340205,129,189,1.19955e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,marg,CompleteHit
5145,Q#2081 - >seq2080,non-specific,335182,35,120,5.78337e-16,69.6391,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,marg,CompleteHit
5146,Q#2081 - >seq2080,superfamily,335182,35,120,5.78337e-16,69.6391,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs7_bushaby.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs7_bushaby,marg,CompleteHit
5147,Q#2083 - >seq2082,specific,238827,520,703,3.38979e-31,122.015,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5148,Q#2083 - >seq2082,superfamily,295487,520,703,3.38979e-31,122.015,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5149,Q#2083 - >seq2082,non-specific,333820,527,680,1.34274e-19,87.7329,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5150,Q#2083 - >seq2082,superfamily,333820,527,680,1.34274e-19,87.7329,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5151,Q#2083 - >seq2082,non-specific,238828,518,677,5.18624e-10,60.6776,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5152,Q#2083 - >seq2082,non-specific,197310,84,113,0.000405288,43.1089,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
5153,Q#2083 - >seq2082,superfamily,351117,84,113,0.000405288,43.1089,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
5154,Q#2083 - >seq2082,non-specific,238185,597,681,0.00394021,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5155,Q#2083 - >seq2082,non-specific,275209,525,677,0.00607895,40.1336,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
5156,Q#2083 - >seq2082,superfamily,275209,525,677,0.00607895,40.1336,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs6_sqmonkey.marg.frame1,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
5157,Q#2085 - >seq2084,non-specific,197310,9,111,0.000277165,43.4941,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5158,Q#2085 - >seq2084,superfamily,351117,9,111,0.000277165,43.4941,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5159,Q#2086 - >seq2085,specific,238827,500,751,1.47414e-45,163.231,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5160,Q#2086 - >seq2085,superfamily,295487,500,751,1.47414e-45,163.231,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5161,Q#2086 - >seq2085,specific,197310,16,231,3.13784e-28,113.986,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5162,Q#2086 - >seq2085,superfamily,351117,16,231,3.13784e-28,113.986,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5163,Q#2086 - >seq2085,non-specific,333820,506,728,5.7545299999999995e-27,108.53399999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5164,Q#2086 - >seq2085,superfamily,333820,506,728,5.7545299999999995e-27,108.53399999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5165,Q#2086 - >seq2085,non-specific,197306,25,231,1.35024e-10,62.4989,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5166,Q#2086 - >seq2085,non-specific,238828,506,725,8.287880000000001e-10,59.9072,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5167,Q#2086 - >seq2085,specific,335306,31,224,2.5336799999999998e-05,46.4694,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5168,Q#2086 - >seq2085,non-specific,197307,31,231,0.000542842,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5169,Q#2086 - >seq2085,non-specific,275209,457,725,0.000572244,43.2152,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5170,Q#2086 - >seq2085,superfamily,275209,457,725,0.000572244,43.2152,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5171,Q#2086 - >seq2085,non-specific,197320,168,203,0.00249686,40.5762,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5172,Q#2086 - >seq2085,non-specific,238185,645,729,0.0053461,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA6,ORF2,hs6_sqmonkey,pars,CompleteHit
5173,Q#2086 - >seq2085,non-specific,223780,171,220,0.00737975,39.5039,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs6_sqmonkey.pars.frame2,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5174,Q#2088 - >seq2087,non-specific,335182,69,163,2.87887e-25,95.0622,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,marg,CompleteHit
5175,Q#2088 - >seq2087,superfamily,335182,69,163,2.87887e-25,95.0622,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,marg,CompleteHit
5176,Q#2088 - >seq2087,non-specific,340205,167,229,1.44829e-21,84.31,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,marg,CompleteHit
5177,Q#2088 - >seq2087,superfamily,340205,167,229,1.44829e-21,84.31,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,marg,CompleteHit
5178,Q#2091 - >seq2090,non-specific,335182,66,160,2.35035e-25,95.0622,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,pars,CompleteHit
5179,Q#2091 - >seq2090,superfamily,335182,66,160,2.35035e-25,95.0622,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,pars,CompleteHit
5180,Q#2091 - >seq2090,non-specific,340205,164,226,1.0160099999999999e-21,84.6952,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,pars,CompleteHit
5181,Q#2091 - >seq2090,superfamily,340205,164,226,1.0160099999999999e-21,84.6952,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs6_sqmonkey.pars.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs6_sqmonkey,pars,CompleteHit
5182,Q#2094 - >seq2093,specific,197310,9,237,2.37638e-36,137.483,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5183,Q#2094 - >seq2093,superfamily,351117,9,237,2.37638e-36,137.483,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5184,Q#2094 - >seq2093,non-specific,197306,9,237,5.934520000000001e-17,81.3736,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5185,Q#2094 - >seq2093,non-specific,238827,510,589,9.26319e-16,77.3314,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5186,Q#2094 - >seq2093,superfamily,295487,510,589,9.26319e-16,77.3314,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5187,Q#2094 - >seq2093,specific,335306,10,230,1.3153499999999998e-09,59.5662,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5188,Q#2094 - >seq2093,non-specific,197307,9,237,9.21525e-09,57.2977,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5189,Q#2094 - >seq2093,non-specific,333820,516,569,7.99173e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5190,Q#2094 - >seq2093,superfamily,333820,516,569,7.99173e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5191,Q#2094 - >seq2093,non-specific,223780,7,226,1.8124e-05,47.5931,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5192,Q#2094 - >seq2093,non-specific,197320,7,209,8.23245e-05,45.5838,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5193,Q#2094 - >seq2093,non-specific,197319,7,237,0.00027085099999999996,43.8045,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5194,Q#2094 - >seq2093,non-specific,272954,7,208,0.00190082,41.2145,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5195,Q#2094 - >seq2093,non-specific,197321,7,237,0.00576388,39.8428,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs6_sqmonkey.marg.frame3,1909130058_L1MA6.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs6_sqmonkey,marg,CompleteHit
5196,Q#2097 - >seq2096,non-specific,335182,66,161,7.133100000000001e-11,57.3127,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs1_chimp.pars.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,pars,CompleteHit
5197,Q#2097 - >seq2096,superfamily,335182,66,161,7.133100000000001e-11,57.3127,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs1_chimp.pars.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,pars,CompleteHit
5198,Q#2097 - >seq2096,non-specific,340205,168,228,2.30494e-05,41.1676,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs1_chimp.pars.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,pars,CompleteHit
5199,Q#2097 - >seq2096,superfamily,340205,168,228,2.30494e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs1_chimp.pars.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,pars,CompleteHit
5200,Q#2100 - >seq2099,non-specific,335182,66,158,8.452949999999999e-08,48.8383,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs1_chimp.marg.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,marg,CompleteHit
5201,Q#2100 - >seq2099,superfamily,335182,66,158,8.452949999999999e-08,48.8383,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs1_chimp.marg.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,marg,CompleteHit
5202,Q#2100 - >seq2099,non-specific,340205,165,225,2.48819e-05,40.7824,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs1_chimp.marg.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,marg,CompleteHit
5203,Q#2100 - >seq2099,superfamily,340205,165,225,2.48819e-05,40.7824,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs1_chimp.marg.frame3,1909130059_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs1_chimp,marg,CompleteHit
5204,Q#2103 - >seq2102,non-specific,335182,65,156,9.56486e-29,103.92200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs0_human.pars.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,pars,CompleteHit
5205,Q#2103 - >seq2102,superfamily,335182,65,156,9.56486e-29,103.92200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs0_human.pars.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,pars,CompleteHit
5206,Q#2103 - >seq2102,non-specific,340205,159,223,4.96748e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs0_human.pars.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,pars,CompleteHit
5207,Q#2103 - >seq2102,superfamily,340205,159,223,4.96748e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs0_human.pars.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,pars,CompleteHit
5208,Q#2106 - >seq2105,non-specific,335182,161,252,9.47991e-26,98.529,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs0_human.marg.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,marg,CompleteHit
5209,Q#2106 - >seq2105,superfamily,335182,161,252,9.47991e-26,98.529,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA6.ORF1.hs0_human.marg.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,marg,CompleteHit
5210,Q#2106 - >seq2105,non-specific,340205,255,319,2.10941e-22,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs0_human.marg.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,marg,CompleteHit
5211,Q#2106 - >seq2105,superfamily,340205,255,319,2.10941e-22,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA6.ORF1.hs0_human.marg.frame3,1909130059_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA6,ORF1,hs0_human,marg,CompleteHit
5212,Q#2107 - >seq2106,specific,238827,500,762,1.8869799999999997e-60,206.373,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5213,Q#2107 - >seq2106,superfamily,295487,500,762,1.8869799999999997e-60,206.373,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5214,Q#2107 - >seq2106,specific,197310,2,230,4.3428099999999994e-54,188.71400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5215,Q#2107 - >seq2106,superfamily,351117,2,230,4.3428099999999994e-54,188.71400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5216,Q#2107 - >seq2106,specific,333820,506,762,3.7621300000000004e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5217,Q#2107 - >seq2106,superfamily,333820,506,762,3.7621300000000004e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5218,Q#2107 - >seq2106,non-specific,197306,2,230,5.589719999999999e-28,113.73,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5219,Q#2107 - >seq2106,non-specific,223780,2,223,1.08697e-16,81.1055,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5220,Q#2107 - >seq2106,non-specific,197307,2,223,5.15877e-16,78.8689,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5221,Q#2107 - >seq2106,non-specific,197320,2,223,1.30181e-14,74.8589,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5222,Q#2107 - >seq2106,specific,335306,3,223,3.3114599999999996e-14,73.0481,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5223,Q#2107 - >seq2106,non-specific,238828,506,726,3.8505e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5224,Q#2107 - >seq2106,non-specific,273186,2,231,1.21102e-10,63.0668,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5225,Q#2107 - >seq2106,non-specific,197319,2,230,4.16642e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5226,Q#2107 - >seq2106,non-specific,272954,2,201,4.67942e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5227,Q#2107 - >seq2106,non-specific,197321,1,223,1.133e-08,57.1768,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5228,Q#2107 - >seq2106,non-specific,275209,457,781,6.653380000000001e-08,55.9268,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5229,Q#2107 - >seq2106,superfamily,275209,457,781,6.653380000000001e-08,55.9268,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5230,Q#2107 - >seq2106,non-specific,197311,31,198,0.000241605,43.4345,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5231,Q#2107 - >seq2106,non-specific,197322,1,223,0.00033628300000000005,43.845,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5232,Q#2107 - >seq2106,non-specific,238185,645,762,0.00174621,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5233,Q#2108 - >seq2107,specific,311990,1156,1174,0.00017240799999999998,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs2_gorilla.marg.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5234,Q#2108 - >seq2107,superfamily,311990,1156,1174,0.00017240799999999998,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs2_gorilla.marg.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA7,ORF2,hs2_gorilla,marg,CompleteHit
5235,Q#2112 - >seq2111,specific,238827,491,753,4.02323e-60,205.218,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5236,Q#2112 - >seq2111,superfamily,295487,491,753,4.02323e-60,205.218,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5237,Q#2112 - >seq2111,specific,197310,2,229,2.6044e-52,183.322,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5238,Q#2112 - >seq2111,superfamily,351117,2,229,2.6044e-52,183.322,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5239,Q#2112 - >seq2111,specific,333820,497,753,8.638799999999999e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5240,Q#2112 - >seq2111,superfamily,333820,497,753,8.638799999999999e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5241,Q#2112 - >seq2111,non-specific,197306,2,229,1.9123599999999997e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5242,Q#2112 - >seq2111,non-specific,223780,2,222,3.05535e-15,76.8683,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5243,Q#2112 - >seq2111,non-specific,197307,2,222,2.78575e-14,73.8613,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5244,Q#2112 - >seq2111,non-specific,197320,2,215,8.500650000000001e-14,72.5478,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5245,Q#2112 - >seq2111,specific,335306,3,222,7.876689999999999e-13,69.1962,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5246,Q#2112 - >seq2111,non-specific,238828,497,717,6.39908e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5247,Q#2112 - >seq2111,non-specific,273186,2,230,1.55969e-09,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5248,Q#2112 - >seq2111,non-specific,272954,2,201,6.83354e-09,57.7781,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5249,Q#2112 - >seq2111,non-specific,197319,2,229,6.18524e-08,54.9753,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5250,Q#2112 - >seq2111,non-specific,275209,448,772,9.996180000000001e-08,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5251,Q#2112 - >seq2111,superfamily,275209,448,772,9.996180000000001e-08,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5252,Q#2112 - >seq2111,non-specific,197321,2,222,2.2614200000000001e-07,53.3248,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5253,Q#2112 - >seq2111,non-specific,197311,31,198,0.00021848400000000002,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5254,Q#2112 - >seq2111,specific,311990,1202,1220,0.00204892,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5255,Q#2112 - >seq2111,superfamily,311990,1202,1220,0.00204892,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5256,Q#2112 - >seq2111,non-specific,238185,636,753,0.00366488,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs2_gorilla,pars,CompleteHit
5257,Q#2116 - >seq2115,non-specific,335182,92,166,1.23145e-16,72.7207,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA7,ORF1,hs2_gorilla,pars,CompleteHit
5258,Q#2116 - >seq2115,superfamily,335182,92,166,1.23145e-16,72.7207,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA7,ORF1,hs2_gorilla,pars,CompleteHit
5259,Q#2116 - >seq2115,non-specific,340205,173,235,2.38094e-13,63.123999999999995,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA7,ORF1,hs2_gorilla,pars,CompleteHit
5260,Q#2116 - >seq2115,superfamily,340205,173,235,2.38094e-13,63.123999999999995,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs2_gorilla.pars.frame2,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA7,ORF1,hs2_gorilla,pars,CompleteHit
5261,Q#2118 - >seq2117,non-specific,335182,100,189,1.96397e-18,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs2_gorilla,marg,CompleteHit
5262,Q#2118 - >seq2117,superfamily,335182,100,189,1.96397e-18,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs2_gorilla,marg,CompleteHit
5263,Q#2118 - >seq2117,non-specific,340205,196,242,2.32828e-12,60.8128,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
5264,Q#2118 - >seq2117,superfamily,340205,196,242,2.32828e-12,60.8128,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs2_gorilla.marg.frame3,1909130101_L1MA7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
5265,Q#2121 - >seq2120,specific,311990,1105,1123,0.000522956,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs4_gibbon.marg.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5266,Q#2121 - >seq2120,superfamily,311990,1105,1123,0.000522956,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs4_gibbon.marg.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5267,Q#2122 - >seq2121,specific,197310,9,237,7.937869999999998e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5268,Q#2122 - >seq2121,superfamily,351117,9,237,7.937869999999998e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5269,Q#2122 - >seq2121,non-specific,197306,9,237,3.66342e-31,122.59,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5270,Q#2122 - >seq2121,non-specific,197307,9,237,4.64315e-18,85.0321,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5271,Q#2122 - >seq2121,non-specific,223780,7,230,1.49731e-16,80.7203,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5272,Q#2122 - >seq2121,non-specific,197320,7,230,3.24407e-15,76.7849,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5273,Q#2122 - >seq2121,specific,335306,10,230,5.278179999999999e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5274,Q#2122 - >seq2121,non-specific,197319,7,237,3.75522e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5275,Q#2122 - >seq2121,non-specific,272954,7,237,5.744310000000001e-13,70.1045,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5276,Q#2122 - >seq2121,non-specific,273186,7,238,2.7494900000000002e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5277,Q#2122 - >seq2121,non-specific,197321,7,237,3.20724e-11,64.8808,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5278,Q#2122 - >seq2121,non-specific,197311,7,237,3.21233e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5279,Q#2122 - >seq2121,non-specific,197336,7,230,3.7681699999999994e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5280,Q#2122 - >seq2121,specific,311990,1155,1173,0.000601765,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5281,Q#2122 - >seq2121,superfamily,311990,1155,1173,0.000601765,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs4_gibbon.pars.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5282,Q#2123 - >seq2122,specific,238827,479,739,6.632919999999999e-61,207.52900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5283,Q#2123 - >seq2122,superfamily,295487,479,739,6.632919999999999e-61,207.52900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5284,Q#2123 - >seq2122,specific,333820,485,708,2.8829000000000002e-30,118.164,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5285,Q#2123 - >seq2122,superfamily,333820,485,708,2.8829000000000002e-30,118.164,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5286,Q#2123 - >seq2122,non-specific,238828,485,705,3.3350799999999996e-09,58.3664,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5287,Q#2123 - >seq2122,non-specific,275209,436,758,1.54028e-05,48.2228,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5288,Q#2123 - >seq2122,superfamily,275209,436,758,1.54028e-05,48.2228,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs4_gibbon,pars,CompleteHit
5289,Q#2123 - >seq2122,non-specific,310000,235,343,0.00438922,41.2413,pfam05110,AF-4,NC,cl25851,"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
5290,Q#2123 - >seq2122,superfamily,310000,235,343,0.00438922,41.2413,cl25851,AF-4 superfamily,NC, - ,"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.",L1MA7.ORF2.hs4_gibbon.pars.frame2,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
5291,Q#2125 - >seq2124,non-specific,335182,64,154,7.72838e-24,91.2102,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs4_gibbon,marg,CompleteHit
5292,Q#2125 - >seq2124,superfamily,335182,64,154,7.72838e-24,91.2102,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs4_gibbon,marg,CompleteHit
5293,Q#2125 - >seq2124,non-specific,340205,162,226,2.00418e-09,51.9532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs4_gibbon,marg,CompleteHit
5294,Q#2125 - >seq2124,superfamily,340205,162,226,2.00418e-09,51.9532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs4_gibbon,marg,CompleteHit
5295,Q#2126 - >seq2125,specific,238827,505,766,4.366849999999999e-60,205.218,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5296,Q#2126 - >seq2125,superfamily,295487,505,766,4.366849999999999e-60,205.218,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5297,Q#2126 - >seq2125,specific,197310,9,235,2.04407e-56,195.263,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5298,Q#2126 - >seq2125,superfamily,351117,9,235,2.04407e-56,195.263,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5299,Q#2126 - >seq2125,specific,333820,511,735,2.40927e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5300,Q#2126 - >seq2125,superfamily,333820,511,735,2.40927e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5301,Q#2126 - >seq2125,non-specific,197306,9,235,1.46171e-28,115.271,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5302,Q#2126 - >seq2125,non-specific,197307,9,235,3.74368e-16,79.2541,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5303,Q#2126 - >seq2125,non-specific,223780,7,228,2.21888e-15,77.2535,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5304,Q#2126 - >seq2125,specific,335306,10,228,1.60737e-13,71.1221,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5305,Q#2126 - >seq2125,non-specific,197320,7,228,2.6360100000000003e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5306,Q#2126 - >seq2125,non-specific,272954,7,207,4.17297e-11,64.7117,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5307,Q#2126 - >seq2125,non-specific,273186,7,236,5.25226e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5308,Q#2126 - >seq2125,non-specific,197319,7,235,1.46147e-10,63.0645,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5309,Q#2126 - >seq2125,non-specific,197321,7,235,3.41805e-09,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5310,Q#2126 - >seq2125,non-specific,238828,511,732,6.089949999999999e-09,57.596000000000004,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5311,Q#2126 - >seq2125,non-specific,197311,7,235,1.54279e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5312,Q#2126 - >seq2125,non-specific,275209,462,785,3.6535400000000005e-06,50.534,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5313,Q#2126 - >seq2125,superfamily,275209,462,785,3.6535400000000005e-06,50.534,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5314,Q#2126 - >seq2125,non-specific,197336,7,228,1.62425e-05,47.6071,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs4_gibbon.marg.frame3,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs4_gibbon,marg,CompleteHit
5315,Q#2129 - >seq2128,non-specific,335182,60,150,1.22617e-24,93.1362,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs4_gibbon.pars.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs4_gibbon,pars,CompleteHit
5316,Q#2129 - >seq2128,superfamily,335182,60,150,1.22617e-24,93.1362,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs4_gibbon.pars.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs4_gibbon,pars,CompleteHit
5317,Q#2129 - >seq2128,non-specific,340205,158,221,2.02237e-08,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs4_gibbon.pars.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs4_gibbon,pars,CompleteHit
5318,Q#2129 - >seq2128,superfamily,340205,158,221,2.02237e-08,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs4_gibbon.pars.frame1,1909130102_L1MA7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs4_gibbon,pars,CompleteHit
5319,Q#2130 - >seq2129,non-specific,340205,134,197,1.81177e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5320,Q#2130 - >seq2129,superfamily,340205,134,197,1.81177e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5321,Q#2130 - >seq2129,non-specific,340205,134,197,1.81177e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5322,Q#2130 - >seq2129,non-specific,335182,35,131,2.6677e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5323,Q#2130 - >seq2129,superfamily,335182,35,131,2.6677e-15,68.0983,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5324,Q#2130 - >seq2129,non-specific,335182,35,131,2.6677e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.marg.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,marg,CompleteHit
5325,Q#2133 - >seq2132,non-specific,340205,134,197,1.81177e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5326,Q#2133 - >seq2132,superfamily,340205,134,197,1.81177e-25,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5327,Q#2133 - >seq2132,non-specific,340205,134,197,1.81177e-25,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5328,Q#2133 - >seq2132,non-specific,335182,35,131,2.6677e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5329,Q#2133 - >seq2132,superfamily,335182,35,131,2.6677e-15,68.0983,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5330,Q#2133 - >seq2132,non-specific,335182,35,131,2.6677e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs3_orang.pars.frame3,1909130102_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs3_orang,pars,CompleteHit
5331,Q#2137 - >seq2136,specific,238827,484,704,7.624029999999999e-37,138.578,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5332,Q#2137 - >seq2136,superfamily,295487,484,704,7.624029999999999e-37,138.578,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5333,Q#2137 - >seq2136,non-specific,333820,490,704,7.76191e-17,79.6438,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5334,Q#2137 - >seq2136,superfamily,333820,490,704,7.76191e-17,79.6438,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5335,Q#2137 - >seq2136,non-specific,238828,534,670,2.8405100000000003e-07,52.5884,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5336,Q#2138 - >seq2137,specific,197310,22,226,3.36074e-47,168.68400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5337,Q#2138 - >seq2137,superfamily,351117,22,226,3.36074e-47,168.68400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5338,Q#2138 - >seq2137,non-specific,197306,14,226,1.172e-22,98.3224,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5339,Q#2138 - >seq2137,non-specific,197307,22,226,1.1037100000000001e-10,63.0757,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5340,Q#2138 - >seq2137,non-specific,197320,96,219,3.30096e-10,61.7622,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5341,Q#2138 - >seq2137,non-specific,223780,44,227,2.7093099999999996e-09,59.1491,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5342,Q#2138 - >seq2137,non-specific,238827,497,535,1.15209e-08,56.5306,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
5343,Q#2138 - >seq2137,superfamily,295487,497,535,1.15209e-08,56.5306,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
5344,Q#2138 - >seq2137,specific,335306,22,219,4.96201e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5345,Q#2138 - >seq2137,non-specific,197319,81,226,1.4112299999999999e-07,53.8197,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5346,Q#2138 - >seq2137,non-specific,273186,22,227,8.861579999999999e-07,51.5108,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5347,Q#2138 - >seq2137,non-specific,272954,14,226,2.16523e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5348,Q#2138 - >seq2137,non-specific,197311,26,226,6.27893e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5349,Q#2138 - >seq2137,non-specific,197321,22,226,0.00012263200000000001,44.8504,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5350,Q#2138 - >seq2137,non-specific,224117,207,488,0.000829345,43.5496,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5351,Q#2138 - >seq2137,superfamily,224117,207,488,0.000829345,43.5496,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5352,Q#2138 - >seq2137,non-specific,214661,246,362,0.00107249,42.7215,smart00435,TOPEUc,N,cl26030,"DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5353,Q#2138 - >seq2137,superfamily,330851,246,362,0.00107249,42.7215,cl26030,Topo_C_assoc superfamily,N, - ,C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.,L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
5354,Q#2138 - >seq2137,non-specific,339261,98,222,0.00124992,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MA7,ORF2,hs5_gmonkey,marg,CompleteHit
5355,Q#2138 - >seq2137,non-specific,333820,503,550,0.00355124,39.583,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
5356,Q#2138 - >seq2137,superfamily,333820,503,550,0.00355124,39.583,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
5357,Q#2138 - >seq2137,non-specific,235175,251,455,0.00917664,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
5358,Q#2138 - >seq2137,superfamily,235175,251,455,0.00917664,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA7.ORF2.hs5_gmonkey.marg.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
5359,Q#2139 - >seq2138,specific,311990,1147,1165,0.00714202,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs5_gmonkey.pars.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5360,Q#2139 - >seq2138,superfamily,311990,1147,1165,0.00714202,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs5_gmonkey.pars.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5361,Q#2140 - >seq2139,specific,238827,482,701,6.81273e-39,144.356,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5362,Q#2140 - >seq2139,superfamily,295487,482,701,6.81273e-39,144.356,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5363,Q#2140 - >seq2139,non-specific,333820,488,701,2.6864499999999998e-17,80.7994,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5364,Q#2140 - >seq2139,superfamily,333820,488,701,2.6864499999999998e-17,80.7994,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5365,Q#2140 - >seq2139,non-specific,238828,510,667,4.71143e-08,54.8996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5366,Q#2140 - >seq2139,non-specific,238185,585,701,0.00962659,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs5_gmonkey.pars.frame2,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5367,Q#2141 - >seq2140,specific,197310,23,223,1.16773e-33,129.779,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5368,Q#2141 - >seq2140,superfamily,351117,23,223,1.16773e-33,129.779,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5369,Q#2141 - >seq2140,non-specific,197306,22,223,4.47879e-19,87.5368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5370,Q#2141 - >seq2140,non-specific,197320,93,216,3.2914599999999996e-10,61.7622,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5371,Q#2141 - >seq2140,non-specific,238827,493,567,1.63817e-08,56.1454,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
5372,Q#2141 - >seq2140,superfamily,295487,493,567,1.63817e-08,56.1454,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
5373,Q#2141 - >seq2140,non-specific,197307,78,223,2.90062e-08,55.7569,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5374,Q#2141 - >seq2140,non-specific,223780,78,224,4.95073e-08,55.2971,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5375,Q#2141 - >seq2140,non-specific,197319,78,223,1.33192e-07,53.8197,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5376,Q#2141 - >seq2140,non-specific,273186,93,224,5.55315e-06,49.1996,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5377,Q#2141 - >seq2140,specific,335306,125,216,8.45435e-05,44.9286,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5378,Q#2141 - >seq2140,non-specific,272954,78,223,0.000681733,42.7553,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5379,Q#2141 - >seq2140,non-specific,214661,243,357,0.000749981,43.1067,smart00435,TOPEUc,N,cl26030,"DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5380,Q#2141 - >seq2140,superfamily,330851,243,357,0.000749981,43.1067,cl26030,Topo_C_assoc superfamily,N, - ,C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.,L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5381,Q#2141 - >seq2140,non-specific,197321,93,223,0.00168616,41.3836,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
5382,Q#2141 - >seq2140,non-specific,339261,95,219,0.00176459,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA7,ORF2,hs5_gmonkey,pars,CompleteHit
5383,Q#2141 - >seq2140,non-specific,235175,248,451,0.00233611,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
5384,Q#2141 - >seq2140,superfamily,235175,248,451,0.00233611,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
5385,Q#2141 - >seq2140,non-specific,333820,499,546,0.00537348,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
5386,Q#2141 - >seq2140,superfamily,333820,499,546,0.00537348,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
5387,Q#2144 - >seq2143,non-specific,335182,22,116,8.24275e-19,76.9579,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs5_gmonkey.marg.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,marg,CompleteHit
5388,Q#2144 - >seq2143,superfamily,335182,22,116,8.24275e-19,76.9579,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs5_gmonkey.marg.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,marg,CompleteHit
5389,Q#2147 - >seq2146,non-specific,335182,22,116,1.2413699999999999e-17,73.8763,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,pars,CompleteHit
5390,Q#2147 - >seq2146,superfamily,335182,22,116,1.2413699999999999e-17,73.8763,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,pars,CompleteHit
5391,Q#2147 - >seq2146,non-specific,340205,122,185,1.19352e-14,65.4352,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,pars,CompleteHit
5392,Q#2147 - >seq2146,superfamily,340205,122,185,1.19352e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs5_gmonkey.pars.frame1,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs5_gmonkey,pars,CompleteHit
5393,Q#2148 - >seq2147,non-specific,340205,114,177,2.31936e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs5_gmonkey,marg,CompleteHit
5394,Q#2148 - >seq2147,superfamily,340205,114,177,2.31936e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs5_gmonkey.marg.frame3,1909130103_L1MA7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs5_gmonkey,marg,CompleteHit
5395,Q#2150 - >seq2149,non-specific,340205,211,275,1.3367300000000003e-25,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs1_chimp.marg.frame2,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs1_chimp,marg,CompleteHit
5396,Q#2150 - >seq2149,superfamily,340205,211,275,1.3367300000000003e-25,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs1_chimp.marg.frame2,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs1_chimp,marg,CompleteHit
5397,Q#2150 - >seq2149,non-specific,335182,133,208,3.05217e-15,69.6391,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs1_chimp.marg.frame2,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
5398,Q#2150 - >seq2149,superfamily,335182,133,208,3.05217e-15,69.6391,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs1_chimp.marg.frame2,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
5399,Q#2154 - >seq2153,non-specific,340205,200,263,1.77483e-26,98.1772,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs1_chimp.pars.frame1,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs1_chimp,pars,CompleteHit
5400,Q#2154 - >seq2153,superfamily,340205,200,263,1.77483e-26,98.1772,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs1_chimp.pars.frame1,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs1_chimp,pars,CompleteHit
5401,Q#2154 - >seq2153,non-specific,335182,122,197,4.46269e-15,68.8687,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs1_chimp.pars.frame1,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
5402,Q#2154 - >seq2153,superfamily,335182,122,197,4.46269e-15,68.8687,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs1_chimp.pars.frame1,1909130104_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
5403,Q#2156 - >seq2155,specific,238827,545,807,2.5443099999999998e-59,202.90599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5404,Q#2156 - >seq2155,superfamily,295487,545,807,2.5443099999999998e-59,202.90599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5405,Q#2156 - >seq2155,specific,197310,73,275,3.3583100000000005e-39,145.957,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5406,Q#2156 - >seq2155,superfamily,351117,73,275,3.3583100000000005e-39,145.957,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5407,Q#2156 - >seq2155,specific,333820,551,775,5.800759999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5408,Q#2156 - >seq2155,superfamily,333820,551,775,5.800759999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5409,Q#2156 - >seq2155,non-specific,197306,65,275,4.0633800000000004e-20,91.0036,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5410,Q#2156 - >seq2155,non-specific,197320,145,268,1.05607e-11,66.3846,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5411,Q#2156 - >seq2155,non-specific,238828,551,772,2.55128e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5412,Q#2156 - >seq2155,non-specific,223780,109,268,1.8481e-09,59.9195,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5413,Q#2156 - >seq2155,specific,335306,73,268,1.08714e-08,56.8698,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5414,Q#2156 - >seq2155,non-specific,197307,130,268,3.7729300000000004e-07,52.6753,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5415,Q#2156 - >seq2155,non-specific,197319,110,275,1.2138e-06,51.1233,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5416,Q#2156 - >seq2155,non-specific,273186,130,276,1.2347399999999998e-06,51.1256,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5417,Q#2156 - >seq2155,non-specific,272954,73,246,2.63039e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5418,Q#2156 - >seq2155,non-specific,197321,73,268,1.98307e-05,47.5468,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5419,Q#2156 - >seq2155,non-specific,275209,622,831,4.08446e-05,47.0672,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5420,Q#2156 - >seq2155,superfamily,275209,622,831,4.08446e-05,47.0672,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5421,Q#2156 - >seq2155,non-specific,339261,147,270,0.000342963,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5422,Q#2156 - >seq2155,specific,311990,1277,1295,0.00318245,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5423,Q#2156 - >seq2155,superfamily,311990,1277,1295,0.00318245,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs6_sqmonkey,marg,CompleteHit
5424,Q#2156 - >seq2155,non-specific,334125,251,448,0.00390982,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5425,Q#2156 - >seq2155,superfamily,334125,251,448,0.00390982,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5426,Q#2156 - >seq2155,non-specific,197311,145,243,0.00642194,39.1973,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs6_sqmonkey.marg.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5427,Q#2157 - >seq2156,specific,238827,519,780,2.2133099999999995e-58,200.21,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5428,Q#2157 - >seq2156,superfamily,295487,519,780,2.2133099999999995e-58,200.21,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5429,Q#2157 - >seq2156,specific,197310,40,247,3.43155e-40,148.654,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5430,Q#2157 - >seq2156,superfamily,351117,40,247,3.43155e-40,148.654,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5431,Q#2157 - >seq2156,specific,333820,525,748,4.184409999999999e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5432,Q#2157 - >seq2156,superfamily,333820,525,748,4.184409999999999e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5433,Q#2157 - >seq2156,non-specific,197306,32,247,7.61661e-21,92.9296,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5434,Q#2157 - >seq2156,non-specific,197320,117,240,1.02652e-11,66.3846,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5435,Q#2157 - >seq2156,non-specific,238828,525,745,1.33408e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5436,Q#2157 - >seq2156,non-specific,223780,104,240,2.6733099999999997e-08,56.0675,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5437,Q#2157 - >seq2156,specific,335306,40,240,4.04669e-08,55.32899999999999,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5438,Q#2157 - >seq2156,non-specific,197307,102,240,3.66894e-07,52.6753,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5439,Q#2157 - >seq2156,non-specific,197319,80,247,9.22667e-07,51.5085,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5440,Q#2157 - >seq2156,non-specific,273186,102,248,1.14725e-06,51.1256,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5441,Q#2157 - >seq2156,non-specific,275209,596,804,5.0765e-06,50.1488,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5442,Q#2157 - >seq2156,superfamily,275209,596,804,5.0765e-06,50.1488,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5443,Q#2157 - >seq2156,non-specific,272954,40,218,6.8234699999999996e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5444,Q#2157 - >seq2156,non-specific,197321,40,240,1.5102e-05,47.931999999999995,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5445,Q#2157 - >seq2156,non-specific,339261,119,242,0.0009392960000000001,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5446,Q#2157 - >seq2156,non-specific,238185,665,724,0.00844148,36.9452,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5447,Q#2157 - >seq2156,non-specific,197311,117,215,0.00917609,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs6_sqmonkey.pars.frame3,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5448,Q#2158 - >seq2157,non-specific,273727,313,500,0.00688169,40.2618,TIGR01642,U2AF_lg,C,cl36941,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA7.ORF2.hs6_sqmonkey.pars.frame2,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5449,Q#2158 - >seq2157,superfamily,273727,313,500,0.00688169,40.2618,cl36941,U2AF_lg superfamily,C, - ,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA7.ORF2.hs6_sqmonkey.pars.frame2,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5450,Q#2159 - >seq2158,specific,311990,1138,1156,0.0006749530000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs6_sqmonkey.pars.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5451,Q#2159 - >seq2158,superfamily,311990,1138,1156,0.0006749530000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs6_sqmonkey.pars.frame1,1909130104_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs6_sqmonkey,pars,CompleteHit
5452,Q#2162 - >seq2161,non-specific,340205,157,220,3.4589499999999996e-28,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs3_orang.marg.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,marg,CompleteHit
5453,Q#2162 - >seq2161,superfamily,340205,157,220,3.4589499999999996e-28,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs3_orang.marg.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,marg,CompleteHit
5454,Q#2162 - >seq2161,non-specific,335182,57,154,1.88156e-25,95.4474,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs3_orang.marg.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,marg,CompleteHit
5455,Q#2162 - >seq2161,superfamily,335182,57,154,1.88156e-25,95.4474,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs3_orang.marg.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,marg,CompleteHit
5456,Q#2165 - >seq2164,non-specific,340205,143,206,7.26168e-28,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs3_orang.pars.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,pars,CompleteHit
5457,Q#2165 - >seq2164,superfamily,340205,143,206,7.26168e-28,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs3_orang.pars.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,pars,CompleteHit
5458,Q#2165 - >seq2164,non-specific,335182,43,140,1.70764e-25,95.0622,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs3_orang.pars.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,pars,CompleteHit
5459,Q#2165 - >seq2164,superfamily,335182,43,140,1.70764e-25,95.0622,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs3_orang.pars.frame3,1909130109_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs3_orang,pars,CompleteHit
5460,Q#2169 - >seq2168,non-specific,340205,229,292,3.1061400000000003e-25,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs2_gorilla.marg.frame1,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs2_gorilla,marg,CompleteHit
5461,Q#2169 - >seq2168,superfamily,340205,229,292,3.1061400000000003e-25,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs2_gorilla.marg.frame1,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs2_gorilla,marg,CompleteHit
5462,Q#2169 - >seq2168,non-specific,335182,130,226,1.12878e-21,86.973,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs2_gorilla.marg.frame1,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs2_gorilla,marg,CompleteHit
5463,Q#2169 - >seq2168,superfamily,335182,130,226,1.12878e-21,86.973,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs2_gorilla.marg.frame1,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs2_gorilla,marg,CompleteHit
5464,Q#2171 - >seq2170,non-specific,340205,167,231,7.324489999999998e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs2_gorilla.pars.frame2,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs2_gorilla,pars,CompleteHit
5465,Q#2171 - >seq2170,superfamily,340205,167,231,7.324489999999998e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs2_gorilla.pars.frame2,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs2_gorilla,pars,CompleteHit
5466,Q#2171 - >seq2170,non-specific,335182,88,164,2.94585e-20,81.9655,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs2_gorilla.pars.frame2,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs2_gorilla,pars,N-TerminusTruncated
5467,Q#2171 - >seq2170,superfamily,335182,88,164,2.94585e-20,81.9655,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs2_gorilla.pars.frame2,1909130109_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs2_gorilla,pars,N-TerminusTruncated
5468,Q#2174 - >seq2173,non-specific,340205,117,180,8.51716e-28,98.9475,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs4_gibbon.marg.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,marg,CompleteHit
5469,Q#2174 - >seq2173,superfamily,340205,117,180,8.51716e-28,98.9475,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs4_gibbon.marg.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,marg,CompleteHit
5470,Q#2174 - >seq2173,non-specific,335182,42,114,1.7610200000000002e-22,86.2026,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs4_gibbon.marg.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,marg,N-TerminusTruncated
5471,Q#2174 - >seq2173,superfamily,335182,42,114,1.7610200000000002e-22,86.2026,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs4_gibbon.marg.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,marg,N-TerminusTruncated
5472,Q#2177 - >seq2176,non-specific,340205,117,181,2.01165e-26,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs4_gibbon.pars.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,pars,CompleteHit
5473,Q#2177 - >seq2176,superfamily,340205,117,181,2.01165e-26,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs4_gibbon.pars.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,pars,CompleteHit
5474,Q#2177 - >seq2176,non-specific,335182,42,114,3.9025899999999997e-22,85.4322,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs4_gibbon.pars.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,pars,N-TerminusTruncated
5475,Q#2177 - >seq2176,superfamily,335182,42,114,3.9025899999999997e-22,85.4322,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs4_gibbon.pars.frame1,1909130110_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs4_gibbon,pars,N-TerminusTruncated
5476,Q#2180 - >seq2179,non-specific,197310,1,33,0.00130759,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs6_sqmonkey.marg.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5477,Q#2180 - >seq2179,superfamily,351117,1,33,0.00130759,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.marg.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5478,Q#2180 - >seq2179,non-specific,197306,1,89,0.00247202,40.9277,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.marg.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5479,Q#2181 - >seq2180,specific,197310,20,224,4.5573800000000004e-30,119.37799999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5480,Q#2181 - >seq2180,superfamily,351117,20,224,4.5573800000000004e-30,119.37799999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5481,Q#2181 - >seq2180,non-specific,197306,41,224,3.0749200000000003e-13,70.5881,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5482,Q#2181 - >seq2180,non-specific,197320,95,197,1.1434100000000001e-05,47.895,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5483,Q#2181 - >seq2180,specific,335306,45,217,0.00034627400000000004,43.3878,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5484,Q#2181 - >seq2180,non-specific,197307,42,197,0.00195585,41.1193,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs6_sqmonkey.marg.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5485,Q#2182 - >seq2181,specific,238827,475,714,2.35415e-55,191.736,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5486,Q#2182 - >seq2181,superfamily,295487,475,714,2.35415e-55,191.736,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5487,Q#2182 - >seq2181,specific,333820,474,688,5.36106e-29,114.697,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5488,Q#2182 - >seq2181,superfamily,333820,474,688,5.36106e-29,114.697,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5489,Q#2182 - >seq2181,non-specific,238828,530,685,2.83482e-07,52.5884,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5490,Q#2182 - >seq2181,specific,311990,1162,1180,0.00695352,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5491,Q#2182 - >seq2181,superfamily,311990,1162,1180,0.00695352,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs6_sqmonkey,marg,CompleteHit
5492,Q#2183 - >seq2182,specific,197310,1,181,8.29044e-28,112.83,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,CompleteHit
5493,Q#2183 - >seq2182,superfamily,351117,1,181,8.29044e-28,112.83,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,CompleteHit
5494,Q#2183 - >seq2182,non-specific,197306,1,146,2.54311e-15,76.7512,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5495,Q#2183 - >seq2182,non-specific,197321,1,104,2.37985e-07,53.3248,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5496,Q#2183 - >seq2182,non-specific,223780,1,132,4.1878900000000003e-07,52.6007,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5497,Q#2183 - >seq2182,non-specific,197307,1,132,1.12214e-06,51.1345,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5498,Q#2183 - >seq2182,specific,335306,1,183,3.6454699999999997e-06,49.1658,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,CompleteHit
5499,Q#2183 - >seq2182,non-specific,272954,1,132,3.30812e-05,46.6073,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5500,Q#2183 - >seq2182,non-specific,197319,1,134,0.000219158,44.1897,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5501,Q#2183 - >seq2182,non-specific,273186,1,110,0.00116731,41.8808,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5502,Q#2183 - >seq2182,non-specific,197336,1,103,0.00545352,39.9031,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs6_sqmonkey.pars.frame3,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5503,Q#2184 - >seq2183,non-specific,238827,612,721,8.98654e-24,100.829,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs6_sqmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5504,Q#2184 - >seq2183,superfamily,295487,612,721,8.98654e-24,100.829,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs6_sqmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5505,Q#2184 - >seq2183,non-specific,333820,612,695,2.59577e-10,60.769,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5506,Q#2184 - >seq2183,superfamily,333820,612,695,2.59577e-10,60.769,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5507,Q#2184 - >seq2183,non-specific,238828,613,692,0.00317905,40.2621,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs6_sqmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5508,Q#2185 - >seq2184,specific,238827,472,571,5.28993e-29,115.851,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5509,Q#2185 - >seq2184,superfamily,295487,472,571,5.28993e-29,115.851,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5510,Q#2185 - >seq2184,non-specific,333820,471,588,9.812310000000001e-14,70.7842,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5511,Q#2185 - >seq2184,superfamily,333820,471,588,9.812310000000001e-14,70.7842,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
5512,Q#2185 - >seq2184,non-specific,197310,143,187,1.43125e-06,50.4277,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5513,Q#2185 - >seq2184,superfamily,351117,143,187,1.43125e-06,50.4277,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5514,Q#2185 - >seq2184,specific,311990,1152,1170,0.00301476,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs6_sqmonkey,pars,CompleteHit
5515,Q#2185 - >seq2184,superfamily,311990,1152,1170,0.00301476,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs6_sqmonkey,pars,CompleteHit
5516,Q#2187 - >seq2186,non-specific,340205,154,217,2.21302e-28,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,marg,CompleteHit
5517,Q#2187 - >seq2186,superfamily,340205,154,217,2.21302e-28,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,marg,CompleteHit
5518,Q#2187 - >seq2186,non-specific,335182,72,151,8.07335e-25,93.5214,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,marg,CompleteHit
5519,Q#2187 - >seq2186,superfamily,335182,72,151,8.07335e-25,93.5214,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs6_sqmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,marg,CompleteHit
5520,Q#2189 - >seq2188,non-specific,340205,132,195,4.64965e-27,97.792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,pars,CompleteHit
5521,Q#2189 - >seq2188,superfamily,340205,132,195,4.64965e-27,97.792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,pars,CompleteHit
5522,Q#2189 - >seq2188,non-specific,335182,49,129,5.80958e-24,90.825,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,pars,CompleteHit
5523,Q#2189 - >seq2188,superfamily,335182,49,129,5.80958e-24,90.825,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs6_sqmonkey.pars.frame1,1909130113_L1MA8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs6_sqmonkey,pars,CompleteHit
5524,Q#2192 - >seq2191,non-specific,340205,116,179,9.523539999999999e-26,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs5_gmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs5_gmonkey,marg,CompleteHit
5525,Q#2192 - >seq2191,superfamily,340205,116,179,9.523539999999999e-26,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs5_gmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs5_gmonkey,marg,CompleteHit
5526,Q#2192 - >seq2191,non-specific,335182,39,110,9.174460000000001e-19,76.9579,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs5_gmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
5527,Q#2192 - >seq2191,superfamily,335182,39,110,9.174460000000001e-19,76.9579,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs5_gmonkey.marg.frame1,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
5528,Q#2194 - >seq2193,non-specific,340205,103,166,1.6257099999999999e-25,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs5_gmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs5_gmonkey,pars,CompleteHit
5529,Q#2194 - >seq2193,superfamily,340205,103,166,1.6257099999999999e-25,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs5_gmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs5_gmonkey,pars,CompleteHit
5530,Q#2194 - >seq2193,non-specific,335182,30,97,1.47915e-16,70.7947,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs5_gmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
5531,Q#2194 - >seq2193,superfamily,335182,30,97,1.47915e-16,70.7947,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs5_gmonkey.pars.frame2,1909130113_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
5532,Q#2197 - >seq2196,specific,238827,522,740,8.845119999999998e-38,141.275,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5533,Q#2197 - >seq2196,superfamily,295487,522,740,8.845119999999998e-38,141.275,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5534,Q#2197 - >seq2196,non-specific,333820,531,714,5.486139999999999e-19,85.8069,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5535,Q#2197 - >seq2196,superfamily,333820,531,714,5.486139999999999e-19,85.8069,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5536,Q#2197 - >seq2196,non-specific,238828,538,711,3.95974e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5537,Q#2197 - >seq2196,non-specific,235175,285,439,0.001038,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5538,Q#2197 - >seq2196,superfamily,235175,285,439,0.001038,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5539,Q#2197 - >seq2196,non-specific,275209,524,711,0.00132342,42.4448,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5540,Q#2197 - >seq2196,superfamily,275209,524,711,0.00132342,42.4448,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5541,Q#2198 - >seq2197,non-specific,238827,458,493,1.1244000000000002e-07,53.449,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs7_bushaby.marg.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5542,Q#2198 - >seq2197,superfamily,295487,458,493,1.1244000000000002e-07,53.449,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs7_bushaby.marg.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5543,Q#2198 - >seq2197,non-specific,197310,6,43,0.0037748000000000005,40.0273,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs7_bushaby.marg.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5544,Q#2198 - >seq2197,superfamily,351117,6,43,0.0037748000000000005,40.0273,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs7_bushaby.marg.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5545,Q#2199 - >seq2198,non-specific,340205,152,216,6.15798e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs0_human.pars.frame1,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs0_human,pars,CompleteHit
5546,Q#2199 - >seq2198,superfamily,340205,152,216,6.15798e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs0_human.pars.frame1,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs0_human,pars,CompleteHit
5547,Q#2199 - >seq2198,non-specific,335182,73,149,1.1663e-13,64.6315,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs0_human.pars.frame1,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs0_human,pars,N-TerminusTruncated
5548,Q#2199 - >seq2198,superfamily,335182,73,149,1.1663e-13,64.6315,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs0_human.pars.frame1,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA8,ORF1,hs0_human,pars,N-TerminusTruncated
5549,Q#2201 - >seq2200,non-specific,340205,168,232,2.79152e-14,65.4352,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs0_human.marg.frame3,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs0_human,marg,CompleteHit
5550,Q#2201 - >seq2200,superfamily,340205,168,232,2.79152e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs0_human.marg.frame3,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs0_human,marg,CompleteHit
5551,Q#2201 - >seq2200,non-specific,335182,91,165,4.45774e-12,60.3943,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs0_human.marg.frame3,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs0_human,marg,N-TerminusTruncated
5552,Q#2201 - >seq2200,superfamily,335182,91,165,4.45774e-12,60.3943,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs0_human.marg.frame3,1909130117_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA8,ORF1,hs0_human,marg,N-TerminusTruncated
5553,Q#2205 - >seq2204,non-specific,197310,160,224,1.49799e-10,62.3689,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs7_bushaby.marg.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA8,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5554,Q#2205 - >seq2204,superfamily,351117,160,224,1.49799e-10,62.3689,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs7_bushaby.marg.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA8,ORF2,hs7_bushaby,marg,N-TerminusTruncated
5555,Q#2205 - >seq2204,specific,311990,1157,1175,0.0006658889999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs7_bushaby.marg.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5556,Q#2205 - >seq2204,superfamily,311990,1157,1175,0.0006658889999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs7_bushaby.marg.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs7_bushaby,marg,CompleteHit
5557,Q#2206 - >seq2205,non-specific,335182,40,105,2.20143e-06,43.8307,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs7_bushaby,pars,N-TerminusTruncated
5558,Q#2206 - >seq2205,superfamily,335182,40,105,2.20143e-06,43.8307,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA8.ORF1.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA8,ORF1,hs7_bushaby,pars,N-TerminusTruncated
5559,Q#2207 - >seq2206,specific,238827,360,581,6.0361e-41,150.134,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5560,Q#2207 - >seq2206,superfamily,295487,360,581,6.0361e-41,150.134,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5561,Q#2207 - >seq2206,non-specific,333820,369,552,1.6244499999999999e-19,86.9625,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5562,Q#2207 - >seq2206,superfamily,333820,369,552,1.6244499999999999e-19,86.9625,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5563,Q#2207 - >seq2206,non-specific,238828,376,549,1.1057799999999999e-09,59.522,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,N-TerminusTruncated
5564,Q#2207 - >seq2206,non-specific,275209,362,549,0.000603801,43.2152,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5565,Q#2207 - >seq2206,superfamily,275209,362,549,0.000603801,43.2152,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs7_bushaby.pars.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5566,Q#2208 - >seq2207,non-specific,340095,113,242,0.00138532,42.5072,pfam17380,DUF5401,NC,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA8.ORF2.hs7_bushaby.pars.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5567,Q#2208 - >seq2207,superfamily,340095,113,242,0.00138532,42.5072,cl38662,DUF5401 superfamily,NC, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA8.ORF2.hs7_bushaby.pars.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5568,Q#2208 - >seq2207,non-specific,274475,142,221,0.00308456,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA8.ORF2.hs7_bushaby.pars.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5569,Q#2208 - >seq2207,superfamily,274475,142,221,0.00308456,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA8.ORF2.hs7_bushaby.pars.frame1,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA8,ORF2,hs7_bushaby,pars,BothTerminiTruncated
5570,Q#2210 - >seq2209,non-specific,340205,167,217,1.87765e-09,51.9532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs7_bushaby,marg,CompleteHit
5571,Q#2210 - >seq2209,superfamily,340205,167,217,1.87765e-09,51.9532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA8,ORF1,hs7_bushaby,marg,CompleteHit
5572,Q#2210 - >seq2209,non-specific,270255,79,205,0.00881963,36.1097,cd13537,PBP2_YvgL_like,C,cl21456,"Substrate binding domain of putative molybdate-binding protein YvgL and similar proteins;the type 2 periplasmic binding protein fold; This subfamily contains domains found in ModA proteins of putative ABC-type transporter. ModA proteins serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate and tungstate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.",L1MA8.ORF1.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA8,ORF1,hs7_bushaby,marg,C-TerminusTruncated
5573,Q#2210 - >seq2209,superfamily,354813,79,205,0.00881963,36.1097,cl21456,Periplasmic_Binding_Protein_Type_2 superfamily,C, - ,"Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating.  The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology.  They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes.  The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.  Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.",L1MA8.ORF1.hs7_bushaby.marg.frame2,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA8,ORF1,hs7_bushaby,marg,C-TerminusTruncated
5574,Q#2212 - >seq2211,non-specific,340205,120,168,5.42775e-08,47.3308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs7_bushaby,pars,CompleteHit
5575,Q#2212 - >seq2211,superfamily,340205,120,168,5.42775e-08,47.3308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA8.ORF1.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA8,ORF1,hs7_bushaby,pars,CompleteHit
5576,Q#2213 - >seq2212,non-specific,238827,342,377,1.0082800000000001e-07,53.449,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5577,Q#2213 - >seq2212,superfamily,295487,342,377,1.0082800000000001e-07,53.449,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs7_bushaby,pars,C-TerminusTruncated
5578,Q#2213 - >seq2212,specific,311990,1021,1039,0.00235157,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5579,Q#2213 - >seq2212,superfamily,311990,1021,1039,0.00235157,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs7_bushaby.pars.frame3,1909130117_L1MA8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA8,ORF2,hs7_bushaby,pars,CompleteHit
5580,Q#2215 - >seq2214,non-specific,340205,217,281,7.070699999999999e-25,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs1_chimp,marg,CompleteHit
5581,Q#2215 - >seq2214,superfamily,340205,217,281,7.070699999999999e-25,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs1_chimp,marg,CompleteHit
5582,Q#2215 - >seq2214,non-specific,335182,119,214,4.12843e-24,93.1362,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs1_chimp,marg,CompleteHit
5583,Q#2215 - >seq2214,superfamily,335182,119,214,4.12843e-24,93.1362,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs1_chimp,marg,CompleteHit
5584,Q#2215 - >seq2214,non-specific,312584,24,88,0.00614576,36.0545,pfam09104,BRCA-2_OB3,N,cl09930,"BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.",L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA9,ORF1,hs1_chimp,marg,N-TerminusTruncated
5585,Q#2215 - >seq2214,superfamily,353029,24,88,0.00614576,36.0545,cl09930,RPA_2b-aaRSs_OBF_like superfamily,N, - ,"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.",L1MA9.ORF1.hs1_chimp.marg.frame2,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MA9,ORF1,hs1_chimp,marg,N-TerminusTruncated
5586,Q#2220 - >seq2219,non-specific,340205,220,284,1.2252299999999999e-23,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs1_chimp.pars.frame3,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs1_chimp,pars,CompleteHit
5587,Q#2220 - >seq2219,superfamily,340205,220,284,1.2252299999999999e-23,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs1_chimp.pars.frame3,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs1_chimp,pars,CompleteHit
5588,Q#2220 - >seq2219,non-specific,335182,137,217,6.344980000000001e-22,87.7434,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs1_chimp.pars.frame3,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs1_chimp,pars,CompleteHit
5589,Q#2220 - >seq2219,superfamily,335182,137,217,6.344980000000001e-22,87.7434,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs1_chimp.pars.frame3,1909130118_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs1_chimp,pars,CompleteHit
5590,Q#2223 - >seq2222,non-specific,340205,192,255,7.688799999999999e-28,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs4_gibbon.marg.frame3,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs4_gibbon,marg,CompleteHit
5591,Q#2223 - >seq2222,superfamily,340205,192,255,7.688799999999999e-28,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs4_gibbon.marg.frame3,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs4_gibbon,marg,CompleteHit
5592,Q#2223 - >seq2222,non-specific,335182,98,189,5.49319e-27,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs4_gibbon.marg.frame3,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs4_gibbon,marg,CompleteHit
5593,Q#2223 - >seq2222,superfamily,335182,98,189,5.49319e-27,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs4_gibbon.marg.frame3,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs4_gibbon,marg,CompleteHit
5594,Q#2225 - >seq2224,non-specific,340205,234,297,6.717599999999999e-28,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs4_gibbon.pars.frame1,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs4_gibbon,pars,CompleteHit
5595,Q#2225 - >seq2224,superfamily,340205,234,297,6.717599999999999e-28,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs4_gibbon.pars.frame1,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs4_gibbon,pars,CompleteHit
5596,Q#2225 - >seq2224,non-specific,335182,141,231,1.30092e-23,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs4_gibbon.pars.frame1,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs4_gibbon,pars,CompleteHit
5597,Q#2225 - >seq2224,superfamily,335182,141,231,1.30092e-23,92.3658,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs4_gibbon.pars.frame1,1909130122_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs4_gibbon,pars,CompleteHit
5598,Q#2228 - >seq2227,non-specific,340205,177,240,3.44678e-23,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs5_gmonkey.pars.frame2,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs5_gmonkey,pars,CompleteHit
5599,Q#2228 - >seq2227,superfamily,340205,177,240,3.44678e-23,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs5_gmonkey.pars.frame2,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs5_gmonkey,pars,CompleteHit
5600,Q#2228 - >seq2227,non-specific,335182,86,154,1.0863700000000001e-12,62.3203,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs5_gmonkey.pars.frame2,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
5601,Q#2228 - >seq2227,superfamily,335182,86,154,1.0863700000000001e-12,62.3203,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs5_gmonkey.pars.frame2,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
5602,Q#2232 - >seq2231,non-specific,340205,196,259,4.649459999999999e-24,91.6288,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs5_gmonkey.marg.frame3,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs5_gmonkey,marg,CompleteHit
5603,Q#2232 - >seq2231,superfamily,340205,196,259,4.649459999999999e-24,91.6288,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs5_gmonkey.marg.frame3,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs5_gmonkey,marg,CompleteHit
5604,Q#2232 - >seq2231,non-specific,335182,105,173,4.67151e-14,66.1723,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs5_gmonkey.marg.frame3,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
5605,Q#2232 - >seq2231,superfamily,335182,105,173,4.67151e-14,66.1723,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs5_gmonkey.marg.frame3,1909130124_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
5606,Q#2233 - >seq2232,non-specific,340205,318,378,2.19679e-18,78.1468,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs6_sqmonkey.marg.frame2,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs6_sqmonkey,marg,CompleteHit
5607,Q#2233 - >seq2232,superfamily,340205,318,378,2.19679e-18,78.1468,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs6_sqmonkey.marg.frame2,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs6_sqmonkey,marg,CompleteHit
5608,Q#2233 - >seq2232,non-specific,335182,238,314,8.58583e-17,75.0319,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs6_sqmonkey.marg.frame2,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
5609,Q#2233 - >seq2232,superfamily,335182,238,314,8.58583e-17,75.0319,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs6_sqmonkey.marg.frame2,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MA9,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
5610,Q#2238 - >seq2237,non-specific,340205,225,285,5.825399999999999e-17,73.1392,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs6_sqmonkey,pars,CompleteHit
5611,Q#2238 - >seq2237,superfamily,340205,225,285,5.825399999999999e-17,73.1392,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs6_sqmonkey,pars,CompleteHit
5612,Q#2238 - >seq2237,non-specific,335182,145,221,4.86262e-16,71.9503,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
5613,Q#2238 - >seq2237,superfamily,335182,145,221,4.86262e-16,71.9503,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
5614,Q#2238 - >seq2237,non-specific,184940,35,133,0.00018522099999999998,42.7055,PRK14977,PRK14977,N,cl33049,bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA9,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
5615,Q#2238 - >seq2237,superfamily,184940,35,133,0.00018522099999999998,42.7055,cl33049,PRK14977 superfamily,N, - ,bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional,L1MA9.ORF1.hs6_sqmonkey.pars.frame1,1909130125_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA9,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
5616,Q#2241 - >seq2240,specific,238827,491,753,6.199519999999999e-63,213.30700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5617,Q#2241 - >seq2240,superfamily,295487,491,753,6.199519999999999e-63,213.30700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5618,Q#2241 - >seq2240,specific,197310,1,221,1.32076e-56,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5619,Q#2241 - >seq2240,superfamily,351117,1,221,1.32076e-56,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5620,Q#2241 - >seq2240,specific,333820,497,753,3.3130199999999995e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5621,Q#2241 - >seq2240,superfamily,333820,497,753,3.3130199999999995e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5622,Q#2241 - >seq2240,non-specific,197306,1,221,1.7343e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5623,Q#2241 - >seq2240,non-specific,197320,15,214,1.62327e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5624,Q#2241 - >seq2240,non-specific,223780,1,214,3.89188e-15,76.4831,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5625,Q#2241 - >seq2240,non-specific,197307,8,214,6.908300000000001e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5626,Q#2241 - >seq2240,specific,335306,12,214,4.41746e-13,69.9666,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5627,Q#2241 - >seq2240,non-specific,238828,497,721,2.31567e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5628,Q#2241 - >seq2240,non-specific,197321,8,214,1.27819e-10,62.9548,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5629,Q#2241 - >seq2240,non-specific,272954,15,192,8.397560000000001e-10,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5630,Q#2241 - >seq2240,non-specific,197319,8,221,2.43681e-09,59.2125,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5631,Q#2241 - >seq2240,non-specific,275209,448,838,7.215709999999999e-09,59.0084,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5632,Q#2241 - >seq2240,superfamily,275209,448,838,7.215709999999999e-09,59.0084,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5633,Q#2241 - >seq2240,non-specific,197311,22,189,8.7787e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5634,Q#2241 - >seq2240,non-specific,238185,637,753,0.000126654,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5635,Q#2241 - >seq2240,non-specific,339261,93,216,0.00045956199999999995,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5636,Q#2241 - >seq2240,non-specific,197336,10,214,0.0021763999999999998,41.0587,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs6_sqmonkey.pars.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,pars,CompleteHit
5637,Q#2244 - >seq2243,specific,238827,503,765,1.6299799999999995e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5638,Q#2244 - >seq2243,superfamily,295487,503,765,1.6299799999999995e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5639,Q#2244 - >seq2243,specific,197310,8,233,5.923929999999999e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5640,Q#2244 - >seq2243,superfamily,351117,8,233,5.923929999999999e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5641,Q#2244 - >seq2243,specific,333820,509,765,5.69668e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5642,Q#2244 - >seq2243,superfamily,333820,509,765,5.69668e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5643,Q#2244 - >seq2243,non-specific,197306,7,233,3.05357e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5644,Q#2244 - >seq2243,non-specific,197320,8,226,7.13934e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5645,Q#2244 - >seq2243,non-specific,223780,8,226,3.3092800000000007e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5646,Q#2244 - >seq2243,specific,335306,7,226,1.35014e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5647,Q#2244 - >seq2243,non-specific,197307,7,226,1.62381e-16,80.4097,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5648,Q#2244 - >seq2243,non-specific,197321,7,226,1.51722e-13,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5649,Q#2244 - >seq2243,non-specific,272954,8,204,3.78343e-11,64.7117,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5650,Q#2244 - >seq2243,non-specific,238828,509,733,3.8242e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5651,Q#2244 - >seq2243,non-specific,273186,7,234,4.50393e-11,64.6076,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5652,Q#2244 - >seq2243,non-specific,197319,10,233,1.7832499999999998e-10,62.6793,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5653,Q#2244 - >seq2243,non-specific,275209,460,789,3.949369999999999e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5654,Q#2244 - >seq2243,superfamily,275209,460,789,3.949369999999999e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5655,Q#2244 - >seq2243,non-specific,197322,8,226,4.93062e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5656,Q#2244 - >seq2243,non-specific,197311,34,201,9.2251e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5657,Q#2244 - >seq2243,non-specific,197336,7,226,9.38886e-07,51.4591,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5658,Q#2244 - >seq2243,non-specific,238185,649,765,0.000132685,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5659,Q#2244 - >seq2243,non-specific,339261,105,228,0.000520423,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs6_sqmonkey.marg.frame3,1909130126_L1MA9.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs6_sqmonkey,marg,CompleteHit
5660,Q#2246 - >seq2245,specific,311990,1011,1029,0.00131728,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5661,Q#2246 - >seq2245,superfamily,311990,1011,1029,0.00131728,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5662,Q#2248 - >seq2247,non-specific,340205,64,126,2.34706e-11,55.42,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs8_ctshrew.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs8_ctshrew,marg,CompleteHit
5663,Q#2248 - >seq2247,superfamily,340205,64,126,2.34706e-11,55.42,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs8_ctshrew.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs8_ctshrew,marg,CompleteHit
5664,Q#2252 - >seq2251,specific,238827,344,605,1.9659399999999996e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5665,Q#2252 - >seq2251,superfamily,295487,344,605,1.9659399999999996e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5666,Q#2252 - >seq2251,specific,333820,350,605,5.03661e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5667,Q#2252 - >seq2251,superfamily,333820,350,605,5.03661e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5668,Q#2252 - >seq2251,non-specific,238828,350,605,7.85033e-13,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5669,Q#2252 - >seq2251,non-specific,275209,301,624,5.502849999999999e-06,49.7636,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5670,Q#2252 - >seq2251,superfamily,275209,301,624,5.502849999999999e-06,49.7636,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5671,Q#2252 - >seq2251,non-specific,238185,484,605,0.00043488800000000003,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs7_bushaby.marg.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs7_bushaby,marg,CompleteHit
5672,Q#2254 - >seq2253,specific,311990,861,879,0.00025104799999999997,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5673,Q#2254 - >seq2253,superfamily,311990,861,879,0.00025104799999999997,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5674,Q#2255 - >seq2254,specific,238827,197,457,2.0641799999999996e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5675,Q#2255 - >seq2254,superfamily,295487,197,457,2.0641799999999996e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5676,Q#2255 - >seq2254,specific,333820,203,457,7.107269999999999e-32,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5677,Q#2255 - >seq2254,superfamily,333820,203,457,7.107269999999999e-32,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5678,Q#2255 - >seq2254,non-specific,238828,203,457,1.04773e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5679,Q#2255 - >seq2254,non-specific,275209,154,476,3.4076099999999996e-06,50.1488,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5680,Q#2255 - >seq2254,superfamily,275209,154,476,3.4076099999999996e-06,50.1488,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5681,Q#2255 - >seq2254,non-specific,238185,336,457,0.00033556300000000004,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs7_bushaby,pars,CompleteHit
5682,Q#2258 - >seq2257,non-specific,335182,235,315,4.8556800000000005e-21,86.973,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,marg,CompleteHit
5683,Q#2258 - >seq2257,superfamily,335182,235,315,4.8556800000000005e-21,86.973,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,marg,CompleteHit
5684,Q#2258 - >seq2257,non-specific,340205,319,389,1.0234500000000001e-07,48.4864,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,marg,CompleteHit
5685,Q#2258 - >seq2257,superfamily,340205,319,389,1.0234500000000001e-07,48.4864,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.marg.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,marg,CompleteHit
5686,Q#2259 - >seq2258,non-specific,335182,9,89,3.2277800000000006e-21,82.3507,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,CompleteHit
5687,Q#2259 - >seq2258,superfamily,335182,9,89,3.2277800000000006e-21,82.3507,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,CompleteHit
5688,Q#2259 - >seq2258,non-specific,340205,93,159,5.16591e-14,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,CompleteHit
5689,Q#2259 - >seq2258,superfamily,340205,93,159,5.16591e-14,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame3,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,CompleteHit
5690,Q#2261 - >seq2260,non-specific,340205,107,123,0.00677975,33.4636,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,BothTerminiTruncated
5691,Q#2261 - >seq2260,superfamily,340205,107,123,0.00677975,33.4636,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs7_bushaby.pars.frame1,1909130128_L1MA9.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs7_bushaby,pars,BothTerminiTruncated
5692,Q#2266 - >seq2265,non-specific,238827,421,455,4.15105e-05,44.9746,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs9_pika.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs9_pika,pars,C-TerminusTruncated
5693,Q#2266 - >seq2265,superfamily,295487,421,455,4.15105e-05,44.9746,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs9_pika.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs9_pika,pars,C-TerminusTruncated
5694,Q#2267 - >seq2266,non-specific,197310,11,196,1.3827999999999999e-21,93.9553,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs9_pika.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs9_pika,pars,CompleteHit
5695,Q#2267 - >seq2266,superfamily,351117,11,196,1.3827999999999999e-21,93.9553,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs9_pika.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs9_pika,pars,CompleteHit
5696,Q#2267 - >seq2266,non-specific,238827,547,638,4.06237e-09,57.301,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs9_pika.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs9_pika,pars,N-TerminusTruncated
5697,Q#2267 - >seq2266,superfamily,295487,547,638,4.06237e-09,57.301,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs9_pika.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs9_pika,pars,N-TerminusTruncated
5698,Q#2267 - >seq2266,non-specific,197306,45,196,0.00474732,39.0017,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs9_pika.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs9_pika,pars,N-TerminusTruncated
5699,Q#2268 - >seq2267,non-specific,238827,463,515,5.47188e-07,50.7526,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs9_pika.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs9_pika,pars,BothTerminiTruncated
5700,Q#2268 - >seq2267,superfamily,295487,463,515,5.47188e-07,50.7526,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs9_pika.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs9_pika,pars,BothTerminiTruncated
5701,Q#2270 - >seq2269,non-specific,340205,62,122,1.4871e-12,58.1164,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs9_pika,marg,CompleteHit
5702,Q#2270 - >seq2269,superfamily,340205,62,122,1.4871e-12,58.1164,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA9,ORF1,hs9_pika,marg,CompleteHit
5703,Q#2271 - >seq2270,specific,238827,515,791,3.84104e-36,136.65200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5704,Q#2271 - >seq2270,superfamily,295487,515,791,3.84104e-36,136.65200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5705,Q#2271 - >seq2270,specific,197310,4,231,5.388769999999999e-34,130.934,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5706,Q#2271 - >seq2270,superfamily,351117,4,231,5.388769999999999e-34,130.934,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5707,Q#2271 - >seq2270,non-specific,333820,521,791,6.772810000000001e-14,71.1694,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5708,Q#2271 - >seq2270,superfamily,333820,521,791,6.772810000000001e-14,71.1694,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5709,Q#2271 - >seq2270,non-specific,197306,4,231,5.1939800000000005e-12,67.1213,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5710,Q#2271 - >seq2270,non-specific,238828,593,760,0.0006855930000000001,42.5733,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MA9,ORF2,hs9_pika,marg,N-TerminusTruncated
5711,Q#2271 - >seq2270,non-specific,180670,301,436,0.00191965,41.5772,PRK06722,PRK06722,N,cl32162,exonuclease; Provisional,L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA9,ORF2,hs9_pika,marg,N-TerminusTruncated
5712,Q#2271 - >seq2270,superfamily,180670,301,436,0.00191965,41.5772,cl32162,PRK06722 superfamily,N, - ,exonuclease; Provisional,L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MA9,ORF2,hs9_pika,marg,N-TerminusTruncated
5713,Q#2271 - >seq2270,specific,311990,1279,1297,0.00614602,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5714,Q#2271 - >seq2270,superfamily,311990,1279,1297,0.00614602,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs9_pika.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs9_pika,marg,CompleteHit
5715,Q#2274 - >seq2273,specific,238827,501,780,4.416529999999999e-45,162.075,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5716,Q#2274 - >seq2273,superfamily,295487,501,780,4.416529999999999e-45,162.075,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5717,Q#2274 - >seq2273,non-specific,333820,507,780,7.32994e-21,91.1997,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5718,Q#2274 - >seq2273,superfamily,333820,507,780,7.32994e-21,91.1997,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5719,Q#2274 - >seq2273,non-specific,238185,652,780,0.00179151,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5720,Q#2274 - >seq2273,non-specific,238828,583,748,0.00891048,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs8_ctshrew.marg.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5721,Q#2276 - >seq2275,specific,197310,6,236,3.12429e-32,125.927,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5722,Q#2276 - >seq2275,superfamily,351117,6,236,3.12429e-32,125.927,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5723,Q#2276 - >seq2275,non-specific,197306,6,236,6.00828e-12,66.7361,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5724,Q#2276 - >seq2275,non-specific,223780,4,229,7.18684e-05,45.6671,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5725,Q#2276 - >seq2275,non-specific,197307,178,229,0.0007499989999999999,42.6601,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5726,Q#2276 - >seq2275,specific,311990,1232,1250,0.00184712,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5727,Q#2276 - >seq2275,superfamily,311990,1232,1250,0.00184712,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5728,Q#2276 - >seq2275,specific,335306,7,229,0.00312631,40.3062,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,CompleteHit
5729,Q#2276 - >seq2275,non-specific,273186,178,237,0.00342737,40.34,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5730,Q#2276 - >seq2275,non-specific,197319,178,236,0.00345649,40.3377,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5731,Q#2276 - >seq2275,non-specific,197320,178,229,0.00533562,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5732,Q#2276 - >seq2275,non-specific,197321,178,229,0.00540889,39.8428,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.marg.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA9,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
5733,Q#2277 - >seq2276,non-specific,197310,63,185,7.51853e-14,71.9989,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5734,Q#2277 - >seq2276,superfamily,351117,63,185,7.51853e-14,71.9989,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5735,Q#2277 - >seq2276,non-specific,197307,133,184,0.000832121,42.2749,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5736,Q#2277 - >seq2276,non-specific,223780,133,184,0.000888483,42.2003,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5737,Q#2277 - >seq2276,non-specific,197320,133,184,0.00464854,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5738,Q#2277 - >seq2276,non-specific,197321,133,184,0.00467072,39.8428,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5739,Q#2277 - >seq2276,non-specific,273186,133,184,0.00626413,39.5696,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs8_ctshrew.pars.frame3,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5740,Q#2278 - >seq2277,non-specific,197310,3,109,5.94483e-09,57.7465,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5741,Q#2278 - >seq2277,superfamily,351117,3,109,5.94483e-09,57.7465,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5742,Q#2278 - >seq2277,non-specific,238827,633,687,8.31558e-06,48.0562,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5743,Q#2278 - >seq2277,superfamily,295487,633,687,8.31558e-06,48.0562,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
5744,Q#2278 - >seq2277,non-specific,224117,220,370,0.000361139,44.7052,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5745,Q#2278 - >seq2277,superfamily,224117,220,370,0.000361139,44.7052,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA9.ORF2.hs8_ctshrew.pars.frame2,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5746,Q#2279 - >seq2278,specific,238827,444,693,2.6552199999999997e-46,165.542,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs8_ctshrew,pars,CompleteHit
5747,Q#2279 - >seq2278,superfamily,295487,444,693,2.6552199999999997e-46,165.542,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs8_ctshrew,pars,CompleteHit
5748,Q#2279 - >seq2278,non-specific,333820,450,642,3.97806e-23,97.7481,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5749,Q#2279 - >seq2278,superfamily,333820,450,642,3.97806e-23,97.7481,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
5750,Q#2279 - >seq2278,non-specific,238828,450,651,1.3741e-06,50.2772,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs8_ctshrew,pars,CompleteHit
5751,Q#2279 - >seq2278,specific,311990,1119,1137,0.0008849169999999999,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA9,ORF2,hs8_ctshrew,pars,CompleteHit
5752,Q#2279 - >seq2278,superfamily,311990,1119,1137,0.0008849169999999999,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs8_ctshrew.pars.frame1,1909130129_L1MA9.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA9,ORF2,hs8_ctshrew,pars,CompleteHit
5753,Q#2281 - >seq2280,non-specific,340205,178,229,6.158180000000001e-13,61.5832,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs1_chimp.marg.frame3,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs1_chimp,marg,CompleteHit
5754,Q#2281 - >seq2280,superfamily,340205,178,229,6.158180000000001e-13,61.5832,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs1_chimp.marg.frame3,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs1_chimp,marg,CompleteHit
5755,Q#2281 - >seq2280,non-specific,335182,87,148,1.91722e-12,61.1647,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs1_chimp.marg.frame3,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
5756,Q#2281 - >seq2280,superfamily,335182,87,148,1.91722e-12,61.1647,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs1_chimp.marg.frame3,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
5757,Q#2286 - >seq2285,non-specific,335182,75,133,6.6321800000000005e-12,59.6239,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs1_chimp.pars.frame1,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
5758,Q#2286 - >seq2285,superfamily,335182,75,133,6.6321800000000005e-12,59.6239,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs1_chimp.pars.frame1,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
5759,Q#2286 - >seq2285,non-specific,340205,163,207,0.000246547,38.086,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs1_chimp.pars.frame1,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs1_chimp,pars,CompleteHit
5760,Q#2286 - >seq2285,superfamily,340205,163,207,0.000246547,38.086,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs1_chimp.pars.frame1,1909130130_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs1_chimp,pars,CompleteHit
5761,Q#2290 - >seq2289,non-specific,340205,166,230,7.65085e-26,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs0_human.pars.frame2,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs0_human,pars,CompleteHit
5762,Q#2290 - >seq2289,superfamily,340205,166,230,7.65085e-26,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs0_human.pars.frame2,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs0_human,pars,CompleteHit
5763,Q#2290 - >seq2289,non-specific,335182,68,163,1.31398e-15,69.6391,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs0_human.pars.frame2,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs0_human,pars,CompleteHit
5764,Q#2290 - >seq2289,superfamily,335182,68,163,1.31398e-15,69.6391,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs0_human.pars.frame2,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MA9,ORF1,hs0_human,pars,CompleteHit
5765,Q#2292 - >seq2291,non-specific,340205,253,317,1.7019600000000001e-25,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs0_human.marg.frame3,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs0_human,marg,CompleteHit
5766,Q#2292 - >seq2291,superfamily,340205,253,317,1.7019600000000001e-25,96.6364,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs0_human.marg.frame3,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs0_human,marg,CompleteHit
5767,Q#2292 - >seq2291,non-specific,335182,155,250,1.59092e-15,70.7947,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs0_human.marg.frame3,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs0_human,marg,CompleteHit
5768,Q#2292 - >seq2291,superfamily,335182,155,250,1.59092e-15,70.7947,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs0_human.marg.frame3,1909130130_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs0_human,marg,CompleteHit
5769,Q#2294 - >seq2293,non-specific,335182,1,74,9.96894e-21,80.4247,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
5770,Q#2294 - >seq2293,superfamily,335182,1,74,9.96894e-21,80.4247,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
5771,Q#2294 - >seq2293,non-specific,335182,1,74,9.96894e-21,80.4247,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
5772,Q#2294 - >seq2293,non-specific,340205,77,140,1.0632099999999999e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,CompleteHit
5773,Q#2294 - >seq2293,superfamily,340205,77,140,1.0632099999999999e-19,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,CompleteHit
5774,Q#2294 - >seq2293,non-specific,340205,77,140,1.0632099999999999e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.pars.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,pars,CompleteHit
5775,Q#2296 - >seq2295,non-specific,335182,1,74,9.96894e-21,80.4247,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
5776,Q#2296 - >seq2295,superfamily,335182,1,74,9.96894e-21,80.4247,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
5777,Q#2296 - >seq2295,non-specific,335182,1,74,9.96894e-21,80.4247,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
5778,Q#2296 - >seq2295,non-specific,340205,77,140,1.0632099999999999e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,CompleteHit
5779,Q#2296 - >seq2295,superfamily,340205,77,140,1.0632099999999999e-19,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,CompleteHit
5780,Q#2296 - >seq2295,non-specific,340205,77,140,1.0632099999999999e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs2_gorilla.marg.frame1,1909130131_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs2_gorilla,marg,CompleteHit
5781,Q#2300 - >seq2299,non-specific,340205,130,191,1.14346e-15,68.1316,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs3_orang.pars.frame2,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs3_orang,pars,CompleteHit
5782,Q#2300 - >seq2299,superfamily,340205,130,191,1.14346e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs3_orang.pars.frame2,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs3_orang,pars,CompleteHit
5783,Q#2301 - >seq2300,non-specific,335182,170,261,3.7901e-25,96.9882,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs3_orang,marg,CompleteHit
5784,Q#2301 - >seq2300,superfamily,335182,170,261,3.7901e-25,96.9882,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs3_orang,marg,CompleteHit
5785,Q#2301 - >seq2300,non-specific,340205,264,327,1.1951399999999998e-18,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs3_orang,marg,CompleteHit
5786,Q#2301 - >seq2300,superfamily,340205,264,327,1.1951399999999998e-18,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs3_orang,marg,CompleteHit
5787,Q#2301 - >seq2300,non-specific,237554,39,140,0.00479749,38.4124,PRK13909,PRK13909,NC,cl36313,putative recombination protein RecB; Provisional,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB1,ORF1,hs3_orang,marg,BothTerminiTruncated
5788,Q#2301 - >seq2300,superfamily,237554,39,140,0.00479749,38.4124,cl36313,PRK13909 superfamily,NC, - ,putative recombination protein RecB; Provisional,L1MB1.ORF1.hs3_orang.marg.frame3,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB1,ORF1,hs3_orang,marg,BothTerminiTruncated
5789,Q#2303 - >seq2302,non-specific,335182,58,111,4.8581e-13,61.9351,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs3_orang.pars.frame1,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs3_orang,pars,N-TerminusTruncated
5790,Q#2303 - >seq2302,superfamily,335182,58,111,4.8581e-13,61.9351,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs3_orang.pars.frame1,1909130132_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs3_orang,pars,N-TerminusTruncated
5791,Q#2305 - >seq2304,non-specific,197310,91,225,2.9518e-26,108.59299999999999,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5792,Q#2305 - >seq2304,superfamily,351117,91,225,2.9518e-26,108.59299999999999,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5793,Q#2305 - >seq2304,non-specific,238827,492,537,1.38699e-09,59.227,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5794,Q#2305 - >seq2304,superfamily,295487,492,537,1.38699e-09,59.227,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5795,Q#2305 - >seq2304,non-specific,197306,62,225,1.6639700000000002e-08,56.3357,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5796,Q#2305 - >seq2304,non-specific,197320,97,218,1.7103400000000003e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5797,Q#2305 - >seq2304,non-specific,223780,97,218,3.82518e-07,52.6007,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5798,Q#2305 - >seq2304,non-specific,197319,93,225,2.13264e-05,47.2713,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5799,Q#2305 - >seq2304,non-specific,197307,97,218,0.000126936,44.9713,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5800,Q#2305 - >seq2304,non-specific,235175,227,448,0.00036454699999999995,44.6696,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5801,Q#2305 - >seq2304,superfamily,235175,227,448,0.00036454699999999995,44.6696,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5802,Q#2305 - >seq2304,non-specific,197321,162,218,0.00288461,40.6132,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5803,Q#2305 - >seq2304,non-specific,238105,250,314,0.00689255,38.4194,cd00179,SynN,C,cl29093,"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5804,Q#2305 - >seq2304,superfamily,355969,250,314,0.00689255,38.4194,cl29093,SynN superfamily,C, - ,"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5805,Q#2305 - >seq2304,non-specific,197874,192,339,0.00953262,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5806,Q#2305 - >seq2304,superfamily,197874,192,339,0.00953262,39.2305,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5807,Q#2305 - >seq2304,non-specific,339261,99,220,0.009632600000000002,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs2_gorilla.marg.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB1,ORF2,hs2_gorilla,marg,CompleteHit
5808,Q#2306 - >seq2305,non-specific,197310,139,212,4.0294600000000006e-15,75.8509,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5809,Q#2306 - >seq2305,superfamily,351117,139,212,4.0294600000000006e-15,75.8509,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5810,Q#2306 - >seq2305,non-specific,197320,145,205,0.00023490900000000002,44.043,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5811,Q#2306 - >seq2305,non-specific,223780,152,205,0.000260593,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5812,Q#2306 - >seq2305,non-specific,197307,152,205,0.00168945,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5813,Q#2306 - >seq2305,non-specific,197321,149,205,0.00210674,40.9984,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5814,Q#2306 - >seq2305,non-specific,197306,129,212,0.0028259,40.5425,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5815,Q#2306 - >seq2305,non-specific,197319,153,212,0.00748648,39.1821,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs2_gorilla.pars.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5816,Q#2307 - >seq2306,specific,238827,484,707,3.356919999999999e-34,130.874,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,CompleteHit
5817,Q#2307 - >seq2306,superfamily,295487,484,707,3.356919999999999e-34,130.874,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,CompleteHit
5818,Q#2307 - >seq2306,non-specific,333820,466,707,2.7541e-15,75.0214,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,CompleteHit
5819,Q#2307 - >seq2306,superfamily,333820,466,707,2.7541e-15,75.0214,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,CompleteHit
5820,Q#2307 - >seq2306,non-specific,238828,517,645,3.8813e-06,49.1216,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5821,Q#2307 - >seq2306,non-specific,197310,85,180,0.00178494,41.1829,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5822,Q#2307 - >seq2306,superfamily,351117,85,180,0.00178494,41.1829,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5823,Q#2307 - >seq2306,non-specific,275209,522,731,0.00204688,41.6744,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5824,Q#2307 - >seq2306,superfamily,275209,522,731,0.00204688,41.6744,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs2_gorilla.pars.frame2,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
5825,Q#2308 - >seq2307,non-specific,197310,9,85,9.26445e-15,74.6953,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs2_gorilla.marg.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5826,Q#2308 - >seq2307,superfamily,351117,9,85,9.26445e-15,74.6953,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.marg.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5827,Q#2308 - >seq2307,non-specific,197306,9,81,0.000534585,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.marg.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
5828,Q#2309 - >seq2308,non-specific,197310,1,79,1.18863e-09,59.6725,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs2_gorilla.pars.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
5829,Q#2309 - >seq2308,superfamily,351117,1,79,1.18863e-09,59.6725,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs2_gorilla.pars.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
5830,Q#2309 - >seq2308,non-specific,238827,480,525,1.5651500000000001e-09,59.227,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs2_gorilla.pars.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
5831,Q#2309 - >seq2308,superfamily,295487,480,525,1.5651500000000001e-09,59.227,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs2_gorilla.pars.frame3,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
5832,Q#2310 - >seq2309,specific,238827,487,710,7.226309999999999e-33,127.022,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,CompleteHit
5833,Q#2310 - >seq2309,superfamily,295487,487,710,7.226309999999999e-33,127.022,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,CompleteHit
5834,Q#2310 - >seq2309,non-specific,333820,487,710,4.86074e-14,71.5546,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,CompleteHit
5835,Q#2310 - >seq2309,superfamily,333820,487,710,4.86074e-14,71.5546,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,CompleteHit
5836,Q#2310 - >seq2309,non-specific,238828,520,648,2.46261e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5837,Q#2310 - >seq2309,non-specific,275209,525,734,0.00890737,39.7484,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5838,Q#2310 - >seq2309,superfamily,275209,525,734,0.00890737,39.7484,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs2_gorilla.marg.frame1,1909130132_L1MB1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
5839,Q#2311 - >seq2310,specific,238827,509,729,5.371289999999999e-41,150.519,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5840,Q#2311 - >seq2310,superfamily,295487,509,729,5.371289999999999e-41,150.519,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5841,Q#2311 - >seq2310,non-specific,333820,513,729,4.8631700000000005e-21,91.5849,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5842,Q#2311 - >seq2310,superfamily,333820,513,729,4.8631700000000005e-21,91.5849,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5843,Q#2311 - >seq2310,non-specific,238828,543,681,6.2374400000000005e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5844,Q#2311 - >seq2310,non-specific,275209,544,693,2.52852e-07,54.0008,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,BothTerminiTruncated
5845,Q#2311 - >seq2310,superfamily,275209,544,693,2.52852e-07,54.0008,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,BothTerminiTruncated
5846,Q#2311 - >seq2310,non-specific,238185,613,729,3.5225500000000003e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5847,Q#2311 - >seq2310,non-specific,197310,9,39,0.00318187,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs3_orang,marg,C-TerminusTruncated
5848,Q#2311 - >seq2310,superfamily,351117,9,39,0.00318187,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.marg.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,marg,C-TerminusTruncated
5849,Q#2312 - >seq2311,specific,197310,26,230,4.5030899999999997e-45,162.52100000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5850,Q#2312 - >seq2311,superfamily,351117,26,230,4.5030899999999997e-45,162.52100000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5851,Q#2312 - >seq2311,non-specific,197306,26,230,5.19971e-18,84.4552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5852,Q#2312 - >seq2311,non-specific,197320,100,215,8.19169e-12,66.3846,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5853,Q#2312 - >seq2311,non-specific,223780,55,219,9.029989999999999e-12,66.4679,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5854,Q#2312 - >seq2311,non-specific,197307,52,223,6.61457e-10,60.7645,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5855,Q#2312 - >seq2311,non-specific,238827,504,551,1.67901e-09,59.227,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs3_orang,marg,C-TerminusTruncated
5856,Q#2312 - >seq2311,superfamily,295487,504,551,1.67901e-09,59.227,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs3_orang,marg,C-TerminusTruncated
5857,Q#2312 - >seq2311,non-specific,197319,66,230,8.101149999999999e-09,57.6717,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5858,Q#2312 - >seq2311,non-specific,272954,16,201,6.567570000000001e-07,52.0001,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5859,Q#2312 - >seq2311,specific,335306,36,223,8.26559e-07,51.0918,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5860,Q#2312 - >seq2311,non-specific,273186,100,231,1.94695e-05,47.2736,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5861,Q#2312 - >seq2311,non-specific,197321,63,223,6.58345e-05,45.6208,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5862,Q#2312 - >seq2311,non-specific,235175,301,463,0.00017324700000000002,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB1,ORF2,hs3_orang,marg,BothTerminiTruncated
5863,Q#2312 - >seq2311,superfamily,235175,301,463,0.00017324700000000002,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB1,ORF2,hs3_orang,marg,BothTerminiTruncated
5864,Q#2312 - >seq2311,non-specific,339261,102,225,0.00043284599999999997,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB1,ORF2,hs3_orang,marg,CompleteHit
5865,Q#2312 - >seq2311,non-specific,197311,66,198,0.000912107,41.8937,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5866,Q#2312 - >seq2311,non-specific,236970,83,201,0.0062657,39.8774,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1MB1.ORF2.hs3_orang.marg.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,marg,N-TerminusTruncated
5867,Q#2314 - >seq2313,specific,311990,1139,1157,0.006809999999999999,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB1.ORF2.hs3_orang.pars.frame2,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5868,Q#2314 - >seq2313,superfamily,311990,1139,1157,0.006809999999999999,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB1.ORF2.hs3_orang.pars.frame2,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5869,Q#2315 - >seq2314,specific,197310,26,230,7.74009e-45,162.136,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5870,Q#2315 - >seq2314,superfamily,351117,26,230,7.74009e-45,162.136,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5871,Q#2315 - >seq2314,non-specific,197306,26,230,1.09126e-17,83.6848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5872,Q#2315 - >seq2314,non-specific,197320,100,215,8.2076e-12,66.3846,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5873,Q#2315 - >seq2314,non-specific,223780,55,219,9.04761e-12,66.4679,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5874,Q#2315 - >seq2314,non-specific,197307,52,223,9.50929e-10,60.3793,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5875,Q#2315 - >seq2314,non-specific,238827,504,551,1.2233e-09,59.6122,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs3_orang,pars,C-TerminusTruncated
5876,Q#2315 - >seq2314,superfamily,295487,504,551,1.2233e-09,59.6122,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs3_orang,pars,C-TerminusTruncated
5877,Q#2315 - >seq2314,non-specific,197319,66,230,1.53245e-08,56.9013,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5878,Q#2315 - >seq2314,specific,335306,36,223,8.2811e-07,51.0918,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5879,Q#2315 - >seq2314,non-specific,272954,16,201,1.13715e-06,51.2297,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5880,Q#2315 - >seq2314,non-specific,273186,100,231,2.33768e-05,47.2736,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5881,Q#2315 - >seq2314,non-specific,197321,63,223,9.99041e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5882,Q#2315 - >seq2314,non-specific,235175,301,463,0.000151552,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB1,ORF2,hs3_orang,pars,BothTerminiTruncated
5883,Q#2315 - >seq2314,superfamily,235175,301,463,0.000151552,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB1,ORF2,hs3_orang,pars,BothTerminiTruncated
5884,Q#2315 - >seq2314,non-specific,339261,102,225,0.000557399,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5885,Q#2315 - >seq2314,non-specific,197311,66,198,0.000913787,41.8937,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5886,Q#2315 - >seq2314,non-specific,236970,83,201,0.00729903,39.4922,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5887,Q#2315 - >seq2314,non-specific,235175,313,496,0.00866362,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs3_orang.pars.frame1,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB1,ORF2,hs3_orang,pars,BothTerminiTruncated
5888,Q#2316 - >seq2315,specific,238827,509,726,2.77299e-40,148.208,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5889,Q#2316 - >seq2315,superfamily,295487,509,726,2.77299e-40,148.208,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5890,Q#2316 - >seq2315,non-specific,333820,513,726,3.24535e-20,89.2737,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5891,Q#2316 - >seq2315,superfamily,333820,513,726,3.24535e-20,89.2737,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5892,Q#2316 - >seq2315,non-specific,238828,543,681,4.41178e-12,66.8408,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,N-TerminusTruncated
5893,Q#2316 - >seq2315,non-specific,275209,544,693,1.73113e-07,54.386,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,BothTerminiTruncated
5894,Q#2316 - >seq2315,superfamily,275209,544,693,1.73113e-07,54.386,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,BothTerminiTruncated
5895,Q#2316 - >seq2315,non-specific,238185,613,726,0.000110641,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs3_orang,pars,CompleteHit
5896,Q#2316 - >seq2315,non-specific,197310,9,39,0.00351905,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs3_orang,pars,C-TerminusTruncated
5897,Q#2316 - >seq2315,superfamily,351117,9,39,0.00351905,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs3_orang.pars.frame3,1909130133_L1MB1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs3_orang,pars,C-TerminusTruncated
5898,Q#2317 - >seq2316,specific,238827,471,715,2.1424099999999999e-47,168.62400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5899,Q#2317 - >seq2316,superfamily,295487,471,715,2.1424099999999999e-47,168.62400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5900,Q#2317 - >seq2316,non-specific,333820,472,683,2.1243600000000002e-23,98.5185,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5901,Q#2317 - >seq2316,superfamily,333820,472,683,2.1243600000000002e-23,98.5185,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5902,Q#2317 - >seq2316,non-specific,238828,508,655,2.9945999999999996e-07,52.5884,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5903,Q#2319 - >seq2318,non-specific,340205,174,230,2.807e-13,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.marg.frame1,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs5_gmonkey,marg,CompleteHit
5904,Q#2319 - >seq2318,superfamily,340205,174,230,2.807e-13,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.marg.frame1,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs5_gmonkey,marg,CompleteHit
5905,Q#2321 - >seq2320,non-specific,340205,114,174,9.10118e-12,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,CompleteHit
5906,Q#2321 - >seq2320,superfamily,340205,114,174,9.10118e-12,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,CompleteHit
5907,Q#2321 - >seq2320,non-specific,335182,87,111,0.00652158,34.5859,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
5908,Q#2321 - >seq2320,superfamily,335182,87,111,0.00652158,34.5859,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
5909,Q#2322 - >seq2321,non-specific,340205,131,166,0.00172972,35.3896,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame1,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
5910,Q#2322 - >seq2321,superfamily,340205,131,166,0.00172972,35.3896,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs5_gmonkey.pars.frame1,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
5911,Q#2323 - >seq2322,specific,197310,8,232,1.94034e-29,117.45200000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5912,Q#2323 - >seq2322,superfamily,351117,8,232,1.94034e-29,117.45200000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5913,Q#2323 - >seq2322,non-specific,197306,8,232,3.34841e-13,70.5881,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5914,Q#2323 - >seq2322,non-specific,197320,103,225,3.97373e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5915,Q#2323 - >seq2322,non-specific,223780,103,225,6.53463e-08,54.9119,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5916,Q#2323 - >seq2322,non-specific,197307,103,225,3.1543900000000004e-06,49.5937,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5917,Q#2323 - >seq2322,non-specific,197319,103,232,7.138510000000001e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5918,Q#2323 - >seq2322,non-specific,273186,104,233,2.5535300000000003e-05,46.8884,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5919,Q#2323 - >seq2322,non-specific,235175,300,455,5.6617e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
5920,Q#2323 - >seq2322,superfamily,235175,300,455,5.6617e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
5921,Q#2323 - >seq2322,non-specific,197321,159,225,8.474459999999999e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5922,Q#2323 - >seq2322,non-specific,235175,301,493,0.00161483,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
5923,Q#2323 - >seq2322,non-specific,237177,284,408,0.00419272,40.917,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
5924,Q#2323 - >seq2322,superfamily,237177,284,408,0.00419272,40.917,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
5925,Q#2323 - >seq2322,non-specific,339261,105,227,0.00446234,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB1,ORF2,hs4_gibbon,marg,CompleteHit
5926,Q#2323 - >seq2322,non-specific,214661,299,365,0.00458832,40.7955,smart00435,TOPEUc,N,cl26030,"DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras",L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5927,Q#2323 - >seq2322,superfamily,330851,299,365,0.00458832,40.7955,cl26030,Topo_C_assoc superfamily,N, - ,C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.,L1MB1.ORF2.hs4_gibbon.marg.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
5928,Q#2324 - >seq2323,non-specific,197310,33,97,4.4493e-06,48.8869,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs4_gibbon.marg.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
5929,Q#2324 - >seq2323,superfamily,351117,33,97,4.4493e-06,48.8869,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs4_gibbon.marg.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
5930,Q#2325 - >seq2324,non-specific,335182,125,149,0.00365935,35.3563,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs5_gmonkey.marg.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
5931,Q#2325 - >seq2324,superfamily,335182,125,149,0.00365935,35.3563,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs5_gmonkey.marg.frame2,1909130134_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
5932,Q#2326 - >seq2325,specific,238827,478,722,3.64634e-47,168.238,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5933,Q#2326 - >seq2325,superfamily,295487,478,722,3.64634e-47,168.238,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5934,Q#2326 - >seq2325,non-specific,333820,479,690,1.8051100000000002e-23,98.9037,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5935,Q#2326 - >seq2325,superfamily,333820,479,690,1.8051100000000002e-23,98.9037,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5936,Q#2326 - >seq2325,non-specific,238828,515,662,2.29118e-07,52.9736,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5937,Q#2330 - >seq2329,non-specific,340205,142,203,1.05983e-12,60.4276,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs4_gibbon,marg,CompleteHit
5938,Q#2330 - >seq2329,superfamily,340205,142,203,1.05983e-12,60.4276,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs4_gibbon,marg,CompleteHit
5939,Q#2330 - >seq2329,non-specific,335182,41,123,7.960939999999999e-12,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs4_gibbon,marg,CompleteHit
5940,Q#2330 - >seq2329,superfamily,335182,41,123,7.960939999999999e-12,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs4_gibbon.marg.frame1,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs4_gibbon,marg,CompleteHit
5941,Q#2331 - >seq2330,non-specific,340205,141,202,1.13259e-12,60.4276,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs4_gibbon,pars,CompleteHit
5942,Q#2331 - >seq2330,superfamily,340205,141,202,1.13259e-12,60.4276,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs4_gibbon,pars,CompleteHit
5943,Q#2331 - >seq2330,non-specific,335182,40,122,1.09182e-11,58.8535,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs4_gibbon,pars,CompleteHit
5944,Q#2331 - >seq2330,superfamily,335182,40,122,1.09182e-11,58.8535,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs4_gibbon.pars.frame3,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs4_gibbon,pars,CompleteHit
5945,Q#2334 - >seq2333,specific,197310,16,242,3.6516199999999997e-44,160.21,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5946,Q#2334 - >seq2333,superfamily,351117,16,242,3.6516199999999997e-44,160.21,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5947,Q#2334 - >seq2333,non-specific,197306,16,242,5.730819999999999e-20,90.2332,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5948,Q#2334 - >seq2333,non-specific,197320,114,235,3.86116e-12,67.5402,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5949,Q#2334 - >seq2333,non-specific,223780,16,235,3.28894e-11,64.9271,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5950,Q#2334 - >seq2333,non-specific,197307,16,235,1.68155e-10,62.6905,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5951,Q#2334 - >seq2333,non-specific,273186,16,243,1.3742e-09,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5952,Q#2334 - >seq2333,specific,335306,16,235,2.00869e-09,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5953,Q#2334 - >seq2333,non-specific,197319,114,242,1.70057e-07,53.8197,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5954,Q#2334 - >seq2333,non-specific,197321,16,235,4.2231400000000003e-07,52.5544,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5955,Q#2334 - >seq2333,non-specific,272954,16,213,1.84415e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5956,Q#2334 - >seq2333,non-specific,235175,310,465,0.00011397700000000001,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
5957,Q#2334 - >seq2333,superfamily,235175,310,465,0.00011397700000000001,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
5958,Q#2334 - >seq2333,non-specific,339261,114,237,0.000174321,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB1,ORF2,hs4_gibbon,pars,CompleteHit
5959,Q#2334 - >seq2333,non-specific,197322,107,235,0.00280489,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5960,Q#2334 - >seq2333,non-specific,237177,294,418,0.00442942,40.917,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1MB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
5961,Q#2334 - >seq2333,superfamily,237177,294,418,0.00442942,40.917,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1MB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
5962,Q#2334 - >seq2333,non-specific,235175,311,503,0.00463888,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
5963,Q#2334 - >seq2333,non-specific,214661,309,375,0.00551999,40.4103,smart00435,TOPEUc,N,cl26030,"DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras",L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5964,Q#2334 - >seq2333,superfamily,330851,309,375,0.00551999,40.4103,cl26030,Topo_C_assoc superfamily,N, - ,C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.,L1MB1.ORF2.hs4_gibbon.pars.frame2,1909130134_L1MB1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
5965,Q#2335 - >seq2334,specific,197310,1,212,3.45639e-30,119.764,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,CompleteHit
5966,Q#2335 - >seq2334,superfamily,351117,1,212,3.45639e-30,119.764,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,CompleteHit
5967,Q#2335 - >seq2334,non-specific,197306,53,212,6.14012e-15,75.5956,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5968,Q#2335 - >seq2334,non-specific,197320,68,197,5.2636900000000005e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5969,Q#2335 - >seq2334,non-specific,223780,68,201,8.063319999999999e-08,54.5267,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5970,Q#2335 - >seq2334,non-specific,197307,68,205,3.22442e-05,46.5121,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5971,Q#2335 - >seq2334,specific,335306,113,205,0.00137159,41.4618,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5972,Q#2335 - >seq2334,non-specific,272954,68,183,0.00384709,40.4441,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5973,Q#2335 - >seq2334,non-specific,197322,33,205,0.00396765,40.3782,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
5974,Q#2335 - >seq2334,non-specific,339261,85,207,0.0065958,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs6_sqmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB1,ORF2,hs6_sqmonkey,pars,CompleteHit
5975,Q#2336 - >seq2335,non-specific,238827,539,659,2.10243e-15,76.561,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs7_bushaby.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5976,Q#2336 - >seq2335,superfamily,295487,539,659,2.10243e-15,76.561,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs7_bushaby.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5977,Q#2336 - >seq2335,non-specific,333820,579,659,1.06066e-06,49.9834,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs7_bushaby.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5978,Q#2336 - >seq2335,superfamily,333820,579,659,1.06066e-06,49.9834,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs7_bushaby.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5979,Q#2336 - >seq2335,non-specific,238828,552,664,0.00133053,41.4177,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs7_bushaby.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
5980,Q#2337 - >seq2336,non-specific,238827,597,717,1.04165e-12,68.4718,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5981,Q#2337 - >seq2336,superfamily,295487,597,717,1.04165e-12,68.4718,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5982,Q#2337 - >seq2336,non-specific,333820,545,717,9.23414e-06,47.287,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5983,Q#2337 - >seq2336,superfamily,333820,545,717,9.23414e-06,47.287,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5984,Q#2337 - >seq2336,non-specific,238828,548,717,1.5865e-05,47.1957,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
5985,Q#2338 - >seq2337,non-specific,238827,481,530,1.57715e-10,62.3086,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5986,Q#2338 - >seq2337,superfamily,295487,481,530,1.57715e-10,62.3086,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5987,Q#2338 - >seq2337,non-specific,333820,487,544,0.00187231,40.3534,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5988,Q#2338 - >seq2337,superfamily,333820,487,544,0.00187231,40.3534,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
5989,Q#2339 - >seq2338,specific,197310,3,222,9.685759999999999e-29,115.52600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5990,Q#2339 - >seq2338,superfamily,351117,3,222,9.685759999999999e-29,115.52600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5991,Q#2339 - >seq2338,non-specific,197306,3,221,6.0347e-13,69.8177,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5992,Q#2339 - >seq2338,non-specific,223780,3,211,1.86588e-10,62.6159,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5993,Q#2339 - >seq2338,non-specific,197320,3,212,3.3578199999999997e-10,61.7622,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5994,Q#2339 - >seq2338,non-specific,238827,537,591,6.25621e-09,57.301,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5995,Q#2339 - >seq2338,superfamily,295487,537,591,6.25621e-09,57.301,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
5996,Q#2339 - >seq2338,non-specific,197307,3,222,8.01919e-07,51.5197,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5997,Q#2339 - >seq2338,specific,335306,4,214,0.00104009,41.847,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5998,Q#2339 - >seq2338,non-specific,273186,3,242,0.00488994,39.9548,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
5999,Q#2339 - >seq2338,non-specific,235602,390,501,0.00952209,39.9756,PRK05776,PRK05776,N,cl35382,DNA topoisomerase I; Provisional,L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6000,Q#2339 - >seq2338,superfamily,235602,390,501,0.00952209,39.9756,cl35382,PRK05776 superfamily,N, - ,DNA topoisomerase I; Provisional,L1MB1.ORF2.hs7_bushaby.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6001,Q#2341 - >seq2340,non-specific,238827,493,711,1.53983e-23,99.67299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,pars,CompleteHit
6002,Q#2341 - >seq2340,superfamily,295487,493,711,1.53983e-23,99.67299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,pars,CompleteHit
6003,Q#2341 - >seq2340,non-specific,197310,2,205,6.05213e-17,80.8585,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs7_bushaby,pars,CompleteHit
6004,Q#2341 - >seq2340,superfamily,351117,2,205,6.05213e-17,80.8585,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs7_bushaby,pars,CompleteHit
6005,Q#2341 - >seq2340,non-specific,333820,526,711,1.2153499999999999e-08,55.3762,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6006,Q#2341 - >seq2340,superfamily,333820,526,711,1.2153499999999999e-08,55.3762,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs7_bushaby.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6007,Q#2342 - >seq2341,non-specific,238827,641,754,2.0869000000000003e-09,58.8418,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs7_bushaby.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6008,Q#2342 - >seq2341,superfamily,295487,641,754,2.0869000000000003e-09,58.8418,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs7_bushaby.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6009,Q#2342 - >seq2341,specific,311990,1215,1233,0.00515413,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB1.ORF2.hs7_bushaby.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
6010,Q#2342 - >seq2341,superfamily,311990,1215,1233,0.00515413,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB1.ORF2.hs7_bushaby.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MB1,ORF2,hs7_bushaby,marg,CompleteHit
6011,Q#2343 - >seq2342,non-specific,238827,587,661,1.93472e-09,58.8418,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
6012,Q#2343 - >seq2342,superfamily,295487,587,661,1.93472e-09,58.8418,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
6013,Q#2343 - >seq2342,non-specific,333820,571,683,0.000114825,44.2054,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6014,Q#2343 - >seq2342,superfamily,333820,571,683,0.000114825,44.2054,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6015,Q#2343 - >seq2342,non-specific,238828,563,661,0.00039291,42.9585,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6016,Q#2344 - >seq2343,non-specific,238827,469,617,4.37951e-09,57.6862,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs7_bushaby.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6017,Q#2344 - >seq2343,superfamily,295487,469,617,4.37951e-09,57.6862,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs7_bushaby.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6018,Q#2345 - >seq2344,non-specific,238827,449,498,1.81278e-10,61.9234,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs6_sqmonkey.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6019,Q#2345 - >seq2344,superfamily,295487,449,498,1.81278e-10,61.9234,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs6_sqmonkey.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6020,Q#2345 - >seq2344,non-specific,333820,455,519,0.000508955,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6021,Q#2345 - >seq2344,superfamily,333820,455,519,0.000508955,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs6_sqmonkey.pars.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6022,Q#2346 - >seq2345,specific,197310,21,231,2.3889799999999995e-38,143.261,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6023,Q#2346 - >seq2345,superfamily,351117,21,231,2.3889799999999995e-38,143.261,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6024,Q#2346 - >seq2345,non-specific,197306,60,231,3.55344e-17,82.14399999999999,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6025,Q#2346 - >seq2345,non-specific,223780,51,220,3.9098699999999993e-10,61.8455,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6026,Q#2346 - >seq2345,non-specific,197320,55,216,1.3094600000000001e-09,59.8362,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6027,Q#2346 - >seq2345,specific,335306,63,224,3.3905e-07,52.2474,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6028,Q#2346 - >seq2345,non-specific,197307,51,224,8.95648e-07,51.5197,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6029,Q#2346 - >seq2345,non-specific,272954,26,202,5.7754e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6030,Q#2346 - >seq2345,non-specific,197321,26,224,0.00108954,42.153999999999996,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6031,Q#2346 - >seq2345,non-specific,197311,68,142,0.00142772,41.1233,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
6032,Q#2346 - >seq2345,non-specific,339261,104,226,0.00481113,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB1,ORF2,hs6_sqmonkey,marg,CompleteHit
6033,Q#2347 - >seq2346,non-specific,307145,185,221,0.00532567,37.1402,pfam00864,P2X_receptor,NC,cl02993,ATP P2X receptor; ATP P2X receptor.  ,L1MB1.ORF1.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
6034,Q#2347 - >seq2346,superfamily,322156,185,221,0.00532567,37.1402,cl02993,P2X_receptor superfamily,NC, - ,ATP P2X receptor; ATP P2X receptor.  ,L1MB1.ORF1.hs6_sqmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
6035,Q#2348 - >seq2347,non-specific,340205,177,242,1.74235e-09,52.3384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,CompleteHit
6036,Q#2348 - >seq2347,superfamily,340205,177,242,1.74235e-09,52.3384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,CompleteHit
6037,Q#2348 - >seq2347,non-specific,335182,89,174,8.22065e-05,40.3639,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,CompleteHit
6038,Q#2348 - >seq2347,superfamily,335182,89,174,8.22065e-05,40.3639,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame1,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,CompleteHit
6039,Q#2350 - >seq2349,non-specific,340205,108,172,1.1887400000000002e-09,51.9532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs6_sqmonkey,pars,CompleteHit
6040,Q#2350 - >seq2349,superfamily,340205,108,172,1.1887400000000002e-09,51.9532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB1,ORF1,hs6_sqmonkey,pars,CompleteHit
6041,Q#2352 - >seq2351,specific,197310,9,236,9.814589999999998e-51,179.084,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6042,Q#2352 - >seq2351,superfamily,351117,9,236,9.814589999999998e-51,179.084,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6043,Q#2352 - >seq2351,non-specific,197306,9,236,5.57614e-21,93.3148,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6044,Q#2352 - >seq2351,non-specific,223780,9,229,8.37582e-11,63.7715,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6045,Q#2352 - >seq2351,non-specific,197307,9,229,1.4093600000000002e-10,62.6905,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6046,Q#2352 - >seq2351,non-specific,197320,107,229,5.93184e-10,60.9918,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6047,Q#2352 - >seq2351,specific,335306,10,229,4.0594299999999996e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6048,Q#2352 - >seq2351,non-specific,197319,9,236,8.46959e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6049,Q#2352 - >seq2351,non-specific,272954,9,207,1.31763e-07,53.9261,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6050,Q#2352 - >seq2351,non-specific,273186,9,237,5.23478e-07,52.2812,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6051,Q#2352 - >seq2351,non-specific,197321,7,229,0.000115453,44.8504,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6052,Q#2352 - >seq2351,non-specific,339261,109,231,0.000202933,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs5_gmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6053,Q#2353 - >seq2352,specific,238827,482,685,2.32261e-40,148.593,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs5_gmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6054,Q#2353 - >seq2352,superfamily,295487,482,685,2.32261e-40,148.593,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs5_gmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6055,Q#2353 - >seq2352,non-specific,333820,488,684,2.43555e-22,95.4369,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs5_gmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6056,Q#2353 - >seq2352,superfamily,333820,488,684,2.43555e-22,95.4369,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs5_gmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6057,Q#2353 - >seq2352,non-specific,238828,488,684,0.000165059,44.1141,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs5_gmonkey.marg.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,marg,CompleteHit
6058,Q#2355 - >seq2354,specific,197310,9,235,2.46731e-47,169.06900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6059,Q#2355 - >seq2354,superfamily,351117,9,235,2.46731e-47,169.06900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6060,Q#2355 - >seq2354,non-specific,197306,9,235,1.81218e-18,85.99600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6061,Q#2355 - >seq2354,non-specific,223780,9,228,5.69967e-09,57.9935,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6062,Q#2355 - >seq2354,non-specific,197307,9,228,2.04901e-08,56.5273,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6063,Q#2355 - >seq2354,non-specific,197320,107,228,2.49501e-07,53.2878,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6064,Q#2355 - >seq2354,specific,335306,10,228,6.31235e-07,51.477,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6065,Q#2355 - >seq2354,non-specific,272954,9,206,8.002849999999999e-06,48.5333,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6066,Q#2355 - >seq2354,non-specific,197319,9,235,1.1641300000000002e-05,48.0417,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6067,Q#2355 - >seq2354,non-specific,197321,172,228,0.00233188,40.9984,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs5_gmonkey.pars.frame3,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6068,Q#2356 - >seq2355,specific,238827,483,686,3.5026e-41,150.905,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs5_gmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6069,Q#2356 - >seq2355,superfamily,295487,483,686,3.5026e-41,150.905,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs5_gmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6070,Q#2356 - >seq2355,non-specific,333820,489,685,9.277379999999999e-23,96.5925,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs5_gmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6071,Q#2356 - >seq2355,superfamily,333820,489,685,9.277379999999999e-23,96.5925,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs5_gmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6072,Q#2356 - >seq2355,non-specific,238828,489,685,0.000103409,44.8845,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs5_gmonkey.pars.frame2,1909130135_L1MB1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB1,ORF2,hs5_gmonkey,pars,CompleteHit
6073,Q#2358 - >seq2357,non-specific,340205,168,202,0.00545252,34.234,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
6074,Q#2358 - >seq2357,superfamily,340205,168,202,0.00545252,34.234,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs6_sqmonkey.marg.frame3,1909130135_L1MB1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
6075,Q#2361 - >seq2360,non-specific,335182,72,130,4.11431e-11,57.6979,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs0_human.marg.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,marg,C-TerminusTruncated
6076,Q#2361 - >seq2360,superfamily,335182,72,130,4.11431e-11,57.6979,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs0_human.marg.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,marg,C-TerminusTruncated
6077,Q#2361 - >seq2360,non-specific,340205,173,231,3.0298700000000003e-10,54.2644,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs0_human.marg.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,marg,CompleteHit
6078,Q#2361 - >seq2360,superfamily,340205,173,231,3.0298700000000003e-10,54.2644,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs0_human.marg.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,marg,CompleteHit
6079,Q#2363 - >seq2362,non-specific,340205,158,221,2.90251e-12,59.6572,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs0_human.pars.frame1,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs0_human,pars,CompleteHit
6080,Q#2363 - >seq2362,superfamily,340205,158,221,2.90251e-12,59.6572,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB1.ORF1.hs0_human.pars.frame1,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB1,ORF1,hs0_human,pars,CompleteHit
6081,Q#2364 - >seq2363,non-specific,335182,75,133,1.63799e-11,58.8535,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs0_human.pars.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,pars,C-TerminusTruncated
6082,Q#2364 - >seq2363,superfamily,335182,75,133,1.63799e-11,58.8535,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB1.ORF1.hs0_human.pars.frame3,1909130136_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB1,ORF1,hs0_human,pars,C-TerminusTruncated
6083,Q#2366 - >seq2365,specific,238827,567,726,9.22448e-30,118.163,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
6084,Q#2366 - >seq2365,superfamily,295487,567,726,9.22448e-30,118.163,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
6085,Q#2366 - >seq2365,specific,197310,119,300,2.60868e-29,117.45200000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs1_chimp,marg,CompleteHit
6086,Q#2366 - >seq2365,superfamily,351117,119,300,2.60868e-29,117.45200000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,marg,CompleteHit
6087,Q#2366 - >seq2365,non-specific,333820,573,719,1.1539799999999999e-15,76.17699999999999,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
6088,Q#2366 - >seq2365,superfamily,333820,573,719,1.1539799999999999e-15,76.17699999999999,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
6089,Q#2366 - >seq2365,non-specific,197306,133,300,1.64998e-11,65.5805,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6090,Q#2366 - >seq2365,non-specific,197320,175,293,3.83689e-11,64.8438,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6091,Q#2366 - >seq2365,non-specific,223780,127,293,9.37537e-09,57.6083,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6092,Q#2366 - >seq2365,specific,335306,117,293,8.903579999999999e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,marg,CompleteHit
6093,Q#2366 - >seq2365,non-specific,273186,175,301,6.44289e-07,51.896,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6094,Q#2366 - >seq2365,non-specific,197307,173,300,8.642480000000001e-07,51.5197,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6095,Q#2366 - >seq2365,non-specific,339261,173,296,5.06793e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB2,ORF2,hs1_chimp,marg,CompleteHit
6096,Q#2366 - >seq2365,non-specific,197319,159,300,5.9472600000000004e-05,46.1157,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6097,Q#2366 - >seq2365,non-specific,235175,330,572,0.000160126,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
6098,Q#2366 - >seq2365,superfamily,235175,330,572,0.000160126,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
6099,Q#2366 - >seq2365,non-specific,272954,170,300,0.000395625,43.5257,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6100,Q#2366 - >seq2365,non-specific,223496,335,559,0.00366192,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1MB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
6101,Q#2366 - >seq2365,superfamily,223496,335,559,0.00366192,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1MB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
6102,Q#2366 - >seq2365,non-specific,334125,276,469,0.00748569,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6103,Q#2366 - >seq2365,superfamily,334125,276,469,0.00748569,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs1_chimp.marg.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6104,Q#2367 - >seq2366,non-specific,238827,654,765,8.98766e-15,74.635,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6105,Q#2367 - >seq2366,superfamily,295487,654,765,8.98766e-15,74.635,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6106,Q#2367 - >seq2366,non-specific,333820,649,742,4.89638e-05,45.361000000000004,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6107,Q#2367 - >seq2366,superfamily,333820,649,742,4.89638e-05,45.361000000000004,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
6108,Q#2368 - >seq2367,specific,197310,69,285,8.4582e-35,133.246,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6109,Q#2368 - >seq2367,superfamily,351117,69,285,8.4582e-35,133.246,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6110,Q#2368 - >seq2367,specific,238827,551,710,8.601799999999999e-30,118.163,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
6111,Q#2368 - >seq2367,superfamily,295487,551,710,8.601799999999999e-30,118.163,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
6112,Q#2368 - >seq2367,non-specific,333820,557,703,8.63828e-16,76.5622,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
6113,Q#2368 - >seq2367,superfamily,333820,557,703,8.63828e-16,76.5622,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
6114,Q#2368 - >seq2367,non-specific,197306,88,285,3.0805799999999998e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6115,Q#2368 - >seq2367,non-specific,197320,160,278,3.75318e-11,64.8438,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6116,Q#2368 - >seq2367,non-specific,223780,73,278,1.56249e-10,63.0011,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6117,Q#2368 - >seq2367,specific,335306,88,278,8.12258e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6118,Q#2368 - >seq2367,non-specific,273186,160,286,6.30431e-07,51.896,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6119,Q#2368 - >seq2367,non-specific,197307,158,285,7.0449e-07,51.9049,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6120,Q#2368 - >seq2367,non-specific,197319,144,285,4.018e-05,46.5009,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6121,Q#2368 - >seq2367,non-specific,339261,158,281,4.96685e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6122,Q#2368 - >seq2367,non-specific,272954,77,285,5.43841e-05,46.2221,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs1_chimp,pars,CompleteHit
6123,Q#2368 - >seq2367,non-specific,235175,315,554,0.000221723,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
6124,Q#2368 - >seq2367,superfamily,235175,315,554,0.000221723,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
6125,Q#2368 - >seq2367,non-specific,223496,320,554,0.00410307,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
6126,Q#2368 - >seq2367,superfamily,223496,320,554,0.00410307,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
6127,Q#2368 - >seq2367,non-specific,334125,261,454,0.00893004,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6128,Q#2368 - >seq2367,superfamily,334125,261,454,0.00893004,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6129,Q#2369 - >seq2368,non-specific,238827,654,765,9.00813e-15,74.635,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs1_chimp.pars.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6130,Q#2369 - >seq2368,superfamily,295487,654,765,9.00813e-15,74.635,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs1_chimp.pars.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6131,Q#2369 - >seq2368,non-specific,333820,649,742,4.42788e-05,45.361000000000004,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.pars.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6132,Q#2369 - >seq2368,superfamily,333820,649,742,4.42788e-05,45.361000000000004,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs1_chimp.pars.frame2,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
6133,Q#2372 - >seq2371,non-specific,340205,180,231,1.4266400000000001e-05,41.5528,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs1_chimp,marg,CompleteHit
6134,Q#2372 - >seq2371,superfamily,340205,180,231,1.4266400000000001e-05,41.5528,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs1_chimp.marg.frame1,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs1_chimp,marg,CompleteHit
6135,Q#2373 - >seq2372,non-specific,340205,113,179,4.7131900000000004e-07,45.0196,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs1_chimp,pars,CompleteHit
6136,Q#2373 - >seq2372,superfamily,340205,113,179,4.7131900000000004e-07,45.0196,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs1_chimp.pars.frame3,1909130137_L1MB2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs1_chimp,pars,CompleteHit
6137,Q#2377 - >seq2376,specific,238827,505,763,3.6562999999999996e-38,142.045,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6138,Q#2377 - >seq2376,superfamily,295487,505,763,3.6562999999999996e-38,142.045,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6139,Q#2377 - >seq2376,non-specific,197310,4,215,7.01135e-22,95.8813,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6140,Q#2377 - >seq2376,superfamily,351117,4,215,7.01135e-22,95.8813,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6141,Q#2377 - >seq2376,non-specific,333820,511,763,6.19746e-18,82.7253,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6142,Q#2377 - >seq2376,superfamily,333820,511,763,6.19746e-18,82.7253,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6143,Q#2377 - >seq2376,non-specific,197306,4,215,1.2647399999999999e-08,56.7209,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs2_gorilla,pars,CompleteHit
6144,Q#2377 - >seq2376,non-specific,197320,70,210,1.1981e-05,47.895,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6145,Q#2377 - >seq2376,non-specific,334125,235,405,0.000338395,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1MB2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6146,Q#2377 - >seq2376,superfamily,334125,235,405,0.000338395,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1MB2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6147,Q#2377 - >seq2376,non-specific,223780,66,197,0.00143308,41.8151,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
6148,Q#2378 - >seq2377,specific,238827,526,788,2.74296e-36,137.037,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6149,Q#2378 - >seq2377,superfamily,295487,526,788,2.74296e-36,137.037,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6150,Q#2378 - >seq2377,non-specific,197310,25,233,1.6107300000000002e-21,94.7257,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6151,Q#2378 - >seq2377,superfamily,351117,25,233,1.6107300000000002e-21,94.7257,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6152,Q#2378 - >seq2377,non-specific,333820,532,788,1.1579800000000001e-15,76.17699999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6153,Q#2378 - >seq2377,superfamily,333820,532,788,1.1579800000000001e-15,76.17699999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6154,Q#2378 - >seq2377,non-specific,197306,25,233,5.31035e-09,57.8765,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs2_gorilla,marg,CompleteHit
6155,Q#2378 - >seq2377,non-specific,197320,88,228,1.2346199999999999e-05,47.895,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6156,Q#2378 - >seq2377,non-specific,334125,253,426,0.0009992389999999999,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6157,Q#2378 - >seq2377,superfamily,334125,253,426,0.0009992389999999999,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6158,Q#2378 - >seq2377,non-specific,223780,84,228,0.00123485,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6159,Q#2378 - >seq2377,non-specific,240271,252,544,0.00410606,41.5704,PTZ00108,PTZ00108,N,cl36510,DNA topoisomerase 2-like protein; Provisional,L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6160,Q#2378 - >seq2377,superfamily,240271,252,544,0.00410606,41.5704,cl36510,PTZ00108 superfamily,N, - ,DNA topoisomerase 2-like protein; Provisional,L1MB2.ORF2.hs2_gorilla.marg.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6161,Q#2384 - >seq2383,non-specific,340205,78,140,2.79842e-07,44.6344,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs2_gorilla.pars.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,pars,CompleteHit
6162,Q#2384 - >seq2383,superfamily,340205,78,140,2.79842e-07,44.6344,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs2_gorilla.pars.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,pars,CompleteHit
6163,Q#2385 - >seq2384,non-specific,335182,6,69,0.000202228,38.0527,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6164,Q#2385 - >seq2384,superfamily,335182,6,69,0.000202228,38.0527,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs2_gorilla.pars.frame2,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6165,Q#2387 - >seq2386,non-specific,340205,180,245,3.93731e-10,54.6496,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs2_gorilla.marg.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,marg,CompleteHit
6166,Q#2387 - >seq2386,superfamily,340205,180,245,3.93731e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs2_gorilla.marg.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,marg,CompleteHit
6167,Q#2387 - >seq2386,non-specific,335182,66,139,7.492960000000001e-08,49.2235,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs2_gorilla.marg.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6168,Q#2387 - >seq2386,superfamily,335182,66,139,7.492960000000001e-08,49.2235,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs2_gorilla.marg.frame1,1909130138_L1MB2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6169,Q#2389 - >seq2388,specific,238827,472,692,1.7989e-31,122.785,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,CompleteHit
6170,Q#2389 - >seq2388,superfamily,295487,472,692,1.7989e-31,122.785,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,CompleteHit
6171,Q#2389 - >seq2388,non-specific,197310,15,200,1.83645e-17,82.7845,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB2,ORF2,hs4_gibbon,pars,CompleteHit
6172,Q#2389 - >seq2388,superfamily,351117,15,200,1.83645e-17,82.7845,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs4_gibbon,pars,CompleteHit
6173,Q#2389 - >seq2388,non-specific,333820,481,635,7.57541e-13,68.0878,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6174,Q#2389 - >seq2388,superfamily,333820,481,635,7.57541e-13,68.0878,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6175,Q#2389 - >seq2388,non-specific,238828,488,646,2.2951999999999997e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
6176,Q#2389 - >seq2388,non-specific,238185,579,658,0.000671638,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,pars,CompleteHit
6177,Q#2389 - >seq2388,non-specific,197320,80,158,0.0008018610000000001,42.5022,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs4_gibbon.pars.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6178,Q#2390 - >seq2389,non-specific,238827,437,475,1.1318e-09,59.6122,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6179,Q#2390 - >seq2389,superfamily,295487,437,475,1.1318e-09,59.6122,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6180,Q#2390 - >seq2389,non-specific,333820,443,475,0.00506,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6181,Q#2390 - >seq2389,superfamily,333820,443,475,0.00506,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6182,Q#2391 - >seq2390,non-specific,238827,478,516,8.166169999999999e-10,59.9974,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6183,Q#2391 - >seq2390,superfamily,295487,478,516,8.166169999999999e-10,59.9974,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6184,Q#2391 - >seq2390,non-specific,333820,484,516,0.00362542,39.583,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6185,Q#2391 - >seq2390,superfamily,333820,484,516,0.00362542,39.583,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6186,Q#2391 - >seq2390,non-specific,340014,928,1039,0.00712935,39.9793,pfam17298,DUF5349,C,cl24283,Family of unknown function (DUF5349); This is a family of unknown function found in Saccharomycetaceae.,L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6187,Q#2391 - >seq2390,superfamily,355175,928,1039,0.00712935,39.9793,cl24283,DUF5349 superfamily,C, - ,Family of unknown function (DUF5349); This is a family of unknown function found in Saccharomycetaceae.,L1MB2.ORF2.hs4_gibbon.marg.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6188,Q#2392 - >seq2391,non-specific,238827,517,707,1.04154e-23,100.443,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6189,Q#2392 - >seq2391,superfamily,295487,517,707,1.04154e-23,100.443,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6190,Q#2392 - >seq2391,non-specific,333820,507,650,6.52987e-13,68.0878,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6191,Q#2392 - >seq2391,superfamily,333820,507,650,6.52987e-13,68.0878,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6192,Q#2392 - >seq2391,non-specific,238828,520,661,2.12051e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6193,Q#2392 - >seq2391,non-specific,238185,594,673,0.000673858,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs4_gibbon.marg.frame2,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs4_gibbon,marg,CompleteHit
6194,Q#2393 - >seq2392,specific,197310,17,242,2.47453e-30,120.149,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs4_gibbon,marg,CompleteHit
6195,Q#2393 - >seq2392,superfamily,351117,17,242,2.47453e-30,120.149,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs4_gibbon,marg,CompleteHit
6196,Q#2393 - >seq2392,non-specific,197306,17,228,7.074010000000001e-09,57.4913,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs4_gibbon,marg,CompleteHit
6197,Q#2393 - >seq2392,non-specific,197320,113,200,8.05427e-07,51.3618,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6198,Q#2393 - >seq2392,non-specific,223780,113,200,9.676870000000001e-05,45.2819,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6199,Q#2393 - >seq2392,non-specific,339261,115,206,0.000646317,40.3983,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6200,Q#2393 - >seq2392,non-specific,197311,99,201,0.00725701,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6201,Q#2396 - >seq2395,non-specific,335182,5,69,1.8799100000000004e-09,51.5347,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs5_gmonkey,pars,CompleteHit
6202,Q#2396 - >seq2395,superfamily,335182,5,69,1.8799100000000004e-09,51.5347,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs5_gmonkey,pars,CompleteHit
6203,Q#2399 - >seq2398,non-specific,238827,398,475,2.25366e-08,55.7602,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs5_gmonkey.pars.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6204,Q#2399 - >seq2398,superfamily,295487,398,475,2.25366e-08,55.7602,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.pars.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6205,Q#2400 - >seq2399,non-specific,238827,409,611,2.63591e-18,84.6502,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs5_gmonkey.pars.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,pars,CompleteHit
6206,Q#2400 - >seq2399,superfamily,295487,409,611,2.63591e-18,84.6502,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.pars.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,pars,CompleteHit
6207,Q#2400 - >seq2399,non-specific,333820,402,622,3.8712900000000003e-10,59.9986,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs5_gmonkey.pars.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,pars,CompleteHit
6208,Q#2400 - >seq2399,superfamily,333820,402,622,3.8712900000000003e-10,59.9986,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs5_gmonkey.pars.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,pars,CompleteHit
6209,Q#2400 - >seq2399,non-specific,238185,533,622,0.00375759,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.pars.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,pars,CompleteHit
6210,Q#2401 - >seq2400,non-specific,197310,11,129,1.57583e-15,77.0065,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6211,Q#2401 - >seq2400,superfamily,351117,11,129,1.57583e-15,77.0065,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6212,Q#2401 - >seq2400,non-specific,197320,2,123,4.822849999999999e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6213,Q#2401 - >seq2400,non-specific,223780,27,123,4.0343e-05,46.4375,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6214,Q#2401 - >seq2400,specific,335306,39,112,0.00257229,40.3062,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6215,Q#2401 - >seq2400,non-specific,197307,39,124,0.00353645,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs5_gmonkey.pars.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6216,Q#2402 - >seq2401,non-specific,197310,108,228,2.0098299999999998e-15,77.0065,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6217,Q#2402 - >seq2401,superfamily,351117,108,228,2.0098299999999998e-15,77.0065,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6218,Q#2402 - >seq2401,non-specific,197320,117,213,2.2108e-06,50.2062,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6219,Q#2402 - >seq2401,non-specific,197307,74,214,4.7561e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6220,Q#2402 - >seq2401,non-specific,223780,117,213,4.78951e-05,46.0523,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6221,Q#2402 - >seq2401,specific,335306,52,202,0.00039380800000000005,43.0026,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs5_gmonkey.marg.frame1,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6222,Q#2403 - >seq2402,non-specific,238827,498,575,6.853110000000001e-08,54.2194,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs5_gmonkey.marg.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6223,Q#2403 - >seq2402,superfamily,295487,498,575,6.853110000000001e-08,54.2194,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.marg.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6224,Q#2403 - >seq2402,non-specific,197310,24,104,1.17521e-05,47.7313,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs5_gmonkey.marg.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6225,Q#2403 - >seq2402,superfamily,351117,24,104,1.17521e-05,47.7313,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs5_gmonkey.marg.frame2,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6226,Q#2404 - >seq2403,non-specific,238827,511,750,5.76738e-23,98.5174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,CompleteHit
6227,Q#2404 - >seq2403,superfamily,295487,511,750,5.76738e-23,98.5174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,CompleteHit
6228,Q#2404 - >seq2403,non-specific,333820,504,714,1.13401e-10,61.9246,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,CompleteHit
6229,Q#2404 - >seq2403,superfamily,333820,504,714,1.13401e-10,61.9246,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,CompleteHit
6230,Q#2404 - >seq2403,non-specific,238828,583,747,0.000680405,42.1881,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6231,Q#2404 - >seq2403,non-specific,238185,635,750,0.00101958,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,CompleteHit
6232,Q#2404 - >seq2403,non-specific,275209,583,787,0.00999913,39.3632,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6233,Q#2404 - >seq2403,superfamily,275209,583,787,0.00999913,39.3632,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs5_gmonkey.marg.frame3,1909130143_L1MB2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6234,Q#2407 - >seq2406,non-specific,335182,65,142,1.1594899999999999e-09,53.8459,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,marg,CompleteHit
6235,Q#2407 - >seq2406,superfamily,335182,65,142,1.1594899999999999e-09,53.8459,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,marg,CompleteHit
6236,Q#2407 - >seq2406,non-specific,340205,170,221,0.000648165,36.9304,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,marg,CompleteHit
6237,Q#2407 - >seq2406,superfamily,340205,170,221,0.000648165,36.9304,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs4_gibbon.marg.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,marg,CompleteHit
6238,Q#2411 - >seq2410,non-specific,340205,134,156,0.00373538,34.234,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs3_orang,pars,N-TerminusTruncated
6239,Q#2411 - >seq2410,superfamily,340205,134,156,0.00373538,34.234,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs3_orang,pars,N-TerminusTruncated
6240,Q#2415 - >seq2414,non-specific,238827,480,697,5.71241e-23,98.5174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs3_orang,pars,CompleteHit
6241,Q#2415 - >seq2414,superfamily,295487,480,697,5.71241e-23,98.5174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs3_orang,pars,CompleteHit
6242,Q#2415 - >seq2414,non-specific,197310,2,131,4.6181000000000004e-17,81.6289,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6243,Q#2415 - >seq2414,superfamily,351117,2,131,4.6181000000000004e-17,81.6289,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6244,Q#2415 - >seq2414,non-specific,333820,486,700,9.86491e-09,56.1466,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs3_orang,pars,CompleteHit
6245,Q#2415 - >seq2414,superfamily,333820,486,700,9.86491e-09,56.1466,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs3_orang,pars,CompleteHit
6246,Q#2415 - >seq2414,non-specific,197306,2,114,6.76101e-08,54.7949,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6247,Q#2415 - >seq2414,non-specific,238828,592,699,0.0039918,39.8769,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6248,Q#2415 - >seq2414,non-specific,223780,2,109,0.00925947,39.1187,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs3_orang.pars.frame1,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6249,Q#2416 - >seq2415,non-specific,340205,147,217,2.3057699999999997e-08,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs3_orang,marg,CompleteHit
6250,Q#2416 - >seq2415,superfamily,340205,147,217,2.3057699999999997e-08,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs3_orang,marg,CompleteHit
6251,Q#2417 - >seq2416,non-specific,197310,101,212,8.53286e-14,71.9989,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6252,Q#2417 - >seq2416,superfamily,351117,101,212,8.53286e-14,71.9989,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6253,Q#2417 - >seq2416,non-specific,197306,82,212,6.50736e-06,48.6317,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6254,Q#2417 - >seq2416,non-specific,197320,101,198,0.000238332,44.043,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6255,Q#2417 - >seq2416,non-specific,197307,102,212,0.00857061,39.1933,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs3_orang.pars.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs3_orang,pars,N-TerminusTruncated
6256,Q#2419 - >seq2418,non-specific,238827,486,666,1.97749e-13,70.783,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs3_orang.marg.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6257,Q#2419 - >seq2418,superfamily,295487,486,666,1.97749e-13,70.783,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs3_orang.marg.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6258,Q#2419 - >seq2418,non-specific,333820,588,669,3.7823899999999995e-05,45.361000000000004,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.marg.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs3_orang,marg,N-TerminusTruncated
6259,Q#2419 - >seq2418,superfamily,333820,588,669,3.7823899999999995e-05,45.361000000000004,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.marg.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs3_orang,marg,N-TerminusTruncated
6260,Q#2419 - >seq2418,non-specific,238828,561,668,0.00179882,41.0325,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs3_orang.marg.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs3_orang,marg,N-TerminusTruncated
6261,Q#2420 - >seq2419,specific,197310,1,226,1.38988e-40,149.809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6262,Q#2420 - >seq2419,superfamily,351117,1,226,1.38988e-40,149.809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6263,Q#2420 - >seq2419,non-specific,238827,496,601,2.35849e-19,88.117,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6264,Q#2420 - >seq2419,superfamily,295487,496,601,2.35849e-19,88.117,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6265,Q#2420 - >seq2419,non-specific,197306,1,226,8.206110000000001e-18,84.07,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6266,Q#2420 - >seq2419,non-specific,197320,1,211,6.87368e-12,66.7698,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6267,Q#2420 - >seq2419,non-specific,223780,1,184,8.508550000000001e-10,60.6899,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6268,Q#2420 - >seq2419,non-specific,197307,1,226,3.80351e-09,58.4533,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6269,Q#2420 - >seq2419,non-specific,333820,502,620,2.2865900000000002e-08,54.99100000000001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6270,Q#2420 - >seq2419,superfamily,333820,502,620,2.2865900000000002e-08,54.99100000000001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6271,Q#2420 - >seq2419,non-specific,273186,1,227,3.994e-08,55.748000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6272,Q#2420 - >seq2419,specific,335306,2,219,0.000149785,44.5434,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6273,Q#2420 - >seq2419,non-specific,339261,98,222,0.00036339900000000004,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6274,Q#2420 - >seq2419,non-specific,272954,1,184,0.000582947,42.7553,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,C-TerminusTruncated
6275,Q#2420 - >seq2419,non-specific,197319,1,226,0.000642406,42.6489,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6276,Q#2420 - >seq2419,non-specific,197311,28,193,0.00125909,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6277,Q#2420 - >seq2419,non-specific,197321,1,184,0.00403501,40.228,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs3_orang.marg.frame3,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs3_orang,marg,CompleteHit
6278,Q#2421 - >seq2420,non-specific,340205,139,163,0.00272506,34.6192,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs4_gibbon.pars.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6279,Q#2421 - >seq2420,superfamily,340205,139,163,0.00272506,34.6192,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs4_gibbon.pars.frame1,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6280,Q#2423 - >seq2422,non-specific,335182,19,91,3.96035e-10,53.8459,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
6281,Q#2423 - >seq2422,superfamily,335182,19,91,3.96035e-10,53.8459,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs4_gibbon.pars.frame3,1909130143_L1MB2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
6282,Q#2424 - >seq2423,non-specific,238827,488,552,1.4404800000000002e-10,62.3086,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs3_orang.pars.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6283,Q#2424 - >seq2423,superfamily,295487,488,552,1.4404800000000002e-10,62.3086,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs3_orang.pars.frame2,1909130143_L1MB2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs3_orang,pars,C-TerminusTruncated
6284,Q#2425 - >seq2424,non-specific,197310,1,142,6.35291e-11,63.5245,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6285,Q#2425 - >seq2424,superfamily,351117,1,142,6.35291e-11,63.5245,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6286,Q#2425 - >seq2424,non-specific,238827,422,460,1.95803e-08,55.7602,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6287,Q#2425 - >seq2424,superfamily,295487,422,460,1.95803e-08,55.7602,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6288,Q#2425 - >seq2424,non-specific,197306,18,101,0.00126845,41.6981,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
6289,Q#2425 - >seq2424,non-specific,333820,428,460,0.00194508,40.3534,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6290,Q#2425 - >seq2424,superfamily,333820,428,460,0.00194508,40.3534,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.pars.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6291,Q#2426 - >seq2425,non-specific,238827,490,526,3.54189e-08,55.375,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs6_sqmonkey.marg.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6292,Q#2426 - >seq2425,superfamily,295487,490,526,3.54189e-08,55.375,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs6_sqmonkey.marg.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6293,Q#2426 - >seq2425,non-specific,333820,496,526,0.00753714,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.marg.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6294,Q#2426 - >seq2425,superfamily,333820,496,526,0.00753714,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.marg.frame3,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6295,Q#2427 - >seq2426,specific,238827,487,694,1.8532599999999997e-36,137.423,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6296,Q#2427 - >seq2426,superfamily,295487,487,694,1.8532599999999997e-36,137.423,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6297,Q#2427 - >seq2426,non-specific,333820,497,679,4.7166100000000005e-18,83.1105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6298,Q#2427 - >seq2426,superfamily,333820,497,679,4.7166100000000005e-18,83.1105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6299,Q#2427 - >seq2426,non-specific,238828,504,680,3.26809e-07,52.2032,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6300,Q#2427 - >seq2426,non-specific,275209,490,745,0.000888683,42.83,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6301,Q#2427 - >seq2426,superfamily,275209,490,745,0.000888683,42.83,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs6_sqmonkey.marg.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6302,Q#2428 - >seq2427,specific,197310,13,238,1.68682e-36,137.868,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6303,Q#2428 - >seq2427,superfamily,351117,13,238,1.68682e-36,137.868,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6304,Q#2428 - >seq2427,non-specific,197306,13,238,6.45332e-15,75.5956,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6305,Q#2428 - >seq2427,non-specific,197307,14,238,3.25531e-09,58.8385,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6306,Q#2428 - >seq2427,non-specific,223780,14,227,5.4177799999999995e-09,58.3787,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6307,Q#2428 - >seq2427,non-specific,197320,108,223,3.59022e-08,55.599,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6308,Q#2428 - >seq2427,specific,335306,31,230,3.2219900000000004e-07,52.2474,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6309,Q#2428 - >seq2427,non-specific,272954,31,209,6.4673e-07,52.0001,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6310,Q#2428 - >seq2427,non-specific,197319,14,238,2.88459e-06,49.9677,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs6_sqmonkey,marg,CompleteHit
6311,Q#2428 - >seq2427,non-specific,224117,76,389,0.00023977299999999998,45.4756,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6312,Q#2428 - >seq2427,superfamily,224117,76,389,0.00023977299999999998,45.4756,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MB2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
6313,Q#2428 - >seq2427,non-specific,234767,160,354,0.00387352,41.361999999999995,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6314,Q#2428 - >seq2427,superfamily,234767,160,354,0.00387352,41.361999999999995,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MB2.ORF2.hs6_sqmonkey.marg.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
6315,Q#2429 - >seq2428,non-specific,197310,86,176,1.57936e-08,56.2057,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs6_sqmonkey.pars.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6316,Q#2429 - >seq2428,superfamily,351117,86,176,1.57936e-08,56.2057,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs6_sqmonkey.pars.frame2,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6317,Q#2430 - >seq2429,specific,238827,443,639,1.34154e-34,132.03,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6318,Q#2430 - >seq2429,superfamily,295487,443,639,1.34154e-34,132.03,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6319,Q#2430 - >seq2429,non-specific,333820,453,642,5.85323e-19,85.8069,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6320,Q#2430 - >seq2429,superfamily,333820,453,642,5.85323e-19,85.8069,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,CompleteHit
6321,Q#2430 - >seq2429,non-specific,238828,460,636,7.549600000000001e-07,51.0476,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6322,Q#2430 - >seq2429,non-specific,275209,446,696,9.28658e-05,45.9116,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6323,Q#2430 - >seq2429,superfamily,275209,446,696,9.28658e-05,45.9116,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs6_sqmonkey.pars.frame1,1909130147_L1MB2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6324,Q#2437 - >seq2436,non-specific,238827,349,396,0.0019756,40.7374,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs7_bushaby.marg.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6325,Q#2437 - >seq2436,superfamily,295487,349,396,0.0019756,40.7374,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.marg.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6326,Q#2438 - >seq2437,non-specific,197310,6,83,1.93591e-12,68.1469,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs7_bushaby.marg.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6327,Q#2438 - >seq2437,superfamily,351117,6,83,1.93591e-12,68.1469,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs7_bushaby.marg.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6328,Q#2438 - >seq2437,non-specific,238827,365,397,3.13548e-06,49.2118,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs7_bushaby.marg.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6329,Q#2438 - >seq2437,superfamily,295487,365,397,3.13548e-06,49.2118,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.marg.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6330,Q#2438 - >seq2437,non-specific,197306,20,83,0.00522303,39.7721,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs7_bushaby.marg.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6331,Q#2439 - >seq2438,specific,238827,399,598,1.34222e-30,120.47399999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6332,Q#2439 - >seq2438,superfamily,295487,399,598,1.34222e-30,120.47399999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6333,Q#2439 - >seq2438,non-specific,333820,405,598,1.7943499999999997e-17,81.1846,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6334,Q#2439 - >seq2438,superfamily,333820,405,598,1.7943499999999997e-17,81.1846,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6335,Q#2439 - >seq2438,non-specific,238828,415,598,3.08615e-08,55.2848,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6336,Q#2439 - >seq2438,non-specific,275209,413,622,2.00531e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6337,Q#2439 - >seq2438,superfamily,275209,413,622,2.00531e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
6338,Q#2439 - >seq2438,non-specific,238185,477,598,7.1527300000000005e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.marg.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB2,ORF2,hs7_bushaby,marg,CompleteHit
6339,Q#2440 - >seq2439,specific,238827,347,571,6.520239999999999e-41,149.749,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6340,Q#2440 - >seq2439,superfamily,295487,347,571,6.520239999999999e-41,149.749,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6341,Q#2440 - >seq2439,non-specific,333820,331,571,1.77127e-19,86.9625,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6342,Q#2440 - >seq2439,superfamily,333820,331,571,1.77127e-19,86.9625,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6343,Q#2440 - >seq2439,non-specific,238828,388,571,1.39957e-08,56.4404,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6344,Q#2440 - >seq2439,non-specific,238185,457,571,6.96807e-08,51.1976,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6345,Q#2440 - >seq2439,non-specific,275209,390,595,3.95685e-06,50.1488,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6346,Q#2440 - >seq2439,superfamily,275209,390,595,3.95685e-06,50.1488,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6347,Q#2440 - >seq2439,non-specific,239569,346,584,2.03439e-05,46.7971,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MB2.ORF2.hs7_bushaby.pars.frame2,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs7_bushaby,pars,CompleteHit
6348,Q#2441 - >seq2440,non-specific,238827,320,352,1.3734399999999999e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs7_bushaby.pars.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6349,Q#2441 - >seq2440,superfamily,295487,320,352,1.3734399999999999e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs7_bushaby.pars.frame1,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6350,Q#2442 - >seq2441,non-specific,197310,1,63,0.00986518,38.4865,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs7_bushaby.pars.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6351,Q#2442 - >seq2441,superfamily,351117,1,63,0.00986518,38.4865,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs7_bushaby.pars.frame3,1909130148_L1MB2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6352,Q#2443 - >seq2442,non-specific,224117,43,229,0.00830811,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs9_pika.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6353,Q#2443 - >seq2442,superfamily,224117,43,229,0.00830811,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs9_pika.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6354,Q#2445 - >seq2444,non-specific,238827,568,762,2.61938e-25,105.066,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,N-TerminusTruncated
6355,Q#2445 - >seq2444,superfamily,295487,568,762,2.61938e-25,105.066,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,N-TerminusTruncated
6356,Q#2445 - >seq2444,non-specific,333820,580,762,9.335120000000001e-17,79.6438,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,N-TerminusTruncated
6357,Q#2445 - >seq2444,superfamily,333820,580,762,9.335120000000001e-17,79.6438,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,N-TerminusTruncated
6358,Q#2445 - >seq2444,non-specific,238828,571,762,1.11182e-11,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,N-TerminusTruncated
6359,Q#2445 - >seq2444,non-specific,275209,571,702,1.39723e-05,48.608000000000004,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,BothTerminiTruncated
6360,Q#2445 - >seq2444,superfamily,275209,571,702,1.39723e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,BothTerminiTruncated
6361,Q#2445 - >seq2444,non-specific,238185,646,762,9.14825e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6362,Q#2446 - >seq2445,specific,197310,53,284,3.5052899999999995e-33,128.623,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6363,Q#2446 - >seq2445,superfamily,351117,53,284,3.5052899999999995e-33,128.623,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6364,Q#2446 - >seq2445,non-specific,238827,559,628,3.16587e-19,87.7318,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,marg,C-TerminusTruncated
6365,Q#2446 - >seq2445,superfamily,295487,559,628,3.16587e-19,87.7318,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,marg,C-TerminusTruncated
6366,Q#2446 - >seq2445,non-specific,197306,53,284,5.51894e-13,69.8177,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6367,Q#2446 - >seq2445,non-specific,197320,52,277,1.02615e-12,69.4662,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6368,Q#2446 - >seq2445,non-specific,223780,50,277,5.32718e-11,64.5419,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6369,Q#2446 - >seq2445,non-specific,333820,565,621,2.44813e-07,51.9094,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,marg,C-TerminusTruncated
6370,Q#2446 - >seq2445,superfamily,333820,565,621,2.44813e-07,51.9094,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,marg,C-TerminusTruncated
6371,Q#2446 - >seq2445,non-specific,272954,50,255,3.24158e-05,46.9925,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs10_snmole.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs10_snmole,marg,CompleteHit
6372,Q#2447 - >seq2446,specific,238827,433,639,5.0771199999999994e-33,127.40700000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6373,Q#2447 - >seq2446,superfamily,295487,433,639,5.0771199999999994e-33,127.40700000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6374,Q#2447 - >seq2446,non-specific,333820,439,634,3.12574e-20,89.2737,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6375,Q#2447 - >seq2446,superfamily,333820,439,634,3.12574e-20,89.2737,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6376,Q#2447 - >seq2446,non-specific,238828,504,634,1.4953999999999998e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,N-TerminusTruncated
6377,Q#2447 - >seq2446,non-specific,275209,509,634,1.89529e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,BothTerminiTruncated
6378,Q#2447 - >seq2446,superfamily,275209,509,634,1.89529e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,BothTerminiTruncated
6379,Q#2447 - >seq2446,non-specific,238185,578,661,0.00408508,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6380,Q#2448 - >seq2447,non-specific,238827,465,498,6.13375e-05,45.3598,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs10_snmole.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6381,Q#2448 - >seq2447,superfamily,295487,465,498,6.13375e-05,45.3598,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs10_snmole.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs10_snmole,pars,C-TerminusTruncated
6382,Q#2448 - >seq2447,specific,311990,1134,1152,0.00678704,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs10_snmole.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6383,Q#2448 - >seq2447,superfamily,311990,1134,1152,0.00678704,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs10_snmole.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6384,Q#2450 - >seq2449,specific,238827,517,721,1.0079599999999999e-27,111.999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6385,Q#2450 - >seq2449,superfamily,295487,517,721,1.0079599999999999e-27,111.999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6386,Q#2450 - >seq2449,non-specific,333820,530,721,8.9718e-17,79.2586,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6387,Q#2450 - >seq2449,superfamily,333820,530,721,8.9718e-17,79.2586,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6388,Q#2450 - >seq2449,non-specific,238828,526,672,1.56781e-08,56.4404,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6389,Q#2450 - >seq2449,non-specific,274328,645,928,0.00020851,45.4525,TIGR02865,spore_II_E,N,cl37180,"stage II sporulation protein E; Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. [Cellular processes, Sporulation and germination]",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6390,Q#2450 - >seq2449,superfamily,274328,645,928,0.00020851,45.4525,cl37180,spore_II_E superfamily,N, - ,"stage II sporulation protein E; Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. [Cellular processes, Sporulation and germination]",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB2,ORF2,hs9_pika,marg,N-TerminusTruncated
6391,Q#2450 - >seq2449,non-specific,238185,599,721,0.000292717,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6392,Q#2450 - >seq2449,non-specific,275209,531,614,0.000650651,43.2152,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,BothTerminiTruncated
6393,Q#2450 - >seq2449,superfamily,275209,531,614,0.000650651,43.2152,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs9_pika.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs9_pika,marg,BothTerminiTruncated
6394,Q#2451 - >seq2450,specific,197310,3,239,7.031069999999999e-37,139.024,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6395,Q#2451 - >seq2450,superfamily,351117,3,239,7.031069999999999e-37,139.024,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6396,Q#2451 - >seq2450,non-specific,238827,516,580,8.625829999999999e-17,80.413,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs9_pika,marg,C-TerminusTruncated
6397,Q#2451 - >seq2450,superfamily,295487,516,580,8.625829999999999e-17,80.413,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs9_pika,marg,C-TerminusTruncated
6398,Q#2451 - >seq2450,non-specific,197306,3,239,2.83645e-14,73.6696,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6399,Q#2451 - >seq2450,non-specific,223780,3,232,2.76533e-11,65.3123,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6400,Q#2451 - >seq2450,non-specific,197320,3,232,4.4563e-09,58.2954,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6401,Q#2451 - >seq2450,non-specific,333820,522,575,4.23029e-06,48.4426,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs9_pika,marg,C-TerminusTruncated
6402,Q#2451 - >seq2450,superfamily,333820,522,575,4.23029e-06,48.4426,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs9_pika,marg,C-TerminusTruncated
6403,Q#2451 - >seq2450,non-specific,272954,3,210,0.000628611,42.7553,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6404,Q#2451 - >seq2450,non-specific,224259,265,474,0.00213588,41.5904,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6405,Q#2451 - >seq2450,superfamily,224259,265,474,0.00213588,41.5904,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs9_pika,marg,CompleteHit
6406,Q#2451 - >seq2450,non-specific,235943,343,560,0.00517278,40.9566,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs9_pika,marg,BothTerminiTruncated
6407,Q#2451 - >seq2450,superfamily,235943,343,560,0.00517278,40.9566,cl35548,PRK07133 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1MB2.ORF2.hs9_pika.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs9_pika,marg,BothTerminiTruncated
6408,Q#2452 - >seq2451,specific,238827,295,488,5.29939e-29,115.46600000000001,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,N-TerminusTruncated
6409,Q#2452 - >seq2451,superfamily,295487,295,488,5.29939e-29,115.46600000000001,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,N-TerminusTruncated
6410,Q#2452 - >seq2451,non-specific,333820,288,488,3.0825700000000003e-19,86.1921,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,CompleteHit
6411,Q#2452 - >seq2451,superfamily,333820,288,488,3.0825700000000003e-19,86.1921,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,CompleteHit
6412,Q#2452 - >seq2451,non-specific,238828,294,488,1.0303599999999999e-08,56.4404,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,N-TerminusTruncated
6413,Q#2452 - >seq2451,non-specific,238185,374,488,2.5224e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,CompleteHit
6414,Q#2452 - >seq2451,non-specific,275209,306,389,0.000896289,42.4448,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,BothTerminiTruncated
6415,Q#2452 - >seq2451,superfamily,275209,306,389,0.000896289,42.4448,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB2.ORF2.hs9_pika.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB2,ORF2,hs9_pika,pars,BothTerminiTruncated
6416,Q#2453 - >seq2452,non-specific,238827,243,307,2.1539699999999996e-17,81.9538,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs9_pika.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6417,Q#2453 - >seq2452,superfamily,295487,243,307,2.1539699999999996e-17,81.9538,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs9_pika.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6418,Q#2453 - >seq2452,non-specific,333820,249,302,2.43515e-06,48.8278,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6419,Q#2453 - >seq2452,superfamily,333820,249,302,2.43515e-06,48.8278,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs9_pika.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs9_pika,pars,C-TerminusTruncated
6420,Q#2454 - >seq2453,non-specific,197310,2,185,1.3633e-23,100.50399999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6421,Q#2454 - >seq2453,superfamily,351117,2,185,1.3633e-23,100.50399999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6422,Q#2454 - >seq2453,non-specific,197306,2,185,6.0726e-07,51.7133,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs10_snmole,pars,CompleteHit
6423,Q#2454 - >seq2453,non-specific,197320,118,178,0.00018671400000000002,44.4282,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs10_snmole,pars,N-TerminusTruncated
6424,Q#2454 - >seq2453,non-specific,223780,125,178,0.000607374,42.5855,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs10_snmole,pars,N-TerminusTruncated
6425,Q#2454 - >seq2453,non-specific,197321,124,178,0.00195229,40.9984,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs10_snmole,pars,N-TerminusTruncated
6426,Q#2454 - >seq2453,non-specific,197307,122,178,0.00643522,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs10_snmole.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB2,ORF2,hs10_snmole,pars,N-TerminusTruncated
6427,Q#2455 - >seq2454,non-specific,238827,468,585,2.8611900000000006e-26,107.762,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6428,Q#2455 - >seq2454,superfamily,295487,468,585,2.8611900000000006e-26,107.762,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6429,Q#2455 - >seq2454,non-specific,333820,457,585,3.31129e-11,63.0802,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6430,Q#2455 - >seq2454,superfamily,333820,457,585,3.31129e-11,63.0802,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6431,Q#2455 - >seq2454,non-specific,238828,453,585,1.21829e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6432,Q#2455 - >seq2454,non-specific,238185,464,585,0.00019255599999999998,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,marg,CompleteHit
6433,Q#2456 - >seq2455,specific,311990,1037,1055,0.0031066999999999996,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MB2,ORF2,hs8_ctshrew,marg,CompleteHit
6434,Q#2456 - >seq2455,superfamily,311990,1037,1055,0.0031066999999999996,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MB2,ORF2,hs8_ctshrew,marg,CompleteHit
6435,Q#2460 - >seq2459,non-specific,340205,184,230,2.5677099999999996e-14,65.4352,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
6436,Q#2460 - >seq2459,superfamily,340205,184,230,2.5677099999999996e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs8_ctshrew.marg.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
6437,Q#2461 - >seq2460,non-specific,335182,66,144,9.7215e-07,44.6011,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs8_ctshrew,pars,CompleteHit
6438,Q#2461 - >seq2460,superfamily,335182,66,144,9.7215e-07,44.6011,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs8_ctshrew,pars,CompleteHit
6439,Q#2462 - >seq2461,specific,238827,225,328,9.49333e-31,120.47399999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6440,Q#2462 - >seq2461,superfamily,295487,225,328,9.49333e-31,120.47399999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6441,Q#2462 - >seq2461,non-specific,333820,231,351,3.19418e-14,71.5546,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6442,Q#2462 - >seq2461,superfamily,333820,231,351,3.19418e-14,71.5546,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.pars.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6443,Q#2463 - >seq2462,specific,238827,352,468,1.6222999999999997e-26,108.147,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6444,Q#2463 - >seq2462,superfamily,295487,352,468,1.6222999999999997e-26,108.147,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6445,Q#2463 - >seq2462,non-specific,333820,342,468,1.33249e-11,64.2358,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6446,Q#2463 - >seq2462,superfamily,333820,342,468,1.33249e-11,64.2358,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6447,Q#2463 - >seq2462,non-specific,238828,342,468,1.8688099999999998e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6448,Q#2463 - >seq2462,non-specific,238185,348,468,5.3266899999999996e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.pars.frame2,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs8_ctshrew,pars,CompleteHit
6449,Q#2464 - >seq2463,specific,311990,909,927,0.00662027,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs8_ctshrew.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MB2,ORF2,hs8_ctshrew,pars,CompleteHit
6450,Q#2464 - >seq2463,superfamily,311990,909,927,0.00662027,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MB2.ORF2.hs8_ctshrew.pars.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MB2,ORF2,hs8_ctshrew,pars,CompleteHit
6451,Q#2465 - >seq2464,specific,238827,368,476,1.3816099999999997e-29,117.39200000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6452,Q#2465 - >seq2464,superfamily,295487,368,476,1.3816099999999997e-29,117.39200000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6453,Q#2465 - >seq2464,non-specific,333820,374,499,1.02346e-11,64.62100000000001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6454,Q#2465 - >seq2464,superfamily,333820,374,499,1.02346e-11,64.62100000000001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6455,Q#2465 - >seq2464,non-specific,197310,7,93,9.3867e-07,51.1981,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6456,Q#2465 - >seq2464,superfamily,351117,7,93,9.3867e-07,51.1981,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6457,Q#2465 - >seq2464,specific,338766,80,221,0.00162373,40.9303,pfam13476,AAA_23,N,cl25403,AAA domain; AAA domain.  ,L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6458,Q#2465 - >seq2464,superfamily,355390,80,221,0.00162373,40.9303,cl25403,ABC_ATPase superfamily,N, - ,"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.",L1MB2.ORF2.hs8_ctshrew.marg.frame1,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6459,Q#2466 - >seq2465,non-specific,335182,74,172,4.10977e-10,55.0015,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs8_ctshrew,marg,CompleteHit
6460,Q#2466 - >seq2465,superfamily,335182,74,172,4.10977e-10,55.0015,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs8_ctshrew,marg,CompleteHit
6461,Q#2466 - >seq2465,non-specific,215214,24,126,0.00396957,37.9563,PLN02381,PLN02381,C,cl33481,valyl-tRNA synthetase,L1MB2.ORF1.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB2,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
6462,Q#2466 - >seq2465,superfamily,215214,24,126,0.00396957,37.9563,cl33481,PLN02381 superfamily,C, - ,valyl-tRNA synthetase,L1MB2.ORF1.hs8_ctshrew.marg.frame3,1909130149_L1MB2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB2,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
6463,Q#2469 - >seq2468,non-specific,340205,211,269,2.0419e-18,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs1_chimp.marg.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,marg,CompleteHit
6464,Q#2469 - >seq2468,superfamily,340205,211,269,2.0419e-18,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs1_chimp.marg.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,marg,CompleteHit
6465,Q#2469 - >seq2468,non-specific,335182,122,187,2.67391e-17,75.0319,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs1_chimp.marg.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,marg,CompleteHit
6466,Q#2469 - >seq2468,superfamily,335182,122,187,2.67391e-17,75.0319,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs1_chimp.marg.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,marg,CompleteHit
6467,Q#2471 - >seq2470,non-specific,335182,30,120,3.07606e-20,80.4247,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs2_gorilla.pars.frame2,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs2_gorilla,pars,CompleteHit
6468,Q#2471 - >seq2470,superfamily,335182,30,120,3.07606e-20,80.4247,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs2_gorilla.pars.frame2,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs2_gorilla,pars,CompleteHit
6469,Q#2474 - >seq2473,non-specific,340205,163,213,1.55277e-12,60.0424,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs2_gorilla.marg.frame2,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6470,Q#2474 - >seq2473,superfamily,340205,163,213,1.55277e-12,60.0424,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs2_gorilla.marg.frame2,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6471,Q#2475 - >seq2474,non-specific,340205,164,222,4.689130000000001e-18,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs1_chimp.pars.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,pars,CompleteHit
6472,Q#2475 - >seq2474,superfamily,340205,164,222,4.689130000000001e-18,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs1_chimp.pars.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,pars,CompleteHit
6473,Q#2475 - >seq2474,non-specific,335182,78,141,3.750069999999999e-14,65.7871,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs1_chimp.pars.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,pars,CompleteHit
6474,Q#2475 - >seq2474,superfamily,335182,78,141,3.750069999999999e-14,65.7871,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs1_chimp.pars.frame2,1909130150_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB3,ORF1,hs1_chimp,pars,CompleteHit
6475,Q#2476 - >seq2475,non-specific,335182,70,160,6.43724e-19,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs2_gorilla.marg.frame3,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs2_gorilla,marg,CompleteHit
6476,Q#2476 - >seq2475,superfamily,335182,70,160,6.43724e-19,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs2_gorilla.marg.frame3,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs2_gorilla,marg,CompleteHit
6477,Q#2477 - >seq2476,non-specific,340205,128,178,6.72073e-13,60.4276,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs2_gorilla.pars.frame1,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
6478,Q#2477 - >seq2476,superfamily,340205,128,178,6.72073e-13,60.4276,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs2_gorilla.pars.frame1,1909130150_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
6479,Q#2479 - >seq2478,non-specific,197310,1,122,1.0917200000000001e-10,62.7541,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs0_human.pars.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,pars,N-TerminusTruncated
6480,Q#2479 - >seq2478,superfamily,351117,1,122,1.0917200000000001e-10,62.7541,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs0_human.pars.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs0_human,pars,N-TerminusTruncated
6481,Q#2480 - >seq2479,non-specific,238827,490,531,2.04084e-05,46.9006,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6482,Q#2480 - >seq2479,superfamily,295487,490,531,2.04084e-05,46.9006,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6483,Q#2480 - >seq2479,non-specific,224117,240,436,0.000809935,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB2,ORF2,hs0_human,marg,BothTerminiTruncated
6484,Q#2480 - >seq2479,superfamily,224117,240,436,0.000809935,43.5496,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MB2,ORF2,hs0_human,marg,BothTerminiTruncated
6485,Q#2480 - >seq2479,non-specific,235175,236,449,0.00150997,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB2,ORF2,hs0_human,marg,BothTerminiTruncated
6486,Q#2480 - >seq2479,superfamily,235175,236,449,0.00150997,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB2.ORF2.hs0_human.marg.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB2,ORF2,hs0_human,marg,BothTerminiTruncated
6487,Q#2481 - >seq2480,non-specific,238827,500,717,9.63078e-16,77.3314,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs0_human,marg,N-TerminusTruncated
6488,Q#2481 - >seq2480,superfamily,295487,500,717,9.63078e-16,77.3314,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs0_human,marg,N-TerminusTruncated
6489,Q#2481 - >seq2480,non-specific,333820,525,717,5.3576699999999994e-08,53.8354,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs0_human,marg,N-TerminusTruncated
6490,Q#2481 - >seq2480,superfamily,333820,525,717,5.3576699999999994e-08,53.8354,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs0_human,marg,N-TerminusTruncated
6491,Q#2481 - >seq2480,non-specific,238828,521,678,1.52645e-05,47.1957,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB2.ORF2.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB2,ORF2,hs0_human,marg,N-TerminusTruncated
6492,Q#2482 - >seq2481,non-specific,238827,492,617,9.36538e-07,50.7526,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs0_human.pars.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs0_human,pars,N-TerminusTruncated
6493,Q#2482 - >seq2481,superfamily,295487,492,617,9.36538e-07,50.7526,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs0_human.pars.frame2,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB2,ORF2,hs0_human,pars,N-TerminusTruncated
6494,Q#2483 - >seq2482,non-specific,238827,368,463,1.26945e-13,71.1682,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB2.ORF2.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs0_human,pars,C-TerminusTruncated
6495,Q#2483 - >seq2482,superfamily,295487,368,463,1.26945e-13,71.1682,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB2.ORF2.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs0_human,pars,C-TerminusTruncated
6496,Q#2483 - >seq2482,non-specific,333820,386,464,0.000371042,42.6646,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs0_human,pars,C-TerminusTruncated
6497,Q#2483 - >seq2482,superfamily,333820,386,464,0.000371042,42.6646,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB2.ORF2.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB2,ORF2,hs0_human,pars,C-TerminusTruncated
6498,Q#2484 - >seq2483,non-specific,340205,70,135,4.14351e-18,73.1392,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,marg,CompleteHit
6499,Q#2484 - >seq2483,superfamily,340205,70,135,4.14351e-18,73.1392,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,marg,CompleteHit
6500,Q#2484 - >seq2483,non-specific,335182,1,51,1.52222e-08,49.2235,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,marg,N-TerminusTruncated
6501,Q#2484 - >seq2483,superfamily,335182,1,51,1.52222e-08,49.2235,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,marg,N-TerminusTruncated
6502,Q#2486 - >seq2485,non-specific,335182,21,58,0.00224979,35.3563,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs0_human,marg,N-TerminusTruncated
6503,Q#2486 - >seq2485,superfamily,335182,21,58,0.00224979,35.3563,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.marg.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB2,ORF1,hs0_human,marg,N-TerminusTruncated
6504,Q#2487 - >seq2486,non-specific,335182,1,47,2.1808199999999998e-07,45.7567,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.pars.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,pars,N-TerminusTruncated
6505,Q#2487 - >seq2486,superfamily,335182,1,47,2.1808199999999998e-07,45.7567,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB2.ORF1.hs0_human.pars.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB2,ORF1,hs0_human,pars,N-TerminusTruncated
6506,Q#2488 - >seq2487,non-specific,340205,77,123,1.7e-11,55.8052,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs0_human,pars,N-TerminusTruncated
6507,Q#2488 - >seq2487,superfamily,340205,77,123,1.7e-11,55.8052,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB2.ORF1.hs0_human.pars.frame1,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB2,ORF1,hs0_human,pars,N-TerminusTruncated
6508,Q#2489 - >seq2488,specific,197310,10,238,1.47631e-42,155.58700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6509,Q#2489 - >seq2488,superfamily,351117,10,238,1.47631e-42,155.58700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6510,Q#2489 - >seq2488,non-specific,197306,10,209,1.2044200000000002e-20,92.1592,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6511,Q#2489 - >seq2488,non-specific,197320,8,210,1.35799e-12,69.081,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6512,Q#2489 - >seq2488,non-specific,223780,8,196,3.4129e-12,68.0087,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6513,Q#2489 - >seq2488,specific,335306,11,209,1.541e-10,62.2626,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6514,Q#2489 - >seq2488,non-specific,272954,8,209,3.4012e-09,58.9337,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6515,Q#2489 - >seq2488,non-specific,273186,8,210,7.3644e-09,57.674,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6516,Q#2489 - >seq2488,non-specific,197307,10,196,1.53783e-07,53.8309,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6517,Q#2489 - >seq2488,non-specific,197321,8,196,5.86782e-07,52.1692,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,CompleteHit
6518,Q#2489 - >seq2488,non-specific,197319,8,149,1.27989e-05,48.0417,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6519,Q#2489 - >seq2488,non-specific,236970,10,148,1.41699e-05,47.9666,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6520,Q#2489 - >seq2488,non-specific,339261,110,169,0.00170324,39.2427,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6521,Q#2489 - >seq2488,non-specific,197336,8,78,0.00261422,40.6735,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6522,Q#2489 - >seq2488,non-specific,197311,27,148,0.00303977,40.3529,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB2.ORF2.hs0_human.marg.frame3,1909130150_L1MB2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB2,ORF2,hs0_human,marg,C-TerminusTruncated
6523,Q#2491 - >seq2490,non-specific,340205,169,228,1.10882e-21,84.6952,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs3_orang.marg.frame3,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs3_orang,marg,CompleteHit
6524,Q#2491 - >seq2490,superfamily,340205,169,228,1.10882e-21,84.6952,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs3_orang.marg.frame3,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs3_orang,marg,CompleteHit
6525,Q#2491 - >seq2490,non-specific,335182,82,156,8.790370000000001e-19,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs3_orang.marg.frame3,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs3_orang,marg,CompleteHit
6526,Q#2491 - >seq2490,superfamily,335182,82,156,8.790370000000001e-19,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs3_orang.marg.frame3,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs3_orang,marg,CompleteHit
6527,Q#2496 - >seq2495,non-specific,340205,168,227,9.7474e-22,84.6952,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs3_orang.pars.frame1,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs3_orang,pars,CompleteHit
6528,Q#2496 - >seq2495,superfamily,340205,168,227,9.7474e-22,84.6952,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs3_orang.pars.frame1,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs3_orang,pars,CompleteHit
6529,Q#2496 - >seq2495,non-specific,335182,81,155,7.586019999999999e-19,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs3_orang.pars.frame1,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs3_orang,pars,CompleteHit
6530,Q#2496 - >seq2495,superfamily,335182,81,155,7.586019999999999e-19,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs3_orang.pars.frame1,1909130151_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs3_orang,pars,CompleteHit
6531,Q#2499 - >seq2498,non-specific,335182,67,145,2.10865e-17,74.6467,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6532,Q#2499 - >seq2498,superfamily,335182,67,145,2.10865e-17,74.6467,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6533,Q#2499 - >seq2498,non-specific,340205,174,236,4.8091600000000004e-17,72.75399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6534,Q#2499 - >seq2498,superfamily,340205,174,236,4.8091600000000004e-17,72.75399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6535,Q#2499 - >seq2498,non-specific,340204,23,65,0.00107017,35.8464,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6536,Q#2499 - >seq2498,superfamily,340204,23,65,0.00107017,35.8464,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs4_gibbon.marg.frame1,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MB3,ORF1,hs4_gibbon,marg,CompleteHit
6537,Q#2502 - >seq2501,non-specific,335182,48,126,9.920930000000002e-18,75.0319,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs4_gibbon,pars,CompleteHit
6538,Q#2502 - >seq2501,superfamily,335182,48,126,9.920930000000002e-18,75.0319,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs4_gibbon,pars,CompleteHit
6539,Q#2502 - >seq2501,non-specific,340205,166,209,1.04074e-15,68.5168,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6540,Q#2502 - >seq2501,superfamily,340205,166,209,1.04074e-15,68.5168,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6541,Q#2502 - >seq2501,non-specific,340204,4,46,0.000853853,35.8464,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MB3,ORF1,hs4_gibbon,pars,CompleteHit
6542,Q#2502 - >seq2501,superfamily,340204,4,46,0.000853853,35.8464,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs4_gibbon.pars.frame3,1909130152_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MB3,ORF1,hs4_gibbon,pars,CompleteHit
6543,Q#2505 - >seq2504,specific,238827,249,507,5.94853e-41,150.134,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,marg,CompleteHit
6544,Q#2505 - >seq2504,superfamily,295487,249,507,5.94853e-41,150.134,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,marg,CompleteHit
6545,Q#2505 - >seq2504,non-specific,333820,264,507,4.6097699999999997e-20,88.5033,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,marg,CompleteHit
6546,Q#2505 - >seq2504,superfamily,333820,264,507,4.6097699999999997e-20,88.5033,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,marg,CompleteHit
6547,Q#2505 - >seq2504,non-specific,238828,326,412,0.00313214,39.8769,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
6548,Q#2507 - >seq2506,non-specific,238827,432,489,1.92527e-06,49.597,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs6_sqmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6549,Q#2507 - >seq2506,superfamily,295487,432,489,1.92527e-06,49.597,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs6_sqmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6550,Q#2508 - >seq2507,specific,238827,246,474,3.6081799999999998e-31,121.62899999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs6_sqmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,pars,CompleteHit
6551,Q#2508 - >seq2507,superfamily,295487,246,474,3.6081799999999998e-31,121.62899999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs6_sqmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,pars,CompleteHit
6552,Q#2508 - >seq2507,non-specific,333820,252,439,2.8824e-19,86.1921,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs6_sqmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6553,Q#2508 - >seq2507,superfamily,333820,252,439,2.8824e-19,86.1921,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs6_sqmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6554,Q#2508 - >seq2507,non-specific,238828,314,443,0.000966525,41.4177,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs6_sqmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
6555,Q#2511 - >seq2510,non-specific,340205,213,256,1.0563e-12,61.5832,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
6556,Q#2511 - >seq2510,superfamily,340205,213,256,1.0563e-12,61.5832,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
6557,Q#2511 - >seq2510,non-specific,335182,94,146,6.6221000000000005e-06,43.8307,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
6558,Q#2511 - >seq2510,superfamily,335182,94,146,6.6221000000000005e-06,43.8307,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs6_sqmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
6559,Q#2512 - >seq2511,non-specific,335182,30,108,1.31757e-13,63.8611,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs6_sqmonkey.pars.frame3,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs6_sqmonkey,pars,CompleteHit
6560,Q#2512 - >seq2511,superfamily,335182,30,108,1.31757e-13,63.8611,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs6_sqmonkey.pars.frame3,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs6_sqmonkey,pars,CompleteHit
6561,Q#2512 - >seq2511,non-specific,340205,150,188,6.03817e-13,61.198,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs6_sqmonkey.pars.frame3,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
6562,Q#2512 - >seq2511,superfamily,340205,150,188,6.03817e-13,61.198,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs6_sqmonkey.pars.frame3,1909130153_L1MB3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
6563,Q#2516 - >seq2515,non-specific,335182,69,147,4.94801e-20,81.5803,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs5_gmonkey,pars,CompleteHit
6564,Q#2516 - >seq2515,superfamily,335182,69,147,4.94801e-20,81.5803,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs5_gmonkey,pars,CompleteHit
6565,Q#2516 - >seq2515,non-specific,340205,191,232,9.399039999999999e-15,66.5908,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6566,Q#2516 - >seq2515,superfamily,340205,191,232,9.399039999999999e-15,66.5908,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6567,Q#2516 - >seq2515,non-specific,340204,22,64,5.92835e-05,39.3132,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1MB3,ORF1,hs5_gmonkey,pars,CompleteHit
6568,Q#2516 - >seq2515,superfamily,340204,22,64,5.92835e-05,39.3132,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1MB3,ORF1,hs5_gmonkey,pars,CompleteHit
6569,Q#2522 - >seq2521,non-specific,197310,37,214,3.4387800000000004e-20,90.8737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6570,Q#2522 - >seq2521,superfamily,351117,37,214,3.4387800000000004e-20,90.8737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6571,Q#2522 - >seq2521,specific,335306,120,213,2.0926100000000003e-05,46.8546,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6572,Q#2522 - >seq2521,non-specific,197306,6,220,0.000491555,42.8537,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6573,Q#2522 - >seq2521,non-specific,197320,123,213,0.00133906,41.7318,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6574,Q#2522 - >seq2521,non-specific,223780,124,213,0.00278194,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6575,Q#2522 - >seq2521,non-specific,197307,12,213,0.00377682,40.3489,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs5_gmonkey.pars.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6576,Q#2523 - >seq2522,specific,238827,468,731,2.2738799999999997e-51,180.18,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6577,Q#2523 - >seq2522,superfamily,295487,468,731,2.2738799999999997e-51,180.18,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6578,Q#2523 - >seq2522,non-specific,333820,474,731,8.730239999999999e-28,111.23,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6579,Q#2523 - >seq2522,superfamily,333820,474,731,8.730239999999999e-28,111.23,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6580,Q#2523 - >seq2522,non-specific,238828,541,696,4.48813e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6581,Q#2523 - >seq2522,non-specific,275209,546,759,3.7057199999999995e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6582,Q#2523 - >seq2522,superfamily,275209,546,759,3.7057199999999995e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6583,Q#2523 - >seq2522,non-specific,238185,615,731,0.000206145,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs5_gmonkey.pars.frame2,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs5_gmonkey,pars,CompleteHit
6584,Q#2525 - >seq2524,specific,238827,498,761,1.2026100000000002e-50,178.25400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6585,Q#2525 - >seq2524,superfamily,295487,498,761,1.2026100000000002e-50,178.25400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6586,Q#2525 - >seq2524,non-specific,333820,504,761,3.0618699999999997e-27,109.689,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6587,Q#2525 - >seq2524,superfamily,333820,504,761,3.0618699999999997e-27,109.689,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6588,Q#2525 - >seq2524,non-specific,197310,41,219,1.48368e-21,94.7257,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6589,Q#2525 - >seq2524,superfamily,351117,41,219,1.48368e-21,94.7257,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6590,Q#2525 - >seq2524,non-specific,238828,571,726,1.6755200000000002e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6591,Q#2525 - >seq2524,non-specific,275209,576,789,1.05674e-08,58.238,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6592,Q#2525 - >seq2524,superfamily,275209,576,789,1.05674e-08,58.238,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6593,Q#2525 - >seq2524,specific,335306,49,218,1.7113900000000002e-05,47.2398,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6594,Q#2525 - >seq2524,non-specific,197320,111,218,0.000102764,45.1986,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6595,Q#2525 - >seq2524,non-specific,238185,645,761,0.000439315,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6596,Q#2525 - >seq2524,non-specific,197306,113,225,0.000606374,42.8537,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6597,Q#2525 - >seq2524,non-specific,223780,129,218,0.00459555,40.2743,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6598,Q#2525 - >seq2524,non-specific,197307,28,218,0.00707826,39.5785,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs5_gmonkey.marg.frame1,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs5_gmonkey,marg,CompleteHit
6599,Q#2526 - >seq2525,non-specific,335182,80,158,1.9652999999999997e-19,80.0395,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs5_gmonkey,marg,CompleteHit
6600,Q#2526 - >seq2525,superfamily,335182,80,158,1.9652999999999997e-19,80.0395,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs5_gmonkey,marg,CompleteHit
6601,Q#2526 - >seq2525,non-specific,340205,204,245,1.66384e-14,66.2056,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6602,Q#2526 - >seq2525,superfamily,340205,204,245,1.66384e-14,66.2056,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6603,Q#2526 - >seq2525,non-specific,340204,33,75,0.00013120799999999998,38.5428,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MB3,ORF1,hs5_gmonkey,marg,CompleteHit
6604,Q#2526 - >seq2525,superfamily,340204,33,75,0.00013120799999999998,38.5428,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB3.ORF1.hs5_gmonkey.marg.frame3,1909130153_L1MB3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MB3,ORF1,hs5_gmonkey,marg,CompleteHit
6605,Q#2527 - >seq2526,specific,238827,442,708,1.6284799999999998e-33,128.94799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6606,Q#2527 - >seq2526,superfamily,295487,442,708,1.6284799999999998e-33,128.94799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6607,Q#2527 - >seq2526,non-specific,333820,443,648,2.34617e-16,78.10300000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6608,Q#2527 - >seq2526,superfamily,333820,443,648,2.34617e-16,78.10300000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6609,Q#2527 - >seq2526,non-specific,197310,19,189,5.439199999999999e-07,51.9685,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6610,Q#2527 - >seq2526,superfamily,351117,19,189,5.439199999999999e-07,51.9685,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs7_bushaby,pars,CompleteHit
6611,Q#2527 - >seq2526,non-specific,238828,509,641,9.46685e-05,44.8845,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs7_bushaby.pars.frame2,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs7_bushaby,pars,N-TerminusTruncated
6612,Q#2529 - >seq2528,specific,238827,540,815,8.419639999999999e-29,115.46600000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs7_bushaby,marg,CompleteHit
6613,Q#2529 - >seq2528,superfamily,295487,540,815,8.419639999999999e-29,115.46600000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs7_bushaby,marg,CompleteHit
6614,Q#2529 - >seq2528,non-specific,197310,57,230,1.84315e-18,85.8661,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs7_bushaby,marg,CompleteHit
6615,Q#2529 - >seq2528,superfamily,351117,57,230,1.84315e-18,85.8661,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs7_bushaby,marg,CompleteHit
6616,Q#2529 - >seq2528,non-specific,333820,541,743,1.4124e-12,67.3174,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6617,Q#2529 - >seq2528,superfamily,333820,541,743,1.4124e-12,67.3174,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs7_bushaby,marg,C-TerminusTruncated
6618,Q#2535 - >seq2534,non-specific,340205,34,96,2.00153e-06,42.3232,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs7_bushaby,marg,CompleteHit
6619,Q#2535 - >seq2534,superfamily,340205,34,96,2.00153e-06,42.3232,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs7_bushaby.marg.frame1,1909130154_L1MB3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs7_bushaby,marg,CompleteHit
6620,Q#2539 - >seq2538,specific,238827,561,748,5.39934e-31,121.62899999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6621,Q#2539 - >seq2538,superfamily,295487,561,748,5.39934e-31,121.62899999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6622,Q#2539 - >seq2538,non-specific,333820,566,748,1.99161e-21,92.7405,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6623,Q#2539 - >seq2538,superfamily,333820,566,748,1.99161e-21,92.7405,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6624,Q#2539 - >seq2538,non-specific,238828,563,711,2.11943e-12,67.9964,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6625,Q#2539 - >seq2538,non-specific,275209,564,772,1.37974e-08,58.238,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6626,Q#2539 - >seq2538,superfamily,275209,564,772,1.37974e-08,58.238,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6627,Q#2539 - >seq2538,non-specific,238185,631,748,2.7606e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.marg.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,marg,CompleteHit
6628,Q#2540 - >seq2539,non-specific,238827,518,583,5.83443e-17,81.1834,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs8_ctshrew.marg.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6629,Q#2540 - >seq2539,superfamily,295487,518,583,5.83443e-17,81.1834,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.marg.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6630,Q#2540 - >seq2539,non-specific,333820,524,592,5.37598e-07,51.138999999999996,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.marg.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6631,Q#2540 - >seq2539,superfamily,333820,524,592,5.37598e-07,51.138999999999996,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.marg.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
6632,Q#2541 - >seq2540,non-specific,197310,15,219,5.580300000000001e-11,63.9097,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs8_ctshrew.marg.frame1,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs8_ctshrew,marg,CompleteHit
6633,Q#2541 - >seq2540,superfamily,351117,15,219,5.580300000000001e-11,63.9097,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs8_ctshrew.marg.frame1,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs8_ctshrew,marg,CompleteHit
6634,Q#2542 - >seq2541,specific,238827,299,485,1.8220099999999997e-32,125.48100000000001,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6635,Q#2542 - >seq2541,superfamily,295487,299,485,1.8220099999999997e-32,125.48100000000001,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6636,Q#2542 - >seq2541,non-specific,333820,304,485,1.04063e-20,90.4293,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6637,Q#2542 - >seq2541,superfamily,333820,304,485,1.04063e-20,90.4293,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6638,Q#2542 - >seq2541,non-specific,238828,299,485,1.84375e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6639,Q#2542 - >seq2541,non-specific,275209,303,509,5.888909999999999e-09,58.6232,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6640,Q#2542 - >seq2541,superfamily,275209,303,509,5.888909999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6641,Q#2542 - >seq2541,non-specific,238185,369,485,6.883960000000001e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs8_ctshrew,pars,CompleteHit
6642,Q#2544 - >seq2543,non-specific,238827,227,292,1.9018499999999998e-17,81.9538,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs8_ctshrew.pars.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6643,Q#2544 - >seq2543,superfamily,295487,227,292,1.9018499999999998e-17,81.9538,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs8_ctshrew.pars.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6644,Q#2544 - >seq2543,non-specific,333820,233,301,3.36923e-07,51.138999999999996,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.pars.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6645,Q#2544 - >seq2543,superfamily,333820,233,301,3.36923e-07,51.138999999999996,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs8_ctshrew.pars.frame2,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
6646,Q#2546 - >seq2545,non-specific,340205,40,82,1.45541e-09,49.2568,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs8_ctshrew.marg.frame1,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
6647,Q#2546 - >seq2545,superfamily,340205,40,82,1.45541e-09,49.2568,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs8_ctshrew.marg.frame1,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB3,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
6648,Q#2547 - >seq2546,non-specific,340205,5,65,1.0509600000000001e-06,41.1676,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs8_ctshrew,pars,CompleteHit
6649,Q#2547 - >seq2546,superfamily,340205,5,65,1.0509600000000001e-06,41.1676,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs8_ctshrew.pars.frame3,1909130155_L1MB3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs8_ctshrew,pars,CompleteHit
6650,Q#2552 - >seq2551,non-specific,197310,142,213,2.75055e-11,64.6801,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs1_chimp.pars.frame1,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
6651,Q#2552 - >seq2551,superfamily,351117,142,213,2.75055e-11,64.6801,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs1_chimp.pars.frame1,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
6652,Q#2552 - >seq2551,non-specific,197320,145,184,0.000347494,43.6578,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs1_chimp.pars.frame1,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
6653,Q#2554 - >seq2553,non-specific,197310,9,132,4.71798e-06,48.8869,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB4,ORF2,hs1_chimp,pars,C-TerminusTruncated
6654,Q#2554 - >seq2553,superfamily,351117,9,132,4.71798e-06,48.8869,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs1_chimp,pars,C-TerminusTruncated
6655,Q#2554 - >seq2553,non-specific,238827,576,684,0.00378681,39.967,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
6656,Q#2554 - >seq2553,superfamily,295487,576,684,0.00378681,39.967,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
6657,Q#2554 - >seq2553,non-specific,234767,47,293,0.00739453,40.5916,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MB4,ORF2,hs1_chimp,pars,C-TerminusTruncated
6658,Q#2554 - >seq2553,superfamily,234767,47,293,0.00739453,40.5916,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MB4.ORF2.hs1_chimp.pars.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MB4,ORF2,hs1_chimp,pars,C-TerminusTruncated
6659,Q#2558 - >seq2557,non-specific,340205,114,161,2.28382e-05,40.3972,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6660,Q#2558 - >seq2557,superfamily,340205,114,161,2.28382e-05,40.3972,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6661,Q#2559 - >seq2558,specific,197310,9,235,2.66365e-34,131.705,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6662,Q#2559 - >seq2558,superfamily,351117,9,235,2.66365e-34,131.705,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6663,Q#2559 - >seq2558,non-specific,197306,9,235,6.46048e-14,72.5141,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6664,Q#2559 - >seq2558,non-specific,197320,68,206,3.0385200000000006e-10,62.1474,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB4,ORF2,hs1_chimp,marg,N-TerminusTruncated
6665,Q#2559 - >seq2558,non-specific,197307,9,228,7.32229e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6666,Q#2559 - >seq2558,specific,335306,10,228,3.8610700000000003e-07,52.2474,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6667,Q#2559 - >seq2558,non-specific,223780,7,205,5.57699e-07,52.2155,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6668,Q#2559 - >seq2558,non-specific,273186,105,236,6.15779e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB4,ORF2,hs1_chimp,marg,N-TerminusTruncated
6669,Q#2559 - >seq2558,non-specific,197321,7,228,0.00021841599999999998,44.08,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6670,Q#2559 - >seq2558,non-specific,339261,107,230,0.00102481,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB4.ORF2.hs1_chimp.marg.frame3,1909130156_L1MB4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB4,ORF2,hs1_chimp,marg,CompleteHit
6671,Q#2561 - >seq2560,non-specific,340205,128,188,0.00323556,34.6192,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.marg.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB4,ORF1,hs2_gorilla,marg,CompleteHit
6672,Q#2561 - >seq2560,superfamily,340205,128,188,0.00323556,34.6192,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.marg.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB4,ORF1,hs2_gorilla,marg,CompleteHit
6673,Q#2563 - >seq2562,non-specific,238827,423,490,0.000695443,41.893,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs2_gorilla.pars.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6674,Q#2563 - >seq2562,superfamily,295487,423,490,0.000695443,41.893,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs2_gorilla.pars.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6675,Q#2564 - >seq2563,non-specific,197310,1,46,0.000721976,41.9533,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6676,Q#2564 - >seq2563,superfamily,351117,1,46,0.000721976,41.9533,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6677,Q#2564 - >seq2563,non-specific,197320,2,27,0.00176986,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6678,Q#2564 - >seq2563,non-specific,132725,182,276,0.00204902,41.467,cd06528,RNAP_A'',NC,cl29012,"A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.",L1MB4.ORF2.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
6679,Q#2564 - >seq2563,superfamily,355888,182,276,0.00204902,41.467,cl29012,RNAP_largest_subunit_C superfamily,NC, - ,"Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.",L1MB4.ORF2.hs2_gorilla.pars.frame3,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
6680,Q#2565 - >seq2564,non-specific,238827,656,734,1.69709e-07,53.0638,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6681,Q#2565 - >seq2564,superfamily,295487,656,734,1.69709e-07,53.0638,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6682,Q#2566 - >seq2565,non-specific,197310,91,230,5.79226e-25,104.741,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6683,Q#2566 - >seq2565,superfamily,351117,91,230,5.79226e-25,104.741,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6684,Q#2566 - >seq2565,non-specific,197320,101,203,7.719839999999999e-10,60.6066,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6685,Q#2566 - >seq2565,non-specific,223780,101,223,4.95547e-08,55.2971,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6686,Q#2566 - >seq2565,non-specific,197306,91,230,1.13562e-07,54.0245,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6687,Q#2566 - >seq2565,non-specific,273186,101,231,1.2921099999999999e-05,48.044,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6688,Q#2566 - >seq2565,non-specific,339261,103,225,1.3798699999999999e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB4,ORF2,hs2_gorilla,marg,CompleteHit
6689,Q#2566 - >seq2565,non-specific,335306,62,223,4.5796999999999995e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6690,Q#2566 - >seq2565,non-specific,197307,101,223,9.77974e-05,45.3565,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6691,Q#2566 - >seq2565,non-specific,272954,101,202,0.000261052,43.9109,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6692,Q#2566 - >seq2565,non-specific,197319,101,230,0.00026274400000000003,43.8045,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6693,Q#2566 - >seq2565,non-specific,197321,101,223,0.00047646,42.9244,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6694,Q#2566 - >seq2565,non-specific,197311,101,199,0.00048210099999999997,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs2_gorilla.marg.frame2,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6695,Q#2569 - >seq2568,non-specific,340205,159,205,0.00100816,36.16,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs2_gorilla,marg,N-TerminusTruncated
6696,Q#2569 - >seq2568,superfamily,340205,159,205,0.00100816,36.16,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs2_gorilla,marg,N-TerminusTruncated
6697,Q#2569 - >seq2568,non-specific,223666,43,152,0.0048201,37.2645,COG0593,DnaA,C,cl33966,"Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair]; ATPase involved in DNA replication initiation [DNA replication, recombination, and repair].",L1MB4.ORF1.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB4,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6698,Q#2569 - >seq2568,superfamily,223666,43,152,0.0048201,37.2645,cl33966,DnaA superfamily,C, - ,"Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair]; ATPase involved in DNA replication initiation [DNA replication, recombination, and repair].",L1MB4.ORF1.hs2_gorilla.marg.frame1,1909130156_L1MB4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB4,ORF1,hs2_gorilla,marg,C-TerminusTruncated
6699,Q#2573 - >seq2572,non-specific,238827,495,617,2.91055e-16,78.8722,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,BothTerminiTruncated
6700,Q#2573 - >seq2572,superfamily,295487,495,617,2.91055e-16,78.8722,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,BothTerminiTruncated
6701,Q#2573 - >seq2572,non-specific,333820,491,613,4.44505e-12,65.7766,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,BothTerminiTruncated
6702,Q#2573 - >seq2572,superfamily,333820,491,613,4.44505e-12,65.7766,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,BothTerminiTruncated
6703,Q#2573 - >seq2572,non-specific,238828,485,613,5.645540000000001e-08,54.5144,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,N-TerminusTruncated
6704,Q#2573 - >seq2572,non-specific,238185,558,647,1.39099e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.pars.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs9_pika,pars,CompleteHit
6705,Q#2574 - >seq2573,non-specific,238827,605,662,7.34109e-07,51.1378,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs9_pika.pars.frame2,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs9_pika,pars,N-TerminusTruncated
6706,Q#2574 - >seq2573,superfamily,295487,605,662,7.34109e-07,51.1378,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.pars.frame2,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs9_pika,pars,N-TerminusTruncated
6707,Q#2574 - >seq2573,non-specific,197310,9,154,2.45399e-06,49.6573,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs9_pika.pars.frame2,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs9_pika,pars,CompleteHit
6708,Q#2574 - >seq2573,superfamily,351117,9,154,2.45399e-06,49.6573,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs9_pika.pars.frame2,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs9_pika,pars,CompleteHit
6709,Q#2575 - >seq2574,non-specific,238827,438,505,6.57616e-14,71.9386,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs9_pika.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs9_pika,pars,C-TerminusTruncated
6710,Q#2575 - >seq2574,superfamily,295487,438,505,6.57616e-14,71.9386,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs9_pika,pars,C-TerminusTruncated
6711,Q#2575 - >seq2574,non-specific,333820,439,485,7.754119999999999e-06,47.287,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs9_pika,pars,C-TerminusTruncated
6712,Q#2575 - >seq2574,superfamily,333820,439,485,7.754119999999999e-06,47.287,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs9_pika,pars,C-TerminusTruncated
6713,Q#2576 - >seq2575,non-specific,197310,38,222,2.07992e-26,108.978,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6714,Q#2576 - >seq2575,superfamily,351117,38,222,2.07992e-26,108.978,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6715,Q#2576 - >seq2575,non-specific,238827,524,774,4.2057999999999997e-22,95.821,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6716,Q#2576 - >seq2575,superfamily,295487,524,774,4.2057999999999997e-22,95.821,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6717,Q#2576 - >seq2575,non-specific,197306,39,248,1.9942e-08,56.3357,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6718,Q#2576 - >seq2575,non-specific,333820,530,588,4.43724e-07,51.5242,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs9_pika,marg,C-TerminusTruncated
6719,Q#2576 - >seq2575,superfamily,333820,530,588,4.43724e-07,51.5242,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs9_pika,marg,C-TerminusTruncated
6720,Q#2576 - >seq2575,non-specific,197320,38,213,9.33606e-07,51.3618,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6721,Q#2576 - >seq2575,non-specific,272954,21,212,1.45582e-06,50.8445,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6722,Q#2576 - >seq2575,non-specific,223780,38,222,2.16616e-06,50.2895,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6723,Q#2576 - >seq2575,non-specific,197307,20,222,6.374869999999999e-06,48.8233,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6724,Q#2576 - >seq2575,specific,335306,38,212,0.000113796,44.9286,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6725,Q#2576 - >seq2575,non-specific,273186,20,234,0.000116762,44.9624,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6726,Q#2576 - >seq2575,non-specific,197321,37,199,0.00537662,39.8428,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs9_pika.marg.frame1,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6727,Q#2578 - >seq2577,non-specific,238827,543,711,6.29688e-17,80.7982,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,N-TerminusTruncated
6728,Q#2578 - >seq2577,superfamily,295487,543,711,6.29688e-17,80.7982,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,N-TerminusTruncated
6729,Q#2578 - >seq2577,non-specific,333820,519,664,5.740479999999999e-13,68.473,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,C-TerminusTruncated
6730,Q#2578 - >seq2577,superfamily,333820,519,664,5.740479999999999e-13,68.473,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,C-TerminusTruncated
6731,Q#2578 - >seq2577,non-specific,238828,535,664,2.74017e-08,55.67,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,N-TerminusTruncated
6732,Q#2578 - >seq2577,non-specific,238185,609,698,5.49379e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs9_pika.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs9_pika,marg,CompleteHit
6733,Q#2582 - >seq2581,non-specific,238827,167,211,5.52585e-09,56.5306,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs10_snmole.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,pars,C-TerminusTruncated
6734,Q#2582 - >seq2581,superfamily,295487,167,211,5.52585e-09,56.5306,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs10_snmole.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,pars,C-TerminusTruncated
6735,Q#2582 - >seq2581,non-specific,333820,171,211,2.79369e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs10_snmole.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,pars,C-TerminusTruncated
6736,Q#2582 - >seq2581,superfamily,333820,171,211,2.79369e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs10_snmole.pars.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,pars,C-TerminusTruncated
6737,Q#2583 - >seq2582,non-specific,238827,208,467,1.84599e-19,87.7318,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs10_snmole.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,marg,CompleteHit
6738,Q#2583 - >seq2582,superfamily,295487,208,467,1.84599e-19,87.7318,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs10_snmole.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,marg,CompleteHit
6739,Q#2583 - >seq2582,non-specific,333820,214,364,4.62169e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs10_snmole.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,marg,C-TerminusTruncated
6740,Q#2583 - >seq2582,superfamily,333820,214,364,4.62169e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs10_snmole.marg.frame3,1909130156_L1MB3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs10_snmole,marg,C-TerminusTruncated
6741,Q#2584 - >seq2583,non-specific,340205,174,218,6.44803e-16,69.2872,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs0_human.pars.frame1,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs0_human,pars,N-TerminusTruncated
6742,Q#2584 - >seq2583,superfamily,340205,174,218,6.44803e-16,69.2872,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs0_human.pars.frame1,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB3,ORF1,hs0_human,pars,N-TerminusTruncated
6743,Q#2587 - >seq2586,non-specific,335182,91,163,6.55109e-14,65.0167,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs0_human.pars.frame3,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs0_human,pars,N-TerminusTruncated
6744,Q#2587 - >seq2586,superfamily,335182,91,163,6.55109e-14,65.0167,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs0_human.pars.frame3,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB3,ORF1,hs0_human,pars,N-TerminusTruncated
6745,Q#2589 - >seq2588,non-specific,340205,162,225,1.6933200000000002e-16,71.2132,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs0_human.marg.frame2,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs0_human,marg,CompleteHit
6746,Q#2589 - >seq2588,superfamily,340205,162,225,1.6933200000000002e-16,71.2132,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB3.ORF1.hs0_human.marg.frame2,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB3,ORF1,hs0_human,marg,CompleteHit
6747,Q#2590 - >seq2589,non-specific,335182,91,163,1.4797e-13,64.6315,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs0_human.marg.frame3,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs0_human,marg,N-TerminusTruncated
6748,Q#2590 - >seq2589,superfamily,335182,91,163,1.4797e-13,64.6315,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB3.ORF1.hs0_human.marg.frame3,1909130156_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB3,ORF1,hs0_human,marg,N-TerminusTruncated
6749,Q#2593 - >seq2592,non-specific,238827,434,472,7.77147e-08,54.2194,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs3_orang.pars.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6750,Q#2593 - >seq2592,superfamily,295487,434,472,7.77147e-08,54.2194,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs3_orang.pars.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6751,Q#2595 - >seq2594,non-specific,238827,452,725,2.1166900000000003e-18,85.0354,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6752,Q#2595 - >seq2594,superfamily,295487,452,725,2.1166900000000003e-18,85.0354,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6753,Q#2595 - >seq2594,non-specific,333820,458,700,0.00559988,39.1978,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6754,Q#2595 - >seq2594,superfamily,333820,458,700,0.00559988,39.1978,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6755,Q#2595 - >seq2594,non-specific,214661,237,334,0.00949806,39.6399,smart00435,TOPEUc,N,cl26030,"DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras",L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB4,ORF2,hs3_orang,marg,N-TerminusTruncated
6756,Q#2595 - >seq2594,superfamily,330851,237,334,0.00949806,39.6399,cl26030,Topo_C_assoc superfamily,N, - ,C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.,L1MB4.ORF2.hs3_orang.marg.frame2,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB4,ORF2,hs3_orang,marg,N-TerminusTruncated
6757,Q#2596 - >seq2595,non-specific,197310,9,53,6.84533e-05,45.4201,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6758,Q#2596 - >seq2595,superfamily,351117,9,53,6.84533e-05,45.4201,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6759,Q#2596 - >seq2595,non-specific,336177,203,363,0.000711339,43.468,pfam05667,DUF812,N,cl25503,Protein of unknown function (DUF812); This family consists of several eukaryotic proteins of unknown function.,L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6760,Q#2596 - >seq2595,superfamily,336177,203,363,0.000711339,43.468,cl25503,DUF812 superfamily,N, - ,Protein of unknown function (DUF812); This family consists of several eukaryotic proteins of unknown function.,L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6761,Q#2596 - >seq2595,non-specific,114219,154,427,0.00927193,40.0901,pfam05483,SCP-1,N,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6762,Q#2596 - >seq2595,superfamily,114219,154,427,0.00927193,40.0901,cl30946,SCP-1 superfamily,N, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MB4.ORF2.hs3_orang.pars.frame3,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6763,Q#2597 - >seq2596,non-specific,197310,43,183,4.552130000000001e-13,70.0729,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs3_orang,pars,CompleteHit
6764,Q#2597 - >seq2596,superfamily,351117,43,183,4.552130000000001e-13,70.0729,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs3_orang,pars,CompleteHit
6765,Q#2597 - >seq2596,non-specific,238827,605,691,7.04063e-08,54.2194,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6766,Q#2597 - >seq2596,superfamily,295487,605,691,7.04063e-08,54.2194,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6767,Q#2597 - >seq2596,non-specific,339261,102,179,4.172310000000001e-05,43.8651,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6768,Q#2597 - >seq2596,non-specific,197306,70,189,6.931649999999999e-05,45.5501,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs3_orang,pars,N-TerminusTruncated
6769,Q#2597 - >seq2596,non-specific,197311,49,140,8.528729999999999e-05,44.9753,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs3_orang.pars.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs3_orang,pars,C-TerminusTruncated
6770,Q#2598 - >seq2597,non-specific,197310,13,192,1.5639800000000002e-17,83.1697,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6771,Q#2598 - >seq2597,superfamily,351117,13,192,1.5639800000000002e-17,83.1697,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6772,Q#2598 - >seq2597,non-specific,197306,13,198,3.53247e-09,58.6469,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs3_orang,marg,CompleteHit
6773,Q#2598 - >seq2597,non-specific,339261,111,188,6.66552e-05,43.4799,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB4.ORF2.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB4,ORF2,hs3_orang,marg,C-TerminusTruncated
6774,Q#2598 - >seq2597,non-specific,197311,58,149,8.39458e-05,44.9753,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB4,ORF2,hs3_orang,marg,C-TerminusTruncated
6775,Q#2600 - >seq2599,non-specific,335182,42,135,0.00312755,35.7415,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs3_orang,marg,CompleteHit
6776,Q#2600 - >seq2599,superfamily,335182,42,135,0.00312755,35.7415,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs3_orang.marg.frame1,1909130158_L1MB4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs3_orang,marg,CompleteHit
6777,Q#2605 - >seq2604,non-specific,197310,15,229,1.92253e-15,77.0065,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs4_gibbon,marg,CompleteHit
6778,Q#2605 - >seq2604,superfamily,351117,15,229,1.92253e-15,77.0065,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,marg,CompleteHit
6779,Q#2605 - >seq2604,non-specific,235175,257,464,3.4968e-06,51.218,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6780,Q#2605 - >seq2604,superfamily,235175,257,464,3.4968e-06,51.218,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6781,Q#2605 - >seq2604,non-specific,197306,12,228,2.90673e-05,46.7057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,marg,CompleteHit
6782,Q#2605 - >seq2604,non-specific,197311,66,140,0.000251709,43.4345,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6783,Q#2605 - >seq2604,non-specific,223780,58,140,0.000880171,42.2003,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6784,Q#2605 - >seq2604,non-specific,274009,272,451,0.00137195,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6785,Q#2605 - >seq2604,superfamily,274009,272,451,0.00137195,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6786,Q#2605 - >seq2604,non-specific,274009,253,451,0.00426034,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
6787,Q#2605 - >seq2604,non-specific,197320,62,140,0.00590796,39.8058,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
6788,Q#2609 - >seq2608,non-specific,197310,28,187,4.16069e-14,73.1545,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
6789,Q#2609 - >seq2608,superfamily,351117,28,187,4.16069e-14,73.1545,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
6790,Q#2609 - >seq2608,non-specific,197306,30,124,0.00014969200000000002,44.3945,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6791,Q#2609 - >seq2608,non-specific,197311,39,111,0.000483339,42.6641,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6792,Q#2609 - >seq2608,specific,335306,13,186,0.00120657,41.4618,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,pars,CompleteHit
6793,Q#2609 - >seq2608,non-specific,274009,240,408,0.00151561,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6794,Q#2609 - >seq2608,superfamily,274009,240,408,0.00151561,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6795,Q#2609 - >seq2608,non-specific,274009,219,408,0.00156778,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6796,Q#2609 - >seq2608,non-specific,223780,31,111,0.0039911,40.2743,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6797,Q#2609 - >seq2608,non-specific,224117,219,408,0.00423226,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6798,Q#2609 - >seq2608,superfamily,224117,219,408,0.00423226,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1MB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
6799,Q#2609 - >seq2608,non-specific,223496,171,416,0.00793066,40.1287,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6800,Q#2609 - >seq2608,superfamily,223496,171,416,0.00793066,40.1287,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB4.ORF2.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
6801,Q#2610 - >seq2609,non-specific,238827,622,701,0.00102919,41.893,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs4_gibbon.marg.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6802,Q#2610 - >seq2609,superfamily,295487,622,701,0.00102919,41.893,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs4_gibbon.marg.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6803,Q#2610 - >seq2609,non-specific,197310,144,195,0.00944602,38.8717,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs4_gibbon.marg.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6804,Q#2610 - >seq2609,superfamily,351117,144,195,0.00944602,38.8717,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs4_gibbon.marg.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
6805,Q#2611 - >seq2610,non-specific,335182,35,107,8.70264e-09,50.7643,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs4_gibbon,marg,CompleteHit
6806,Q#2611 - >seq2610,superfamily,335182,35,107,8.70264e-09,50.7643,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs4_gibbon.marg.frame2,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs4_gibbon,marg,CompleteHit
6807,Q#2612 - >seq2611,non-specific,340205,145,201,1.22331e-05,41.5528,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs4_gibbon.marg.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs4_gibbon,marg,CompleteHit
6808,Q#2612 - >seq2611,superfamily,340205,145,201,1.22331e-05,41.5528,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs4_gibbon.marg.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs4_gibbon,marg,CompleteHit
6809,Q#2613 - >seq2612,non-specific,340205,120,170,2.18158e-05,40.3972,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs4_gibbon.pars.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6810,Q#2613 - >seq2612,superfamily,340205,120,170,2.18158e-05,40.3972,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs4_gibbon.pars.frame3,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs4_gibbon,pars,N-TerminusTruncated
6811,Q#2615 - >seq2614,non-specific,335182,11,102,3.8531000000000004e-06,43.0603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs4_gibbon,pars,CompleteHit
6812,Q#2615 - >seq2614,superfamily,335182,11,102,3.8531000000000004e-06,43.0603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs4_gibbon.pars.frame1,1909130200_L1MB4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs4_gibbon,pars,CompleteHit
6813,Q#2618 - >seq2617,non-specific,238827,570,847,1.3919299999999999e-18,85.8058,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs6_sqmonkey,marg,CompleteHit
6814,Q#2618 - >seq2617,superfamily,295487,570,847,1.3919299999999999e-18,85.8058,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs6_sqmonkey,marg,CompleteHit
6815,Q#2618 - >seq2617,non-specific,333820,576,847,4.6976000000000005e-07,51.5242,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs6_sqmonkey,marg,CompleteHit
6816,Q#2618 - >seq2617,superfamily,333820,576,847,4.6976000000000005e-07,51.5242,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs6_sqmonkey,marg,CompleteHit
6817,Q#2623 - >seq2622,non-specific,340205,5,48,6.7428300000000005e-06,38.8564,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs7_bushaby.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs7_bushaby,pars,C-TerminusTruncated
6818,Q#2623 - >seq2622,superfamily,340205,5,48,6.7428300000000005e-06,38.8564,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs7_bushaby.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs7_bushaby,pars,C-TerminusTruncated
6819,Q#2626 - >seq2625,non-specific,238827,527,565,0.0064319,38.4262,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs7_bushaby.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs7_bushaby,pars,BothTerminiTruncated
6820,Q#2626 - >seq2625,superfamily,295487,527,565,0.0064319,38.4262,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs7_bushaby.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs7_bushaby,pars,BothTerminiTruncated
6821,Q#2627 - >seq2626,non-specific,238827,401,449,1.3404000000000003e-07,52.6786,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs7_bushaby.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6822,Q#2627 - >seq2626,superfamily,295487,401,449,1.3404000000000003e-07,52.6786,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs7_bushaby.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6823,Q#2627 - >seq2626,non-specific,333820,402,448,0.00348563,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs7_bushaby.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6824,Q#2627 - >seq2626,superfamily,333820,402,448,0.00348563,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs7_bushaby.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6825,Q#2628 - >seq2627,non-specific,236304,230,378,0.00315083,40.5415,PRK08581,PRK08581,C,cl35718,N-acetylmuramoyl-L-alanine amidase; Validated,L1MB4.ORF2.hs7_bushaby.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6826,Q#2628 - >seq2627,superfamily,236304,230,378,0.00315083,40.5415,cl35718,PRK08581 superfamily,C, - ,N-acetylmuramoyl-L-alanine amidase; Validated,L1MB4.ORF2.hs7_bushaby.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
6827,Q#2629 - >seq2628,specific,197310,17,236,9.0196e-29,116.29700000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB4,ORF2,hs7_bushaby,marg,CompleteHit
6828,Q#2629 - >seq2628,superfamily,351117,17,236,9.0196e-29,116.29700000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs7_bushaby,marg,CompleteHit
6829,Q#2629 - >seq2628,non-specific,238827,528,797,3.10946e-12,67.7014,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs7_bushaby,marg,CompleteHit
6830,Q#2629 - >seq2628,superfamily,295487,528,797,3.10946e-12,67.7014,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs7_bushaby,marg,CompleteHit
6831,Q#2629 - >seq2628,non-specific,197306,26,236,2.1450299999999997e-08,56.7209,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs7_bushaby,marg,CompleteHit
6832,Q#2631 - >seq2630,non-specific,238827,425,505,9.11288e-14,71.5534,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs6_sqmonkey.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6833,Q#2631 - >seq2630,superfamily,295487,425,505,9.11288e-14,71.5534,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs6_sqmonkey.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6834,Q#2631 - >seq2630,non-specific,333820,431,485,0.00027246599999999996,43.0498,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs6_sqmonkey.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6835,Q#2631 - >seq2630,superfamily,333820,431,485,0.00027246599999999996,43.0498,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs6_sqmonkey.pars.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
6836,Q#2632 - >seq2631,non-specific,340205,4,68,7.45035e-12,54.2644,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs7_bushaby,marg,CompleteHit
6837,Q#2632 - >seq2631,superfamily,340205,4,68,7.45035e-12,54.2644,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs7_bushaby.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs7_bushaby,marg,CompleteHit
6838,Q#2635 - >seq2634,non-specific,335182,42,127,2.6946499999999996e-10,55.0015,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs6_sqmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs6_sqmonkey,marg,CompleteHit
6839,Q#2635 - >seq2634,superfamily,335182,42,127,2.6946499999999996e-10,55.0015,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs6_sqmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs6_sqmonkey,marg,CompleteHit
6840,Q#2637 - >seq2636,non-specific,335182,27,87,0.000200765,38.0527,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6841,Q#2637 - >seq2636,superfamily,335182,27,87,0.000200765,38.0527,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6842,Q#2639 - >seq2638,non-specific,340205,154,200,4.97626e-06,42.7084,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs5_gmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6843,Q#2639 - >seq2638,superfamily,340205,154,200,4.97626e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs5_gmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6844,Q#2640 - >seq2639,non-specific,335182,53,120,2.3747900000000003e-06,44.2159,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6845,Q#2640 - >seq2639,superfamily,335182,53,120,2.3747900000000003e-06,44.2159,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
6846,Q#2642 - >seq2641,non-specific,197310,48,212,2.55188e-07,52.7389,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6847,Q#2642 - >seq2641,superfamily,351117,48,212,2.55188e-07,52.7389,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6848,Q#2642 - >seq2641,non-specific,274009,285,432,0.0007295689999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6849,Q#2642 - >seq2641,superfamily,274009,285,432,0.0007295689999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
6850,Q#2642 - >seq2641,non-specific,223496,230,433,0.00163311,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
6851,Q#2642 - >seq2641,superfamily,223496,230,433,0.00163311,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
6852,Q#2642 - >seq2641,specific,335306,48,181,0.00299388,40.3062,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB4.ORF2.hs5_gmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
6853,Q#2644 - >seq2643,non-specific,340205,120,161,5.4208e-05,39.2416,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs5_gmonkey.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6854,Q#2644 - >seq2643,superfamily,340205,120,161,5.4208e-05,39.2416,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs5_gmonkey.pars.frame3,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
6855,Q#2646 - >seq2645,non-specific,197310,44,220,5.61997e-08,55.0501,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB4,ORF2,hs5_gmonkey,marg,CompleteHit
6856,Q#2646 - >seq2645,superfamily,351117,44,220,5.61997e-08,55.0501,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs5_gmonkey,marg,CompleteHit
6857,Q#2646 - >seq2645,non-specific,274009,343,487,0.00191306,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6858,Q#2646 - >seq2645,superfamily,274009,343,487,0.00191306,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB4.ORF2.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
6859,Q#2646 - >seq2645,specific,335306,63,211,0.0021205,41.0766,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB4.ORF2.hs5_gmonkey.marg.frame2,1909130202_L1MB4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
6860,Q#2648 - >seq2647,non-specific,340205,119,165,6.738889999999999e-10,52.3384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs6_sqmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs6_sqmonkey,pars,CompleteHit
6861,Q#2648 - >seq2647,superfamily,340205,119,165,6.738889999999999e-10,52.3384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs6_sqmonkey.pars.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs6_sqmonkey,pars,CompleteHit
6862,Q#2651 - >seq2650,non-specific,340205,158,209,2.68998e-12,59.6572,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs6_sqmonkey,marg,CompleteHit
6863,Q#2651 - >seq2650,superfamily,340205,158,209,2.68998e-12,59.6572,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs6_sqmonkey.marg.frame1,1909130202_L1MB4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs6_sqmonkey,marg,CompleteHit
6864,Q#2653 - >seq2652,non-specific,335182,69,127,0.00354594,35.3563,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs9_pika.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs9_pika,marg,BothTerminiTruncated
6865,Q#2653 - >seq2652,superfamily,335182,69,127,0.00354594,35.3563,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs9_pika.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs9_pika,marg,BothTerminiTruncated
6866,Q#2654 - >seq2653,non-specific,340205,145,196,1.03102e-12,60.4276,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs9_pika.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs9_pika,marg,CompleteHit
6867,Q#2654 - >seq2653,superfamily,340205,145,196,1.03102e-12,60.4276,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs9_pika.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs9_pika,marg,CompleteHit
6868,Q#2656 - >seq2655,non-specific,238827,422,469,0.00043226800000000003,42.2782,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs9_pika.pars.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs9_pika,pars,N-TerminusTruncated
6869,Q#2656 - >seq2655,superfamily,295487,422,469,0.00043226800000000003,42.2782,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs9_pika.pars.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB4,ORF2,hs9_pika,pars,N-TerminusTruncated
6870,Q#2660 - >seq2659,non-specific,238827,375,620,6.41401e-14,72.3238,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs9_pika.marg.frame3,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB4,ORF2,hs9_pika,marg,CompleteHit
6871,Q#2660 - >seq2659,superfamily,295487,375,620,6.41401e-14,72.3238,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs9_pika.marg.frame3,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB4,ORF2,hs9_pika,marg,CompleteHit
6872,Q#2662 - >seq2661,non-specific,238827,358,408,5.23107e-05,45.3598,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs9_pika.pars.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs9_pika,pars,BothTerminiTruncated
6873,Q#2662 - >seq2661,superfamily,295487,358,408,5.23107e-05,45.3598,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs9_pika.pars.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs9_pika,pars,BothTerminiTruncated
6874,Q#2663 - >seq2662,non-specific,340205,65,105,6.813689999999999e-07,42.7084,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs9_pika.pars.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs9_pika,pars,C-TerminusTruncated
6875,Q#2663 - >seq2662,superfamily,340205,65,105,6.813689999999999e-07,42.7084,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs9_pika.pars.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs9_pika,pars,C-TerminusTruncated
6876,Q#2665 - >seq2664,non-specific,238827,491,769,6.50899e-20,89.6578,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6877,Q#2665 - >seq2664,superfamily,295487,491,769,6.50899e-20,89.6578,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6878,Q#2665 - >seq2664,non-specific,333820,644,769,9.03255e-07,50.3686,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6879,Q#2665 - >seq2664,superfamily,333820,644,769,9.03255e-07,50.3686,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6880,Q#2665 - >seq2664,non-specific,238828,607,728,0.000236495,43.7289,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6881,Q#2665 - >seq2664,non-specific,238185,645,769,0.00404228,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs8_ctshrew.marg.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6882,Q#2669 - >seq2668,non-specific,340205,70,133,1.4503099999999999e-13,61.198,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs8_ctshrew,marg,CompleteHit
6883,Q#2669 - >seq2668,superfamily,340205,70,133,1.4503099999999999e-13,61.198,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB4.ORF1.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB4,ORF1,hs8_ctshrew,marg,CompleteHit
6884,Q#2673 - >seq2672,non-specific,238827,509,575,2.0021099999999997e-06,49.597,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs8_ctshrew.pars.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6885,Q#2673 - >seq2672,superfamily,295487,509,575,2.0021099999999997e-06,49.597,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs8_ctshrew.pars.frame2,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
6886,Q#2674 - >seq2673,non-specific,238827,482,523,9.66709e-07,50.7526,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs8_ctshrew.pars.frame3,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB4,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
6887,Q#2674 - >seq2673,superfamily,295487,482,523,9.66709e-07,50.7526,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs8_ctshrew.pars.frame3,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB4,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
6888,Q#2675 - >seq2674,non-specific,197310,10,223,8.09918e-25,104.35600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6889,Q#2675 - >seq2674,superfamily,351117,10,223,8.09918e-25,104.35600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6890,Q#2675 - >seq2674,non-specific,197306,10,213,1.1351300000000002e-09,60.1877,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs8_ctshrew,marg,CompleteHit
6891,Q#2675 - >seq2674,non-specific,197320,135,214,0.000772753,42.5022,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB4.ORF2.hs8_ctshrew.marg.frame1,1909130203_L1MB4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB4,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
6892,Q#2677 - >seq2676,non-specific,197310,50,166,5.5076000000000005e-17,81.2437,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6893,Q#2677 - >seq2676,superfamily,351117,50,166,5.5076000000000005e-17,81.2437,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6894,Q#2677 - >seq2676,non-specific,197320,54,157,9.71912e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6895,Q#2677 - >seq2676,non-specific,238827,442,480,3.53804e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs1_chimp,pars,C-TerminusTruncated
6896,Q#2677 - >seq2676,superfamily,295487,442,480,3.53804e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs1_chimp,pars,C-TerminusTruncated
6897,Q#2677 - >seq2676,non-specific,197306,50,159,0.000370088,43.2389,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6898,Q#2677 - >seq2676,specific,335306,72,165,0.000745419,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6899,Q#2677 - >seq2676,non-specific,223780,50,165,0.00163702,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
6900,Q#2678 - >seq2677,non-specific,340205,158,221,4.3465199999999994e-18,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,marg,CompleteHit
6901,Q#2678 - >seq2677,superfamily,340205,158,221,4.3465199999999994e-18,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,marg,CompleteHit
6902,Q#2678 - >seq2677,non-specific,335182,89,141,0.00104101,37.2823,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
6903,Q#2678 - >seq2677,superfamily,335182,89,141,0.00104101,37.2823,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
6904,Q#2679 - >seq2678,non-specific,197310,83,199,1.35692e-17,83.1697,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6905,Q#2679 - >seq2678,superfamily,351117,83,199,1.35692e-17,83.1697,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6906,Q#2679 - >seq2678,non-specific,238827,513,671,1.74549e-13,70.783,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6907,Q#2679 - >seq2678,superfamily,295487,513,671,1.74549e-13,70.783,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6908,Q#2679 - >seq2678,non-specific,333820,526,671,3.10089e-09,57.6874,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6909,Q#2679 - >seq2678,superfamily,333820,526,671,3.10089e-09,57.6874,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6910,Q#2679 - >seq2678,non-specific,197320,87,190,9.927910000000001e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6911,Q#2679 - >seq2678,non-specific,197306,83,192,0.00020806,44.0093,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6912,Q#2679 - >seq2678,specific,335306,105,198,0.0007610319999999999,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6913,Q#2679 - >seq2678,non-specific,238828,525,656,0.0007931160000000001,42.1881,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6914,Q#2679 - >seq2678,non-specific,223780,83,198,0.000978287,42.2003,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6915,Q#2679 - >seq2678,non-specific,273186,82,198,0.00861333,39.1844,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6916,Q#2679 - >seq2678,non-specific,197321,83,198,0.00951313,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs1_chimp,marg,N-TerminusTruncated
6917,Q#2681 - >seq2680,non-specific,238827,473,511,2.87888e-05,46.5154,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs1_chimp.marg.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs1_chimp,marg,C-TerminusTruncated
6918,Q#2681 - >seq2680,superfamily,295487,473,511,2.87888e-05,46.5154,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs1_chimp.marg.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs1_chimp,marg,C-TerminusTruncated
6919,Q#2684 - >seq2683,non-specific,340205,69,127,3.37907e-17,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,pars,CompleteHit
6920,Q#2684 - >seq2683,superfamily,340205,69,127,3.37907e-17,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,pars,CompleteHit
6921,Q#2684 - >seq2683,non-specific,335182,1,52,0.00036579699999999995,36.8971,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6922,Q#2684 - >seq2683,superfamily,335182,1,52,0.00036579699999999995,36.8971,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs2_gorilla,pars,N-TerminusTruncated
6923,Q#2688 - >seq2687,specific,197310,9,237,6.607639999999998e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6924,Q#2688 - >seq2687,superfamily,351117,9,237,6.607639999999998e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6925,Q#2688 - >seq2687,non-specific,197306,9,237,5.91228e-29,116.427,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6926,Q#2688 - >seq2687,non-specific,223780,7,230,1.2326399999999998e-22,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6927,Q#2688 - >seq2687,specific,335306,10,230,6.53491e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6928,Q#2688 - >seq2687,non-specific,197320,7,230,1.3217099999999998e-18,86.8001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6929,Q#2688 - >seq2687,non-specific,197307,9,230,5.97712e-17,81.9505,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6930,Q#2688 - >seq2687,non-specific,197321,7,230,1.79099e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6931,Q#2688 - >seq2687,non-specific,272954,7,208,1.03157e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6932,Q#2688 - >seq2687,non-specific,273186,7,238,3.07479e-13,70.7708,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6933,Q#2688 - >seq2687,non-specific,197319,7,237,8.99591e-13,69.6129,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6934,Q#2688 - >seq2687,non-specific,197336,7,230,1.24418e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6935,Q#2688 - >seq2687,non-specific,238827,505,542,1.91822e-09,58.8418,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6936,Q#2688 - >seq2687,superfamily,295487,505,542,1.91822e-09,58.8418,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6937,Q#2688 - >seq2687,non-specific,197311,7,205,1.7768400000000003e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6938,Q#2688 - >seq2687,non-specific,224117,75,496,3.9839300000000005e-06,51.2536,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6939,Q#2688 - >seq2687,superfamily,224117,75,496,3.9839300000000005e-06,51.2536,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6940,Q#2688 - >seq2687,non-specific,339261,109,232,1.91902e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6941,Q#2688 - >seq2687,non-specific,236970,9,230,2.4123899999999998e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6942,Q#2688 - >seq2687,non-specific,197318,9,231,7.65086e-05,45.3651,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6943,Q#2688 - >seq2687,non-specific,274009,307,453,0.00015478,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6944,Q#2688 - >seq2687,superfamily,274009,307,453,0.00015478,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6945,Q#2688 - >seq2687,non-specific,224259,263,463,0.000267624,44.2868,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6946,Q#2688 - >seq2687,superfamily,224259,263,463,0.000267624,44.2868,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6947,Q#2688 - >seq2687,non-specific,333820,511,548,0.000510215,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6948,Q#2688 - >seq2687,superfamily,333820,511,548,0.000510215,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
6949,Q#2688 - >seq2687,non-specific,274009,125,451,0.000604064,43.9031,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6950,Q#2688 - >seq2687,non-specific,235175,308,458,0.000860332,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6951,Q#2688 - >seq2687,superfamily,235175,308,458,0.000860332,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6952,Q#2688 - >seq2687,non-specific,197874,222,395,0.00289566,41.1565,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6953,Q#2688 - >seq2687,superfamily,197874,222,395,0.00289566,41.1565,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6954,Q#2688 - >seq2687,non-specific,223496,251,495,0.00399551,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6955,Q#2688 - >seq2687,superfamily,223496,251,495,0.00399551,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB5.ORF2.hs2_gorilla.marg.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6956,Q#2689 - >seq2688,specific,197310,9,237,7.37626e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6957,Q#2689 - >seq2688,superfamily,351117,9,237,7.37626e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6958,Q#2689 - >seq2688,specific,238827,507,772,6.12582e-46,164.77200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6959,Q#2689 - >seq2688,superfamily,295487,507,772,6.12582e-46,164.77200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6960,Q#2689 - >seq2688,non-specific,197306,9,237,2.59711e-29,117.58200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6961,Q#2689 - >seq2688,non-specific,333820,513,772,2.3781799999999998e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6962,Q#2689 - >seq2688,superfamily,333820,513,772,2.3781799999999998e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6963,Q#2689 - >seq2688,non-specific,223780,7,230,2.69101e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6964,Q#2689 - >seq2688,specific,335306,10,230,6.73128e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6965,Q#2689 - >seq2688,non-specific,197320,7,230,1.6618299999999999e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6966,Q#2689 - >seq2688,non-specific,197307,9,230,1.0063899999999999e-16,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6967,Q#2689 - >seq2688,non-specific,197321,7,230,2.51778e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6968,Q#2689 - >seq2688,non-specific,272954,7,208,1.1351500000000001e-13,72.0305,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6969,Q#2689 - >seq2688,non-specific,273186,7,238,3.1393e-13,70.7708,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6970,Q#2689 - >seq2688,non-specific,197319,7,237,1.52112e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6971,Q#2689 - >seq2688,non-specific,197336,7,230,1.2819799999999996e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6972,Q#2689 - >seq2688,non-specific,238828,585,739,4.82472e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6973,Q#2689 - >seq2688,non-specific,197311,7,205,1.5901099999999999e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6974,Q#2689 - >seq2688,non-specific,339261,109,232,4.84708e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6975,Q#2689 - >seq2688,non-specific,275209,586,800,8.32243e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6976,Q#2689 - >seq2688,superfamily,275209,586,800,8.32243e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6977,Q#2689 - >seq2688,non-specific,224117,75,498,9.415110000000001e-06,50.098,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6978,Q#2689 - >seq2688,superfamily,224117,75,498,9.415110000000001e-06,50.098,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MB5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
6979,Q#2689 - >seq2688,non-specific,236970,9,230,2.50699e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6980,Q#2689 - >seq2688,non-specific,197318,9,231,7.87731e-05,45.3651,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6981,Q#2689 - >seq2688,non-specific,235175,308,466,0.000396162,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,pars,BothTerminiTruncated
6982,Q#2689 - >seq2688,superfamily,235175,308,466,0.000396162,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB5,ORF2,hs2_gorilla,pars,BothTerminiTruncated
6983,Q#2689 - >seq2688,non-specific,238185,655,772,0.000918443,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6984,Q#2689 - >seq2688,non-specific,185746,154,425,0.00384003,40.7884,cd08915,V_Alix_like, - ,cl14654,"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6985,Q#2689 - >seq2688,superfamily,353824,154,425,0.00384003,40.7884,cl14654,V_Alix_like superfamily, - , - ,"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain.",L1MB5.ORF2.hs2_gorilla.pars.frame3,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB5,ORF2,hs2_gorilla,pars,CompleteHit
6986,Q#2690 - >seq2689,specific,238827,483,672,9.943899999999999e-28,111.999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6987,Q#2690 - >seq2689,superfamily,295487,483,672,9.943899999999999e-28,111.999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6988,Q#2690 - >seq2689,non-specific,333820,486,668,1.59077e-16,78.4882,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6989,Q#2690 - >seq2689,superfamily,333820,486,668,1.59077e-16,78.4882,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6990,Q#2690 - >seq2689,non-specific,238828,511,668,3.97661e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
6991,Q#2690 - >seq2689,non-specific,275209,516,667,0.000432983,43.6004,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6992,Q#2690 - >seq2689,superfamily,275209,516,667,0.000432983,43.6004,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
6993,Q#2690 - >seq2689,non-specific,238185,585,665,0.00331162,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs2_gorilla.marg.frame1,1909130204_L1MB5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs2_gorilla,marg,CompleteHit
6994,Q#2693 - >seq2692,non-specific,340205,160,223,2.96805e-19,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs3_orang.pars.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,pars,CompleteHit
6995,Q#2693 - >seq2692,superfamily,340205,160,223,2.96805e-19,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs3_orang.pars.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,pars,CompleteHit
6996,Q#2693 - >seq2692,non-specific,335182,76,156,2.9100599999999996e-14,66.1723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs3_orang.pars.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,pars,CompleteHit
6997,Q#2693 - >seq2692,superfamily,335182,76,156,2.9100599999999996e-14,66.1723,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs3_orang.pars.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,pars,CompleteHit
6998,Q#2696 - >seq2695,non-specific,335182,105,201,2.13198e-20,83.5063,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs3_orang.marg.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,marg,CompleteHit
6999,Q#2696 - >seq2695,superfamily,335182,105,201,2.13198e-20,83.5063,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs3_orang.marg.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,marg,CompleteHit
7000,Q#2696 - >seq2695,non-specific,340205,204,268,2.38396e-19,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs3_orang.marg.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,marg,CompleteHit
7001,Q#2696 - >seq2695,superfamily,340205,204,268,2.38396e-19,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs3_orang.marg.frame1,1909130204_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs3_orang,marg,CompleteHit
7002,Q#2700 - >seq2699,non-specific,238827,478,627,1.02645e-11,65.3902,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs1_chimp.pars.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
7003,Q#2700 - >seq2699,superfamily,295487,478,627,1.02645e-11,65.3902,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs1_chimp.pars.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
7004,Q#2700 - >seq2699,non-specific,333820,482,627,1.76412e-09,58.0726,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs1_chimp.pars.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
7005,Q#2700 - >seq2699,superfamily,333820,482,627,1.76412e-09,58.0726,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs1_chimp.pars.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
7006,Q#2700 - >seq2699,non-specific,238828,481,612,0.000435913,42.9585,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs1_chimp.pars.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs1_chimp,pars,N-TerminusTruncated
7007,Q#2701 - >seq2700,non-specific,335182,17,97,4.3818800000000003e-07,45.7567,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs0_human.pars.frame1,1909130204_L1MB4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs0_human,pars,CompleteHit
7008,Q#2701 - >seq2700,superfamily,335182,17,97,4.3818800000000003e-07,45.7567,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs0_human.pars.frame1,1909130204_L1MB4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB4,ORF1,hs0_human,pars,CompleteHit
7009,Q#2704 - >seq2703,non-specific,238827,333,535,3.71195e-23,98.5174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs10_snmole.pars.frame2,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs10_snmole,pars,CompleteHit
7010,Q#2704 - >seq2703,superfamily,295487,333,535,3.71195e-23,98.5174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs10_snmole.pars.frame2,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs10_snmole,pars,CompleteHit
7011,Q#2704 - >seq2703,non-specific,333820,339,548,4.6217300000000004e-10,59.6134,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs10_snmole.pars.frame2,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs10_snmole,pars,CompleteHit
7012,Q#2704 - >seq2703,superfamily,333820,339,548,4.6217300000000004e-10,59.6134,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs10_snmole.pars.frame2,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs10_snmole,pars,CompleteHit
7013,Q#2704 - >seq2703,non-specific,238828,418,514,0.00455423,39.4917,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB4.ORF2.hs10_snmole.pars.frame2,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB4,ORF2,hs10_snmole,pars,N-TerminusTruncated
7014,Q#2706 - >seq2705,non-specific,238827,525,816,1.4824e-12,68.0866,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs10_snmole,marg,CompleteHit
7015,Q#2706 - >seq2705,superfamily,295487,525,816,1.4824e-12,68.0866,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs10_snmole,marg,CompleteHit
7016,Q#2706 - >seq2705,non-specific,197310,20,161,4.651719999999999e-10,61.2133,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB4,ORF2,hs10_snmole,marg,C-TerminusTruncated
7017,Q#2706 - >seq2705,superfamily,351117,20,161,4.651719999999999e-10,61.2133,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB4,ORF2,hs10_snmole,marg,C-TerminusTruncated
7018,Q#2706 - >seq2705,non-specific,333820,703,816,0.00133218,41.1238,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs10_snmole,marg,N-TerminusTruncated
7019,Q#2706 - >seq2705,superfamily,333820,703,816,0.00133218,41.1238,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB4.ORF2.hs10_snmole.marg.frame1,1909130204_L1MB4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB4,ORF2,hs10_snmole,marg,N-TerminusTruncated
7020,Q#2712 - >seq2711,non-specific,335182,35,112,3.3552899999999997e-10,54.2311,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs0_human.marg.frame2,1909130204_L1MB4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs0_human,marg,CompleteHit
7021,Q#2712 - >seq2711,superfamily,335182,35,112,3.3552899999999997e-10,54.2311,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB4.ORF1.hs0_human.marg.frame2,1909130204_L1MB4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB4,ORF1,hs0_human,marg,CompleteHit
7022,Q#2715 - >seq2714,non-specific,340205,108,170,7.624939999999999e-06,41.5528,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs1_chimp,marg,CompleteHit
7023,Q#2715 - >seq2714,superfamily,340205,108,170,7.624939999999999e-06,41.5528,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs1_chimp.marg.frame1,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs1_chimp,marg,CompleteHit
7024,Q#2719 - >seq2718,non-specific,335182,1,50,5.191189999999999e-05,39.2083,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs1_chimp,pars,N-TerminusTruncated
7025,Q#2719 - >seq2718,superfamily,335182,1,50,5.191189999999999e-05,39.2083,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs1_chimp.pars.frame3,1909130204_L1MB5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs1_chimp,pars,N-TerminusTruncated
7026,Q#2725 - >seq2724,specific,197310,9,230,1.6354099999999998e-45,164.062,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7027,Q#2725 - >seq2724,superfamily,351117,9,230,1.6354099999999998e-45,164.062,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7028,Q#2725 - >seq2724,specific,238827,503,741,7.404579999999999e-43,155.52700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7029,Q#2725 - >seq2724,superfamily,295487,503,741,7.404579999999999e-43,155.52700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7030,Q#2725 - >seq2724,non-specific,333820,499,714,1.7022100000000001e-25,104.682,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7031,Q#2725 - >seq2724,superfamily,333820,499,714,1.7022100000000001e-25,104.682,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7032,Q#2725 - >seq2724,non-specific,197306,9,236,1.4951299999999999e-24,103.715,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7033,Q#2725 - >seq2724,non-specific,197320,7,221,2.51631e-15,77.1701,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7034,Q#2725 - >seq2724,non-specific,223780,9,225,3.34441e-13,70.7051,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7035,Q#2725 - >seq2724,non-specific,197307,9,229,6.1626599999999995e-12,66.9277,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7036,Q#2725 - >seq2724,specific,335306,10,212,2.80211e-10,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7037,Q#2725 - >seq2724,non-specific,238828,562,714,3.36497e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,N-TerminusTruncated
7038,Q#2725 - >seq2724,non-specific,197321,7,229,1.60358e-09,59.8732,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7039,Q#2725 - >seq2724,non-specific,273186,7,237,3.35332e-09,58.8296,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7040,Q#2725 - >seq2724,non-specific,272954,7,207,1.46596e-08,57.0077,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7041,Q#2725 - >seq2724,non-specific,197311,27,204,1.2469200000000002e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7042,Q#2725 - >seq2724,non-specific,197319,7,236,2.48997e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7043,Q#2725 - >seq2724,non-specific,197336,7,194,4.2404900000000005e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7044,Q#2725 - >seq2724,non-specific,339261,108,230,9.02933e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs3_orang,marg,CompleteHit
7045,Q#2725 - >seq2724,non-specific,275209,563,768,1.1188699999999998e-05,48.9932,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,N-TerminusTruncated
7046,Q#2725 - >seq2724,superfamily,275209,563,768,1.1188699999999998e-05,48.9932,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs3_orang,marg,N-TerminusTruncated
7047,Q#2725 - >seq2724,non-specific,197322,91,217,0.000517306,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs3_orang,marg,N-TerminusTruncated
7048,Q#2725 - >seq2724,non-specific,197317,124,229,0.00224145,41.0484,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB5.ORF2.hs3_orang.marg.frame3,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,marg,N-TerminusTruncated
7049,Q#2727 - >seq2726,specific,238827,483,684,3.04208e-40,148.208,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,C-TerminusTruncated
7050,Q#2727 - >seq2726,superfamily,295487,483,684,3.04208e-40,148.208,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,C-TerminusTruncated
7051,Q#2727 - >seq2726,specific,197310,22,216,6.6699e-40,147.88299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7052,Q#2727 - >seq2726,superfamily,351117,22,216,6.6699e-40,147.88299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7053,Q#2727 - >seq2726,non-specific,197306,12,224,9.734130000000001e-22,95.626,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7054,Q#2727 - >seq2726,non-specific,333820,489,683,7.711609999999999e-21,91.1997,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,C-TerminusTruncated
7055,Q#2727 - >seq2726,superfamily,333820,489,683,7.711609999999999e-21,91.1997,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,C-TerminusTruncated
7056,Q#2727 - >seq2726,non-specific,197320,24,215,1.8959799999999998e-12,68.3106,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7057,Q#2727 - >seq2726,non-specific,223780,20,215,7.46848e-10,60.6899,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7058,Q#2727 - >seq2726,specific,335306,18,206,1.3354200000000001e-08,56.4846,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7059,Q#2727 - >seq2726,non-specific,197307,18,216,2.25048e-08,56.1421,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7060,Q#2727 - >seq2726,non-specific,197311,19,198,5.3186400000000006e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7061,Q#2727 - >seq2726,non-specific,238828,554,684,8.26645e-08,54.1292,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,N-TerminusTruncated
7062,Q#2727 - >seq2726,non-specific,272954,24,201,9.02055e-06,48.5333,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7063,Q#2727 - >seq2726,non-specific,273186,24,215,6.30716e-05,45.7328,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7064,Q#2727 - >seq2726,non-specific,197321,19,188,6.58589e-05,45.6208,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7065,Q#2727 - >seq2726,non-specific,339261,102,208,0.000197717,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7066,Q#2727 - >seq2726,non-specific,197322,85,211,0.000517794,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,N-TerminusTruncated
7067,Q#2727 - >seq2726,non-specific,197319,20,217,0.00179964,41.4933,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs3_orang,pars,CompleteHit
7068,Q#2727 - >seq2726,non-specific,275209,559,676,0.00292536,41.2892,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,BothTerminiTruncated
7069,Q#2727 - >seq2726,superfamily,275209,559,676,0.00292536,41.2892,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs3_orang,pars,BothTerminiTruncated
7070,Q#2727 - >seq2726,non-specific,197317,118,216,0.00920556,39.1224,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB5.ORF2.hs3_orang.pars.frame2,1909130205_L1MB5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs3_orang,pars,N-TerminusTruncated
7071,Q#2732 - >seq2731,non-specific,238827,477,573,4.14058e-13,69.6274,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7072,Q#2732 - >seq2731,superfamily,295487,477,573,4.14058e-13,69.6274,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7073,Q#2732 - >seq2731,non-specific,333820,483,573,1.2518800000000001e-05,46.9018,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7074,Q#2732 - >seq2731,superfamily,333820,483,573,1.2518800000000001e-05,46.9018,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7075,Q#2733 - >seq2732,specific,197310,9,236,6.26753e-48,170.995,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7076,Q#2733 - >seq2732,superfamily,351117,9,236,6.26753e-48,170.995,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7077,Q#2733 - >seq2732,non-specific,238827,507,764,1.5925599999999998e-25,105.836,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7078,Q#2733 - >seq2732,superfamily,295487,507,764,1.5925599999999998e-25,105.836,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7079,Q#2733 - >seq2732,non-specific,197306,9,236,8.66985e-20,89.848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7080,Q#2733 - >seq2732,non-specific,333820,513,734,4.29797e-17,80.4142,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7081,Q#2733 - >seq2732,superfamily,333820,513,734,4.29797e-17,80.4142,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7082,Q#2733 - >seq2732,non-specific,223780,9,225,5.67082e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7083,Q#2733 - >seq2732,non-specific,197320,7,217,6.07351e-12,67.155,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7084,Q#2733 - >seq2732,specific,335306,10,229,5.75677e-10,60.7218,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7085,Q#2733 - >seq2732,non-specific,197307,9,229,3.72705e-08,55.7569,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7086,Q#2733 - >seq2732,non-specific,197311,7,204,1.60167e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7087,Q#2733 - >seq2732,non-specific,339261,108,231,1.48401e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7088,Q#2733 - >seq2732,non-specific,272954,7,207,1.7299300000000002e-05,47.7629,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7089,Q#2733 - >seq2732,non-specific,197321,7,229,3.43148e-05,46.7764,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7090,Q#2733 - >seq2732,non-specific,238828,580,734,4.92621e-05,46.0401,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7091,Q#2733 - >seq2732,non-specific,273186,7,218,5.6022e-05,46.118,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7092,Q#2733 - >seq2732,non-specific,197319,7,236,0.000443375,43.4193,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7093,Q#2733 - >seq2732,non-specific,197336,7,194,0.0007234969999999999,42.5995,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs4_gibbon,marg,CompleteHit
7094,Q#2733 - >seq2732,non-specific,335313,86,151,0.00297319,41.2732,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7095,Q#2733 - >seq2732,superfamily,354836,86,151,0.00297319,41.2732,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1MB5.ORF2.hs4_gibbon.marg.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7096,Q#2734 - >seq2733,non-specific,197310,38,85,2.28103e-05,46.9609,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7097,Q#2734 - >seq2733,superfamily,351117,38,85,2.28103e-05,46.9609,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7098,Q#2734 - >seq2733,non-specific,238827,594,694,7.29113e-05,45.3598,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7099,Q#2734 - >seq2733,superfamily,295487,594,694,7.29113e-05,45.3598,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7100,Q#2736 - >seq2735,specific,197310,79,227,1.1791999999999999e-30,120.919,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7101,Q#2736 - >seq2735,superfamily,351117,79,227,1.1791999999999999e-30,120.919,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7102,Q#2736 - >seq2735,non-specific,197306,82,227,7.58603e-14,72.5141,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7103,Q#2736 - >seq2735,non-specific,197320,97,208,3.0941399999999995e-10,61.7622,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7104,Q#2736 - >seq2735,non-specific,223780,58,216,9.11322e-09,57.6083,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7105,Q#2736 - >seq2735,non-specific,339261,99,222,9.31951e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB5,ORF2,hs4_gibbon,pars,CompleteHit
7106,Q#2736 - >seq2735,non-specific,197311,93,195,5.94519e-05,45.3605,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7107,Q#2736 - >seq2735,non-specific,197307,82,220,0.000152478,44.5861,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7108,Q#2736 - >seq2735,non-specific,273186,97,209,0.00017608900000000001,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7109,Q#2736 - >seq2735,non-specific,335306,103,220,0.00080883,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7110,Q#2736 - >seq2735,non-specific,197319,82,227,0.0025956,40.7229,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7111,Q#2737 - >seq2736,non-specific,335182,83,151,0.000173117,39.2083,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7112,Q#2737 - >seq2736,superfamily,335182,83,151,0.000173117,39.2083,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs4_gibbon.pars.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7113,Q#2738 - >seq2737,non-specific,335182,166,239,5.02522e-05,41.5195,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs4_gibbon.marg.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs4_gibbon,marg,CompleteHit
7114,Q#2738 - >seq2737,superfamily,335182,166,239,5.02522e-05,41.5195,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs4_gibbon.marg.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs4_gibbon,marg,CompleteHit
7115,Q#2739 - >seq2738,non-specific,340205,261,334,1.30312e-07,48.1012,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs4_gibbon,marg,CompleteHit
7116,Q#2739 - >seq2738,superfamily,340205,261,334,1.30312e-07,48.1012,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs4_gibbon,marg,CompleteHit
7117,Q#2739 - >seq2738,non-specific,236327,92,147,0.00112622,40.5045,PRK08661,PRK08661,N,cl35734,prolyl-tRNA synthetase; Provisional,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB5,ORF1,hs4_gibbon,marg,N-TerminusTruncated
7118,Q#2739 - >seq2738,superfamily,236327,92,147,0.00112622,40.5045,cl35734,PRK08661 superfamily,N, - ,prolyl-tRNA synthetase; Provisional,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB5,ORF1,hs4_gibbon,marg,N-TerminusTruncated
7119,Q#2739 - >seq2738,non-specific,237177,72,143,0.00572663,38.2206,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MB5,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7120,Q#2739 - >seq2738,superfamily,237177,72,143,0.00572663,38.2206,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MB5.ORF1.hs4_gibbon.marg.frame1,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MB5,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7121,Q#2740 - >seq2739,non-specific,236327,1,56,0.000965644,39.7341,PRK08661,PRK08661,N,cl35734,prolyl-tRNA synthetase; Provisional,L1MB5.ORF1.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7122,Q#2740 - >seq2739,superfamily,236327,1,56,0.000965644,39.7341,cl35734,PRK08661 superfamily,N, - ,prolyl-tRNA synthetase; Provisional,L1MB5.ORF1.hs4_gibbon.pars.frame3,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7123,Q#2741 - >seq2740,non-specific,340205,162,206,0.000320061,37.7008,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7124,Q#2741 - >seq2740,superfamily,340205,162,206,0.000320061,37.7008,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs4_gibbon.pars.frame2,1909130206_L1MB5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7125,Q#2743 - >seq2742,non-specific,293312,306,393,0.000387107,42.7408,pfam16707,CagS,C,cl25057,Cag pathogenicity island protein S of Helicobacter pylori; CagS is a family of proteins from the pathogenicity island of Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known.,L1MB5.ORF2.hs5_gmonkey.marg.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7126,Q#2743 - >seq2742,superfamily,293312,306,393,0.000387107,42.7408,cl25057,CagS superfamily,C, - ,Cag pathogenicity island protein S of Helicobacter pylori; CagS is a family of proteins from the pathogenicity island of Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known.,L1MB5.ORF2.hs5_gmonkey.marg.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MB5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7127,Q#2744 - >seq2743,non-specific,238827,472,706,2.55247e-22,96.5914,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,marg,CompleteHit
7128,Q#2744 - >seq2743,superfamily,295487,472,706,2.55247e-22,96.5914,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,marg,CompleteHit
7129,Q#2744 - >seq2743,non-specific,333820,489,703,2.89637e-13,69.2434,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,marg,CompleteHit
7130,Q#2744 - >seq2743,superfamily,333820,489,703,2.89637e-13,69.2434,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,marg,CompleteHit
7131,Q#2744 - >seq2743,non-specific,197310,19,114,1.32049e-09,59.6725,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7132,Q#2744 - >seq2743,superfamily,351117,19,114,1.32049e-09,59.6725,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7133,Q#2744 - >seq2743,non-specific,238828,546,700,0.000180531,44.1141,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs5_gmonkey.marg.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7134,Q#2745 - >seq2744,non-specific,197310,105,228,1.4054e-13,71.6137,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs5_gmonkey.marg.frame1,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7135,Q#2745 - >seq2744,superfamily,351117,105,228,1.4054e-13,71.6137,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs5_gmonkey.marg.frame1,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7136,Q#2745 - >seq2744,non-specific,197306,102,228,0.000147303,44.3945,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs5_gmonkey.marg.frame1,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7137,Q#2745 - >seq2744,specific,335306,128,221,0.00199168,41.0766,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs5_gmonkey.marg.frame1,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7138,Q#2746 - >seq2745,non-specific,238827,555,723,1.06972e-14,74.2498,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7139,Q#2746 - >seq2745,superfamily,295487,555,723,1.06972e-14,74.2498,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7140,Q#2746 - >seq2745,non-specific,197310,109,225,9.87237e-10,60.0577,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7141,Q#2746 - >seq2745,superfamily,351117,109,225,9.87237e-10,60.0577,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7142,Q#2746 - >seq2745,non-specific,333820,570,720,4.17321e-09,57.3022,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7143,Q#2746 - >seq2745,superfamily,333820,570,720,4.17321e-09,57.3022,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7144,Q#2746 - >seq2745,non-specific,238828,565,717,0.000112046,44.8845,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs5_gmonkey.pars.frame2,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7145,Q#2748 - >seq2747,non-specific,197310,13,109,1.4199100000000001e-05,47.3461,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7146,Q#2748 - >seq2747,superfamily,351117,13,109,1.4199100000000001e-05,47.3461,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7147,Q#2748 - >seq2747,non-specific,238827,475,530,0.000705879,42.2782,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7148,Q#2748 - >seq2747,superfamily,295487,475,530,0.000705879,42.2782,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7149,Q#2751 - >seq2750,non-specific,340205,141,205,2.1861799999999998e-16,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,pars,CompleteHit
7150,Q#2751 - >seq2750,superfamily,340205,141,205,2.1861799999999998e-16,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,pars,CompleteHit
7151,Q#2751 - >seq2750,non-specific,335182,52,138,1.96329e-09,52.6903,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,pars,CompleteHit
7152,Q#2751 - >seq2750,superfamily,335182,52,138,1.96329e-09,52.6903,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs5_gmonkey.pars.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,pars,CompleteHit
7153,Q#2754 - >seq2753,non-specific,340205,1,59,1.73821e-14,60.4276,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs5_gmonkey.marg.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,marg,CompleteHit
7154,Q#2754 - >seq2753,superfamily,340205,1,59,1.73821e-14,60.4276,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs5_gmonkey.marg.frame3,1909130208_L1MB5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs5_gmonkey,marg,CompleteHit
7155,Q#2756 - >seq2755,non-specific,335182,87,168,1.42619e-11,58.8535,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs7_bushaby,marg,CompleteHit
7156,Q#2756 - >seq2755,superfamily,335182,87,168,1.42619e-11,58.8535,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs7_bushaby,marg,CompleteHit
7157,Q#2757 - >seq2756,non-specific,340205,173,222,7.80673e-06,42.3232,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs7_bushaby,marg,N-TerminusTruncated
7158,Q#2757 - >seq2756,superfamily,340205,173,222,7.80673e-06,42.3232,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs7_bushaby,marg,N-TerminusTruncated
7159,Q#2759 - >seq2758,non-specific,197310,10,228,3.55523e-07,52.7389,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7160,Q#2759 - >seq2758,superfamily,351117,10,228,3.55523e-07,52.7389,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7161,Q#2759 - >seq2758,non-specific,238827,546,572,0.000609869,42.6634,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
7162,Q#2759 - >seq2758,superfamily,295487,546,572,0.000609869,42.6634,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs7_bushaby.marg.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs7_bushaby,marg,C-TerminusTruncated
7163,Q#2761 - >seq2760,specific,238827,513,768,9.78636e-32,123.941,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7164,Q#2761 - >seq2760,superfamily,295487,513,768,9.78636e-32,123.941,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7165,Q#2761 - >seq2760,non-specific,333820,504,768,2.7916000000000002e-18,83.8809,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7166,Q#2761 - >seq2760,superfamily,333820,504,768,2.7916000000000002e-18,83.8809,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,CompleteHit
7167,Q#2761 - >seq2760,non-specific,238828,564,698,1.6837299999999998e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7168,Q#2761 - >seq2760,non-specific,275209,569,702,2.8686e-05,47.4524,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7169,Q#2761 - >seq2760,superfamily,275209,569,702,2.8686e-05,47.4524,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs7_bushaby.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7170,Q#2763 - >seq2762,non-specific,335182,85,125,0.00146687,36.1267,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs7_bushaby,pars,N-TerminusTruncated
7171,Q#2763 - >seq2762,superfamily,335182,85,125,0.00146687,36.1267,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs7_bushaby,pars,N-TerminusTruncated
7172,Q#2765 - >seq2764,non-specific,340205,149,188,0.00249953,35.0044,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs7_bushaby.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs7_bushaby,pars,N-TerminusTruncated
7173,Q#2765 - >seq2764,superfamily,340205,149,188,0.00249953,35.0044,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs7_bushaby.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs7_bushaby,pars,N-TerminusTruncated
7174,Q#2766 - >seq2765,specific,238827,239,475,1.2767899999999998e-43,156.297,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,CompleteHit
7175,Q#2766 - >seq2765,superfamily,295487,239,475,1.2767899999999998e-43,156.297,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,CompleteHit
7176,Q#2766 - >seq2765,non-specific,333820,240,475,2.2027399999999998e-26,106.223,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,CompleteHit
7177,Q#2766 - >seq2765,superfamily,333820,240,475,2.2027399999999998e-26,106.223,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,CompleteHit
7178,Q#2766 - >seq2765,non-specific,238828,293,475,2.38982e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7179,Q#2766 - >seq2765,non-specific,275209,298,496,7.27165e-07,51.6896,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7180,Q#2766 - >seq2765,superfamily,275209,298,496,7.27165e-07,51.6896,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7181,Q#2766 - >seq2765,non-specific,238185,370,475,3.16212e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs7_bushaby.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs7_bushaby,pars,CompleteHit
7182,Q#2767 - >seq2766,non-specific,238827,630,701,1.1836299999999999e-08,56.5306,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
7183,Q#2767 - >seq2766,superfamily,295487,630,701,1.1836299999999999e-08,56.5306,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
7184,Q#2769 - >seq2768,non-specific,340205,77,137,1.87112e-11,55.42,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,pars,CompleteHit
7185,Q#2769 - >seq2768,superfamily,340205,77,137,1.87112e-11,55.42,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,pars,CompleteHit
7186,Q#2770 - >seq2769,non-specific,238827,452,561,2.26918e-23,99.67299999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs6_sqmonkey.marg.frame3,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7187,Q#2770 - >seq2769,superfamily,295487,452,561,2.26918e-23,99.67299999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs6_sqmonkey.marg.frame3,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7188,Q#2770 - >seq2769,non-specific,333820,458,567,1.57965e-10,61.1542,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.marg.frame3,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7189,Q#2770 - >seq2769,superfamily,333820,458,567,1.57965e-10,61.1542,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.marg.frame3,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7190,Q#2772 - >seq2771,non-specific,340205,111,178,1.2096799999999998e-08,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,marg,CompleteHit
7191,Q#2772 - >seq2771,superfamily,340205,111,178,1.2096799999999998e-08,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,marg,CompleteHit
7192,Q#2772 - >seq2771,non-specific,335182,20,95,6.37414e-06,42.6751,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,marg,CompleteHit
7193,Q#2772 - >seq2771,superfamily,335182,20,95,6.37414e-06,42.6751,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs6_sqmonkey.marg.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs6_sqmonkey,marg,CompleteHit
7194,Q#2774 - >seq2773,non-specific,238827,395,516,4.97273e-16,78.1018,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7195,Q#2774 - >seq2773,superfamily,295487,395,516,4.97273e-16,78.1018,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7196,Q#2774 - >seq2773,non-specific,333820,401,516,4.74214e-06,48.0574,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7197,Q#2774 - >seq2773,superfamily,333820,401,516,4.74214e-06,48.0574,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7198,Q#2774 - >seq2773,non-specific,237049,450,572,0.00892975,39.8515,PRK12300,leuS,N,cl36101,leucyl-tRNA synthetase; Reviewed,L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7199,Q#2774 - >seq2773,superfamily,237049,450,572,0.00892975,39.8515,cl36101,leuS superfamily,N, - ,leucyl-tRNA synthetase; Reviewed,L1MB5.ORF2.hs6_sqmonkey.pars.frame1,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MB5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7200,Q#2775 - >seq2774,non-specific,238827,274,328,8.47687e-14,71.5534,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7201,Q#2775 - >seq2774,superfamily,295487,274,328,8.47687e-14,71.5534,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7202,Q#2775 - >seq2774,non-specific,333820,280,329,3.33731e-06,48.4426,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7203,Q#2775 - >seq2774,superfamily,333820,280,329,3.33731e-06,48.4426,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs6_sqmonkey.pars.frame2,1909130210_L1MB5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7204,Q#2779 - >seq2778,non-specific,335182,51,127,1.81078e-06,44.9863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs9_pika.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs9_pika,marg,CompleteHit
7205,Q#2779 - >seq2778,superfamily,335182,51,127,1.81078e-06,44.9863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs9_pika.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs9_pika,marg,CompleteHit
7206,Q#2781 - >seq2780,non-specific,340205,161,200,4.98827e-08,48.1012,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs9_pika.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs9_pika,marg,N-TerminusTruncated
7207,Q#2781 - >seq2780,superfamily,340205,161,200,4.98827e-08,48.1012,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs9_pika.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs9_pika,marg,N-TerminusTruncated
7208,Q#2784 - >seq2783,non-specific,340205,135,196,6.185650000000001e-18,74.2948,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs9_pika.pars.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs9_pika,pars,CompleteHit
7209,Q#2784 - >seq2783,superfamily,340205,135,196,6.185650000000001e-18,74.2948,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs9_pika.pars.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs9_pika,pars,CompleteHit
7210,Q#2785 - >seq2784,non-specific,238827,502,679,3.7593800000000004e-22,96.2062,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7211,Q#2785 - >seq2784,superfamily,295487,502,679,3.7593800000000004e-22,96.2062,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7212,Q#2785 - >seq2784,non-specific,238828,562,689,1.2285299999999999e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7213,Q#2785 - >seq2784,non-specific,333820,502,670,1.50206e-05,46.9018,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7214,Q#2785 - >seq2784,superfamily,333820,502,670,1.50206e-05,46.9018,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7215,Q#2785 - >seq2784,non-specific,238185,624,699,0.00613026,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs8_ctshrew.marg.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,marg,CompleteHit
7216,Q#2786 - >seq2785,non-specific,197310,171,229,1.54592e-09,59.6725,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7217,Q#2786 - >seq2785,superfamily,351117,171,229,1.54592e-09,59.6725,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7218,Q#2786 - >seq2785,non-specific,235175,266,494,0.00484372,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB5,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
7219,Q#2786 - >seq2785,superfamily,235175,266,494,0.00484372,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB5,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
7220,Q#2786 - >seq2785,non-specific,224117,267,534,0.00708816,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB5,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7221,Q#2786 - >seq2785,superfamily,224117,267,534,0.00708816,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB5.ORF2.hs8_ctshrew.marg.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MB5,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7222,Q#2788 - >seq2787,non-specific,197310,45,209,1.59246e-11,65.4505,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs8_ctshrew.pars.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB5,ORF2,hs8_ctshrew,pars,CompleteHit
7223,Q#2788 - >seq2787,superfamily,351117,45,209,1.59246e-11,65.4505,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs8_ctshrew.pars.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB5,ORF2,hs8_ctshrew,pars,CompleteHit
7224,Q#2788 - >seq2787,non-specific,197320,150,188,0.0058699,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs8_ctshrew.pars.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB5,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7225,Q#2791 - >seq2790,non-specific,340205,139,198,1.38452e-15,68.1316,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs8_ctshrew.marg.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,marg,CompleteHit
7226,Q#2791 - >seq2790,superfamily,340205,139,198,1.38452e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs8_ctshrew.marg.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,marg,CompleteHit
7227,Q#2791 - >seq2790,non-specific,335182,45,121,2.26229e-07,46.9123,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs8_ctshrew.marg.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,marg,CompleteHit
7228,Q#2791 - >seq2790,superfamily,335182,45,121,2.26229e-07,46.9123,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs8_ctshrew.marg.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,marg,CompleteHit
7229,Q#2794 - >seq2793,non-specific,335182,42,127,1.81005e-08,49.6087,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs8_ctshrew.pars.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,pars,CompleteHit
7230,Q#2794 - >seq2793,superfamily,335182,42,127,1.81005e-08,49.6087,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs8_ctshrew.pars.frame2,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs8_ctshrew,pars,CompleteHit
7231,Q#2795 - >seq2794,non-specific,340205,132,176,5.06143e-11,55.42,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs8_ctshrew.pars.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
7232,Q#2795 - >seq2794,superfamily,340205,132,176,5.06143e-11,55.42,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs8_ctshrew.pars.frame1,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB5,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
7233,Q#2796 - >seq2795,non-specific,238827,472,647,4.6742e-12,66.5458,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs8_ctshrew.pars.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7234,Q#2796 - >seq2795,superfamily,295487,472,647,4.6742e-12,66.5458,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs8_ctshrew.pars.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7235,Q#2796 - >seq2795,non-specific,333820,473,647,1.8018299999999998e-06,49.213,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs8_ctshrew.pars.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7236,Q#2796 - >seq2795,superfamily,333820,473,647,1.8018299999999998e-06,49.213,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs8_ctshrew.pars.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7237,Q#2796 - >seq2795,non-specific,238828,597,683,0.00244093,40.6473,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs8_ctshrew.pars.frame3,1909130211_L1MB5.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB5,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7238,Q#2800 - >seq2799,non-specific,335182,1,52,0.000608128,36.5119,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs0_human,pars,N-TerminusTruncated
7239,Q#2800 - >seq2799,superfamily,335182,1,52,0.000608128,36.5119,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs0_human,pars,N-TerminusTruncated
7240,Q#2801 - >seq2800,non-specific,335182,82,139,0.00010239899999999999,39.9787,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs0_human,marg,N-TerminusTruncated
7241,Q#2801 - >seq2800,superfamily,335182,82,139,0.00010239899999999999,39.9787,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs0_human,marg,N-TerminusTruncated
7242,Q#2803 - >seq2802,non-specific,238827,470,725,2.19344e-20,90.8134,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7243,Q#2803 - >seq2802,superfamily,295487,470,725,2.19344e-20,90.8134,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7244,Q#2803 - >seq2802,non-specific,333820,476,689,6.4499e-13,68.0878,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7245,Q#2803 - >seq2802,superfamily,333820,476,689,6.4499e-13,68.0878,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7246,Q#2803 - >seq2802,non-specific,238185,602,691,0.000459598,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7247,Q#2803 - >seq2802,non-specific,238828,566,692,0.00711951,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs0_human.marg.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs0_human,marg,N-TerminusTruncated
7248,Q#2804 - >seq2803,non-specific,238827,465,518,9.57307e-10,59.6122,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs0_human.pars.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs0_human,pars,C-TerminusTruncated
7249,Q#2804 - >seq2803,superfamily,295487,465,518,9.57307e-10,59.6122,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.pars.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs0_human,pars,C-TerminusTruncated
7250,Q#2804 - >seq2803,non-specific,333820,471,559,0.00134388,40.7386,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.pars.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs0_human,pars,C-TerminusTruncated
7251,Q#2804 - >seq2803,superfamily,333820,471,559,0.00134388,40.7386,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.pars.frame1,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB5,ORF2,hs0_human,pars,C-TerminusTruncated
7252,Q#2805 - >seq2804,non-specific,238827,494,713,1.02626e-18,86.191,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,CompleteHit
7253,Q#2805 - >seq2804,superfamily,295487,494,713,1.02626e-18,86.191,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,CompleteHit
7254,Q#2805 - >seq2804,non-specific,333820,525,677,2.95852e-08,54.6058,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7255,Q#2805 - >seq2804,superfamily,333820,525,677,2.95852e-08,54.6058,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7256,Q#2805 - >seq2804,non-specific,238828,526,660,4.3484e-05,46.0401,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7257,Q#2805 - >seq2804,non-specific,238185,588,679,0.00194465,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.pars.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs0_human,pars,CompleteHit
7258,Q#2806 - >seq2805,specific,197310,4,226,2.18469e-38,143.261,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7259,Q#2806 - >seq2805,superfamily,351117,4,226,2.18469e-38,143.261,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7260,Q#2806 - >seq2805,non-specific,197306,4,226,1.17119e-15,77.5216,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7261,Q#2806 - >seq2805,non-specific,197320,97,199,2.46545e-11,65.229,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7262,Q#2806 - >seq2805,specific,335306,5,219,8.636889999999999e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7263,Q#2806 - >seq2805,non-specific,223780,82,198,9.02895e-08,54.5267,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7264,Q#2806 - >seq2805,non-specific,197311,2,226,5.20163e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7265,Q#2806 - >seq2805,non-specific,339261,99,221,5.56696e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs0_human,pars,CompleteHit
7266,Q#2806 - >seq2805,non-specific,197307,4,219,0.000101086,44.9713,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7267,Q#2806 - >seq2805,non-specific,273186,98,199,0.000277201,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7268,Q#2806 - >seq2805,non-specific,197322,82,219,0.0012277000000000002,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7269,Q#2806 - >seq2805,non-specific,197319,82,226,0.00136756,41.4933,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,N-TerminusTruncated
7270,Q#2806 - >seq2805,non-specific,272954,2,198,0.0016663000000000001,41.2145,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7271,Q#2806 - >seq2805,non-specific,197321,2,219,0.00220103,40.9984,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.pars.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,pars,CompleteHit
7272,Q#2807 - >seq2806,non-specific,238827,500,554,8.453120000000001e-05,44.9746,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs0_human.marg.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs0_human,marg,C-TerminusTruncated
7273,Q#2807 - >seq2806,superfamily,295487,500,554,8.453120000000001e-05,44.9746,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs0_human.marg.frame2,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB5,ORF2,hs0_human,marg,C-TerminusTruncated
7274,Q#2808 - >seq2807,specific,197310,8,234,3.0657499999999993e-41,151.735,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7275,Q#2808 - >seq2807,superfamily,351117,8,234,3.0657499999999993e-41,151.735,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7276,Q#2808 - >seq2807,non-specific,197306,8,234,8.50985e-17,80.9884,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7277,Q#2808 - >seq2807,non-specific,197320,105,207,2.48029e-11,65.229,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,marg,N-TerminusTruncated
7278,Q#2808 - >seq2807,specific,335306,9,227,2.06479e-09,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7279,Q#2808 - >seq2807,non-specific,223780,6,206,2.0439500000000002e-08,56.4527,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7280,Q#2808 - >seq2807,non-specific,197311,6,234,1.28207e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7281,Q#2808 - >seq2807,non-specific,197307,8,227,1.73e-06,50.3641,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7282,Q#2808 - >seq2807,non-specific,339261,107,229,6.99321e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB5,ORF2,hs0_human,marg,CompleteHit
7283,Q#2808 - >seq2807,non-specific,273186,6,207,0.00013209999999999999,44.9624,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7284,Q#2808 - >seq2807,non-specific,272954,6,206,0.00024141,43.9109,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7285,Q#2808 - >seq2807,non-specific,197321,6,227,0.000294018,43.6948,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,CompleteHit
7286,Q#2808 - >seq2807,non-specific,197322,90,227,0.00123491,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,N-TerminusTruncated
7287,Q#2808 - >seq2807,non-specific,197319,90,234,0.00154543,41.4933,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB5.ORF2.hs0_human.marg.frame3,1909130212_L1MB5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB5,ORF2,hs0_human,marg,N-TerminusTruncated
7288,Q#2811 - >seq2810,non-specific,238827,29,276,1.21061e-20,90.8134,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs10_snmole,marg,CompleteHit
7289,Q#2811 - >seq2810,superfamily,295487,29,276,1.21061e-20,90.8134,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs10_snmole,marg,CompleteHit
7290,Q#2811 - >seq2810,non-specific,333820,33,276,2.0810399999999997e-09,57.3022,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs10_snmole,marg,CompleteHit
7291,Q#2811 - >seq2810,superfamily,333820,33,276,2.0810399999999997e-09,57.3022,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs10_snmole,marg,CompleteHit
7292,Q#2813 - >seq2812,non-specific,238827,66,156,1.96547e-11,63.4642,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs10_snmole,pars,N-TerminusTruncated
7293,Q#2813 - >seq2812,superfamily,295487,66,156,1.96547e-11,63.4642,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs10_snmole,pars,N-TerminusTruncated
7294,Q#2813 - >seq2812,non-specific,333820,66,156,0.00129823,39.9682,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs10_snmole,pars,N-TerminusTruncated
7295,Q#2813 - >seq2812,superfamily,333820,66,156,0.00129823,39.9682,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB5.ORF2.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB5,ORF2,hs10_snmole,pars,N-TerminusTruncated
7296,Q#2815 - >seq2814,non-specific,340205,138,188,3.6217699999999995e-17,72.75399999999999,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs10_snmole.marg.frame3,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs10_snmole,marg,C-TerminusTruncated
7297,Q#2815 - >seq2814,superfamily,340205,138,188,3.6217699999999995e-17,72.75399999999999,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs10_snmole.marg.frame3,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB5,ORF1,hs10_snmole,marg,C-TerminusTruncated
7298,Q#2817 - >seq2816,non-specific,335182,49,141,1.40092e-14,66.5575,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs10_snmole,marg,CompleteHit
7299,Q#2817 - >seq2816,superfamily,335182,49,141,1.40092e-14,66.5575,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs10_snmole.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB5,ORF1,hs10_snmole,marg,CompleteHit
7300,Q#2818 - >seq2817,non-specific,335182,40,105,5.5894900000000006e-08,48.4531,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs10_snmole.pars.frame3,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs10_snmole,pars,N-TerminusTruncated
7301,Q#2818 - >seq2817,superfamily,335182,40,105,5.5894900000000006e-08,48.4531,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB5.ORF1.hs10_snmole.pars.frame3,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB5,ORF1,hs10_snmole,pars,N-TerminusTruncated
7302,Q#2819 - >seq2818,non-specific,340205,102,162,8.265120000000001e-19,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs10_snmole,pars,CompleteHit
7303,Q#2819 - >seq2818,superfamily,340205,102,162,8.265120000000001e-19,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB5.ORF1.hs10_snmole.pars.frame2,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB5,ORF1,hs10_snmole,pars,CompleteHit
7304,Q#2823 - >seq2822,non-specific,197310,1,123,3.53744e-14,73.1545,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB5,ORF2,hs9_pika,marg,N-TerminusTruncated
7305,Q#2823 - >seq2822,superfamily,351117,1,123,3.53744e-14,73.1545,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs9_pika,marg,N-TerminusTruncated
7306,Q#2823 - >seq2822,non-specific,238827,379,522,8.307410000000001e-08,53.8342,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs9_pika,marg,C-TerminusTruncated
7307,Q#2823 - >seq2822,superfamily,295487,379,522,8.307410000000001e-08,53.8342,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB5,ORF2,hs9_pika,marg,C-TerminusTruncated
7308,Q#2823 - >seq2822,non-specific,223780,1,116,0.000692435,42.5855,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB5,ORF2,hs9_pika,marg,N-TerminusTruncated
7309,Q#2823 - >seq2822,specific,335306,11,123,0.00562971,39.5358,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB5.ORF2.hs9_pika.marg.frame1,1909130212_L1MB5.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB5,ORF2,hs9_pika,marg,N-TerminusTruncated
7310,Q#2827 - >seq2826,non-specific,340205,236,300,5.0727200000000007e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs1_chimp.marg.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,marg,CompleteHit
7311,Q#2827 - >seq2826,superfamily,340205,236,300,5.0727200000000007e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs1_chimp.marg.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,marg,CompleteHit
7312,Q#2827 - >seq2826,non-specific,335182,141,233,4.35465e-12,61.1647,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs1_chimp.marg.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,marg,CompleteHit
7313,Q#2827 - >seq2826,superfamily,335182,141,233,4.35465e-12,61.1647,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs1_chimp.marg.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,marg,CompleteHit
7314,Q#2832 - >seq2831,non-specific,340205,212,276,6.260009999999999e-23,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,pars,CompleteHit
7315,Q#2832 - >seq2831,superfamily,340205,212,276,6.260009999999999e-23,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,pars,CompleteHit
7316,Q#2832 - >seq2831,non-specific,335182,118,209,3.06497e-10,55.7719,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,pars,CompleteHit
7317,Q#2832 - >seq2831,superfamily,335182,118,209,3.06497e-10,55.7719,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs1_chimp,pars,CompleteHit
7318,Q#2832 - >seq2831,non-specific,153362,139,224,0.00745712,36.9095,cd07678,F-BAR_FCHSD1,NC,cl12013,"The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 1 (FCHSD1); F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 1 (FCHSD1) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.",L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB7,ORF1,hs1_chimp,pars,BothTerminiTruncated
7319,Q#2832 - >seq2831,superfamily,353336,139,224,0.00745712,36.9095,cl12013,BAR superfamily,NC, - ,"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively.",L1MB7.ORF1.hs1_chimp.pars.frame3,1909130213_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MB7,ORF1,hs1_chimp,pars,BothTerminiTruncated
7320,Q#2836 - >seq2835,specific,238827,434,694,1.23892e-27,111.61399999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs1_chimp,pars,CompleteHit
7321,Q#2836 - >seq2835,superfamily,295487,434,694,1.23892e-27,111.61399999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs1_chimp,pars,CompleteHit
7322,Q#2836 - >seq2835,non-specific,197310,1,162,1.72078e-24,103.2,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7323,Q#2836 - >seq2835,superfamily,351117,1,162,1.72078e-24,103.2,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7324,Q#2836 - >seq2835,non-specific,333820,440,639,1.81192e-11,63.8506,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs1_chimp,pars,C-TerminusTruncated
7325,Q#2836 - >seq2835,superfamily,333820,440,639,1.81192e-11,63.8506,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs1_chimp,pars,C-TerminusTruncated
7326,Q#2836 - >seq2835,non-specific,197306,1,162,7.21433e-08,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7327,Q#2836 - >seq2835,non-specific,197320,65,155,2.32977e-05,47.1246,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7328,Q#2836 - >seq2835,non-specific,238828,499,639,5.3881899999999997e-05,45.6549,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7329,Q#2836 - >seq2835,non-specific,223780,56,163,0.000191955,44.1263,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7330,Q#2836 - >seq2835,non-specific,197307,66,162,0.00129033,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7331,Q#2836 - >seq2835,non-specific,197321,101,162,0.008637700000000002,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.pars.frame3,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs1_chimp,pars,N-TerminusTruncated
7332,Q#2838 - >seq2837,specific,197310,9,233,2.6490599999999996e-42,154.817,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7333,Q#2838 - >seq2837,superfamily,351117,9,233,2.6490599999999996e-42,154.817,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7334,Q#2838 - >seq2837,specific,238827,506,765,1.5895e-28,114.311,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7335,Q#2838 - >seq2837,superfamily,295487,506,765,1.5895e-28,114.311,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7336,Q#2838 - >seq2837,non-specific,197306,9,233,2.93981e-18,85.2256,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7337,Q#2838 - >seq2837,non-specific,333820,512,711,1.33674e-11,64.2358,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs1_chimp,marg,C-TerminusTruncated
7338,Q#2838 - >seq2837,superfamily,333820,512,711,1.33674e-11,64.2358,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs1_chimp,marg,C-TerminusTruncated
7339,Q#2838 - >seq2837,non-specific,223780,9,234,2.87597e-11,64.9271,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7340,Q#2838 - >seq2837,specific,335306,12,226,2.09888e-09,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7341,Q#2838 - >seq2837,non-specific,197320,13,226,2.6407199999999995e-09,59.0658,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7342,Q#2838 - >seq2837,non-specific,197307,9,233,5.28274e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7343,Q#2838 - >seq2837,non-specific,272954,9,233,2.09075e-05,47.3777,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7344,Q#2838 - >seq2837,non-specific,238828,571,711,5.55419e-05,45.6549,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs1_chimp,marg,N-TerminusTruncated
7345,Q#2838 - >seq2837,non-specific,197321,7,233,0.000338947,43.6948,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs1_chimp.marg.frame2,1909130214_L1MB7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs1_chimp,marg,CompleteHit
7346,Q#2839 - >seq2838,specific,238827,455,685,9.58578e-28,111.999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs2_gorilla,marg,CompleteHit
7347,Q#2839 - >seq2838,superfamily,295487,455,685,9.58578e-28,111.999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs2_gorilla,marg,CompleteHit
7348,Q#2839 - >seq2838,non-specific,333820,461,680,3.26661e-15,75.0214,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs2_gorilla,marg,CompleteHit
7349,Q#2839 - >seq2838,superfamily,333820,461,680,3.26661e-15,75.0214,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs2_gorilla,marg,CompleteHit
7350,Q#2839 - >seq2838,non-specific,197310,9,84,9.34598e-11,63.1393,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
7351,Q#2839 - >seq2838,superfamily,351117,9,84,9.34598e-11,63.1393,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
7352,Q#2839 - >seq2838,non-specific,197306,9,113,1.60117e-05,47.4761,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
7353,Q#2839 - >seq2838,non-specific,238828,532,669,0.000220822,43.7289,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7354,Q#2839 - >seq2838,non-specific,223780,7,81,0.00554424,39.8891,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
7355,Q#2840 - >seq2839,non-specific,340205,160,223,2.0308299999999998e-24,91.6288,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.marg.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,marg,CompleteHit
7356,Q#2840 - >seq2839,superfamily,340205,160,223,2.0308299999999998e-24,91.6288,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.marg.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,marg,CompleteHit
7357,Q#2840 - >seq2839,non-specific,335182,68,157,2.89135e-11,58.0831,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs3_orang.marg.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,marg,CompleteHit
7358,Q#2840 - >seq2839,superfamily,335182,68,157,2.89135e-11,58.0831,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs3_orang.marg.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,marg,CompleteHit
7359,Q#2841 - >seq2840,non-specific,340205,161,207,1.3307000000000001e-15,68.1316,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.pars.frame1,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs3_orang,pars,N-TerminusTruncated
7360,Q#2841 - >seq2840,superfamily,340205,161,207,1.3307000000000001e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.pars.frame1,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs3_orang,pars,N-TerminusTruncated
7361,Q#2842 - >seq2841,non-specific,197310,85,226,1.94275e-26,108.978,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7362,Q#2842 - >seq2841,superfamily,351117,85,226,1.94275e-26,108.978,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7363,Q#2842 - >seq2841,non-specific,197306,84,226,2.6368400000000005e-10,61.7285,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7364,Q#2842 - >seq2841,non-specific,197320,99,215,2.34481e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7365,Q#2842 - >seq2841,non-specific,223780,99,215,3.7182800000000003e-06,49.5191,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7366,Q#2842 - >seq2841,non-specific,197307,96,226,4.8436e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7367,Q#2842 - >seq2841,non-specific,273186,99,227,0.00020340400000000002,44.192,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7368,Q#2842 - >seq2841,specific,335306,102,219,0.000846022,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7369,Q#2842 - >seq2841,non-specific,197321,101,226,0.00215379,40.9984,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7370,Q#2842 - >seq2841,non-specific,197319,96,226,0.0031605,40.7229,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB7.ORF2.hs2_gorilla.marg.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7371,Q#2843 - >seq2842,non-specific,335182,68,157,2.53195e-11,58.0831,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs3_orang.pars.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,pars,CompleteHit
7372,Q#2843 - >seq2842,superfamily,335182,68,157,2.53195e-11,58.0831,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs3_orang.pars.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,pars,CompleteHit
7373,Q#2843 - >seq2842,non-specific,340205,160,180,0.00926774,33.4636,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.pars.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,pars,C-TerminusTruncated
7374,Q#2843 - >seq2842,superfamily,340205,160,180,0.00926774,33.4636,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs3_orang.pars.frame3,1909130215_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs3_orang,pars,C-TerminusTruncated
7375,Q#2848 - >seq2847,non-specific,340205,164,227,2.3321999999999998e-21,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs2_gorilla,marg,CompleteHit
7376,Q#2848 - >seq2847,superfamily,340205,164,227,2.3321999999999998e-21,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs2_gorilla,marg,CompleteHit
7377,Q#2848 - >seq2847,non-specific,335182,90,161,2.00921e-14,66.5575,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
7378,Q#2848 - >seq2847,superfamily,335182,90,161,2.00921e-14,66.5575,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs2_gorilla.marg.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
7379,Q#2849 - >seq2848,specific,238827,501,733,2.40891e-27,111.229,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs2_gorilla,pars,CompleteHit
7380,Q#2849 - >seq2848,superfamily,295487,501,733,2.40891e-27,111.229,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs2_gorilla,pars,CompleteHit
7381,Q#2849 - >seq2848,non-specific,197310,85,226,1.0433599999999999e-26,109.74799999999999,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7382,Q#2849 - >seq2848,superfamily,351117,85,226,1.0433599999999999e-26,109.74799999999999,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7383,Q#2849 - >seq2848,non-specific,333820,507,728,6.25185e-15,74.251,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs2_gorilla,pars,CompleteHit
7384,Q#2849 - >seq2848,superfamily,333820,507,728,6.25185e-15,74.251,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs2_gorilla,pars,CompleteHit
7385,Q#2849 - >seq2848,non-specific,197306,84,226,2.66411e-10,61.7285,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7386,Q#2849 - >seq2848,non-specific,197320,99,215,2.39146e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7387,Q#2849 - >seq2848,non-specific,223780,99,215,6.07145e-06,49.1339,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7388,Q#2849 - >seq2848,non-specific,197307,96,226,5.3084399999999996e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7389,Q#2849 - >seq2848,non-specific,273186,99,227,0.00021689700000000002,44.192,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7390,Q#2849 - >seq2848,non-specific,238828,578,717,0.000813068,42.1881,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7391,Q#2849 - >seq2848,specific,335306,102,219,0.0008621939999999999,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7392,Q#2849 - >seq2848,non-specific,197321,101,226,0.00169338,41.3836,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7393,Q#2849 - >seq2848,non-specific,197319,96,226,0.00219262,41.1081,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB7.ORF2.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7394,Q#2854 - >seq2853,non-specific,340205,157,218,9.42583e-19,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs2_gorilla,pars,CompleteHit
7395,Q#2854 - >seq2853,superfamily,340205,157,218,9.42583e-19,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs2_gorilla,pars,CompleteHit
7396,Q#2854 - >seq2853,non-specific,335182,83,154,7.45439e-14,64.6315,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
7397,Q#2854 - >seq2853,superfamily,335182,83,154,7.45439e-14,64.6315,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs2_gorilla.pars.frame2,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
7398,Q#2856 - >seq2855,non-specific,197310,9,84,7.10895e-11,63.5245,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs2_gorilla.pars.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
7399,Q#2856 - >seq2855,superfamily,351117,9,84,7.10895e-11,63.5245,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.pars.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
7400,Q#2856 - >seq2855,non-specific,197306,9,113,1.11929e-05,47.8613,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs2_gorilla.pars.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
7401,Q#2856 - >seq2855,non-specific,223780,7,81,0.00548036,39.8891,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs2_gorilla.pars.frame3,1909130215_L1MB7.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
7402,Q#2857 - >seq2856,non-specific,197310,5,136,7.55047e-23,98.5776,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7403,Q#2857 - >seq2856,superfamily,351117,5,136,7.55047e-23,98.5776,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7404,Q#2857 - >seq2856,non-specific,197306,9,137,1.18916e-06,50.9429,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7405,Q#2857 - >seq2856,non-specific,197320,17,135,8.244360000000001e-05,45.1986,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7406,Q#2857 - >seq2856,non-specific,223780,6,163,0.00010410700000000001,45.2819,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7407,Q#2857 - >seq2856,non-specific,197307,6,139,0.000595432,42.6601,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7408,Q#2857 - >seq2856,non-specific,197311,27,135,0.00242325,40.3529,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs3_orang.marg.frame2,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs3_orang,marg,C-TerminusTruncated
7409,Q#2858 - >seq2857,non-specific,197310,150,209,3.0057300000000003e-07,52.7389,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs3_orang.marg.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB7,ORF2,hs3_orang,marg,N-TerminusTruncated
7410,Q#2858 - >seq2857,superfamily,351117,150,209,3.0057300000000003e-07,52.7389,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs3_orang.marg.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,marg,N-TerminusTruncated
7411,Q#2859 - >seq2858,specific,238827,451,675,3.7275599999999997e-34,130.489,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs3_orang.marg.frame3,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs3_orang,marg,CompleteHit
7412,Q#2859 - >seq2858,superfamily,295487,451,675,3.7275599999999997e-34,130.489,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs3_orang.marg.frame3,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs3_orang,marg,CompleteHit
7413,Q#2859 - >seq2858,non-specific,333820,456,675,1.2905900000000001e-15,76.17699999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs3_orang.marg.frame3,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs3_orang,marg,CompleteHit
7414,Q#2859 - >seq2858,superfamily,333820,456,675,1.2905900000000001e-15,76.17699999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs3_orang.marg.frame3,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs3_orang,marg,CompleteHit
7415,Q#2859 - >seq2858,non-specific,238828,525,650,0.000237767,43.7289,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs3_orang.marg.frame3,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs3_orang,marg,N-TerminusTruncated
7416,Q#2861 - >seq2860,specific,238827,487,711,3.5769299999999996e-33,127.79299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7417,Q#2861 - >seq2860,superfamily,295487,487,711,3.5769299999999996e-33,127.79299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7418,Q#2861 - >seq2860,non-specific,197310,24,220,1.77798e-24,103.2,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7419,Q#2861 - >seq2860,superfamily,351117,24,220,1.77798e-24,103.2,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7420,Q#2861 - >seq2860,non-specific,333820,492,711,3.11227e-15,75.0214,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7421,Q#2861 - >seq2860,superfamily,333820,492,711,3.11227e-15,75.0214,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7422,Q#2861 - >seq2860,non-specific,197306,2,220,8.43933e-10,60.1877,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7423,Q#2861 - >seq2860,non-specific,238828,561,686,0.0005598959999999999,42.5733,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs3_orang,pars,N-TerminusTruncated
7424,Q#2861 - >seq2860,non-specific,197320,99,145,0.000815203,42.5022,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB7,ORF2,hs3_orang,pars,BothTerminiTruncated
7425,Q#2861 - >seq2860,specific,335306,26,213,0.00157118,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs3_orang,pars,CompleteHit
7426,Q#2861 - >seq2860,non-specific,197311,30,138,0.00250382,40.3529,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs3_orang,pars,C-TerminusTruncated
7427,Q#2861 - >seq2860,non-specific,197307,99,213,0.00390133,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB7,ORF2,hs3_orang,pars,N-TerminusTruncated
7428,Q#2861 - >seq2860,non-specific,274009,316,436,0.00531386,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB7,ORF2,hs3_orang,pars,BothTerminiTruncated
7429,Q#2861 - >seq2860,superfamily,274009,316,436,0.00531386,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs3_orang.pars.frame1,1909130216_L1MB7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MB7,ORF2,hs3_orang,pars,BothTerminiTruncated
7430,Q#2863 - >seq2862,non-specific,340205,158,226,1.60562e-07,46.9456,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs5_gmonkey,marg,CompleteHit
7431,Q#2863 - >seq2862,superfamily,340205,158,226,1.60562e-07,46.9456,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs5_gmonkey,marg,CompleteHit
7432,Q#2863 - >seq2862,non-specific,340204,21,63,0.000776526,36.2316,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MB7,ORF1,hs5_gmonkey,marg,CompleteHit
7433,Q#2863 - >seq2862,superfamily,340204,21,63,0.000776526,36.2316,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MB7,ORF1,hs5_gmonkey,marg,CompleteHit
7434,Q#2864 - >seq2863,non-specific,238827,524,688,4.98645e-17,81.1834,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs5_gmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7435,Q#2864 - >seq2863,superfamily,295487,524,688,4.98645e-17,81.1834,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs5_gmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7436,Q#2864 - >seq2863,non-specific,333820,533,680,3.05804e-08,54.6058,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7437,Q#2864 - >seq2863,superfamily,333820,533,680,3.05804e-08,54.6058,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7438,Q#2864 - >seq2863,non-specific,238828,528,692,0.00134799,41.4177,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs5_gmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7439,Q#2865 - >seq2864,non-specific,238827,477,536,1.60536e-17,82.7242,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs5_gmonkey.pars.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7440,Q#2865 - >seq2864,superfamily,295487,477,536,1.60536e-17,82.7242,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs5_gmonkey.pars.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7441,Q#2865 - >seq2864,non-specific,333820,483,552,8.427819999999999e-07,50.3686,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.pars.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7442,Q#2865 - >seq2864,superfamily,333820,483,552,8.427819999999999e-07,50.3686,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.pars.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7443,Q#2866 - >seq2865,non-specific,197310,40,235,1.4757499999999998e-24,103.585,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs5_gmonkey,pars,CompleteHit
7444,Q#2866 - >seq2865,superfamily,351117,40,235,1.4757499999999998e-24,103.585,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,CompleteHit
7445,Q#2866 - >seq2865,non-specific,197306,46,235,1.0942000000000001e-10,62.8841,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,CompleteHit
7446,Q#2866 - >seq2865,non-specific,197307,50,235,1.9743200000000002e-07,53.4457,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,CompleteHit
7447,Q#2866 - >seq2865,non-specific,197320,123,228,1.13301e-06,50.9766,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7448,Q#2866 - >seq2865,non-specific,197321,121,235,6.10017e-05,46.006,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7449,Q#2866 - >seq2865,specific,335306,130,228,0.00010051899999999999,44.9286,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7450,Q#2866 - >seq2865,non-specific,223780,139,228,0.000102541,45.2819,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7451,Q#2866 - >seq2865,non-specific,197319,121,235,0.000573587,43.0341,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB7.ORF2.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7452,Q#2867 - >seq2866,non-specific,238827,544,708,2.5245700000000004e-17,81.9538,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs5_gmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7453,Q#2867 - >seq2866,superfamily,295487,544,708,2.5245700000000004e-17,81.9538,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs5_gmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7454,Q#2867 - >seq2866,non-specific,333820,553,700,2.06362e-08,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7455,Q#2867 - >seq2866,superfamily,333820,553,700,2.06362e-08,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7456,Q#2867 - >seq2866,non-specific,238828,548,712,0.00136698,41.4177,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs5_gmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7457,Q#2868 - >seq2867,specific,197310,9,254,3.78129e-27,110.904,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs5_gmonkey,marg,CompleteHit
7458,Q#2868 - >seq2867,superfamily,351117,9,254,3.78129e-27,110.904,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,CompleteHit
7459,Q#2868 - >seq2867,non-specific,238827,529,588,2.93354e-17,81.9538,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7460,Q#2868 - >seq2867,superfamily,295487,529,588,2.93354e-17,81.9538,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7461,Q#2868 - >seq2867,non-specific,197306,9,254,1.06324e-12,69.0473,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,CompleteHit
7462,Q#2868 - >seq2867,non-specific,197307,9,254,8.45641e-08,54.6013,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,CompleteHit
7463,Q#2868 - >seq2867,non-specific,333820,535,604,1.14116e-06,49.9834,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7464,Q#2868 - >seq2867,superfamily,333820,535,604,1.14116e-06,49.9834,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
7465,Q#2868 - >seq2867,non-specific,197320,148,247,1.2247e-06,50.9766,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7466,Q#2868 - >seq2867,specific,335306,145,247,3.92919e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7467,Q#2868 - >seq2867,non-specific,223780,158,247,0.00020757799999999998,44.1263,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7468,Q#2868 - >seq2867,non-specific,197321,158,254,0.00042151,43.3096,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7469,Q#2868 - >seq2867,non-specific,197319,137,254,0.00875756,39.1821,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB7.ORF2.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7470,Q#2872 - >seq2871,non-specific,340205,176,243,2.8603e-17,73.9096,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs6_sqmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,marg,CompleteHit
7471,Q#2872 - >seq2871,superfamily,340205,176,243,2.8603e-17,73.9096,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs6_sqmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,marg,CompleteHit
7472,Q#2872 - >seq2871,non-specific,335182,89,141,1.4669200000000001e-09,53.8459,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs6_sqmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
7473,Q#2872 - >seq2871,superfamily,335182,89,141,1.4669200000000001e-09,53.8459,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs6_sqmonkey.marg.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
7474,Q#2874 - >seq2873,non-specific,335182,78,115,0.00037438,38.4379,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
7475,Q#2874 - >seq2873,superfamily,335182,78,115,0.00037438,38.4379,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs5_gmonkey.marg.frame2,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
7476,Q#2875 - >seq2874,non-specific,340205,138,205,2.3014799999999998e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs6_sqmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,pars,CompleteHit
7477,Q#2875 - >seq2874,superfamily,340205,138,205,2.3014799999999998e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs6_sqmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,pars,CompleteHit
7478,Q#2875 - >seq2874,non-specific,335182,51,103,2.12556e-10,55.7719,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs6_sqmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
7479,Q#2875 - >seq2874,superfamily,335182,51,103,2.12556e-10,55.7719,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs6_sqmonkey.pars.frame1,1909130217_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
7480,Q#2879 - >seq2878,non-specific,335182,32,75,0.00922696,33.8155,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
7481,Q#2879 - >seq2878,superfamily,335182,32,75,0.00922696,33.8155,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs5_gmonkey.pars.frame3,1909130217_L1MB7.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
7482,Q#2880 - >seq2879,non-specific,340205,178,239,8.48499e-18,74.68,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,CompleteHit
7483,Q#2880 - >seq2879,superfamily,340205,178,239,8.48499e-18,74.68,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,CompleteHit
7484,Q#2880 - >seq2879,non-specific,335182,126,174,0.00010345100000000001,39.9787,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7485,Q#2880 - >seq2879,superfamily,335182,126,174,0.00010345100000000001,39.9787,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
7486,Q#2881 - >seq2880,non-specific,335182,85,136,0.00259034,36.1267,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
7487,Q#2881 - >seq2880,superfamily,335182,85,136,0.00259034,36.1267,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
7488,Q#2884 - >seq2883,non-specific,335182,96,183,2.21967e-15,69.2539,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.marg.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,marg,CompleteHit
7489,Q#2884 - >seq2883,superfamily,335182,96,183,2.21967e-15,69.2539,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs4_gibbon.marg.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,marg,CompleteHit
7490,Q#2884 - >seq2883,non-specific,340205,195,241,9.20666e-11,55.8052,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs4_gibbon.marg.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7491,Q#2884 - >seq2883,superfamily,340205,195,241,9.20666e-11,55.8052,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs4_gibbon.marg.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7492,Q#2886 - >seq2885,non-specific,197310,18,81,0.0007858769999999999,42.3385,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7493,Q#2886 - >seq2885,superfamily,351117,18,81,0.0007858769999999999,42.3385,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs4_gibbon.pars.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7494,Q#2887 - >seq2886,non-specific,197310,93,222,1.69857e-21,94.7257,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7495,Q#2887 - >seq2886,superfamily,351117,93,222,1.69857e-21,94.7257,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7496,Q#2887 - >seq2886,non-specific,197320,95,207,1.44904e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7497,Q#2887 - >seq2886,non-specific,197306,89,222,1.01124e-06,50.9429,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7498,Q#2887 - >seq2886,non-specific,235175,292,454,6.33722e-06,50.4476,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
7499,Q#2887 - >seq2886,superfamily,235175,292,454,6.33722e-06,50.4476,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
7500,Q#2887 - >seq2886,non-specific,274009,306,444,1.22409e-05,49.6811,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7501,Q#2887 - >seq2886,superfamily,274009,306,444,1.22409e-05,49.6811,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7502,Q#2887 - >seq2886,non-specific,223780,95,207,3.0979099999999996e-05,46.8227,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7503,Q#2887 - >seq2886,specific,335306,122,215,0.000251177,43.773,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7504,Q#2887 - >seq2886,non-specific,235175,268,454,0.00213937,41.9732,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7505,Q#2887 - >seq2886,non-specific,197307,95,215,0.00313679,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7506,Q#2887 - >seq2886,non-specific,197322,126,208,0.00869709,39.6078,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs4_gibbon.pars.frame3,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7507,Q#2889 - >seq2888,specific,197310,18,232,2.8204700000000002e-30,120.149,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7508,Q#2889 - >seq2888,superfamily,351117,18,232,2.8204700000000002e-30,120.149,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7509,Q#2889 - >seq2888,specific,238827,501,755,1.56379e-26,108.91799999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7510,Q#2889 - >seq2888,superfamily,295487,501,755,1.56379e-26,108.91799999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7511,Q#2889 - >seq2888,non-specific,333820,507,728,4.1800800000000003e-16,77.7178,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7512,Q#2889 - >seq2888,superfamily,333820,507,728,4.1800800000000003e-16,77.7178,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7513,Q#2889 - >seq2888,non-specific,197306,19,232,6.80524e-09,57.8765,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7514,Q#2889 - >seq2888,non-specific,197320,105,217,1.03546e-08,57.525,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7515,Q#2889 - >seq2888,non-specific,223780,22,217,3.896040000000001e-06,49.5191,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7516,Q#2889 - >seq2888,non-specific,274009,316,494,2.9213699999999998e-05,48.5255,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB7,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7517,Q#2889 - >seq2888,superfamily,274009,316,494,2.9213699999999998e-05,48.5255,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB7,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7518,Q#2889 - >seq2888,non-specific,238828,575,711,5.6080200000000006e-05,45.6549,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7519,Q#2889 - >seq2888,non-specific,273186,94,233,7.55826e-05,45.7328,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7520,Q#2889 - >seq2888,specific,335306,22,225,0.00198792,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs4_gibbon.marg.frame2,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs4_gibbon,marg,CompleteHit
7521,Q#2892 - >seq2891,specific,238827,445,699,8.54928e-27,109.303,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs4_gibbon.pars.frame1,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs4_gibbon,pars,CompleteHit
7522,Q#2892 - >seq2891,superfamily,295487,445,699,8.54928e-27,109.303,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs4_gibbon.pars.frame1,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs4_gibbon,pars,CompleteHit
7523,Q#2892 - >seq2891,non-specific,333820,451,672,4.48676e-16,77.3326,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs4_gibbon.pars.frame1,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs4_gibbon,pars,CompleteHit
7524,Q#2892 - >seq2891,superfamily,333820,451,672,4.48676e-16,77.3326,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs4_gibbon.pars.frame1,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs4_gibbon,pars,CompleteHit
7525,Q#2892 - >seq2891,non-specific,238828,519,655,2.8957600000000002e-05,46.4253,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs4_gibbon.pars.frame1,1909130217_L1MB7.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7526,Q#2893 - >seq2892,non-specific,238827,472,668,7.24321e-15,75.0202,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs6_sqmonkey.marg.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7527,Q#2893 - >seq2892,superfamily,295487,472,668,7.24321e-15,75.0202,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs6_sqmonkey.marg.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7528,Q#2893 - >seq2892,non-specific,333820,478,667,5.9832e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs6_sqmonkey.marg.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7529,Q#2893 - >seq2892,superfamily,333820,478,667,5.9832e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs6_sqmonkey.marg.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
7530,Q#2894 - >seq2893,non-specific,197310,8,225,4.63404e-24,102.044,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs6_sqmonkey.marg.frame2,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs6_sqmonkey,marg,CompleteHit
7531,Q#2894 - >seq2893,superfamily,351117,8,225,4.63404e-24,102.044,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs6_sqmonkey.marg.frame2,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs6_sqmonkey,marg,CompleteHit
7532,Q#2894 - >seq2893,non-specific,197306,6,225,7.283209999999999e-10,60.5729,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs6_sqmonkey.marg.frame2,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs6_sqmonkey,marg,CompleteHit
7533,Q#2896 - >seq2895,non-specific,197310,7,237,2.2412200000000005e-24,102.815,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs6_sqmonkey.pars.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs6_sqmonkey,pars,CompleteHit
7534,Q#2896 - >seq2895,superfamily,351117,7,237,2.2412200000000005e-24,102.815,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs6_sqmonkey.pars.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs6_sqmonkey,pars,CompleteHit
7535,Q#2896 - >seq2895,non-specific,197306,5,237,6.39617e-10,60.5729,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs6_sqmonkey.pars.frame3,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs6_sqmonkey,pars,CompleteHit
7536,Q#2897 - >seq2896,non-specific,238827,483,688,1.9983700000000003e-14,73.4794,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs6_sqmonkey.pars.frame1,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7537,Q#2897 - >seq2896,superfamily,295487,483,688,1.9983700000000003e-14,73.4794,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs6_sqmonkey.pars.frame1,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7538,Q#2897 - >seq2896,non-specific,333820,489,687,7.32158e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs6_sqmonkey.pars.frame1,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7539,Q#2897 - >seq2896,superfamily,333820,489,687,7.32158e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs6_sqmonkey.pars.frame1,1909130218_L1MB7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
7540,Q#2899 - >seq2898,non-specific,238827,448,661,4.8017899999999996e-26,107.37700000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs7_bushaby.pars.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,pars,C-TerminusTruncated
7541,Q#2899 - >seq2898,superfamily,295487,448,661,4.8017899999999996e-26,107.37700000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs7_bushaby.pars.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,pars,C-TerminusTruncated
7542,Q#2899 - >seq2898,non-specific,333820,465,653,5.0899e-14,71.5546,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs7_bushaby.pars.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,pars,CompleteHit
7543,Q#2899 - >seq2898,superfamily,333820,465,653,5.0899e-14,71.5546,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs7_bushaby.pars.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,pars,CompleteHit
7544,Q#2899 - >seq2898,non-specific,238828,519,683,2.25574e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs7_bushaby.pars.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7545,Q#2900 - >seq2899,specific,197310,4,237,4.1827599999999997e-38,142.49,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7546,Q#2900 - >seq2899,superfamily,351117,4,237,4.1827599999999997e-38,142.49,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7547,Q#2900 - >seq2899,non-specific,197306,4,237,1.07053e-14,74.8252,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7548,Q#2900 - >seq2899,non-specific,197320,108,222,1.4455e-11,65.9994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7549,Q#2900 - >seq2899,non-specific,223780,108,222,5.50229e-09,58.3787,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7550,Q#2900 - >seq2899,non-specific,197307,4,230,2.0006499999999999e-07,53.4457,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7551,Q#2900 - >seq2899,non-specific,197319,108,237,6.8858e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7552,Q#2900 - >seq2899,specific,335306,5,230,7.46372e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7553,Q#2900 - >seq2899,non-specific,273186,108,238,0.00016994,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7554,Q#2900 - >seq2899,non-specific,197311,104,205,0.000307805,43.0493,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7555,Q#2900 - >seq2899,non-specific,339261,110,232,0.0005618180000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7556,Q#2900 - >seq2899,non-specific,272954,4,208,0.00072184,42.3701,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7557,Q#2900 - >seq2899,non-specific,197321,4,230,0.00116127,41.7688,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,CompleteHit
7558,Q#2900 - >seq2899,non-specific,197322,109,223,0.00195062,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs7_bushaby.marg.frame3,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7559,Q#2901 - >seq2900,non-specific,238827,516,664,2.39821e-13,70.3978,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs7_bushaby.marg.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7560,Q#2901 - >seq2900,superfamily,295487,516,664,2.39821e-13,70.3978,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs7_bushaby.marg.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7561,Q#2901 - >seq2900,non-specific,333820,531,656,6.720910000000001e-08,53.4502,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs7_bushaby.marg.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7562,Q#2901 - >seq2900,superfamily,333820,531,656,6.720910000000001e-08,53.4502,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs7_bushaby.marg.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7563,Q#2901 - >seq2900,non-specific,238828,522,686,1.23368e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs7_bushaby.marg.frame2,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7564,Q#2902 - >seq2901,non-specific,238827,466,516,2.6185999999999996e-09,58.4566,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs7_bushaby,marg,C-TerminusTruncated
7565,Q#2902 - >seq2901,superfamily,295487,466,516,2.6185999999999996e-09,58.4566,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs7_bushaby,marg,C-TerminusTruncated
7566,Q#2904 - >seq2903,non-specific,197310,42,176,2.7479199999999998e-09,58.5169,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs7_bushaby.pars.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7567,Q#2904 - >seq2903,superfamily,351117,42,176,2.7479199999999998e-09,58.5169,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs7_bushaby.pars.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7568,Q#2906 - >seq2905,non-specific,340205,182,255,1.2500500000000002e-08,50.4124,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,marg,CompleteHit
7569,Q#2906 - >seq2905,superfamily,340205,182,255,1.2500500000000002e-08,50.4124,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,marg,CompleteHit
7570,Q#2906 - >seq2905,non-specific,335182,67,165,6.72707e-06,43.4455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,marg,CompleteHit
7571,Q#2906 - >seq2905,superfamily,335182,67,165,6.72707e-06,43.4455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs7_bushaby.marg.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,marg,CompleteHit
7572,Q#2909 - >seq2908,non-specific,340205,76,127,2.0740700000000003e-12,58.1164,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs7_bushaby.pars.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,pars,CompleteHit
7573,Q#2909 - >seq2908,superfamily,340205,76,127,2.0740700000000003e-12,58.1164,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs7_bushaby.pars.frame1,1909130219_L1MB7.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs7_bushaby,pars,CompleteHit
7574,Q#2911 - >seq2910,specific,238827,443,700,1.3580299999999997e-48,172.09,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7575,Q#2911 - >seq2910,superfamily,295487,443,700,1.3580299999999997e-48,172.09,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7576,Q#2911 - >seq2910,non-specific,333820,449,700,1.94522e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7577,Q#2911 - >seq2910,superfamily,333820,449,700,1.94522e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7578,Q#2911 - >seq2910,non-specific,238828,496,652,8.26149e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7579,Q#2911 - >seq2910,non-specific,275209,518,602,1.51254e-06,51.6896,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,BothTerminiTruncated
7580,Q#2911 - >seq2910,superfamily,275209,518,602,1.51254e-06,51.6896,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,BothTerminiTruncated
7581,Q#2911 - >seq2910,non-specific,238185,587,700,0.000166689,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7582,Q#2912 - >seq2911,non-specific,197310,143,200,9.672110000000001e-07,51.1981,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7583,Q#2912 - >seq2911,superfamily,351117,143,200,9.672110000000001e-07,51.1981,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7584,Q#2912 - >seq2911,non-specific,274009,227,375,0.000361221,44.6735,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7585,Q#2912 - >seq2911,superfamily,274009,227,375,0.000361221,44.6735,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7586,Q#2912 - >seq2911,non-specific,224117,214,452,0.00196873,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7587,Q#2912 - >seq2911,superfamily,224117,214,452,0.00196873,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7588,Q#2912 - >seq2911,non-specific,223496,263,376,0.0024936999999999997,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MB7,ORF2,hs9_pika,pars,BothTerminiTruncated
7589,Q#2912 - >seq2911,superfamily,223496,263,376,0.0024936999999999997,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MB7,ORF2,hs9_pika,pars,BothTerminiTruncated
7590,Q#2912 - >seq2911,non-specific,224117,197,348,0.00251623,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs9_pika,pars,N-TerminusTruncated
7591,Q#2912 - >seq2911,non-specific,224117,226,378,0.00677104,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB7,ORF2,hs9_pika,pars,C-TerminusTruncated
7592,Q#2913 - >seq2912,non-specific,197310,72,236,1.30754e-19,88.9477,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7593,Q#2913 - >seq2912,superfamily,351117,72,236,1.30754e-19,88.9477,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7594,Q#2913 - >seq2912,non-specific,197306,63,236,4.0439099999999994e-08,55.1801,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7595,Q#2913 - >seq2912,non-specific,235175,262,462,7.14161e-07,53.5291,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7596,Q#2913 - >seq2912,superfamily,235175,262,462,7.14161e-07,53.5291,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7597,Q#2913 - >seq2912,non-specific,223496,299,456,5.7129799999999996e-05,47.4475,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7598,Q#2913 - >seq2912,superfamily,223496,299,456,5.7129799999999996e-05,47.4475,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7599,Q#2913 - >seq2912,non-specific,274009,288,457,9.313319999999999e-05,46.5995,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7600,Q#2913 - >seq2912,superfamily,274009,288,457,9.313319999999999e-05,46.5995,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7601,Q#2913 - >seq2912,non-specific,224117,250,461,9.503139999999999e-05,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7602,Q#2913 - >seq2912,superfamily,224117,250,461,9.503139999999999e-05,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7603,Q#2913 - >seq2912,non-specific,224117,262,462,0.00010255,46.6312,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7604,Q#2913 - >seq2912,non-specific,224117,293,461,0.000113508,46.246,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7605,Q#2913 - >seq2912,non-specific,224259,262,504,0.000388929,43.5164,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7606,Q#2913 - >seq2912,superfamily,224259,262,504,0.000388929,43.5164,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7607,Q#2913 - >seq2912,non-specific,274009,320,457,0.00039236699999999997,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7608,Q#2913 - >seq2912,non-specific,225288,290,462,0.00044655300000000003,44.31,COG2433,COG2433,N,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7609,Q#2913 - >seq2912,superfamily,331991,290,462,0.00044655300000000003,44.31,cl27170,DUF460 superfamily,N, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7610,Q#2913 - >seq2912,non-specific,274009,263,448,0.00057413,43.9031,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7611,Q#2913 - >seq2912,non-specific,308206,297,455,0.00103133,43.4221,pfam02463,SMC_N,C,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7612,Q#2913 - >seq2912,superfamily,308206,297,455,0.00103133,43.4221,cl37666,SMC_N superfamily,C, - ,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7613,Q#2913 - >seq2912,non-specific,308206,315,461,0.00137497,43.0369,pfam02463,SMC_N,C,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7614,Q#2913 - >seq2912,non-specific,308206,250,462,0.00167024,42.6517,pfam02463,SMC_N,NC,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7615,Q#2913 - >seq2912,non-specific,197320,173,229,0.00197476,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7616,Q#2913 - >seq2912,non-specific,224117,233,384,0.00199724,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7617,Q#2913 - >seq2912,non-specific,224117,319,456,0.00304854,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,C-TerminusTruncated
7618,Q#2913 - >seq2912,non-specific,274008,217,475,0.00354283,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7619,Q#2913 - >seq2912,superfamily,274008,217,475,0.00354283,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7620,Q#2913 - >seq2912,non-specific,223496,248,457,0.00406571,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7621,Q#2913 - >seq2912,non-specific,223780,71,229,0.00564182,39.8891,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7622,Q#2914 - >seq2913,specific,238827,469,701,7.165239999999998e-49,172.861,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7623,Q#2914 - >seq2913,superfamily,295487,469,701,7.165239999999998e-49,172.861,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7624,Q#2914 - >seq2913,non-specific,333820,475,683,8.42433e-25,102.37100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7625,Q#2914 - >seq2913,superfamily,333820,475,683,8.42433e-25,102.37100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,CompleteHit
7626,Q#2914 - >seq2913,non-specific,238828,522,681,4.65334e-13,69.5372,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,N-TerminusTruncated
7627,Q#2914 - >seq2913,non-specific,275209,544,681,3.73705e-07,53.6156,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7628,Q#2914 - >seq2913,superfamily,275209,544,681,3.73705e-07,53.6156,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs9_pika.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB7,ORF2,hs9_pika,marg,BothTerminiTruncated
7629,Q#2916 - >seq2915,non-specific,238827,471,535,0.0024088,40.3522,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs11_armadillo.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs11_armadillo,pars,BothTerminiTruncated
7630,Q#2916 - >seq2915,superfamily,295487,471,535,0.0024088,40.3522,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs11_armadillo.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs11_armadillo,pars,BothTerminiTruncated
7631,Q#2917 - >seq2916,non-specific,197310,60,115,5.1156e-13,69.6877,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7632,Q#2917 - >seq2916,superfamily,351117,60,115,5.1156e-13,69.6877,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7633,Q#2917 - >seq2916,non-specific,197320,61,114,5.23342e-05,45.5838,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7634,Q#2917 - >seq2916,non-specific,223780,61,114,0.000409224,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7635,Q#2917 - >seq2916,non-specific,197306,58,114,0.00079903,42.0833,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7636,Q#2917 - >seq2916,non-specific,197307,61,114,0.00317768,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs11_armadillo.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs11_armadillo,pars,N-TerminusTruncated
7637,Q#2918 - >seq2917,non-specific,238827,361,415,0.000274043,43.0486,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs11_armadillo.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs11_armadillo,pars,C-TerminusTruncated
7638,Q#2918 - >seq2917,superfamily,295487,361,415,0.000274043,43.0486,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs11_armadillo.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs11_armadillo,pars,C-TerminusTruncated
7639,Q#2921 - >seq2920,non-specific,340205,143,205,4.58293e-22,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs0_human.pars.frame1,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs0_human,pars,CompleteHit
7640,Q#2921 - >seq2920,superfamily,340205,143,205,4.58293e-22,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs0_human.pars.frame1,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs0_human,pars,CompleteHit
7641,Q#2921 - >seq2920,non-specific,335182,71,140,3.82182e-05,41.1343,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs0_human.pars.frame1,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs0_human,pars,N-TerminusTruncated
7642,Q#2921 - >seq2920,superfamily,335182,71,140,3.82182e-05,41.1343,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs0_human.pars.frame1,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs0_human,pars,N-TerminusTruncated
7643,Q#2926 - >seq2925,non-specific,340205,219,281,4.40882e-22,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs0_human.marg.frame3,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs0_human,marg,CompleteHit
7644,Q#2926 - >seq2925,superfamily,340205,219,281,4.40882e-22,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs0_human.marg.frame3,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs0_human,marg,CompleteHit
7645,Q#2926 - >seq2925,non-specific,335182,123,216,1.4919999999999999e-06,45.7567,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs0_human.marg.frame3,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs0_human,marg,CompleteHit
7646,Q#2926 - >seq2925,superfamily,335182,123,216,1.4919999999999999e-06,45.7567,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs0_human.marg.frame3,1909130220_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB7,ORF1,hs0_human,marg,CompleteHit
7647,Q#2927 - >seq2926,non-specific,197310,57,205,2.7901e-15,76.6213,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB7,ORF2,hs11_armadillo,marg,N-TerminusTruncated
7648,Q#2927 - >seq2926,superfamily,351117,57,205,2.7901e-15,76.6213,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs11_armadillo,marg,N-TerminusTruncated
7649,Q#2927 - >seq2926,non-specific,238827,494,772,2.46447e-11,64.6198,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs11_armadillo,marg,CompleteHit
7650,Q#2927 - >seq2926,superfamily,295487,494,772,2.46447e-11,64.6198,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB7,ORF2,hs11_armadillo,marg,CompleteHit
7651,Q#2927 - >seq2926,non-specific,340095,297,440,0.0008075539999999999,43.6628,pfam17380,DUF5401,N,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs11_armadillo,marg,N-TerminusTruncated
7652,Q#2927 - >seq2926,superfamily,340095,297,440,0.0008075539999999999,43.6628,cl38662,DUF5401 superfamily,N, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB7,ORF2,hs11_armadillo,marg,N-TerminusTruncated
7653,Q#2927 - >seq2926,non-specific,197320,148,204,0.00426375,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs11_armadillo.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB7,ORF2,hs11_armadillo,marg,N-TerminusTruncated
7654,Q#2928 - >seq2927,non-specific,197310,7,171,1.9826300000000002e-10,61.9837,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs9_pika.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7655,Q#2928 - >seq2927,superfamily,351117,7,171,1.9826300000000002e-10,61.9837,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs9_pika.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7656,Q#2928 - >seq2927,non-specific,197306,7,171,0.00131363,41.6981,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs9_pika.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs9_pika,pars,CompleteHit
7657,Q#2931 - >seq2930,non-specific,340205,96,128,2.70038e-09,49.641999999999996,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
7658,Q#2931 - >seq2930,superfamily,340205,96,128,2.70038e-09,49.641999999999996,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
7659,Q#2931 - >seq2930,non-specific,335182,14,93,0.00035060699999999996,36.8971,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs8_ctshrew,pars,CompleteHit
7660,Q#2931 - >seq2930,superfamily,335182,14,93,0.00035060699999999996,36.8971,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB7,ORF1,hs8_ctshrew,pars,CompleteHit
7661,Q#2936 - >seq2935,specific,197310,5,217,1.71351e-34,132.09,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7662,Q#2936 - >seq2935,superfamily,351117,5,217,1.71351e-34,132.09,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7663,Q#2936 - >seq2935,non-specific,238827,530,681,3.90646e-21,93.1246,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
7664,Q#2936 - >seq2935,superfamily,295487,530,681,3.90646e-21,93.1246,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
7665,Q#2936 - >seq2935,non-specific,197306,5,217,1.55943e-14,74.44,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7666,Q#2936 - >seq2935,non-specific,333820,544,684,4.91129e-13,68.473,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7667,Q#2936 - >seq2935,superfamily,333820,544,684,4.91129e-13,68.473,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7668,Q#2936 - >seq2935,non-specific,197320,5,210,1.17972e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7669,Q#2936 - >seq2935,non-specific,238828,535,684,3.12204e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7670,Q#2936 - >seq2935,non-specific,223780,5,210,9.501539999999999e-08,54.5267,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7671,Q#2936 - >seq2935,non-specific,273186,5,218,1.17554e-06,51.1256,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7672,Q#2936 - >seq2935,non-specific,197307,5,210,1.32672e-06,50.7493,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7673,Q#2936 - >seq2935,specific,335306,6,210,6.35732e-06,48.3954,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7674,Q#2936 - >seq2935,non-specific,197322,72,210,1.6837e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7675,Q#2936 - >seq2935,non-specific,272954,5,188,0.000234787,43.9109,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7676,Q#2936 - >seq2935,non-specific,275209,540,747,0.000579358,43.2152,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7677,Q#2936 - >seq2935,superfamily,275209,540,747,0.000579358,43.2152,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB7,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7678,Q#2936 - >seq2935,non-specific,339261,89,212,0.000713981,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB7.ORF2.hs8_ctshrew.pars.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB7,ORF2,hs8_ctshrew,pars,CompleteHit
7679,Q#2938 - >seq2937,non-specific,340205,160,192,3.34699e-09,50.7976,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
7680,Q#2938 - >seq2937,superfamily,340205,160,192,3.34699e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
7681,Q#2938 - >seq2937,non-specific,335182,98,157,0.00036591900000000003,38.0527,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
7682,Q#2938 - >seq2937,superfamily,335182,98,157,0.00036591900000000003,38.0527,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB7,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
7683,Q#2940 - >seq2939,specific,197310,11,229,4.371689999999999e-33,128.238,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7684,Q#2940 - >seq2939,superfamily,351117,11,229,4.371689999999999e-33,128.238,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7685,Q#2940 - >seq2939,non-specific,197306,11,229,3.867519999999999e-15,76.366,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7686,Q#2940 - >seq2939,non-specific,197320,9,222,1.5597e-10,62.9178,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7687,Q#2940 - >seq2939,non-specific,223780,9,222,3.67361e-09,58.7639,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7688,Q#2940 - >seq2939,non-specific,273186,9,230,4.76918e-07,52.2812,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7689,Q#2940 - >seq2939,specific,335306,12,222,1.3006799999999998e-06,50.7066,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7690,Q#2940 - >seq2939,non-specific,197307,11,222,3.7184600000000002e-06,49.5937,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7691,Q#2940 - >seq2939,non-specific,272954,9,200,1.27295e-05,47.7629,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7692,Q#2940 - >seq2939,non-specific,197322,84,222,1.68531e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7693,Q#2940 - >seq2939,non-specific,339261,101,224,0.00238819,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB7.ORF2.hs8_ctshrew.marg.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7694,Q#2941 - >seq2940,specific,238827,461,679,1.7686199999999997e-29,117.39200000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7695,Q#2941 - >seq2940,superfamily,295487,461,679,1.7686199999999997e-29,117.39200000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7696,Q#2941 - >seq2940,non-specific,333820,467,682,4.54718e-16,77.3326,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7697,Q#2941 - >seq2940,superfamily,333820,467,682,4.54718e-16,77.3326,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,CompleteHit
7698,Q#2941 - >seq2940,non-specific,238828,537,682,2.70344e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7699,Q#2941 - >seq2940,non-specific,275209,542,745,7.3835699999999995e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7700,Q#2941 - >seq2940,superfamily,275209,542,745,7.3835699999999995e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB7.ORF2.hs8_ctshrew.marg.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7701,Q#2943 - >seq2942,non-specific,335182,28,94,2.96044e-07,45.7567,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs9_pika,pars,N-TerminusTruncated
7702,Q#2943 - >seq2942,superfamily,335182,28,94,2.96044e-07,45.7567,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs9_pika.pars.frame2,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB7,ORF1,hs9_pika,pars,N-TerminusTruncated
7703,Q#2945 - >seq2944,non-specific,335182,42,90,4.07666e-07,46.1419,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs9_pika,marg,BothTerminiTruncated
7704,Q#2945 - >seq2944,superfamily,335182,42,90,4.07666e-07,46.1419,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB7.ORF1.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs9_pika,marg,BothTerminiTruncated
7705,Q#2945 - >seq2944,non-specific,340205,140,196,3.72978e-06,42.7084,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs9_pika,marg,N-TerminusTruncated
7706,Q#2945 - >seq2944,superfamily,340205,140,196,3.72978e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB7.ORF1.hs9_pika.marg.frame1,1909130220_L1MB7.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB7,ORF1,hs9_pika,marg,N-TerminusTruncated
7707,Q#2946 - >seq2945,non-specific,238827,456,513,0.00024545,43.4338,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs8_ctshrew.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7708,Q#2946 - >seq2945,superfamily,295487,456,513,0.00024545,43.4338,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs8_ctshrew.pars.frame3,1909130220_L1MB7.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7709,Q#2948 - >seq2947,non-specific,197310,107,225,3.9816300000000005e-20,90.4885,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7710,Q#2948 - >seq2947,superfamily,351117,107,225,3.9816300000000005e-20,90.4885,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7711,Q#2948 - >seq2947,non-specific,197320,111,218,3.4295499999999996e-07,52.5174,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7712,Q#2948 - >seq2947,non-specific,197306,114,225,6.307230000000001e-06,48.6317,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7713,Q#2948 - >seq2947,specific,335306,85,218,9.52411e-06,48.0102,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7714,Q#2948 - >seq2947,non-specific,197307,111,218,1.88346e-05,47.2825,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7715,Q#2948 - >seq2947,non-specific,223780,111,218,0.00010075200000000001,45.2819,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7716,Q#2948 - >seq2947,non-specific,197317,113,218,0.00145454,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB7.ORF2.hs0_human.pars.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,N-TerminusTruncated
7717,Q#2949 - >seq2948,specific,238827,486,711,4.2773400000000004e-32,124.711,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs0_human,pars,CompleteHit
7718,Q#2949 - >seq2948,superfamily,295487,486,711,4.2773400000000004e-32,124.711,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs0_human,pars,CompleteHit
7719,Q#2949 - >seq2948,non-specific,197310,9,126,1.00097e-14,74.6953,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB7,ORF2,hs0_human,pars,C-TerminusTruncated
7720,Q#2949 - >seq2948,superfamily,351117,9,126,1.00097e-14,74.6953,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,C-TerminusTruncated
7721,Q#2949 - >seq2948,non-specific,333820,492,708,1.2581200000000002e-14,73.0954,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs0_human,pars,CompleteHit
7722,Q#2949 - >seq2948,superfamily,333820,492,708,1.2581200000000002e-14,73.0954,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB7,ORF2,hs0_human,pars,CompleteHit
7723,Q#2949 - >seq2948,non-specific,197306,9,117,2.50371e-05,47.0909,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.pars.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,pars,C-TerminusTruncated
7724,Q#2951 - >seq2950,non-specific,197310,101,219,3.27788e-20,90.8737,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7725,Q#2951 - >seq2950,superfamily,351117,101,219,3.27788e-20,90.8737,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7726,Q#2951 - >seq2950,non-specific,197320,105,212,3.41577e-07,52.5174,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7727,Q#2951 - >seq2950,non-specific,197306,108,219,7.7498e-06,48.2465,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7728,Q#2951 - >seq2950,specific,335306,80,212,1.26186e-05,47.625,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7729,Q#2951 - >seq2950,non-specific,197307,105,212,1.60799e-05,47.6677,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7730,Q#2951 - >seq2950,non-specific,223780,105,212,9.00907e-05,45.2819,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7731,Q#2951 - >seq2950,non-specific,197317,107,212,0.00158465,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB7.ORF2.hs0_human.marg.frame2,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,N-TerminusTruncated
7732,Q#2952 - >seq2951,specific,238827,475,700,2.77358e-32,125.48100000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs0_human,marg,CompleteHit
7733,Q#2952 - >seq2951,superfamily,295487,475,700,2.77358e-32,125.48100000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs0_human,marg,CompleteHit
7734,Q#2952 - >seq2951,non-specific,333820,481,697,1.16476e-14,73.4806,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs0_human,marg,CompleteHit
7735,Q#2952 - >seq2951,superfamily,333820,481,697,1.16476e-14,73.4806,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB7,ORF2,hs0_human,marg,CompleteHit
7736,Q#2952 - >seq2951,non-specific,197310,5,115,5.91449e-11,63.9097,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB7,ORF2,hs0_human,marg,C-TerminusTruncated
7737,Q#2952 - >seq2951,superfamily,351117,5,115,5.91449e-11,63.9097,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,C-TerminusTruncated
7738,Q#2952 - >seq2951,non-specific,197306,5,106,0.000472346,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB7.ORF2.hs0_human.marg.frame3,1909130222_L1MB7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB7,ORF2,hs0_human,marg,C-TerminusTruncated
7739,Q#2960 - >seq2959,non-specific,238827,521,703,5.83207e-16,78.1018,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs1_chimp.pars.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,pars,N-TerminusTruncated
7740,Q#2960 - >seq2959,superfamily,295487,521,703,5.83207e-16,78.1018,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs1_chimp.pars.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,pars,N-TerminusTruncated
7741,Q#2960 - >seq2959,non-specific,333820,505,703,8.636450000000001e-07,50.3686,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.pars.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7742,Q#2960 - >seq2959,superfamily,333820,505,703,8.636450000000001e-07,50.3686,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.pars.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7743,Q#2961 - >seq2960,specific,197310,9,237,1.1415199999999999e-41,152.891,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7744,Q#2961 - >seq2960,superfamily,351117,9,237,1.1415199999999999e-41,152.891,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7745,Q#2961 - >seq2960,non-specific,197306,9,237,1.13908e-15,77.5216,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7746,Q#2961 - >seq2960,non-specific,238827,512,568,4.69228e-14,72.3238,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,pars,C-TerminusTruncated
7747,Q#2961 - >seq2960,superfamily,295487,512,568,4.69228e-14,72.3238,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,pars,C-TerminusTruncated
7748,Q#2961 - >seq2960,specific,335306,10,230,1.61726e-08,56.0994,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7749,Q#2961 - >seq2960,non-specific,223780,9,222,8.47601e-08,54.5267,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7750,Q#2961 - >seq2960,non-specific,197320,105,209,4.63942e-06,49.0506,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs1_chimp,pars,N-TerminusTruncated
7751,Q#2961 - >seq2960,non-specific,339261,107,232,8.517110000000001e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7752,Q#2961 - >seq2960,non-specific,333820,518,562,0.000327855,42.6646,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,pars,C-TerminusTruncated
7753,Q#2961 - >seq2960,superfamily,333820,518,562,0.000327855,42.6646,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,pars,C-TerminusTruncated
7754,Q#2961 - >seq2960,non-specific,197307,9,230,0.000640846,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7755,Q#2961 - >seq2960,non-specific,197311,71,145,0.00225463,40.3529,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs1_chimp,pars,BothTerminiTruncated
7756,Q#2961 - >seq2960,non-specific,273186,9,230,0.00314784,40.34,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs1_chimp.pars.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs1_chimp,pars,CompleteHit
7757,Q#2962 - >seq2961,specific,197310,6,225,6.17059e-37,139.024,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7758,Q#2962 - >seq2961,superfamily,351117,6,225,6.17059e-37,139.024,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7759,Q#2962 - >seq2961,non-specific,197306,6,225,1.7102e-14,74.0548,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7760,Q#2962 - >seq2961,specific,335306,6,218,2.5945099999999997e-06,49.551,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7761,Q#2962 - >seq2961,non-specific,223780,7,210,4.02598e-05,46.4375,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7762,Q#2962 - >seq2961,non-specific,339261,101,220,0.000600962,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB8,ORF2,hs1_chimp,marg,CompleteHit
7763,Q#2962 - >seq2961,non-specific,197311,65,193,0.00195056,40.7381,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs1_chimp.marg.frame1,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs1_chimp,marg,N-TerminusTruncated
7764,Q#2963 - >seq2962,non-specific,238827,513,684,2.87868e-10,61.153,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs1_chimp.marg.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,marg,N-TerminusTruncated
7765,Q#2963 - >seq2962,superfamily,295487,513,684,2.87868e-10,61.153,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs1_chimp.marg.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,marg,N-TerminusTruncated
7766,Q#2963 - >seq2962,non-specific,333820,513,684,0.00667464,38.8126,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.marg.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,marg,N-TerminusTruncated
7767,Q#2963 - >seq2962,superfamily,333820,513,684,0.00667464,38.8126,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.marg.frame2,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs1_chimp,marg,N-TerminusTruncated
7768,Q#2964 - >seq2963,non-specific,238827,451,507,1.30262e-14,73.8646,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs1_chimp.marg.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,marg,C-TerminusTruncated
7769,Q#2964 - >seq2963,superfamily,295487,451,507,1.30262e-14,73.8646,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs1_chimp.marg.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,marg,C-TerminusTruncated
7770,Q#2964 - >seq2963,non-specific,333820,457,501,0.000205482,43.435,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.marg.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,marg,C-TerminusTruncated
7771,Q#2964 - >seq2963,superfamily,333820,457,501,0.000205482,43.435,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs1_chimp.marg.frame3,1909130224_L1MB8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs1_chimp,marg,C-TerminusTruncated
7772,Q#2965 - >seq2964,non-specific,340205,176,237,4.483569999999999e-09,51.1828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs2_gorilla.marg.frame1,1909130225_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs2_gorilla,marg,CompleteHit
7773,Q#2965 - >seq2964,superfamily,340205,176,237,4.483569999999999e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs2_gorilla.marg.frame1,1909130225_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs2_gorilla,marg,CompleteHit
7774,Q#2966 - >seq2965,non-specific,340205,95,152,4.78091e-06,41.938,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs2_gorilla.pars.frame1,1909130225_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs2_gorilla,pars,CompleteHit
7775,Q#2966 - >seq2965,superfamily,340205,95,152,4.78091e-06,41.938,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs2_gorilla.pars.frame1,1909130225_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs2_gorilla,pars,CompleteHit
7776,Q#2971 - >seq2970,non-specific,238827,452,683,2.76867e-20,90.4282,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs2_gorilla.marg.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7777,Q#2971 - >seq2970,superfamily,295487,452,683,2.76867e-20,90.4282,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs2_gorilla.marg.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7778,Q#2971 - >seq2970,non-specific,333820,470,683,1.1843099999999999e-06,49.9834,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs2_gorilla.marg.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7779,Q#2971 - >seq2970,superfamily,333820,470,683,1.1843099999999999e-06,49.9834,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs2_gorilla.marg.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7780,Q#2971 - >seq2970,non-specific,238828,524,670,0.00585255,39.4917,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs2_gorilla.marg.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7781,Q#2972 - >seq2971,specific,197310,1,214,4.97412e-28,113.6,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7782,Q#2972 - >seq2971,superfamily,351117,1,214,4.97412e-28,113.6,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7783,Q#2972 - >seq2971,non-specific,197306,1,220,9.72163e-10,60.1877,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7784,Q#2972 - >seq2971,non-specific,223780,92,213,1.35909e-07,54.1415,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7785,Q#2972 - >seq2971,specific,335306,116,213,1.3323399999999999e-05,47.625,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7786,Q#2972 - >seq2971,non-specific,273186,92,221,1.33295e-05,47.6588,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7787,Q#2972 - >seq2971,non-specific,197307,92,213,8.27125e-05,45.3565,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7788,Q#2972 - >seq2971,non-specific,197319,92,220,8.32092e-05,45.3453,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7789,Q#2972 - >seq2971,non-specific,339261,94,214,0.00204169,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB8,ORF2,hs2_gorilla,marg,CompleteHit
7790,Q#2972 - >seq2971,non-specific,272954,92,191,0.00664055,39.6737,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs2_gorilla.marg.frame1,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
7791,Q#2974 - >seq2973,non-specific,238827,465,695,2.41586e-21,93.5098,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs2_gorilla.pars.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7792,Q#2974 - >seq2973,superfamily,295487,465,695,2.41586e-21,93.5098,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs2_gorilla.pars.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7793,Q#2974 - >seq2973,non-specific,333820,483,695,7.16741e-08,53.4502,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs2_gorilla.pars.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7794,Q#2974 - >seq2973,superfamily,333820,483,695,7.16741e-08,53.4502,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs2_gorilla.pars.frame2,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7795,Q#2976 - >seq2975,specific,197310,1,221,1.0008899999999999e-30,121.304,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7796,Q#2976 - >seq2975,superfamily,351117,1,221,1.0008899999999999e-30,121.304,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7797,Q#2976 - >seq2975,non-specific,197306,1,227,3.51217e-11,64.4249,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7798,Q#2976 - >seq2975,specific,335306,1,220,4.47987e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7799,Q#2976 - >seq2975,non-specific,223780,96,220,5.54978e-07,52.2155,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7800,Q#2976 - >seq2975,non-specific,339261,98,221,1.0556300000000001e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB8,ORF2,hs2_gorilla,pars,CompleteHit
7801,Q#2976 - >seq2975,non-specific,273186,96,228,3.78772e-05,46.5032,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7802,Q#2976 - >seq2975,non-specific,197307,96,220,0.000332861,43.4305,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7803,Q#2976 - >seq2975,non-specific,197311,91,227,0.00654896,39.1973,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7804,Q#2976 - >seq2975,non-specific,272954,96,198,0.00969363,38.9033,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs2_gorilla.pars.frame3,1909130226_L1MB8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
7805,Q#2977 - >seq2976,non-specific,335182,87,153,2.96653e-08,49.6087,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs3_orang.marg.frame3,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB8,ORF1,hs3_orang,marg,N-TerminusTruncated
7806,Q#2977 - >seq2976,superfamily,335182,87,153,2.96653e-08,49.6087,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs3_orang.marg.frame3,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB8,ORF1,hs3_orang,marg,N-TerminusTruncated
7807,Q#2979 - >seq2978,non-specific,340205,140,199,1.3572799999999998e-12,60.0424,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs3_orang.marg.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,marg,CompleteHit
7808,Q#2979 - >seq2978,superfamily,340205,140,199,1.3572799999999998e-12,60.0424,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs3_orang.marg.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,marg,CompleteHit
7809,Q#2980 - >seq2979,non-specific,340205,139,187,1.10295e-12,60.0424,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs3_orang.pars.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,pars,CompleteHit
7810,Q#2980 - >seq2979,superfamily,340205,139,187,1.10295e-12,60.0424,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs3_orang.pars.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,pars,CompleteHit
7811,Q#2980 - >seq2979,non-specific,335182,59,93,5.5633599999999995e-05,40.3639,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs3_orang.pars.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,pars,BothTerminiTruncated
7812,Q#2980 - >seq2979,superfamily,335182,59,93,5.5633599999999995e-05,40.3639,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs3_orang.pars.frame1,1909130228_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs3_orang,pars,BothTerminiTruncated
7813,Q#2983 - >seq2982,non-specific,197310,791,924,1.7697499999999998e-10,63.1393,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs4_gibbon.marg.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7814,Q#2983 - >seq2982,superfamily,351117,791,924,1.7697499999999998e-10,63.1393,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs4_gibbon.marg.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7815,Q#2983 - >seq2982,non-specific,238827,1291,1378,7.94272e-07,51.9082,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs4_gibbon.marg.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7816,Q#2983 - >seq2982,superfamily,295487,1291,1378,7.94272e-07,51.9082,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs4_gibbon.marg.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
7817,Q#2987 - >seq2986,non-specific,340205,107,155,1.67696e-10,53.8792,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
7818,Q#2987 - >seq2986,superfamily,340205,107,155,1.67696e-10,53.8792,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
7819,Q#2988 - >seq2987,non-specific,340205,126,174,1.28464e-10,54.6496,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs5_gmonkey.marg.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
7820,Q#2988 - >seq2987,superfamily,340205,126,174,1.28464e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs5_gmonkey.marg.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
7821,Q#2988 - >seq2987,non-specific,273614,19,71,0.00187705,37.8973,TIGR01421,gluta_reduc_1,C,cl30699,"glutathione-disulfide reductase, animal/bacterial; The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of animals, yeast, and a number of animal-resident bacteria. [Energy metabolism, Electron transport]",L1MB8.ORF1.hs5_gmonkey.marg.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
7822,Q#2988 - >seq2987,superfamily,357575,19,71,0.00187705,37.8973,cl30699,Lpd superfamily,C, - ,"Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component or related enzyme [Energy production and conversion]; Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion].",L1MB8.ORF1.hs5_gmonkey.marg.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MB8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
7823,Q#2990 - >seq2989,non-specific,197310,168,295,6.090909999999999e-17,80.8585,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7824,Q#2990 - >seq2989,superfamily,351117,168,295,6.090909999999999e-17,80.8585,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7825,Q#2990 - >seq2989,specific,335306,192,294,0.000285847,43.0026,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7826,Q#2990 - >seq2989,non-specific,197306,178,301,0.000744278,42.0833,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7827,Q#2990 - >seq2989,non-specific,223780,193,294,0.00521714,39.5039,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7828,Q#2990 - >seq2989,non-specific,197320,201,286,0.00896232,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs5_gmonkey.pars.frame1,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7829,Q#2991 - >seq2990,non-specific,238827,513,624,1.27825e-15,76.561,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs5_gmonkey.pars.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7830,Q#2991 - >seq2990,superfamily,295487,513,624,1.27825e-15,76.561,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs5_gmonkey.pars.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7831,Q#2991 - >seq2990,non-specific,333820,519,570,1.0291600000000002e-05,46.9018,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.pars.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7832,Q#2991 - >seq2990,superfamily,333820,519,570,1.0291600000000002e-05,46.9018,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.pars.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7833,Q#2992 - >seq2991,non-specific,197310,75,191,1.78567e-13,70.8433,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7834,Q#2992 - >seq2991,superfamily,351117,75,191,1.78567e-13,70.8433,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
7835,Q#2992 - >seq2991,non-specific,238827,687,802,1.20908e-11,65.005,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7836,Q#2992 - >seq2991,superfamily,295487,687,802,1.20908e-11,65.005,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7837,Q#2992 - >seq2991,non-specific,333820,686,768,3.1455199999999997e-05,45.361000000000004,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7838,Q#2992 - >seq2991,superfamily,333820,686,768,3.1455199999999997e-05,45.361000000000004,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
7839,Q#2992 - >seq2991,non-specific,197306,140,217,0.00127819,41.3129,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.pars.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
7840,Q#2994 - >seq2993,specific,238827,481,709,4.853479999999999e-31,121.62899999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs5_gmonkey.marg.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7841,Q#2994 - >seq2993,superfamily,295487,481,709,4.853479999999999e-31,121.62899999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs5_gmonkey.marg.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7842,Q#2994 - >seq2993,non-specific,333820,487,709,1.1417599999999999e-13,70.399,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.marg.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7843,Q#2994 - >seq2993,superfamily,333820,487,709,1.1417599999999999e-13,70.399,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs5_gmonkey.marg.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7844,Q#2994 - >seq2993,non-specific,238828,582,697,0.004142,39.8769,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs5_gmonkey.marg.frame2,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7845,Q#2995 - >seq2994,non-specific,197310,883,995,1.5279000000000002e-11,66.2209,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs4_gibbon.marg.frame1,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7846,Q#2995 - >seq2994,superfamily,351117,883,995,1.5279000000000002e-11,66.2209,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs4_gibbon.marg.frame1,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7847,Q#2995 - >seq2994,non-specific,197306,868,988,0.000490787,43.6241,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs4_gibbon.marg.frame1,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
7848,Q#2997 - >seq2996,specific,197310,2,227,2.2514599999999998e-40,149.039,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7849,Q#2997 - >seq2996,superfamily,351117,2,227,2.2514599999999998e-40,149.039,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7850,Q#2997 - >seq2996,non-specific,197306,2,233,4.12566e-14,73.2844,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7851,Q#2997 - >seq2996,non-specific,223780,59,226,6.94131e-09,57.9935,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7852,Q#2997 - >seq2996,specific,335306,3,226,9.364839999999999e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7853,Q#2997 - >seq2996,non-specific,197320,59,218,1.09964e-06,51.3618,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7854,Q#2997 - >seq2996,non-specific,197307,50,226,4.77002e-05,46.1269,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7855,Q#2997 - >seq2996,non-specific,197321,48,226,0.00201049,40.9984,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs5_gmonkey,marg,CompleteHit
7856,Q#2997 - >seq2996,non-specific,273186,59,234,0.00532191,39.9548,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs5_gmonkey.marg.frame3,1909130229_L1MB8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
7857,Q#2998 - >seq2997,specific,197310,9,227,1.52767e-29,117.838,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs4_gibbon,pars,CompleteHit
7858,Q#2998 - >seq2997,superfamily,351117,9,227,1.52767e-29,117.838,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs4_gibbon,pars,CompleteHit
7859,Q#2998 - >seq2997,non-specific,197306,9,220,8.905249999999999e-10,60.1877,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs4_gibbon,pars,CompleteHit
7860,Q#2998 - >seq2997,non-specific,197320,106,208,6.43868e-07,51.747,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7861,Q#2998 - >seq2997,non-specific,223780,7,207,1.66701e-06,50.6747,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs4_gibbon,pars,CompleteHit
7862,Q#2998 - >seq2997,non-specific,197311,74,204,0.00028371799999999997,43.0493,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7863,Q#2998 - >seq2997,non-specific,197307,9,208,0.0008556589999999999,42.2749,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs4_gibbon,pars,CompleteHit
7864,Q#2998 - >seq2997,non-specific,273186,94,208,0.000976227,41.8808,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7865,Q#2998 - >seq2997,non-specific,272954,94,207,0.00295984,40.4441,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs4_gibbon.pars.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
7866,Q#2999 - >seq2998,non-specific,238827,491,578,1.2265399999999999e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs4_gibbon.pars.frame1,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7867,Q#2999 - >seq2998,superfamily,295487,491,578,1.2265399999999999e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs4_gibbon.pars.frame1,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
7868,Q#3001 - >seq3000,non-specific,238827,465,695,1.6897400000000005e-10,61.9234,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs3_orang.pars.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7869,Q#3001 - >seq3000,superfamily,295487,465,695,1.6897400000000005e-10,61.9234,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs3_orang.pars.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7870,Q#3001 - >seq3000,non-specific,333820,490,669,9.07587e-06,47.287,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs3_orang.pars.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs3_orang,pars,C-TerminusTruncated
7871,Q#3001 - >seq3000,superfamily,333820,490,669,9.07587e-06,47.287,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs3_orang.pars.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs3_orang,pars,C-TerminusTruncated
7872,Q#3001 - >seq3000,non-specific,238828,540,669,1.32016e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs3_orang.pars.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs3_orang,pars,N-TerminusTruncated
7873,Q#3002 - >seq3001,specific,197310,9,230,7.047869999999999e-34,130.549,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7874,Q#3002 - >seq3001,superfamily,351117,9,230,7.047869999999999e-34,130.549,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7875,Q#3002 - >seq3001,non-specific,197306,9,202,3.42423e-11,64.4249,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7876,Q#3002 - >seq3001,non-specific,223780,9,199,2.21773e-06,50.2895,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7877,Q#3002 - >seq3001,specific,335306,12,201,2.46173e-06,49.551,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7878,Q#3002 - >seq3001,non-specific,197321,7,188,4.88609e-05,46.006,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7879,Q#3002 - >seq3001,non-specific,197311,70,141,9.536780000000001e-05,44.5901,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,pars,BothTerminiTruncated
7880,Q#3002 - >seq3001,non-specific,197307,9,201,0.0009305139999999999,42.2749,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7881,Q#3002 - >seq3001,non-specific,273186,9,199,0.00262163,40.7252,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7882,Q#3002 - >seq3001,non-specific,272954,9,201,0.00712013,39.2885,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs3_orang.pars.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,pars,CompleteHit
7883,Q#3003 - >seq3002,non-specific,224117,207,459,0.00745283,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs3_orang.marg.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs3_orang,marg,BothTerminiTruncated
7884,Q#3003 - >seq3002,superfamily,224117,207,459,0.00745283,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs3_orang.marg.frame2,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MB8,ORF2,hs3_orang,marg,BothTerminiTruncated
7885,Q#3004 - >seq3003,specific,197310,9,231,2.54601e-34,131.705,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7886,Q#3004 - >seq3003,superfamily,351117,9,231,2.54601e-34,131.705,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7887,Q#3004 - >seq3003,non-specific,238827,500,700,2.52855e-12,67.3162,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7888,Q#3004 - >seq3003,superfamily,295487,500,700,2.52855e-12,67.3162,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7889,Q#3004 - >seq3003,non-specific,197306,9,203,9.83806e-11,63.2693,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7890,Q#3004 - >seq3003,non-specific,333820,498,698,2.8401999999999998e-09,57.6874,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7891,Q#3004 - >seq3003,superfamily,333820,498,698,2.8401999999999998e-09,57.6874,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7892,Q#3004 - >seq3003,non-specific,238828,550,689,5.39722e-08,54.8996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs3_orang,marg,N-TerminusTruncated
7893,Q#3004 - >seq3003,non-specific,223780,9,200,1.25381e-06,51.0599,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7894,Q#3004 - >seq3003,specific,335306,12,202,1.76623e-06,50.3214,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7895,Q#3004 - >seq3003,non-specific,197321,7,189,0.000130865,44.8504,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7896,Q#3004 - >seq3003,non-specific,197307,9,202,0.000418798,43.4305,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7897,Q#3004 - >seq3003,non-specific,197311,70,142,0.00138035,41.1233,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,marg,BothTerminiTruncated
7898,Q#3004 - >seq3003,non-specific,272954,9,202,0.00814905,39.2885,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs3_orang.marg.frame3,1909130229_L1MB8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs3_orang,marg,CompleteHit
7899,Q#3006 - >seq3005,non-specific,340205,149,189,2.7031799999999997e-06,43.0936,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs4_gibbon.pars.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
7900,Q#3006 - >seq3005,superfamily,340205,149,189,2.7031799999999997e-06,43.0936,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs4_gibbon.pars.frame2,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MB8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
7901,Q#3010 - >seq3009,non-specific,340205,154,200,7.980159999999999e-07,44.6344,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs4_gibbon.marg.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7902,Q#3010 - >seq3009,superfamily,340205,154,200,7.980159999999999e-07,44.6344,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs4_gibbon.marg.frame3,1909130229_L1MB8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MB8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
7903,Q#3013 - >seq3012,non-specific,238827,476,730,1.40941e-13,71.1682,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs6_sqmonkey,pars,CompleteHit
7904,Q#3013 - >seq3012,superfamily,295487,476,730,1.40941e-13,71.1682,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs6_sqmonkey,pars,CompleteHit
7905,Q#3013 - >seq3012,non-specific,197310,75,181,4.78416e-08,55.0501,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7906,Q#3013 - >seq3012,superfamily,351117,75,181,4.78416e-08,55.0501,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7907,Q#3013 - >seq3012,non-specific,197306,42,181,1.1621800000000001e-05,47.8613,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7908,Q#3013 - >seq3012,non-specific,333820,609,695,0.0014015999999999998,40.7386,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7909,Q#3013 - >seq3012,superfamily,333820,609,695,0.0014015999999999998,40.7386,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs6_sqmonkey.pars.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
7910,Q#3014 - >seq3013,non-specific,197310,144,344,7.06348e-16,78.5473,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs6_sqmonkey,marg,CompleteHit
7911,Q#3014 - >seq3013,superfamily,351117,144,344,7.06348e-16,78.5473,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs6_sqmonkey,marg,CompleteHit
7912,Q#3014 - >seq3013,non-specific,238827,645,871,1.9609400000000003e-12,68.0866,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs6_sqmonkey,marg,CompleteHit
7913,Q#3014 - >seq3013,superfamily,295487,645,871,1.9609400000000003e-12,68.0866,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs6_sqmonkey,marg,CompleteHit
7914,Q#3014 - >seq3013,non-specific,197306,122,344,5.4303599999999994e-09,58.2617,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs6_sqmonkey,marg,CompleteHit
7915,Q#3014 - >seq3013,non-specific,333820,772,871,0.00215048,40.3534,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
7916,Q#3014 - >seq3013,superfamily,333820,772,871,0.00215048,40.3534,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs6_sqmonkey.marg.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
7917,Q#3020 - >seq3019,non-specific,340205,104,168,6.0877e-20,78.532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs6_sqmonkey.marg.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs6_sqmonkey,marg,CompleteHit
7918,Q#3020 - >seq3019,superfamily,340205,104,168,6.0877e-20,78.532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs6_sqmonkey.marg.frame1,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs6_sqmonkey,marg,CompleteHit
7919,Q#3021 - >seq3020,non-specific,340205,65,129,2.7766299999999996e-20,77.7616,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs6_sqmonkey.pars.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs6_sqmonkey,pars,CompleteHit
7920,Q#3021 - >seq3020,superfamily,340205,65,129,2.7766299999999996e-20,77.7616,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs6_sqmonkey.pars.frame3,1909130230_L1MB8.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs6_sqmonkey,pars,CompleteHit
7921,Q#3027 - >seq3026,specific,197310,10,238,2.449e-38,143.261,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7922,Q#3027 - >seq3026,superfamily,351117,10,238,2.449e-38,143.261,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7923,Q#3027 - >seq3026,non-specific,197306,10,238,1.78689e-16,80.218,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7924,Q#3027 - >seq3026,specific,335306,10,231,2.25191e-13,70.7369,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7925,Q#3027 - >seq3026,non-specific,197307,10,231,8.70489e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7926,Q#3027 - >seq3026,non-specific,238827,537,809,1.1155899999999999e-09,59.6122,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7927,Q#3027 - >seq3026,superfamily,295487,537,809,1.1155899999999999e-09,59.6122,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7928,Q#3027 - >seq3026,non-specific,197320,11,209,3.6421500000000003e-09,58.6806,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7929,Q#3027 - >seq3026,non-specific,223780,10,208,4.2336300000000003e-07,52.6007,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7930,Q#3027 - >seq3026,non-specific,273186,10,239,0.00032392900000000004,43.8068,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs7_bushaby,marg,CompleteHit
7931,Q#3027 - >seq3026,non-specific,197321,10,44,0.0055912,39.8428,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs7_bushaby,marg,C-TerminusTruncated
7932,Q#3027 - >seq3026,non-specific,197322,119,231,0.00765639,39.6078,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB8,ORF2,hs7_bushaby,marg,N-TerminusTruncated
7933,Q#3027 - >seq3026,non-specific,235175,348,476,0.00913331,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7934,Q#3027 - >seq3026,superfamily,235175,348,476,0.00913331,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB8.ORF2.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB8,ORF2,hs7_bushaby,marg,BothTerminiTruncated
7935,Q#3029 - >seq3028,non-specific,197310,12,68,2.46822e-08,55.4353,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs7_bushaby.pars.frame2,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7936,Q#3029 - >seq3028,superfamily,351117,12,68,2.46822e-08,55.4353,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs7_bushaby.pars.frame2,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7937,Q#3029 - >seq3028,non-specific,238827,453,532,3.3445099999999996e-07,51.9082,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs7_bushaby.pars.frame2,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7938,Q#3029 - >seq3028,superfamily,295487,453,532,3.3445099999999996e-07,51.9082,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs7_bushaby.pars.frame2,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs7_bushaby,pars,N-TerminusTruncated
7939,Q#3032 - >seq3031,non-specific,340205,126,190,1.03521e-11,57.7312,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs7_bushaby,marg,CompleteHit
7940,Q#3032 - >seq3031,superfamily,340205,126,190,1.03521e-11,57.7312,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs7_bushaby,marg,CompleteHit
7941,Q#3032 - >seq3031,non-specific,335182,50,80,0.00061855,37.6675,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs7_bushaby,marg,BothTerminiTruncated
7942,Q#3032 - >seq3031,superfamily,335182,50,80,0.00061855,37.6675,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs7_bushaby.marg.frame1,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MB8,ORF1,hs7_bushaby,marg,BothTerminiTruncated
7943,Q#3033 - >seq3032,non-specific,340205,60,121,2.21305e-12,57.7312,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs7_bushaby.pars.frame3,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs7_bushaby,pars,CompleteHit
7944,Q#3033 - >seq3032,superfamily,340205,60,121,2.21305e-12,57.7312,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs7_bushaby.pars.frame3,1909130235_L1MB8.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs7_bushaby,pars,CompleteHit
7945,Q#3042 - >seq3041,non-specific,335182,1,49,2.0740400000000002e-06,42.6751,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs8_ctshrew.pars.frame3,1909130236_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
7946,Q#3042 - >seq3041,superfamily,335182,1,49,2.0740400000000002e-06,42.6751,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MB8.ORF1.hs8_ctshrew.pars.frame3,1909130236_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MB8,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
7947,Q#3043 - >seq3042,specific,238827,452,703,8.7987e-34,129.719,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,CompleteHit
7948,Q#3043 - >seq3042,superfamily,295487,452,703,8.7987e-34,129.719,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,CompleteHit
7949,Q#3043 - >seq3042,non-specific,333820,458,678,2.97906e-16,78.10300000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,CompleteHit
7950,Q#3043 - >seq3042,superfamily,333820,458,678,2.97906e-16,78.10300000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,CompleteHit
7951,Q#3043 - >seq3042,non-specific,238828,506,681,3.63108e-09,58.3664,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7952,Q#3043 - >seq3042,non-specific,275209,528,735,7.63957e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7953,Q#3043 - >seq3042,superfamily,275209,528,735,7.63957e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs8_ctshrew.pars.frame1,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7954,Q#3044 - >seq3043,non-specific,197310,77,204,8.82615e-19,86.6365,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7955,Q#3044 - >seq3043,superfamily,351117,77,204,8.82615e-19,86.6365,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7956,Q#3044 - >seq3043,non-specific,197320,57,177,1.8374199999999998e-07,53.2878,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7957,Q#3044 - >seq3043,non-specific,339261,78,200,5.19733e-07,49.2579,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB8,ORF2,hs8_ctshrew,pars,CompleteHit
7958,Q#3044 - >seq3043,non-specific,335306,40,197,7.07655e-06,48.3954,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7959,Q#3044 - >seq3043,non-specific,197307,57,204,1.27249e-05,47.6677,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7960,Q#3044 - >seq3043,non-specific,197306,81,204,4.3801099999999996e-05,45.9353,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7961,Q#3044 - >seq3043,non-specific,223780,80,197,0.000223563,44.1263,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7962,Q#3044 - >seq3043,non-specific,197322,80,204,0.00023067099999999997,44.2302,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7963,Q#3044 - >seq3043,non-specific,197311,80,204,0.000553011,42.2789,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7964,Q#3044 - >seq3043,non-specific,273186,80,205,0.00195896,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
7965,Q#3044 - >seq3043,non-specific,238827,474,512,0.00215784,40.7374,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7966,Q#3044 - >seq3043,superfamily,295487,474,512,0.00215784,40.7374,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs8_ctshrew.pars.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
7967,Q#3047 - >seq3046,specific,238827,524,757,5.22725e-33,127.40700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7968,Q#3047 - >seq3046,superfamily,295487,524,757,5.22725e-33,127.40700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7969,Q#3047 - >seq3046,specific,197310,11,241,1.93388e-29,117.838,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7970,Q#3047 - >seq3046,superfamily,351117,11,241,1.93388e-29,117.838,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7971,Q#3047 - >seq3046,non-specific,333820,530,750,5.55345e-16,77.3326,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7972,Q#3047 - >seq3046,superfamily,333820,530,750,5.55345e-16,77.3326,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7973,Q#3047 - >seq3046,non-specific,197306,77,241,6.3619700000000005e-09,57.8765,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7974,Q#3047 - >seq3046,non-specific,238828,578,753,8.50727e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7975,Q#3047 - >seq3046,non-specific,197320,81,213,2.71354e-08,55.9842,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7976,Q#3047 - >seq3046,non-specific,197307,93,241,7.98344e-08,54.6013,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7977,Q#3047 - >seq3046,non-specific,223780,93,234,2.56804e-07,53.3711,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7978,Q#3047 - >seq3046,non-specific,197322,93,241,1.19598e-06,51.549,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7979,Q#3047 - >seq3046,non-specific,197311,76,241,3.2044e-06,49.2125,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7980,Q#3047 - >seq3046,non-specific,339261,111,237,1.10543e-05,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB8,ORF2,hs8_ctshrew,marg,CompleteHit
7981,Q#3047 - >seq3046,non-specific,335306,76,234,3.3184e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7982,Q#3047 - >seq3046,non-specific,275209,600,754,7.10447e-05,46.2968,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
7983,Q#3047 - >seq3046,superfamily,275209,600,754,7.10447e-05,46.2968,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
7984,Q#3047 - >seq3046,non-specific,273186,81,242,0.000145621,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7985,Q#3047 - >seq3046,non-specific,197321,76,241,0.00286423,40.6132,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs8_ctshrew.marg.frame2,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
7986,Q#3048 - >seq3047,non-specific,238827,474,512,0.00177158,41.1226,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs8_ctshrew.marg.frame3,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7987,Q#3048 - >seq3047,superfamily,295487,474,512,0.00177158,41.1226,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs8_ctshrew.marg.frame3,1909130237_L1MB8.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MB8,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
7988,Q#3050 - >seq3049,specific,197310,16,237,3.54227e-33,128.238,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7989,Q#3050 - >seq3049,superfamily,351117,16,237,3.54227e-33,128.238,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7990,Q#3050 - >seq3049,non-specific,238827,503,608,2.60118e-12,67.3162,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs9_pika,marg,C-TerminusTruncated
7991,Q#3050 - >seq3049,superfamily,295487,503,608,2.60118e-12,67.3162,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs9_pika,marg,C-TerminusTruncated
7992,Q#3050 - >seq3049,non-specific,197306,18,237,1.81585e-11,65.1953,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7993,Q#3050 - >seq3049,non-specific,223780,74,230,2.37122e-07,53.3711,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
7994,Q#3050 - >seq3049,non-specific,197320,74,230,5.39084e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
7995,Q#3050 - >seq3049,non-specific,197307,16,237,2.29704e-06,50.3641,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7996,Q#3050 - >seq3049,specific,335306,23,230,3.5302099999999995e-06,49.1658,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7997,Q#3050 - >seq3049,non-specific,197311,9,237,1.17449e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7998,Q#3050 - >seq3049,non-specific,339261,110,233,0.00023549,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB8,ORF2,hs9_pika,marg,CompleteHit
7999,Q#3050 - >seq3049,non-specific,224117,72,454,0.000633885,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8000,Q#3050 - >seq3049,superfamily,224117,72,454,0.000633885,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8001,Q#3050 - >seq3049,non-specific,273186,177,238,0.0017553,41.4956,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8002,Q#3050 - >seq3049,non-specific,274009,325,453,0.00413146,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,marg,BothTerminiTruncated
8003,Q#3050 - >seq3049,superfamily,274009,325,453,0.00413146,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,marg,BothTerminiTruncated
8004,Q#3050 - >seq3049,non-specific,224259,262,462,0.005696199999999999,40.0496,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8005,Q#3050 - >seq3049,superfamily,224259,262,462,0.005696199999999999,40.0496,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8006,Q#3050 - >seq3049,non-specific,235175,263,463,0.00873796,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,marg,BothTerminiTruncated
8007,Q#3050 - >seq3049,superfamily,235175,263,463,0.00873796,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB8.ORF2.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,marg,BothTerminiTruncated
8008,Q#3051 - >seq3050,non-specific,238827,597,689,3.18348e-20,90.4282,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs9_pika.marg.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8009,Q#3051 - >seq3050,superfamily,295487,597,689,3.18348e-20,90.4282,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs9_pika.marg.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8010,Q#3051 - >seq3050,non-specific,333820,597,674,3.64781e-09,57.3022,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs9_pika.marg.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8011,Q#3051 - >seq3050,superfamily,333820,597,674,3.64781e-09,57.3022,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs9_pika.marg.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8012,Q#3051 - >seq3050,non-specific,238828,597,677,0.00159718,41.0325,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs9_pika.marg.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs9_pika,marg,N-TerminusTruncated
8013,Q#3052 - >seq3051,non-specific,224117,219,418,0.000592995,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8014,Q#3052 - >seq3051,superfamily,224117,219,418,0.000592995,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8015,Q#3052 - >seq3051,non-specific,274009,275,410,0.000879773,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,pars,BothTerminiTruncated
8016,Q#3052 - >seq3051,superfamily,274009,275,410,0.000879773,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,pars,BothTerminiTruncated
8017,Q#3052 - >seq3051,non-specific,224259,228,419,0.00104634,42.3608,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8018,Q#3052 - >seq3051,superfamily,224259,228,419,0.00104634,42.3608,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8019,Q#3052 - >seq3051,non-specific,235175,191,415,0.00582946,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,pars,BothTerminiTruncated
8020,Q#3052 - >seq3051,superfamily,235175,191,415,0.00582946,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB8.ORF2.hs9_pika.pars.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB8,ORF2,hs9_pika,pars,BothTerminiTruncated
8021,Q#3053 - >seq3052,non-specific,197310,8,208,4.63404e-24,102.044,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8022,Q#3053 - >seq3052,superfamily,351117,8,208,4.63404e-24,102.044,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8023,Q#3053 - >seq3052,non-specific,197306,8,208,3.6669400000000004e-08,55.5653,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8024,Q#3053 - >seq3052,specific,335306,8,201,4.97767e-07,51.8622,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8025,Q#3053 - >seq3052,non-specific,197320,109,201,5.1466000000000005e-05,45.968999999999994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8026,Q#3053 - >seq3052,non-specific,223780,107,201,0.000477436,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8027,Q#3053 - >seq3052,non-specific,197307,113,208,0.000483388,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8028,Q#3053 - >seq3052,non-specific,339261,83,204,0.00118986,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8029,Q#3053 - >seq3052,non-specific,273186,148,209,0.00185115,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs9_pika.pars.frame3,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8030,Q#3054 - >seq3053,specific,238827,472,668,1.7145799999999997e-28,114.311,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8031,Q#3054 - >seq3053,superfamily,295487,472,668,1.7145799999999997e-28,114.311,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8032,Q#3054 - >seq3053,non-specific,333820,470,653,1.67852e-14,72.7102,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8033,Q#3054 - >seq3053,superfamily,333820,470,653,1.67852e-14,72.7102,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs9_pika,pars,CompleteHit
8034,Q#3054 - >seq3053,non-specific,238828,481,656,5.932330000000001e-07,51.4328,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB8,ORF2,hs9_pika,pars,N-TerminusTruncated
8035,Q#3056 - >seq3055,non-specific,340205,160,214,8.44802e-19,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB8,ORF1,hs9_pika,marg,CompleteHit
8036,Q#3056 - >seq3055,superfamily,340205,160,214,8.44802e-19,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs9_pika.marg.frame2,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MB8,ORF1,hs9_pika,marg,CompleteHit
8037,Q#3059 - >seq3058,non-specific,340205,150,185,4.84602e-10,53.1088,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs9_pika,pars,C-TerminusTruncated
8038,Q#3059 - >seq3058,superfamily,340205,150,185,4.84602e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MB8.ORF1.hs9_pika.pars.frame1,1909130239_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MB8,ORF1,hs9_pika,pars,C-TerminusTruncated
8039,Q#3062 - >seq3061,specific,238827,375,568,2.4867799999999997e-30,119.318,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8040,Q#3062 - >seq3061,superfamily,295487,375,568,2.4867799999999997e-30,119.318,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8041,Q#3062 - >seq3061,non-specific,333820,387,568,4.73477e-15,74.251,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8042,Q#3062 - >seq3061,superfamily,333820,387,568,4.73477e-15,74.251,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8043,Q#3062 - >seq3061,non-specific,238828,378,536,1.62021e-12,67.9964,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8044,Q#3062 - >seq3061,non-specific,275209,383,562,3.4993300000000005e-06,50.1488,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8045,Q#3062 - >seq3061,superfamily,275209,383,562,3.4993300000000005e-06,50.1488,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,N-TerminusTruncated
8046,Q#3062 - >seq3061,non-specific,238185,445,568,0.000490684,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.pars.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,pars,CompleteHit
8047,Q#3063 - >seq3062,non-specific,238827,335,381,1.19954e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs10_snmole.pars.frame3,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs10_snmole,pars,C-TerminusTruncated
8048,Q#3063 - >seq3062,superfamily,295487,335,381,1.19954e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.pars.frame3,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs10_snmole,pars,C-TerminusTruncated
8049,Q#3064 - >seq3063,non-specific,238827,426,455,0.000306733,43.4338,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs10_snmole.marg.frame1,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs10_snmole,marg,C-TerminusTruncated
8050,Q#3064 - >seq3063,superfamily,295487,426,455,0.000306733,43.4338,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.marg.frame1,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MB8,ORF2,hs10_snmole,marg,C-TerminusTruncated
8051,Q#3065 - >seq3064,specific,238827,441,664,6.1181700000000005e-37,138.578,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,CompleteHit
8052,Q#3065 - >seq3064,superfamily,295487,441,664,6.1181700000000005e-37,138.578,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,CompleteHit
8053,Q#3065 - >seq3064,non-specific,333820,442,664,6.60959e-16,76.9474,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,CompleteHit
8054,Q#3065 - >seq3064,superfamily,333820,442,664,6.60959e-16,76.9474,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,CompleteHit
8055,Q#3065 - >seq3064,non-specific,238828,451,632,5.85706e-13,69.152,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,N-TerminusTruncated
8056,Q#3065 - >seq3064,non-specific,275209,473,658,1.99053e-05,47.8376,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,N-TerminusTruncated
8057,Q#3065 - >seq3064,superfamily,275209,473,658,1.99053e-05,47.8376,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,N-TerminusTruncated
8058,Q#3065 - >seq3064,non-specific,238185,550,664,0.000660997,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs10_snmole.marg.frame2,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs10_snmole,marg,CompleteHit
8059,Q#3066 - >seq3065,non-specific,197310,103,158,0.00031742900000000004,43.4941,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs10_snmole.marg.frame3,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB8,ORF2,hs10_snmole,marg,N-TerminusTruncated
8060,Q#3066 - >seq3065,superfamily,351117,103,158,0.00031742900000000004,43.4941,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs10_snmole.marg.frame3,1909130240_L1MB8.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB8,ORF2,hs10_snmole,marg,N-TerminusTruncated
8061,Q#3073 - >seq3072,non-specific,340205,163,227,3.50696e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs1_chimp.marg.frame3,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs1_chimp,marg,CompleteHit
8062,Q#3073 - >seq3072,superfamily,340205,163,227,3.50696e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs1_chimp.marg.frame3,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs1_chimp,marg,CompleteHit
8063,Q#3074 - >seq3073,non-specific,317697,96,191,0.000496526,40.2123,pfam15324,TALPID3,NC,cl25881,Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.,L1MC1.ORF1.hs1_chimp.marg.frame2,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MC1,ORF1,hs1_chimp,marg,BothTerminiTruncated
8064,Q#3074 - >seq3073,superfamily,317697,96,191,0.000496526,40.2123,cl25881,TALPID3 superfamily,NC, - ,Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.,L1MC1.ORF1.hs1_chimp.marg.frame2,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MC1,ORF1,hs1_chimp,marg,BothTerminiTruncated
8065,Q#3076 - >seq3075,non-specific,340205,111,175,2.50106e-24,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs1_chimp.pars.frame3,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs1_chimp,pars,CompleteHit
8066,Q#3076 - >seq3075,superfamily,340205,111,175,2.50106e-24,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs1_chimp.pars.frame3,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs1_chimp,pars,CompleteHit
8067,Q#3077 - >seq3076,non-specific,317697,48,143,0.000629364,39.4419,pfam15324,TALPID3,NC,cl25881,Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.,L1MC1.ORF1.hs1_chimp.pars.frame2,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC1,ORF1,hs1_chimp,pars,BothTerminiTruncated
8068,Q#3077 - >seq3076,superfamily,317697,48,143,0.000629364,39.4419,cl25881,TALPID3 superfamily,NC, - ,Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.,L1MC1.ORF1.hs1_chimp.pars.frame2,1909130243_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC1,ORF1,hs1_chimp,pars,BothTerminiTruncated
8069,Q#3081 - >seq3080,specific,238827,476,724,9.369309999999999e-27,109.303,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs0_human.pars.frame3,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs0_human,pars,CompleteHit
8070,Q#3081 - >seq3080,superfamily,295487,476,724,9.369309999999999e-27,109.303,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs0_human.pars.frame3,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs0_human,pars,CompleteHit
8071,Q#3081 - >seq3080,non-specific,333820,474,724,1.13488e-10,61.9246,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs0_human.pars.frame3,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs0_human,pars,CompleteHit
8072,Q#3081 - >seq3080,superfamily,333820,474,724,1.13488e-10,61.9246,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs0_human.pars.frame3,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs0_human,pars,CompleteHit
8073,Q#3081 - >seq3080,non-specific,238828,528,661,0.00514178,39.4917,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB8.ORF2.hs0_human.pars.frame3,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8074,Q#3082 - >seq3081,specific,197310,65,240,3.23603e-33,128.623,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8075,Q#3082 - >seq3081,superfamily,351117,65,240,3.23603e-33,128.623,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8076,Q#3082 - >seq3081,non-specific,197306,83,240,5.75888e-13,69.8177,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8077,Q#3082 - >seq3081,non-specific,223780,104,241,2.93974e-08,56.0675,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8078,Q#3082 - >seq3081,non-specific,197320,104,233,5.2972e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8079,Q#3082 - >seq3081,specific,335306,70,233,7.58352e-07,51.0918,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8080,Q#3082 - >seq3081,non-specific,273186,114,241,1.29158e-05,48.044,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8081,Q#3082 - >seq3081,non-specific,197311,81,154,0.00021030099999999998,43.8197,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,pars,BothTerminiTruncated
8082,Q#3082 - >seq3081,non-specific,197307,114,240,0.00023657,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8083,Q#3082 - >seq3081,non-specific,197319,114,240,0.0006226080000000001,42.6489,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB8.ORF2.hs0_human.pars.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,pars,N-TerminusTruncated
8084,Q#3084 - >seq3083,specific,197310,53,228,2.0382299999999998e-32,126.31200000000001,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8085,Q#3084 - >seq3083,superfamily,351117,53,228,2.0382299999999998e-32,126.31200000000001,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8086,Q#3084 - >seq3083,specific,238827,535,783,1.0696899999999998e-26,109.303,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs0_human,marg,CompleteHit
8087,Q#3084 - >seq3083,superfamily,295487,535,783,1.0696899999999998e-26,109.303,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs0_human,marg,CompleteHit
8088,Q#3084 - >seq3083,non-specific,197306,71,228,6.42695e-13,69.8177,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8089,Q#3084 - >seq3083,non-specific,333820,533,783,3.4116399999999997e-10,60.3838,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs0_human,marg,CompleteHit
8090,Q#3084 - >seq3083,superfamily,333820,533,783,3.4116399999999997e-10,60.3838,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MB8,ORF2,hs0_human,marg,CompleteHit
8091,Q#3084 - >seq3083,non-specific,197320,92,221,4.2817199999999996e-08,55.599,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8092,Q#3084 - >seq3083,non-specific,223780,92,229,8.03101e-08,54.9119,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8093,Q#3084 - >seq3083,specific,335306,58,221,7.76882e-07,51.477,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8094,Q#3084 - >seq3083,non-specific,273186,102,229,8.73211e-06,48.4292,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8095,Q#3084 - >seq3083,non-specific,197311,69,142,0.000223355,43.8197,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,marg,BothTerminiTruncated
8096,Q#3084 - >seq3083,non-specific,197307,102,228,0.000498368,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8097,Q#3084 - >seq3083,non-specific,197319,102,228,0.00121819,41.8785,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB8,ORF2,hs0_human,marg,N-TerminusTruncated
8098,Q#3084 - >seq3083,non-specific,339261,104,224,0.00946144,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB8.ORF2.hs0_human.marg.frame2,1909130243_L1MB8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB8,ORF2,hs0_human,marg,CompleteHit
8099,Q#3086 - >seq3085,non-specific,340205,163,227,1.48399e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs2_gorilla.marg.frame3,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs2_gorilla,marg,CompleteHit
8100,Q#3086 - >seq3085,superfamily,340205,163,227,1.48399e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs2_gorilla.marg.frame3,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs2_gorilla,marg,CompleteHit
8101,Q#3086 - >seq3085,non-specific,335182,84,158,9.67084e-10,53.8459,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs2_gorilla.marg.frame3,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
8102,Q#3086 - >seq3085,superfamily,335182,84,158,9.67084e-10,53.8459,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs2_gorilla.marg.frame3,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
8103,Q#3088 - >seq3087,non-specific,340205,155,216,2.3493800000000003e-21,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs2_gorilla.pars.frame2,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs2_gorilla,pars,CompleteHit
8104,Q#3088 - >seq3087,superfamily,340205,155,216,2.3493800000000003e-21,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs2_gorilla.pars.frame2,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs2_gorilla,pars,CompleteHit
8105,Q#3088 - >seq3087,non-specific,335182,76,150,2.05367e-09,53.0755,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs2_gorilla.pars.frame2,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
8106,Q#3088 - >seq3087,superfamily,335182,76,150,2.05367e-09,53.0755,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs2_gorilla.pars.frame2,1909130245_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
8107,Q#3091 - >seq3090,non-specific,340205,133,194,2.16897e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs3_orang.pars.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,pars,CompleteHit
8108,Q#3091 - >seq3090,superfamily,340205,133,194,2.16897e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs3_orang.pars.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,pars,CompleteHit
8109,Q#3091 - >seq3090,non-specific,335182,15,128,4.20079e-07,46.5271,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs3_orang.pars.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,pars,CompleteHit
8110,Q#3091 - >seq3090,superfamily,335182,15,128,4.20079e-07,46.5271,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs3_orang.pars.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,pars,CompleteHit
8111,Q#3094 - >seq3093,non-specific,340205,113,177,3.7099e-25,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs3_orang.marg.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,marg,CompleteHit
8112,Q#3094 - >seq3093,superfamily,340205,113,177,3.7099e-25,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs3_orang.marg.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,marg,CompleteHit
8113,Q#3094 - >seq3093,non-specific,335182,15,108,1.20544e-12,60.7795,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs3_orang.marg.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,marg,CompleteHit
8114,Q#3094 - >seq3093,superfamily,335182,15,108,1.20544e-12,60.7795,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs3_orang.marg.frame1,1909130248_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs3_orang,marg,CompleteHit
8115,Q#3097 - >seq3096,non-specific,340205,176,238,1.6365999999999999e-22,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs4_gibbon.marg.frame3,1909130251_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs4_gibbon,marg,CompleteHit
8116,Q#3097 - >seq3096,superfamily,340205,176,238,1.6365999999999999e-22,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs4_gibbon.marg.frame3,1909130251_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs4_gibbon,marg,CompleteHit
8117,Q#3101 - >seq3100,non-specific,340205,156,218,1.04543e-22,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs4_gibbon.pars.frame1,1909130251_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs4_gibbon,pars,CompleteHit
8118,Q#3101 - >seq3100,superfamily,340205,156,218,1.04543e-22,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs4_gibbon.pars.frame1,1909130251_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs4_gibbon,pars,CompleteHit
8119,Q#3106 - >seq3105,non-specific,197310,128,226,3.04092e-05,46.5757,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs7_bushaby.pars.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
8120,Q#3106 - >seq3105,superfamily,351117,128,226,3.04092e-05,46.5757,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs7_bushaby.pars.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
8121,Q#3107 - >seq3106,non-specific,238827,494,756,7.249610000000001e-24,101.214,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8122,Q#3107 - >seq3106,superfamily,295487,494,756,7.249610000000001e-24,101.214,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8123,Q#3107 - >seq3106,non-specific,333820,500,724,3.5783600000000003e-13,69.2434,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8124,Q#3107 - >seq3106,superfamily,333820,500,724,3.5783600000000003e-13,69.2434,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8125,Q#3107 - >seq3106,non-specific,238828,586,697,2.9168000000000003e-07,52.5884,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
8126,Q#3107 - >seq3106,non-specific,275209,585,658,0.00042856,43.9856,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
8127,Q#3107 - >seq3106,superfamily,275209,585,658,0.00042856,43.9856,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs7_bushaby.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
8128,Q#3108 - >seq3107,non-specific,197310,33,250,7.26125e-14,72.3841,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs7_bushaby.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8129,Q#3108 - >seq3107,superfamily,351117,33,250,7.26125e-14,72.3841,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs7_bushaby.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs7_bushaby,marg,CompleteHit
8130,Q#3110 - >seq3109,non-specific,340205,145,164,0.00145031,35.3896,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs8_ctshrew.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
8131,Q#3110 - >seq3109,superfamily,340205,145,164,0.00145031,35.3896,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs8_ctshrew.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
8132,Q#3111 - >seq3110,non-specific,335182,53,95,0.00154714,35.7415,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs8_ctshrew.pars.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
8133,Q#3111 - >seq3110,superfamily,335182,53,95,0.00154714,35.7415,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs8_ctshrew.pars.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
8134,Q#3114 - >seq3113,non-specific,340205,15,34,0.000142944,34.234,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs8_ctshrew.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
8135,Q#3114 - >seq3113,superfamily,340205,15,34,0.000142944,34.234,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs8_ctshrew.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
8136,Q#3117 - >seq3116,non-specific,238827,502,725,2.63407e-25,105.066,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,CompleteHit
8137,Q#3117 - >seq3116,superfamily,295487,502,725,2.63407e-25,105.066,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,CompleteHit
8138,Q#3117 - >seq3116,non-specific,333820,553,693,2.2458099999999997e-10,60.769,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
8139,Q#3117 - >seq3116,superfamily,333820,553,693,2.2458099999999997e-10,60.769,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
8140,Q#3117 - >seq3116,non-specific,238828,555,666,3.23339e-07,52.2032,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
8141,Q#3117 - >seq3116,non-specific,275209,554,627,0.000666704,43.2152,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,BothTerminiTruncated
8142,Q#3117 - >seq3116,superfamily,275209,554,627,0.000666704,43.2152,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs7_bushaby.pars.frame2,1909130252_L1MC1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs7_bushaby,pars,BothTerminiTruncated
8143,Q#3119 - >seq3118,non-specific,340205,169,235,1.60325e-11,58.1164,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs5_gmonkey.pars.frame1,1909130252_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs5_gmonkey,pars,CompleteHit
8144,Q#3119 - >seq3118,superfamily,340205,169,235,1.60325e-11,58.1164,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs5_gmonkey.pars.frame1,1909130252_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs5_gmonkey,pars,CompleteHit
8145,Q#3122 - >seq3121,non-specific,340205,183,249,3.21956e-11,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs5_gmonkey.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs5_gmonkey,marg,CompleteHit
8146,Q#3122 - >seq3121,superfamily,340205,183,249,3.21956e-11,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs5_gmonkey.marg.frame1,1909130252_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs5_gmonkey,marg,CompleteHit
8147,Q#3125 - >seq3124,non-specific,340205,177,240,6.1902e-18,75.0652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs6_sqmonkey.pars.frame1,1909130252_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs6_sqmonkey,pars,CompleteHit
8148,Q#3125 - >seq3124,superfamily,340205,177,240,6.1902e-18,75.0652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs6_sqmonkey.pars.frame1,1909130252_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs6_sqmonkey,pars,CompleteHit
8149,Q#3130 - >seq3129,non-specific,340205,213,276,2.71583e-18,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs6_sqmonkey.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs6_sqmonkey,marg,CompleteHit
8150,Q#3130 - >seq3129,superfamily,340205,213,276,2.71583e-18,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs6_sqmonkey.marg.frame3,1909130252_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs6_sqmonkey,marg,CompleteHit
8151,Q#3133 - >seq3132,non-specific,238827,529,568,0.00431445,39.967,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs8_ctshrew.marg.frame2,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8152,Q#3133 - >seq3132,superfamily,295487,529,568,0.00431445,39.967,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.marg.frame2,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8153,Q#3134 - >seq3133,specific,197310,14,245,5.35212e-33,127.853,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs8_ctshrew,marg,CompleteHit
8154,Q#3134 - >seq3133,superfamily,351117,14,245,5.35212e-33,127.853,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,CompleteHit
8155,Q#3134 - >seq3133,non-specific,238827,519,584,1.78193e-18,85.4206,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8156,Q#3134 - >seq3133,superfamily,295487,519,584,1.78193e-18,85.4206,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8157,Q#3134 - >seq3133,non-specific,197306,77,245,3.457e-15,76.366,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8158,Q#3134 - >seq3133,non-specific,197320,77,230,6.4807899999999995e-09,57.9102,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8159,Q#3134 - >seq3133,non-specific,223780,73,230,1.35575e-08,57.2231,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8160,Q#3134 - >seq3133,non-specific,333820,525,579,1.06815e-07,53.065,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8161,Q#3134 - >seq3133,superfamily,333820,525,579,1.06815e-07,53.065,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8162,Q#3134 - >seq3133,non-specific,197322,117,231,2.3865999999999998e-05,47.696999999999996,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8163,Q#3134 - >seq3133,specific,335306,75,238,3.93216e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8164,Q#3134 - >seq3133,non-specific,273186,116,246,0.00012995200000000002,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8165,Q#3134 - >seq3133,non-specific,197307,101,231,0.000289738,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8166,Q#3134 - >seq3133,non-specific,339261,118,241,0.00367804,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MC1,ORF2,hs8_ctshrew,marg,CompleteHit
8167,Q#3134 - >seq3133,non-specific,272954,101,216,0.00490446,40.0589,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs8_ctshrew.marg.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8168,Q#3135 - >seq3134,non-specific,238827,595,712,1.61597e-22,96.9766,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8169,Q#3135 - >seq3134,superfamily,295487,595,712,1.61597e-22,96.9766,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8170,Q#3135 - >seq3134,non-specific,333820,581,712,7.439450000000001e-10,59.2282,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8171,Q#3135 - >seq3134,superfamily,333820,581,712,7.439450000000001e-10,59.2282,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8172,Q#3135 - >seq3134,non-specific,238828,585,690,0.000881753,41.8029,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8173,Q#3135 - >seq3134,non-specific,238185,596,690,0.0091375,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.marg.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,marg,CompleteHit
8174,Q#3137 - >seq3136,non-specific,238827,477,542,7.94592e-19,86.191,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs8_ctshrew.pars.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8175,Q#3137 - >seq3136,superfamily,295487,477,542,7.94592e-19,86.191,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.pars.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8176,Q#3137 - >seq3136,non-specific,333820,483,537,5.230659999999999e-08,53.8354,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.pars.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8177,Q#3137 - >seq3136,superfamily,333820,483,537,5.230659999999999e-08,53.8354,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.pars.frame1,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8178,Q#3138 - >seq3137,non-specific,238827,517,700,1.03927e-23,100.443,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
8179,Q#3138 - >seq3137,superfamily,295487,517,700,1.03927e-23,100.443,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
8180,Q#3138 - >seq3137,non-specific,333820,509,700,6.35768e-11,62.3098,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,pars,CompleteHit
8181,Q#3138 - >seq3137,superfamily,333820,509,700,6.35768e-11,62.3098,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs8_ctshrew,pars,CompleteHit
8182,Q#3138 - >seq3137,non-specific,197310,88,187,2.8503700000000003e-06,49.6573,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
8183,Q#3138 - >seq3137,superfamily,351117,88,187,2.8503700000000003e-06,49.6573,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs8_ctshrew.pars.frame3,1909130255_L1MC1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
8184,Q#3139 - >seq3138,non-specific,238827,602,657,1.4484299999999999e-08,56.5306,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs9_pika,marg,BothTerminiTruncated
8185,Q#3139 - >seq3138,superfamily,295487,602,657,1.4484299999999999e-08,56.5306,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs9_pika,marg,BothTerminiTruncated
8186,Q#3139 - >seq3138,non-specific,333820,602,658,0.00037581199999999995,42.6646,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs9_pika,marg,BothTerminiTruncated
8187,Q#3139 - >seq3138,superfamily,333820,602,658,0.00037581199999999995,42.6646,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs9_pika,marg,BothTerminiTruncated
8188,Q#3140 - >seq3139,specific,238827,462,613,2.0620799999999998e-33,128.563,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs9_pika.marg.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs9_pika,marg,C-TerminusTruncated
8189,Q#3140 - >seq3139,superfamily,295487,462,613,2.0620799999999998e-33,128.563,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs9_pika.marg.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs9_pika,marg,C-TerminusTruncated
8190,Q#3140 - >seq3139,non-specific,333820,468,613,1.81584e-16,78.4882,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.marg.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs9_pika,marg,C-TerminusTruncated
8191,Q#3140 - >seq3139,superfamily,333820,468,613,1.81584e-16,78.4882,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.marg.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs9_pika,marg,C-TerminusTruncated
8192,Q#3140 - >seq3139,non-specific,238828,468,613,9.577919999999998e-08,54.1292,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs9_pika.marg.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs9_pika,marg,C-TerminusTruncated
8193,Q#3141 - >seq3140,specific,197310,30,233,1.20145e-44,161.365,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8194,Q#3141 - >seq3140,superfamily,351117,30,233,1.20145e-44,161.365,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8195,Q#3141 - >seq3140,non-specific,197306,27,233,3.64522e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8196,Q#3141 - >seq3140,non-specific,223780,31,234,3.48006e-13,71.0903,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8197,Q#3141 - >seq3140,specific,335306,31,226,2.84156e-12,67.6554,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8198,Q#3141 - >seq3140,non-specific,197320,31,218,3.01516e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8199,Q#3141 - >seq3140,non-specific,197307,25,233,1.1541300000000002e-09,60.3793,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8200,Q#3141 - >seq3140,non-specific,273186,31,234,1.24317e-08,57.2888,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8201,Q#3141 - >seq3140,non-specific,197322,104,233,5.10071e-07,52.7046,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,N-TerminusTruncated
8202,Q#3141 - >seq3140,non-specific,197321,31,233,5.46164e-06,49.0876,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8203,Q#3141 - >seq3140,non-specific,272954,32,233,1.27472e-05,48.1481,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8204,Q#3141 - >seq3140,non-specific,197319,25,233,0.000136675,44.9601,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8205,Q#3141 - >seq3140,non-specific,339261,105,229,0.000794702,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MC1,ORF2,hs9_pika,marg,CompleteHit
8206,Q#3141 - >seq3140,non-specific,238827,674,730,0.00230757,40.7374,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs9_pika,marg,N-TerminusTruncated
8207,Q#3141 - >seq3140,superfamily,295487,674,730,0.00230757,40.7374,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs9_pika,marg,N-TerminusTruncated
8208,Q#3144 - >seq3143,specific,238827,503,749,5.922179999999999e-48,170.55,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8209,Q#3144 - >seq3143,superfamily,295487,503,749,5.922179999999999e-48,170.55,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8210,Q#3144 - >seq3143,specific,197310,28,231,8.392519999999999e-45,161.75,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8211,Q#3144 - >seq3143,superfamily,351117,28,231,8.392519999999999e-45,161.75,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8212,Q#3144 - >seq3143,non-specific,333820,509,727,6.99723e-23,96.9777,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8213,Q#3144 - >seq3143,superfamily,333820,509,727,6.99723e-23,96.9777,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8214,Q#3144 - >seq3143,non-specific,197306,25,231,3.4983300000000007e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8215,Q#3144 - >seq3143,non-specific,223780,29,232,1.29977e-13,72.2459,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8216,Q#3144 - >seq3143,non-specific,238828,509,663,6.522979999999999e-13,69.152,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,C-TerminusTruncated
8217,Q#3144 - >seq3143,specific,335306,29,224,2.6544099999999998e-12,67.6554,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8218,Q#3144 - >seq3143,non-specific,197320,29,216,2.47111e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8219,Q#3144 - >seq3143,non-specific,197307,23,231,6.59467e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8220,Q#3144 - >seq3143,non-specific,273186,29,232,5.7633800000000004e-09,58.0592,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8221,Q#3144 - >seq3143,non-specific,197322,102,231,4.75636e-07,52.7046,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,N-TerminusTruncated
8222,Q#3144 - >seq3143,non-specific,275209,462,663,5.8027e-07,52.8452,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,C-TerminusTruncated
8223,Q#3144 - >seq3143,superfamily,275209,462,663,5.8027e-07,52.8452,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,C-TerminusTruncated
8224,Q#3144 - >seq3143,non-specific,197321,29,231,1.31445e-06,51.0136,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8225,Q#3144 - >seq3143,non-specific,272954,30,231,1.37668e-05,47.7629,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8226,Q#3144 - >seq3143,non-specific,197319,23,231,8.43526e-05,45.3453,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8227,Q#3144 - >seq3143,non-specific,339261,103,227,0.000216596,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8228,Q#3144 - >seq3143,specific,225881,508,735,0.00211658,41.3629,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,N-TerminusTruncated
8229,Q#3144 - >seq3143,superfamily,225881,508,735,0.00211658,41.3629,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs9_pika,pars,N-TerminusTruncated
8230,Q#3144 - >seq3143,non-specific,235175,205,443,0.00465226,41.2028,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs9_pika,pars,C-TerminusTruncated
8231,Q#3144 - >seq3143,superfamily,235175,205,443,0.00465226,41.2028,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs9_pika,pars,C-TerminusTruncated
8232,Q#3144 - >seq3143,non-specific,274009,301,422,0.00757439,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs9_pika,pars,N-TerminusTruncated
8233,Q#3144 - >seq3143,superfamily,274009,301,422,0.00757439,40.4363,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs9_pika,pars,N-TerminusTruncated
8234,Q#3144 - >seq3143,non-specific,197311,29,199,0.00881802,38.8121,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs9_pika.pars.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs9_pika,pars,CompleteHit
8235,Q#3146 - >seq3145,non-specific,340205,150,179,1.33828e-05,41.1676,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs9_pika,marg,BothTerminiTruncated
8236,Q#3146 - >seq3145,superfamily,340205,150,179,1.33828e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.marg.frame1,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC1,ORF1,hs9_pika,marg,BothTerminiTruncated
8237,Q#3148 - >seq3147,non-specific,340205,53,98,4.5156899999999994e-13,58.5016,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.pars.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs9_pika,pars,N-TerminusTruncated
8238,Q#3148 - >seq3147,superfamily,340205,53,98,4.5156899999999994e-13,58.5016,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.pars.frame2,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC1,ORF1,hs9_pika,pars,N-TerminusTruncated
8239,Q#3150 - >seq3149,non-specific,335182,59,132,6.366319999999999e-06,43.0603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs9_pika,marg,CompleteHit
8240,Q#3150 - >seq3149,superfamily,335182,59,132,6.366319999999999e-06,43.0603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs9_pika,marg,CompleteHit
8241,Q#3150 - >seq3149,non-specific,340205,139,193,0.000429576,37.3156,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs9_pika,marg,CompleteHit
8242,Q#3150 - >seq3149,superfamily,340205,139,193,0.000429576,37.3156,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs9_pika.marg.frame3,1909130256_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs9_pika,marg,CompleteHit
8243,Q#3151 - >seq3150,specific,238827,505,684,8.38207e-29,115.46600000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,C-TerminusTruncated
8244,Q#3151 - >seq3150,superfamily,295487,505,684,8.38207e-29,115.46600000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,C-TerminusTruncated
8245,Q#3151 - >seq3150,non-specific,333820,504,684,3.27374e-17,80.7994,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,C-TerminusTruncated
8246,Q#3151 - >seq3150,superfamily,333820,504,684,3.27374e-17,80.7994,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,C-TerminusTruncated
8247,Q#3151 - >seq3150,non-specific,238828,493,729,1.31975e-07,53.744,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,CompleteHit
8248,Q#3151 - >seq3150,non-specific,275209,558,729,5.6428900000000004e-05,46.681999999999995,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,BothTerminiTruncated
8249,Q#3151 - >seq3150,superfamily,275209,558,729,5.6428900000000004e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs10_snmole.marg.frame2,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC1,ORF2,hs10_snmole,marg,BothTerminiTruncated
8250,Q#3154 - >seq3153,non-specific,340205,176,240,6.93446e-26,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs0_human.marg.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,marg,CompleteHit
8251,Q#3154 - >seq3153,superfamily,340205,176,240,6.93446e-26,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs0_human.marg.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,marg,CompleteHit
8252,Q#3154 - >seq3153,non-specific,335182,79,173,2.18826e-06,44.9863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs0_human.marg.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,marg,CompleteHit
8253,Q#3154 - >seq3153,superfamily,335182,79,173,2.18826e-06,44.9863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs0_human.marg.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,marg,CompleteHit
8254,Q#3155 - >seq3154,non-specific,340205,171,230,2.60206e-21,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs0_human.pars.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,pars,CompleteHit
8255,Q#3155 - >seq3154,superfamily,340205,171,230,2.60206e-21,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs0_human.pars.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,pars,CompleteHit
8256,Q#3155 - >seq3154,non-specific,335182,74,168,1.7068700000000001e-06,44.9863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs0_human.pars.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,pars,CompleteHit
8257,Q#3155 - >seq3154,superfamily,335182,74,168,1.7068700000000001e-06,44.9863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs0_human.pars.frame3,1909130258_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC1,ORF1,hs0_human,pars,CompleteHit
8258,Q#3159 - >seq3158,specific,197310,12,242,3.21127e-27,111.289,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs10_snmole.marg.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC1,ORF2,hs10_snmole,marg,CompleteHit
8259,Q#3159 - >seq3158,superfamily,351117,12,242,3.21127e-27,111.289,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs10_snmole.marg.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs10_snmole,marg,CompleteHit
8260,Q#3159 - >seq3158,non-specific,197306,19,242,0.000436165,43.2389,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs10_snmole.marg.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs10_snmole,marg,CompleteHit
8261,Q#3159 - >seq3158,non-specific,130673,242,638,0.00215249,42.346000000000004,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1MC1.ORF2.hs10_snmole.marg.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC1,ORF2,hs10_snmole,marg,BothTerminiTruncated
8262,Q#3159 - >seq3158,superfamily,130673,242,638,0.00215249,42.346000000000004,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1MC1.ORF2.hs10_snmole.marg.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC1,ORF2,hs10_snmole,marg,BothTerminiTruncated
8263,Q#3162 - >seq3161,non-specific,238827,494,573,9.582069999999999e-13,68.4718,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8264,Q#3162 - >seq3161,superfamily,295487,494,573,9.582069999999999e-13,68.4718,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8265,Q#3162 - >seq3161,non-specific,197310,31,131,3.50684e-11,64.2949,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8266,Q#3162 - >seq3161,superfamily,351117,31,131,3.50684e-11,64.2949,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8267,Q#3162 - >seq3161,non-specific,333820,476,573,2.58893e-06,48.8278,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8268,Q#3162 - >seq3161,superfamily,333820,476,573,2.58893e-06,48.8278,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8269,Q#3162 - >seq3161,non-specific,238828,453,571,6.03885e-06,48.3513,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8270,Q#3162 - >seq3161,non-specific,197306,1,131,2.4574499999999997e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8271,Q#3162 - >seq3161,non-specific,223780,23,124,0.00122738,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC1,ORF2,hs10_snmole,pars,N-TerminusTruncated
8272,Q#3163 - >seq3162,non-specific,340205,169,220,1.52622e-11,57.7312,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs10_snmole.marg.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs10_snmole,marg,N-TerminusTruncated
8273,Q#3163 - >seq3162,superfamily,340205,169,220,1.52622e-11,57.7312,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs10_snmole.marg.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs10_snmole,marg,N-TerminusTruncated
8274,Q#3163 - >seq3162,non-specific,335182,68,150,1.94739e-08,50.3791,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs10_snmole.marg.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs10_snmole,marg,CompleteHit
8275,Q#3163 - >seq3162,superfamily,335182,68,150,1.94739e-08,50.3791,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC1.ORF1.hs10_snmole.marg.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC1,ORF1,hs10_snmole,marg,CompleteHit
8276,Q#3167 - >seq3166,non-specific,340205,132,172,4.29061e-05,40.012,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs10_snmole,pars,C-TerminusTruncated
8277,Q#3167 - >seq3166,superfamily,340205,132,172,4.29061e-05,40.012,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC1.ORF1.hs10_snmole.pars.frame1,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC1,ORF1,hs10_snmole,pars,C-TerminusTruncated
8278,Q#3168 - >seq3167,non-specific,238827,352,450,5.0403000000000004e-20,89.6578,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs10_snmole.pars.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs10_snmole,pars,C-TerminusTruncated
8279,Q#3168 - >seq3167,superfamily,295487,352,450,5.0403000000000004e-20,89.6578,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs10_snmole.pars.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs10_snmole,pars,C-TerminusTruncated
8280,Q#3168 - >seq3167,non-specific,333820,368,455,5.257579999999999e-09,56.5318,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.pars.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs10_snmole,pars,C-TerminusTruncated
8281,Q#3168 - >seq3167,superfamily,333820,368,455,5.257579999999999e-09,56.5318,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs10_snmole.pars.frame3,1909130258_L1MC1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs10_snmole,pars,C-TerminusTruncated
8282,Q#3171 - >seq3170,non-specific,340205,172,225,3.1645599999999993e-14,65.4352,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs3_orang.marg.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs3_orang,marg,C-TerminusTruncated
8283,Q#3171 - >seq3170,superfamily,340205,172,225,3.1645599999999993e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs3_orang.marg.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs3_orang,marg,C-TerminusTruncated
8284,Q#3174 - >seq3173,non-specific,238827,507,696,1.9242700000000003e-24,102.755,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8285,Q#3174 - >seq3173,superfamily,295487,507,696,1.9242700000000003e-24,102.755,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8286,Q#3174 - >seq3173,non-specific,333820,514,665,2.3675e-13,69.6286,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8287,Q#3174 - >seq3173,superfamily,333820,514,665,2.3675e-13,69.6286,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8288,Q#3174 - >seq3173,non-specific,238828,510,635,5.6918599999999995e-12,66.4556,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,BothTerminiTruncated
8289,Q#3174 - >seq3173,non-specific,275209,515,599,1.1449e-08,58.238,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,BothTerminiTruncated
8290,Q#3174 - >seq3173,superfamily,275209,515,599,1.1449e-08,58.238,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs3_orang.pars.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs3_orang,pars,BothTerminiTruncated
8291,Q#3175 - >seq3174,specific,197310,60,210,4.61077e-27,110.904,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8292,Q#3175 - >seq3174,superfamily,351117,60,210,4.61077e-27,110.904,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8293,Q#3175 - >seq3174,non-specific,238827,528,725,3.7075699999999996e-14,72.709,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8294,Q#3175 - >seq3174,superfamily,295487,528,725,3.7075699999999996e-14,72.709,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8295,Q#3175 - >seq3174,non-specific,197306,60,207,9.70969e-11,63.2693,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8296,Q#3175 - >seq3174,non-specific,223780,64,199,1.15915e-09,60.3047,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8297,Q#3175 - >seq3174,non-specific,197320,98,200,4.89387e-09,58.2954,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8298,Q#3175 - >seq3174,non-specific,238828,548,666,4.76515e-08,54.8996,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
8299,Q#3175 - >seq3174,non-specific,333820,548,665,7.04239e-07,50.7538,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
8300,Q#3175 - >seq3174,superfamily,333820,548,665,7.04239e-07,50.7538,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
8301,Q#3175 - >seq3174,non-specific,197307,83,210,1.1761100000000001e-06,51.1345,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8302,Q#3175 - >seq3174,non-specific,273186,98,200,1.1801700000000001e-05,48.044,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8303,Q#3175 - >seq3174,non-specific,272954,83,199,5.39522e-05,45.8369,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8304,Q#3175 - >seq3174,specific,335306,64,204,6.3122e-05,45.3138,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8305,Q#3175 - >seq3174,non-specific,197322,99,200,7.042390000000001e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8306,Q#3175 - >seq3174,non-specific,339261,100,199,0.00382124,38.4723,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
8307,Q#3175 - >seq3174,non-specific,275209,549,633,0.004704600000000001,40.5188,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
8308,Q#3175 - >seq3174,superfamily,275209,549,633,0.004704600000000001,40.5188,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs2_gorilla.marg.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
8309,Q#3176 - >seq3175,non-specific,340205,164,224,9.65196e-14,63.5092,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs3_orang.pars.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs3_orang,pars,CompleteHit
8310,Q#3176 - >seq3175,superfamily,340205,164,224,9.65196e-14,63.5092,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs3_orang.pars.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs3_orang,pars,CompleteHit
8311,Q#3176 - >seq3175,non-specific,335182,75,160,0.000146847,39.5935,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs3_orang.pars.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs3_orang,pars,CompleteHit
8312,Q#3176 - >seq3175,superfamily,335182,75,160,0.000146847,39.5935,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs3_orang.pars.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs3_orang,pars,CompleteHit
8313,Q#3177 - >seq3176,specific,197310,30,220,5.425599999999999e-30,118.993,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs3_orang,pars,CompleteHit
8314,Q#3177 - >seq3176,superfamily,351117,30,220,5.425599999999999e-30,118.993,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,pars,CompleteHit
8315,Q#3177 - >seq3176,non-specific,197306,59,220,2.1707e-14,74.0548,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8316,Q#3177 - >seq3176,non-specific,238827,488,538,5.55813e-10,60.3826,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs3_orang,pars,C-TerminusTruncated
8317,Q#3177 - >seq3176,superfamily,295487,488,538,5.55813e-10,60.3826,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs3_orang,pars,C-TerminusTruncated
8318,Q#3177 - >seq3176,non-specific,223780,75,213,6.440030000000001e-10,61.0751,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8319,Q#3177 - >seq3176,non-specific,197320,90,205,1.4409799999999999e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8320,Q#3177 - >seq3176,non-specific,273186,91,220,4.5960700000000005e-07,52.2812,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8321,Q#3177 - >seq3176,non-specific,197307,75,220,2.42291e-06,49.9789,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8322,Q#3177 - >seq3176,non-specific,197322,75,220,1.10952e-05,48.4674,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8323,Q#3177 - >seq3176,specific,335306,49,213,1.99247e-05,46.8546,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8324,Q#3177 - >seq3176,non-specific,339261,92,216,3.54835e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MC2,ORF2,hs3_orang,pars,CompleteHit
8325,Q#3177 - >seq3176,non-specific,272954,75,191,0.00116067,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs3_orang,pars,N-TerminusTruncated
8326,Q#3177 - >seq3176,non-specific,333820,494,537,0.00144675,40.7386,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs3_orang,pars,C-TerminusTruncated
8327,Q#3177 - >seq3176,superfamily,333820,494,537,0.00144675,40.7386,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.pars.frame2,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs3_orang,pars,C-TerminusTruncated
8328,Q#3179 - >seq3178,non-specific,238827,471,520,6.83261e-08,54.2194,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs3_orang.marg.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs3_orang,marg,C-TerminusTruncated
8329,Q#3179 - >seq3178,superfamily,295487,471,520,6.83261e-08,54.2194,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs3_orang.marg.frame1,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs3_orang,marg,C-TerminusTruncated
8330,Q#3180 - >seq3179,specific,197310,11,237,8.47458e-39,144.416,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8331,Q#3180 - >seq3179,superfamily,351117,11,237,8.47458e-39,144.416,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8332,Q#3180 - >seq3179,non-specific,238827,540,729,1.6444799999999998e-24,102.755,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8333,Q#3180 - >seq3179,superfamily,295487,540,729,1.6444799999999998e-24,102.755,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8334,Q#3180 - >seq3179,non-specific,197306,11,237,2.6562399999999997e-17,82.5292,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8335,Q#3180 - >seq3179,non-specific,333820,547,698,9.780499999999999e-14,70.7842,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8336,Q#3180 - >seq3179,superfamily,333820,547,698,9.780499999999999e-14,70.7842,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8337,Q#3180 - >seq3179,non-specific,238828,543,668,5.67217e-12,66.4556,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,BothTerminiTruncated
8338,Q#3180 - >seq3179,non-specific,223780,92,230,4.93376e-10,61.4603,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8339,Q#3180 - >seq3179,non-specific,197320,43,222,2.24187e-09,59.451,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8340,Q#3180 - >seq3179,non-specific,275209,548,632,8.99858e-09,58.6232,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,BothTerminiTruncated
8341,Q#3180 - >seq3179,superfamily,275209,548,632,8.99858e-09,58.6232,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs3_orang,marg,BothTerminiTruncated
8342,Q#3180 - >seq3179,specific,335306,12,230,2.4804099999999996e-07,52.6326,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8343,Q#3180 - >seq3179,non-specific,273186,108,237,4.85986e-07,52.2812,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8344,Q#3180 - >seq3179,non-specific,197307,92,237,2.29625e-06,49.9789,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8345,Q#3180 - >seq3179,non-specific,197322,92,237,1.13135e-05,48.4674,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs3_orang,marg,N-TerminusTruncated
8346,Q#3180 - >seq3179,non-specific,339261,109,233,5.915270000000001e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8347,Q#3180 - >seq3179,non-specific,272954,43,208,0.000299744,43.9109,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs3_orang.marg.frame3,1909130259_L1MC2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs3_orang,marg,CompleteHit
8348,Q#3181 - >seq3180,non-specific,340205,96,134,6.61012e-07,44.2492,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs4_gibbon.pars.frame2,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
8349,Q#3181 - >seq3180,superfamily,340205,96,134,6.61012e-07,44.2492,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs4_gibbon.pars.frame2,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
8350,Q#3182 - >seq3181,non-specific,335182,32,85,1.36971e-06,44.2159,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs4_gibbon.pars.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
8351,Q#3182 - >seq3181,superfamily,335182,32,85,1.36971e-06,44.2159,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs4_gibbon.pars.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
8352,Q#3185 - >seq3184,non-specific,335182,90,182,3.82832e-09,52.6903,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs4_gibbon.marg.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,marg,CompleteHit
8353,Q#3185 - >seq3184,superfamily,335182,90,182,3.82832e-09,52.6903,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs4_gibbon.marg.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,marg,CompleteHit
8354,Q#3185 - >seq3184,non-specific,340205,185,226,0.000129179,39.2416,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs4_gibbon.marg.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8355,Q#3185 - >seq3184,superfamily,340205,185,226,0.000129179,39.2416,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs4_gibbon.marg.frame3,1909130259_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8356,Q#3190 - >seq3189,non-specific,238827,494,606,7.3080900000000006e-09,57.301,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs2_gorilla.pars.frame2,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
8357,Q#3190 - >seq3189,superfamily,295487,494,606,7.3080900000000006e-09,57.301,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs2_gorilla.pars.frame2,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
8358,Q#3190 - >seq3189,non-specific,238828,510,600,1.7887599999999997e-06,49.891999999999996,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs2_gorilla.pars.frame2,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
8359,Q#3190 - >seq3189,non-specific,333820,514,603,2.1934600000000002e-05,46.1314,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs2_gorilla.pars.frame2,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
8360,Q#3190 - >seq3189,superfamily,333820,514,603,2.1934600000000002e-05,46.1314,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs2_gorilla.pars.frame2,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
8361,Q#3193 - >seq3192,non-specific,340205,162,212,1.14628e-07,46.9456,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs1_chimp,pars,C-TerminusTruncated
8362,Q#3193 - >seq3192,superfamily,340205,162,212,1.14628e-07,46.9456,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs1_chimp,pars,C-TerminusTruncated
8363,Q#3195 - >seq3194,non-specific,340205,173,223,5.3623699999999995e-08,48.1012,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs1_chimp.marg.frame2,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC2,ORF1,hs1_chimp,marg,C-TerminusTruncated
8364,Q#3195 - >seq3194,superfamily,340205,173,223,5.3623699999999995e-08,48.1012,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs1_chimp.marg.frame2,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC2,ORF1,hs1_chimp,marg,C-TerminusTruncated
8365,Q#3198 - >seq3197,non-specific,197310,3,121,2.2046799999999997e-05,46.9609,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs2_gorilla.pars.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
8366,Q#3198 - >seq3197,superfamily,351117,3,121,2.2046799999999997e-05,46.9609,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs2_gorilla.pars.frame3,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
8367,Q#3200 - >seq3199,specific,197310,44,228,6.476349999999999e-30,118.993,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8368,Q#3200 - >seq3199,superfamily,351117,44,228,6.476349999999999e-30,118.993,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8369,Q#3200 - >seq3199,specific,238827,493,743,5.29479e-29,115.851,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8370,Q#3200 - >seq3199,superfamily,295487,493,743,5.29479e-29,115.851,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8371,Q#3200 - >seq3199,non-specific,333820,499,720,1.3858399999999999e-12,67.3174,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8372,Q#3200 - >seq3199,superfamily,333820,499,720,1.3858399999999999e-12,67.3174,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8373,Q#3200 - >seq3199,non-specific,197306,48,228,1.1148e-10,62.8841,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8374,Q#3200 - >seq3199,non-specific,223780,64,213,3.97241e-08,55.6823,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8375,Q#3200 - >seq3199,non-specific,197320,98,213,5.64198e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8376,Q#3200 - >seq3199,non-specific,273186,98,229,9.74075e-06,48.4292,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8377,Q#3200 - >seq3199,non-specific,197322,99,228,9.75118e-05,45.771,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8378,Q#3200 - >seq3199,non-specific,197307,50,228,0.000298623,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
8379,Q#3200 - >seq3199,non-specific,274009,252,438,0.00156795,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
8380,Q#3200 - >seq3199,superfamily,274009,252,438,0.00156795,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
8381,Q#3200 - >seq3199,non-specific,339261,100,224,0.00242187,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC2.ORF2.hs1_chimp.pars.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC2,ORF2,hs1_chimp,pars,CompleteHit
8382,Q#3202 - >seq3201,specific,197310,45,237,9.609669999999999e-32,124.38600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8383,Q#3202 - >seq3201,superfamily,351117,45,237,9.609669999999999e-32,124.38600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8384,Q#3202 - >seq3201,non-specific,197306,57,237,8.06041e-11,63.2693,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8385,Q#3202 - >seq3201,non-specific,223780,73,222,1.68171e-08,56.8379,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8386,Q#3202 - >seq3201,non-specific,197320,107,222,5.49784e-08,55.2138,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8387,Q#3202 - >seq3201,non-specific,273186,107,238,7.99161e-06,48.4292,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8388,Q#3202 - >seq3201,non-specific,197322,108,237,9.50258e-05,45.771,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8389,Q#3202 - >seq3201,non-specific,197307,59,237,0.000150822,44.5861,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
8390,Q#3202 - >seq3201,non-specific,339261,109,233,0.00365055,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC2.ORF2.hs1_chimp.marg.frame3,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8391,Q#3209 - >seq3208,non-specific,197310,49,201,4.04039e-14,72.7693,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs2_gorilla.pars.frame1,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
8392,Q#3209 - >seq3208,superfamily,351117,49,201,4.04039e-14,72.7693,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs2_gorilla.pars.frame1,1909130259_L1MC2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
8393,Q#3210 - >seq3209,specific,238827,471,730,1.7585299999999996e-30,120.089,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs1_chimp.marg.frame1,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8394,Q#3210 - >seq3209,superfamily,295487,471,730,1.7585299999999996e-30,120.089,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs1_chimp.marg.frame1,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8395,Q#3210 - >seq3209,non-specific,333820,477,698,3.4580099999999997e-12,66.1618,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs1_chimp.marg.frame1,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8396,Q#3210 - >seq3209,superfamily,333820,477,698,3.4580099999999997e-12,66.1618,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs1_chimp.marg.frame1,1909130259_L1MC2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs1_chimp,marg,CompleteHit
8397,Q#3212 - >seq3211,specific,197310,10,235,1.1376400000000002e-37,141.335,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC2,ORF2,hs4_gibbon,marg,CompleteHit
8398,Q#3212 - >seq3211,superfamily,351117,10,235,1.1376400000000002e-37,141.335,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,CompleteHit
8399,Q#3212 - >seq3211,non-specific,238827,571,765,2.48333e-25,105.066,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8400,Q#3212 - >seq3211,superfamily,295487,571,765,2.48333e-25,105.066,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8401,Q#3212 - >seq3211,non-specific,197306,10,235,4.1819099999999997e-17,82.14399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,CompleteHit
8402,Q#3212 - >seq3211,non-specific,333820,583,734,2.66651e-15,75.0214,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8403,Q#3212 - >seq3211,superfamily,333820,583,734,2.66651e-15,75.0214,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8404,Q#3212 - >seq3211,non-specific,238828,579,709,4.0237800000000005e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8405,Q#3212 - >seq3211,non-specific,223780,61,228,6.877660000000001e-10,61.0751,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8406,Q#3212 - >seq3211,non-specific,275209,584,779,1.5730200000000001e-06,51.6896,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8407,Q#3212 - >seq3211,superfamily,275209,584,779,1.5730200000000001e-06,51.6896,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8408,Q#3212 - >seq3211,non-specific,197307,91,235,7.291419999999999e-06,48.8233,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8409,Q#3212 - >seq3211,non-specific,197320,29,220,1.1670299999999999e-05,47.895,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,CompleteHit
8410,Q#3212 - >seq3211,specific,335306,30,228,0.00023202599999999998,43.773,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC2.ORF2.hs4_gibbon.marg.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,marg,CompleteHit
8411,Q#3213 - >seq3212,non-specific,238827,471,512,0.00150458,41.1226,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs4_gibbon.marg.frame1,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
8412,Q#3213 - >seq3212,superfamily,295487,471,512,0.00150458,41.1226,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs4_gibbon.marg.frame1,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
8413,Q#3214 - >seq3213,specific,197310,11,212,9.732849999999998e-36,135.55700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8414,Q#3214 - >seq3213,superfamily,351117,11,212,9.732849999999998e-36,135.55700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8415,Q#3214 - >seq3213,non-specific,197306,7,212,5.25339e-15,75.5956,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8416,Q#3214 - >seq3213,non-specific,223780,19,205,2.94948e-10,61.8455,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8417,Q#3214 - >seq3213,non-specific,197307,9,212,4.37243e-07,52.2901,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8418,Q#3214 - >seq3213,non-specific,197320,8,197,5.30582e-07,52.1322,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8419,Q#3214 - >seq3213,specific,335306,9,205,0.000226842,43.773,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8420,Q#3214 - >seq3213,non-specific,272954,9,212,0.0007577230000000001,42.3701,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC2,ORF2,hs4_gibbon,pars,CompleteHit
8421,Q#3214 - >seq3213,non-specific,238827,473,514,0.0036885999999999998,39.967,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
8422,Q#3214 - >seq3213,superfamily,295487,473,514,0.0036885999999999998,39.967,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs4_gibbon.pars.frame3,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
8423,Q#3215 - >seq3214,non-specific,238827,525,710,1.1056e-24,103.525,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
8424,Q#3215 - >seq3214,superfamily,295487,525,710,1.1056e-24,103.525,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
8425,Q#3215 - >seq3214,non-specific,333820,537,688,2.01501e-15,75.4066,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
8426,Q#3215 - >seq3214,superfamily,333820,537,688,2.01501e-15,75.4066,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
8427,Q#3215 - >seq3214,non-specific,238828,533,663,3.0872000000000005e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
8428,Q#3215 - >seq3214,non-specific,275209,538,688,1.9691900000000003e-06,51.3044,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
8429,Q#3215 - >seq3214,superfamily,275209,538,688,1.9691900000000003e-06,51.3044,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs4_gibbon.pars.frame2,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
8430,Q#3216 - >seq3215,non-specific,340095,240,334,0.00289794,41.7368,pfam17380,DUF5401,NC,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MC2.ORF2.hs4_gibbon.pars.frame1,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
8431,Q#3216 - >seq3215,superfamily,340095,240,334,0.00289794,41.7368,cl38662,DUF5401 superfamily,NC, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MC2.ORF2.hs4_gibbon.pars.frame1,1909130304_L1MC2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
8432,Q#3220 - >seq3219,specific,238827,470,720,1.2877199999999998e-29,117.39200000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs5_gmonkey,pars,CompleteHit
8433,Q#3220 - >seq3219,superfamily,295487,470,720,1.2877199999999998e-29,117.39200000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs5_gmonkey,pars,CompleteHit
8434,Q#3220 - >seq3219,non-specific,197310,29,166,5.95212e-16,78.5473,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8435,Q#3220 - >seq3219,superfamily,351117,29,166,5.95212e-16,78.5473,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8436,Q#3220 - >seq3219,non-specific,333820,476,698,7.579500000000001e-14,70.7842,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs5_gmonkey,pars,CompleteHit
8437,Q#3220 - >seq3219,superfamily,333820,476,698,7.579500000000001e-14,70.7842,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs5_gmonkey,pars,CompleteHit
8438,Q#3220 - >seq3219,non-specific,197322,83,166,0.000840512,42.6894,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8439,Q#3220 - >seq3219,non-specific,223780,50,166,0.00105052,42.2003,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8440,Q#3220 - >seq3219,non-specific,197320,83,164,0.00401912,40.191,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8441,Q#3220 - >seq3219,non-specific,197311,53,123,0.00675164,39.1973,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs5_gmonkey.pars.frame2,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8442,Q#3222 - >seq3221,specific,238827,516,775,2.12808e-30,119.70299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8443,Q#3222 - >seq3221,superfamily,295487,516,775,2.12808e-30,119.70299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8444,Q#3222 - >seq3221,non-specific,197310,32,222,2.6996499999999997e-18,85.4809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8445,Q#3222 - >seq3221,superfamily,351117,32,222,2.6996499999999997e-18,85.4809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8446,Q#3222 - >seq3221,non-specific,333820,522,744,2.48683e-14,72.325,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8447,Q#3222 - >seq3221,superfamily,333820,522,744,2.48683e-14,72.325,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs5_gmonkey,marg,CompleteHit
8448,Q#3222 - >seq3221,non-specific,197306,8,178,2.67602e-05,46.7057,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8449,Q#3222 - >seq3221,non-specific,197322,95,178,0.000896117,42.6894,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8450,Q#3222 - >seq3221,non-specific,197320,45,176,0.00196671,41.3466,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8451,Q#3222 - >seq3221,non-specific,223780,97,178,0.00415212,40.2743,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8452,Q#3224 - >seq3223,non-specific,340205,178,245,9.043719999999999e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs5_gmonkey,marg,CompleteHit
8453,Q#3224 - >seq3223,superfamily,340205,178,245,9.043719999999999e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs5_gmonkey,marg,CompleteHit
8454,Q#3224 - >seq3223,non-specific,335182,78,175,2.39237e-05,41.9047,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs5_gmonkey,marg,CompleteHit
8455,Q#3224 - >seq3223,superfamily,335182,78,175,2.39237e-05,41.9047,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs5_gmonkey.marg.frame1,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs5_gmonkey,marg,CompleteHit
8456,Q#3225 - >seq3224,non-specific,340205,147,205,7.167819999999999e-17,71.5984,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs5_gmonkey.pars.frame3,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs5_gmonkey,pars,CompleteHit
8457,Q#3225 - >seq3224,superfamily,340205,147,205,7.167819999999999e-17,71.5984,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs5_gmonkey.pars.frame3,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs5_gmonkey,pars,CompleteHit
8458,Q#3225 - >seq3224,non-specific,335182,52,145,1.55967e-07,47.6827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs5_gmonkey.pars.frame3,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs5_gmonkey,pars,CompleteHit
8459,Q#3225 - >seq3224,superfamily,335182,52,145,1.55967e-07,47.6827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs5_gmonkey.pars.frame3,1909130305_L1MC2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs5_gmonkey,pars,CompleteHit
8460,Q#3230 - >seq3229,non-specific,340205,71,130,3.6191e-17,70.0576,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs6_sqmonkey.pars.frame2,1909130306_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs6_sqmonkey,pars,CompleteHit
8461,Q#3230 - >seq3229,superfamily,340205,71,130,3.6191e-17,70.0576,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs6_sqmonkey.pars.frame2,1909130306_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs6_sqmonkey,pars,CompleteHit
8462,Q#3232 - >seq3231,non-specific,340205,114,180,5.10775e-15,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs6_sqmonkey.marg.frame1,1909130306_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs6_sqmonkey,marg,CompleteHit
8463,Q#3232 - >seq3231,superfamily,340205,114,180,5.10775e-15,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs6_sqmonkey.marg.frame1,1909130306_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs6_sqmonkey,marg,CompleteHit
8464,Q#3235 - >seq3234,non-specific,238827,133,171,3.51652e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs6_sqmonkey.marg.frame2,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8465,Q#3235 - >seq3234,superfamily,295487,133,171,3.51652e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs6_sqmonkey.marg.frame2,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8466,Q#3236 - >seq3235,non-specific,238827,186,251,1.5314e-05,46.9006,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs6_sqmonkey.marg.frame3,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8467,Q#3236 - >seq3235,superfamily,295487,186,251,1.5314e-05,46.9006,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs6_sqmonkey.marg.frame3,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8468,Q#3238 - >seq3237,non-specific,238827,179,248,1.38185e-05,46.9006,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs6_sqmonkey.pars.frame2,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8469,Q#3238 - >seq3237,superfamily,295487,179,248,1.38185e-05,46.9006,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs6_sqmonkey.pars.frame2,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8470,Q#3239 - >seq3238,non-specific,238827,129,167,4.91534e-05,45.3598,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs6_sqmonkey.pars.frame1,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8471,Q#3239 - >seq3238,superfamily,295487,129,167,4.91534e-05,45.3598,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs6_sqmonkey.pars.frame1,1909130307_L1MC2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8472,Q#3241 - >seq3240,non-specific,238827,141,254,2.04986e-15,75.7906,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8473,Q#3241 - >seq3240,superfamily,295487,141,254,2.04986e-15,75.7906,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8474,Q#3241 - >seq3240,non-specific,333820,147,252,1.57125e-06,49.213,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8475,Q#3241 - >seq3240,superfamily,333820,147,252,1.57125e-06,49.213,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8476,Q#3242 - >seq3241,non-specific,340205,90,139,5.41604e-08,46.5604,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs7_bushaby.pars.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,pars,CompleteHit
8477,Q#3242 - >seq3241,superfamily,340205,90,139,5.41604e-08,46.5604,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs7_bushaby.pars.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,pars,CompleteHit
8478,Q#3243 - >seq3242,non-specific,335182,8,82,4.47822e-05,39.9787,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
8479,Q#3243 - >seq3242,superfamily,335182,8,82,4.47822e-05,39.9787,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs7_bushaby.pars.frame2,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC2,ORF1,hs7_bushaby,pars,N-TerminusTruncated
8480,Q#3245 - >seq3244,non-specific,340205,169,224,8.71258e-17,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,marg,CompleteHit
8481,Q#3245 - >seq3244,superfamily,340205,169,224,8.71258e-17,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,marg,CompleteHit
8482,Q#3245 - >seq3244,non-specific,335182,74,166,0.000881397,37.2823,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,marg,CompleteHit
8483,Q#3245 - >seq3244,superfamily,335182,74,166,0.000881397,37.2823,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs7_bushaby,marg,CompleteHit
8484,Q#3250 - >seq3249,non-specific,238827,507,787,3.6695e-17,81.5686,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs7_bushaby,marg,CompleteHit
8485,Q#3250 - >seq3249,superfamily,295487,507,787,3.6695e-17,81.5686,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs7_bushaby,marg,CompleteHit
8486,Q#3250 - >seq3249,non-specific,333820,513,620,7.49316e-07,50.7538,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
8487,Q#3250 - >seq3249,superfamily,333820,513,620,7.49316e-07,50.7538,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
8488,Q#3250 - >seq3249,non-specific,197310,63,220,6.888789999999999e-06,48.5017,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
8489,Q#3250 - >seq3249,superfamily,351117,63,220,6.888789999999999e-06,48.5017,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
8490,Q#3250 - >seq3249,non-specific,197306,70,208,0.0015924000000000001,41.3129,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs7_bushaby.marg.frame1,1909130310_L1MC2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
8491,Q#3254 - >seq3253,non-specific,197310,10,240,7.39494e-25,104.741,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs8_ctshrew,marg,CompleteHit
8492,Q#3254 - >seq3253,superfamily,351117,10,240,7.39494e-25,104.741,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs8_ctshrew,marg,CompleteHit
8493,Q#3254 - >seq3253,non-specific,197306,10,232,7.4391400000000004e-09,57.8765,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs8_ctshrew,marg,CompleteHit
8494,Q#3254 - >seq3253,non-specific,238827,549,861,1.85305e-06,50.3674,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs8_ctshrew,marg,CompleteHit
8495,Q#3254 - >seq3253,superfamily,295487,549,861,1.85305e-06,50.3674,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs8_ctshrew,marg,CompleteHit
8496,Q#3254 - >seq3253,non-specific,197322,114,238,0.00013168200000000002,45.3858,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8497,Q#3254 - >seq3253,non-specific,273186,113,238,0.000490609,43.4216,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8498,Q#3254 - >seq3253,non-specific,223780,100,229,0.0006646569999999999,42.9707,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8499,Q#3254 - >seq3253,non-specific,197320,113,229,0.00761805,39.4206,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC2.ORF2.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8500,Q#3255 - >seq3254,non-specific,238827,224,307,6.221469999999999e-10,59.9974,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs8_ctshrew.pars.frame2,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8501,Q#3255 - >seq3254,superfamily,295487,224,307,6.221469999999999e-10,59.9974,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs8_ctshrew.pars.frame2,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8502,Q#3255 - >seq3254,non-specific,333820,230,283,0.00336468,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs8_ctshrew.pars.frame2,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8503,Q#3255 - >seq3254,superfamily,333820,230,283,0.00336468,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs8_ctshrew.pars.frame2,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8504,Q#3261 - >seq3260,non-specific,340205,80,145,2.34057e-16,68.5168,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs8_ctshrew,marg,CompleteHit
8505,Q#3261 - >seq3260,superfamily,340205,80,145,2.34057e-16,68.5168,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs8_ctshrew,marg,CompleteHit
8506,Q#3261 - >seq3260,non-specific,335182,1,75,9.192910000000001e-07,44.6011,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
8507,Q#3261 - >seq3260,superfamily,335182,1,75,9.192910000000001e-07,44.6011,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs8_ctshrew.marg.frame1,1909130311_L1MC2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
8508,Q#3265 - >seq3264,non-specific,340205,128,169,9.83283e-07,43.864,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs2_gorilla.pars.frame3,1909130312_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs2_gorilla,pars,N-TerminusTruncated
8509,Q#3265 - >seq3264,superfamily,340205,128,169,9.83283e-07,43.864,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs2_gorilla.pars.frame3,1909130312_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs2_gorilla,pars,N-TerminusTruncated
8510,Q#3268 - >seq3267,non-specific,335182,159,185,2.94867e-05,41.9047,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs1_chimp.marg.frame2,1909130312_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC3,ORF1,hs1_chimp,marg,C-TerminusTruncated
8511,Q#3268 - >seq3267,superfamily,335182,159,185,2.94867e-05,41.9047,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs1_chimp.marg.frame2,1909130312_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC3,ORF1,hs1_chimp,marg,C-TerminusTruncated
8512,Q#3268 - >seq3267,non-specific,340204,115,156,0.000292249,37.7724,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC3.ORF1.hs1_chimp.marg.frame2,1909130312_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Trimerization,L1MC3,ORF1,hs1_chimp,marg,CompleteHit
8513,Q#3268 - >seq3267,superfamily,340204,115,156,0.000292249,37.7724,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC3.ORF1.hs1_chimp.marg.frame2,1909130312_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Trimerization,L1MC3,ORF1,hs1_chimp,marg,CompleteHit
8514,Q#3272 - >seq3271,non-specific,340205,147,188,1.3577799999999998e-06,43.864,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs2_gorilla.marg.frame1,1909130312_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
8515,Q#3272 - >seq3271,superfamily,340205,147,188,1.3577799999999998e-06,43.864,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs2_gorilla.marg.frame1,1909130312_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
8516,Q#3278 - >seq3277,non-specific,340205,84,146,4.0948500000000003e-14,63.123999999999995,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs3_orang.pars.frame3,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs3_orang,pars,CompleteHit
8517,Q#3278 - >seq3277,superfamily,340205,84,146,4.0948500000000003e-14,63.123999999999995,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs3_orang.pars.frame3,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs3_orang,pars,CompleteHit
8518,Q#3278 - >seq3277,non-specific,335182,16,81,3.7073400000000006e-08,48.4531,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs3_orang.pars.frame3,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs3_orang,pars,N-TerminusTruncated
8519,Q#3278 - >seq3277,superfamily,335182,16,81,3.7073400000000006e-08,48.4531,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs3_orang.pars.frame3,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs3_orang,pars,N-TerminusTruncated
8520,Q#3279 - >seq3278,non-specific,335182,151,248,5.8768e-19,80.4247,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8521,Q#3279 - >seq3278,superfamily,335182,151,248,5.8768e-19,80.4247,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8522,Q#3279 - >seq3278,non-specific,340205,251,315,7.10762e-16,70.828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8523,Q#3279 - >seq3278,superfamily,340205,251,315,7.10762e-16,70.828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8524,Q#3279 - >seq3278,non-specific,340204,110,148,9.67031e-07,44.706,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8525,Q#3279 - >seq3278,superfamily,340204,110,148,9.67031e-07,44.706,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC3.ORF1.hs3_orang.marg.frame1,1909130312_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC3,ORF1,hs3_orang,marg,CompleteHit
8526,Q#3283 - >seq3282,non-specific,309995,10,48,0.00176021,36.5165,pfam05104,Rib_recp_KP_reg,C,cl25527,Ribosome receptor lysine/proline rich region; This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear.,L1MC2.ORF1.hs9_pika.marg.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC2,ORF1,hs9_pika,marg,C-TerminusTruncated
8527,Q#3283 - >seq3282,superfamily,309995,10,48,0.00176021,36.5165,cl25527,Rib_recp_KP_reg superfamily,C, - ,Ribosome receptor lysine/proline rich region; This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear.,L1MC2.ORF1.hs9_pika.marg.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC2,ORF1,hs9_pika,marg,C-TerminusTruncated
8528,Q#3284 - >seq3283,non-specific,340205,237,300,6.79898e-22,87.0064,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs0_human.marg.frame2,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC2,ORF1,hs0_human,marg,CompleteHit
8529,Q#3284 - >seq3283,superfamily,340205,237,300,6.79898e-22,87.0064,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs0_human.marg.frame2,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC2,ORF1,hs0_human,marg,CompleteHit
8530,Q#3289 - >seq3288,non-specific,335182,44,121,2.03842e-06,43.8307,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs9_pika,marg,N-TerminusTruncated
8531,Q#3289 - >seq3288,superfamily,335182,44,121,2.03842e-06,43.8307,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs9_pika,marg,N-TerminusTruncated
8532,Q#3293 - >seq3292,specific,238827,534,744,3.71623e-37,139.349,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8533,Q#3293 - >seq3292,superfamily,295487,534,744,3.71623e-37,139.349,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8534,Q#3293 - >seq3292,non-specific,333820,540,739,3.58702e-19,86.5773,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8535,Q#3293 - >seq3292,superfamily,333820,540,739,3.58702e-19,86.5773,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8536,Q#3293 - >seq3292,non-specific,197310,10,229,1.51309e-12,68.5321,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC2,ORF2,hs9_pika,marg,CompleteHit
8537,Q#3293 - >seq3292,superfamily,351117,10,229,1.51309e-12,68.5321,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC2,ORF2,hs9_pika,marg,CompleteHit
8538,Q#3293 - >seq3292,non-specific,238828,606,736,2.85343e-06,49.5068,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC2,ORF2,hs9_pika,marg,BothTerminiTruncated
8539,Q#3293 - >seq3292,non-specific,274009,257,494,0.000481545,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC2,ORF2,hs9_pika,marg,BothTerminiTruncated
8540,Q#3293 - >seq3292,superfamily,274009,257,494,0.000481545,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC2.ORF2.hs9_pika.marg.frame1,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC2,ORF2,hs9_pika,marg,BothTerminiTruncated
8541,Q#3294 - >seq3293,non-specific,234665,53,141,0.0070072,39.3387,PRK00145,PRK00145,C,cl00489,putative inner membrane protein translocase component YidC; Provisional,L1MC2.ORF2.hs9_pika.marg.frame2,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8542,Q#3294 - >seq3293,superfamily,351116,53,141,0.0070072,39.3387,cl00489,60KD_IMP superfamily,C, - ,60Kd inner membrane protein; 60Kd inner membrane protein.  ,L1MC2.ORF2.hs9_pika.marg.frame2,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MC2,ORF2,hs9_pika,marg,C-TerminusTruncated
8543,Q#3296 - >seq3295,non-specific,340205,124,185,8.102310000000001e-22,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs0_human.pars.frame1,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC2,ORF1,hs0_human,pars,CompleteHit
8544,Q#3296 - >seq3295,superfamily,340205,124,185,8.102310000000001e-22,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC2.ORF1.hs0_human.pars.frame1,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC2,ORF1,hs0_human,pars,CompleteHit
8545,Q#3298 - >seq3297,non-specific,335182,37,113,2.4774700000000002e-08,49.2235,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs0_human.pars.frame3,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs0_human,pars,C-TerminusTruncated
8546,Q#3298 - >seq3297,superfamily,335182,37,113,2.4774700000000002e-08,49.2235,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs0_human.pars.frame3,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC2,ORF1,hs0_human,pars,C-TerminusTruncated
8547,Q#3299 - >seq3298,non-specific,335182,183,246,8.632340000000001e-05,40.7491,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs0_human.marg.frame1,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs0_human,marg,C-TerminusTruncated
8548,Q#3299 - >seq3298,superfamily,335182,183,246,8.632340000000001e-05,40.7491,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC2.ORF1.hs0_human.marg.frame1,1909130312_L1MC2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC2,ORF1,hs0_human,marg,C-TerminusTruncated
8549,Q#3300 - >seq3299,specific,238827,430,614,2.6622999999999997e-32,125.096,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,C-TerminusTruncated
8550,Q#3300 - >seq3299,superfamily,295487,430,614,2.6622999999999997e-32,125.096,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,C-TerminusTruncated
8551,Q#3300 - >seq3299,non-specific,333820,428,613,4.32398e-18,83.1105,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,C-TerminusTruncated
8552,Q#3300 - >seq3299,superfamily,333820,428,613,4.32398e-18,83.1105,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,C-TerminusTruncated
8553,Q#3300 - >seq3299,non-specific,238828,482,613,3.1538699999999996e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,N-TerminusTruncated
8554,Q#3300 - >seq3299,non-specific,275209,487,572,0.00427156,40.1336,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,BothTerminiTruncated
8555,Q#3300 - >seq3299,superfamily,275209,487,572,0.00427156,40.1336,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC2.ORF2.hs9_pika.pars.frame3,1909130312_L1MC2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC2,ORF2,hs9_pika,pars,BothTerminiTruncated
8556,Q#3302 - >seq3301,non-specific,335182,61,133,2.00658e-12,60.7795,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs4_gibbon.marg.frame1,1909130313_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs4_gibbon,marg,CompleteHit
8557,Q#3302 - >seq3301,superfamily,335182,61,133,2.00658e-12,60.7795,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs4_gibbon.marg.frame1,1909130313_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs4_gibbon,marg,CompleteHit
8558,Q#3310 - >seq3309,non-specific,238827,398,596,1.03373e-16,80.0278,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,CompleteHit
8559,Q#3310 - >seq3309,superfamily,295487,398,596,1.03373e-16,80.0278,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,CompleteHit
8560,Q#3310 - >seq3309,non-specific,333820,434,554,3.76733e-09,56.917,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8561,Q#3310 - >seq3309,superfamily,333820,434,554,3.76733e-09,56.917,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8562,Q#3310 - >seq3309,non-specific,238828,430,519,4.27645e-08,54.8996,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8563,Q#3310 - >seq3309,non-specific,275209,435,519,0.000143132,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8564,Q#3310 - >seq3309,superfamily,275209,435,519,0.000143132,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs6_sqmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8565,Q#3311 - >seq3310,non-specific,197310,1,96,1.4308499999999999e-09,59.2873,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs6_sqmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
8566,Q#3311 - >seq3310,superfamily,351117,1,96,1.4308499999999999e-09,59.2873,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs6_sqmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
8567,Q#3311 - >seq3310,non-specific,197306,1,96,0.008357,39.0017,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs6_sqmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
8568,Q#3312 - >seq3311,non-specific,238827,550,737,1.80942e-15,76.561,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8569,Q#3312 - >seq3311,superfamily,295487,550,737,1.80942e-15,76.561,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8570,Q#3312 - >seq3311,non-specific,333820,575,695,1.4676799999999999e-08,55.7614,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
8571,Q#3312 - >seq3311,superfamily,333820,575,695,1.4676799999999999e-08,55.7614,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
8572,Q#3312 - >seq3311,non-specific,238828,575,660,9.54084e-08,54.1292,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
8573,Q#3312 - >seq3311,non-specific,275209,576,660,0.000136219,45.5264,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
8574,Q#3312 - >seq3311,superfamily,275209,576,660,0.000136219,45.5264,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs6_sqmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
8575,Q#3314 - >seq3313,non-specific,197310,113,239,1.4072799999999998e-14,74.3101,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs6_sqmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8576,Q#3314 - >seq3313,superfamily,351117,113,239,1.4072799999999998e-14,74.3101,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs6_sqmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8577,Q#3314 - >seq3313,non-specific,197306,67,239,1.0642100000000001e-05,47.8613,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs6_sqmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8578,Q#3315 - >seq3314,non-specific,340205,85,144,2.13068e-11,55.8052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs7_bushaby.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,pars,CompleteHit
8579,Q#3315 - >seq3314,superfamily,340205,85,144,2.13068e-11,55.8052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs7_bushaby.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,pars,CompleteHit
8580,Q#3315 - >seq3314,non-specific,335182,16,82,4.55536e-07,44.9863,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs7_bushaby.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,pars,N-TerminusTruncated
8581,Q#3315 - >seq3314,superfamily,335182,16,82,4.55536e-07,44.9863,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs7_bushaby.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,pars,N-TerminusTruncated
8582,Q#3318 - >seq3317,non-specific,335182,39,145,2.8398900000000003e-14,65.7871,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs7_bushaby.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,marg,CompleteHit
8583,Q#3318 - >seq3317,superfamily,335182,39,145,2.8398900000000003e-14,65.7871,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs7_bushaby.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,marg,CompleteHit
8584,Q#3318 - >seq3317,non-specific,340205,148,212,9.66404e-08,47.3308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs7_bushaby.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,marg,CompleteHit
8585,Q#3318 - >seq3317,superfamily,340205,148,212,9.66404e-08,47.3308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs7_bushaby.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs7_bushaby,marg,CompleteHit
8586,Q#3322 - >seq3321,specific,197310,23,235,1.1725799999999999e-36,138.253,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,CompleteHit
8587,Q#3322 - >seq3321,superfamily,351117,23,235,1.1725799999999999e-36,138.253,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,CompleteHit
8588,Q#3322 - >seq3321,non-specific,197306,71,235,3.41838e-28,114.116,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8589,Q#3322 - >seq3321,non-specific,197307,71,235,5.35237e-13,70.0093,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8590,Q#3322 - >seq3321,non-specific,223780,71,237,8.847639999999999e-13,69.5495,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8591,Q#3322 - >seq3321,non-specific,197320,71,235,8.47711e-11,63.303000000000004,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8592,Q#3322 - >seq3321,non-specific,273186,71,236,1.5239200000000003e-08,56.9036,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8593,Q#3322 - >seq3321,non-specific,339261,107,231,4.56637e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MC3,ORF2,hs5_gmonkey,pars,CompleteHit
8594,Q#3322 - >seq3321,non-specific,236970,71,237,6.45367e-08,54.9002,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8595,Q#3322 - >seq3321,non-specific,197321,71,235,8.82726e-08,54.4804,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8596,Q#3322 - >seq3321,non-specific,335306,71,228,7.29378e-07,51.0918,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8597,Q#3322 - >seq3321,non-specific,197322,90,235,1.7825400000000001e-06,51.1638,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8598,Q#3322 - >seq3321,non-specific,197319,71,235,3.33685e-06,49.5825,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8599,Q#3322 - >seq3321,non-specific,272954,71,235,2.70477e-05,46.9925,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8600,Q#3322 - >seq3321,non-specific,197311,71,235,4.40317e-05,45.7457,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8601,Q#3322 - >seq3321,non-specific,197317,138,228,0.0011283,41.8188,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC3.ORF2.hs5_gmonkey.pars.frame2,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8602,Q#2 - >seq3325,non-specific,335182,37,106,9.58448e-07,44.9863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs5_gmonkey,pars,CompleteHit
8603,Q#2 - >seq3325,superfamily,335182,37,106,9.58448e-07,44.9863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC3,ORF1,hs5_gmonkey,pars,CompleteHit
8604,Q#3 - >seq3326,non-specific,335182,168,257,2.88335e-12,61.9351,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs5_gmonkey,marg,CompleteHit
8605,Q#3 - >seq3326,superfamily,335182,168,257,2.88335e-12,61.9351,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs5_gmonkey,marg,CompleteHit
8606,Q#5 - >seq3328,non-specific,340205,262,310,1.24411e-12,61.9684,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8607,Q#5 - >seq3328,superfamily,340205,262,310,1.24411e-12,61.9684,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8608,Q#6 - >seq3329,non-specific,340205,119,182,2.2226399999999998e-17,72.3688,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs5_gmonkey.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs5_gmonkey,pars,CompleteHit
8609,Q#6 - >seq3329,superfamily,340205,119,182,2.2226399999999998e-17,72.3688,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs5_gmonkey.pars.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC3,ORF1,hs5_gmonkey,pars,CompleteHit
8610,Q#7 - >seq3330,non-specific,238827,475,634,3.17374e-18,84.6502,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8611,Q#7 - >seq3330,superfamily,295487,475,634,3.17374e-18,84.6502,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8612,Q#7 - >seq3330,non-specific,197310,8,81,1.37386e-12,68.5321,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8613,Q#7 - >seq3330,superfamily,351117,8,81,1.37386e-12,68.5321,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8614,Q#7 - >seq3330,non-specific,197306,8,80,1.41575e-11,65.5805,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8615,Q#7 - >seq3330,non-specific,333820,481,635,2.85833e-11,63.4654,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8616,Q#7 - >seq3330,superfamily,333820,481,635,2.85833e-11,63.4654,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8617,Q#7 - >seq3330,non-specific,238828,536,660,8.79306e-10,59.9072,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8618,Q#7 - >seq3330,superfamily,295487,536,660,8.79306e-10,59.9072,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8619,Q#7 - >seq3330,non-specific,275209,547,677,1.7884699999999999e-07,54.386,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8620,Q#7 - >seq3330,superfamily,275209,547,677,1.7884699999999999e-07,54.386,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8621,Q#7 - >seq3330,non-specific,223780,8,48,6.53366e-05,45.6671,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8622,Q#7 - >seq3330,non-specific,197336,6,42,0.00165879,41.4439,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8623,Q#7 - >seq3330,non-specific,197321,6,48,0.00222228,40.9984,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8624,Q#7 - >seq3330,non-specific,197320,7,48,0.006462899999999999,39.4206,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8625,Q#7 - >seq3330,specific,335306,9,52,0.0064941,39.1506,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC3.ORF2.hs5_gmonkey.pars.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8626,Q#8 - >seq3331,non-specific,238827,472,724,2.5386900000000003e-24,102.369,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8627,Q#8 - >seq3331,superfamily,295487,472,724,2.5386900000000003e-24,102.369,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8628,Q#8 - >seq3331,non-specific,333820,478,667,3.57342e-13,68.8582,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8629,Q#8 - >seq3331,superfamily,333820,478,667,3.57342e-13,68.8582,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8630,Q#8 - >seq3331,non-specific,238828,533,667,5.63318e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8631,Q#8 - >seq3331,non-specific,275209,544,632,1.48985e-07,54.7712,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8632,Q#8 - >seq3331,superfamily,275209,544,632,1.48985e-07,54.7712,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs5_gmonkey.marg.frame1,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8633,Q#10 - >seq3333,specific,197310,8,237,3.810640000000001e-56,194.49200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8634,Q#10 - >seq3333,superfamily,351117,8,237,3.810640000000001e-56,194.49200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8635,Q#10 - >seq3333,non-specific,197306,8,237,1.3168e-47,169.97,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8636,Q#10 - >seq3333,non-specific,223780,8,239,1.1159900000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8637,Q#10 - >seq3333,non-specific,197307,8,237,3.27768e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8638,Q#10 - >seq3333,non-specific,197321,6,237,9.26745e-19,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8639,Q#10 - >seq3333,non-specific,197320,7,237,5.63101e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8640,Q#10 - >seq3333,specific,335306,9,230,1.07146e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8641,Q#10 - >seq3333,non-specific,273186,8,238,5.36461e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8642,Q#10 - >seq3333,non-specific,197319,7,237,3.00847e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8643,Q#10 - >seq3333,non-specific,197336,6,236,5.79369e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8644,Q#10 - >seq3333,non-specific,272954,8,237,2.8442e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8645,Q#10 - >seq3333,non-specific,197322,8,237,3.940109999999999e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8646,Q#10 - >seq3333,non-specific,236970,8,239,1.9238e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8647,Q#10 - >seq3333,non-specific,339261,109,233,6.21214e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8648,Q#10 - >seq3333,non-specific,197311,6,237,5.61273e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs5_gmonkey,marg,CompleteHit
8649,Q#10 - >seq3333,non-specific,197317,140,230,0.00172417,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC3.ORF2.hs5_gmonkey.marg.frame3,1909130314_L1MC3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8650,Q#13 - >seq3336,non-specific,162719,674,738,0.00545653,39.382,TIGR02129,hisA_euk,NC,cl21457,"phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, eukaryotic type; This enzyme acts in the biosynthesis of histidine and has been characterized in S. cerevisiae and Arabidopsis where it complements the E. coli HisA gene. In eukaryotes the gene is known as HIS6. In bacteria, this gene is found in Fibrobacter succinogenes, presumably due to lateral gene transfer from plants in the rumen gut. [Amino acid biosynthesis, Histidine family]",L1MC3.ORF2.hs7_bushaby.marg.frame3,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC3,ORF2,hs7_bushaby,marg,BothTerminiTruncated
8651,Q#13 - >seq3336,superfamily,354814,674,738,0.00545653,39.382,cl21457,DRE_TIM_metallolyase superfamily,NC, - ,"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM"".",L1MC3.ORF2.hs7_bushaby.marg.frame3,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC3,ORF2,hs7_bushaby,marg,BothTerminiTruncated
8652,Q#15 - >seq3338,non-specific,238827,265,472,0.00043529800000000003,42.6634,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs7_bushaby.marg.frame1,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs7_bushaby,marg,CompleteHit
8653,Q#15 - >seq3338,superfamily,295487,265,472,0.00043529800000000003,42.6634,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs7_bushaby.marg.frame1,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs7_bushaby,marg,CompleteHit
8654,Q#18 - >seq3341,non-specific,238827,127,334,0.000643747,41.893,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs7_bushaby.pars.frame2,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs7_bushaby,pars,CompleteHit
8655,Q#18 - >seq3341,superfamily,295487,127,334,0.000643747,41.893,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs7_bushaby.pars.frame2,1909130315_L1MC3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs7_bushaby,pars,CompleteHit
8656,Q#21 - >seq3344,non-specific,238827,302,358,5.657800000000001e-09,56.9158,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs8_ctshrew.marg.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8657,Q#21 - >seq3344,superfamily,295487,302,358,5.657800000000001e-09,56.9158,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs8_ctshrew.marg.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8658,Q#21 - >seq3344,non-specific,238828,252,361,0.000136852,44.1141,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs8_ctshrew.marg.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
8659,Q#21 - >seq3344,non-specific,333820,297,354,0.00170995,40.3534,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs8_ctshrew.marg.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8660,Q#21 - >seq3344,superfamily,333820,297,354,0.00170995,40.3534,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs8_ctshrew.marg.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
8661,Q#23 - >seq3346,non-specific,238827,16,215,1.6918299999999998e-13,70.0126,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs8_ctshrew.pars.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8662,Q#23 - >seq3346,superfamily,295487,16,215,1.6918299999999998e-13,70.0126,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs8_ctshrew.pars.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
8663,Q#23 - >seq3346,non-specific,238828,115,218,0.00368649,39.4917,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs8_ctshrew.pars.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
8664,Q#23 - >seq3346,non-specific,333820,159,211,0.00511963,38.4274,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs8_ctshrew.pars.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
8665,Q#23 - >seq3346,superfamily,333820,159,211,0.00511963,38.4274,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs8_ctshrew.pars.frame1,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
8666,Q#24 - >seq3347,non-specific,238827,172,238,0.00137766,41.1226,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs8_ctshrew.marg.frame3,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8667,Q#24 - >seq3347,superfamily,295487,172,238,0.00137766,41.1226,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs8_ctshrew.marg.frame3,1909130316_L1MC3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
8668,Q#35 - >seq3358,non-specific,340205,91,137,7.126060000000001e-08,46.1752,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs0_human.marg.frame2,1909130317_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC3,ORF1,hs0_human,marg,N-TerminusTruncated
8669,Q#35 - >seq3358,superfamily,340205,91,137,7.126060000000001e-08,46.1752,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs0_human.marg.frame2,1909130317_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC3,ORF1,hs0_human,marg,N-TerminusTruncated
8670,Q#39 - >seq3362,specific,238827,215,467,2.90789e-35,133.571,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs10_snmole.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,marg,CompleteHit
8671,Q#39 - >seq3362,superfamily,295487,215,467,2.90789e-35,133.571,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs10_snmole.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,marg,CompleteHit
8672,Q#39 - >seq3362,non-specific,333820,221,467,5.174100000000001e-15,73.8658,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs10_snmole.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,marg,CompleteHit
8673,Q#39 - >seq3362,superfamily,333820,221,467,5.174100000000001e-15,73.8658,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs10_snmole.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,marg,CompleteHit
8674,Q#45 - >seq3368,non-specific,340205,57,103,1.5423e-07,44.6344,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs0_human.pars.frame2,1909130317_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC3,ORF1,hs0_human,pars,N-TerminusTruncated
8675,Q#45 - >seq3368,superfamily,340205,57,103,1.5423e-07,44.6344,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC3.ORF1.hs0_human.pars.frame2,1909130317_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC3,ORF1,hs0_human,pars,N-TerminusTruncated
8676,Q#46 - >seq3369,specific,238827,144,390,3.18143e-33,127.40700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs10_snmole.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,pars,CompleteHit
8677,Q#46 - >seq3369,superfamily,295487,144,390,3.18143e-33,127.40700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs10_snmole.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,pars,CompleteHit
8678,Q#46 - >seq3369,non-specific,333820,150,374,2.15936e-16,77.7178,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs10_snmole.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,pars,CompleteHit
8679,Q#46 - >seq3369,superfamily,333820,150,374,2.15936e-16,77.7178,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs10_snmole.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs10_snmole,pars,CompleteHit
8680,Q#48 - >seq3371,non-specific,238827,162,326,3.74454e-12,66.1606,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs9_pika.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs9_pika,pars,N-TerminusTruncated
8681,Q#48 - >seq3371,superfamily,295487,162,326,3.74454e-12,66.1606,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs9_pika.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs9_pika,pars,N-TerminusTruncated
8682,Q#48 - >seq3371,non-specific,333820,177,326,1.34784e-07,52.2946,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs9_pika,pars,N-TerminusTruncated
8683,Q#48 - >seq3371,superfamily,333820,177,326,1.34784e-07,52.2946,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs9_pika,pars,N-TerminusTruncated
8684,Q#48 - >seq3371,non-specific,238828,182,332,0.00019857799999999998,43.3437,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs9_pika.pars.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC3,ORF2,hs9_pika,pars,N-TerminusTruncated
8685,Q#49 - >seq3372,non-specific,238827,105,169,2.29317e-16,78.487,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs9_pika.pars.frame3,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs9_pika,pars,C-TerminusTruncated
8686,Q#49 - >seq3372,superfamily,295487,105,169,2.29317e-16,78.487,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs9_pika.pars.frame3,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs9_pika,pars,C-TerminusTruncated
8687,Q#49 - >seq3372,non-specific,333820,111,165,8.908660000000001e-08,52.6798,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.pars.frame3,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs9_pika,pars,C-TerminusTruncated
8688,Q#49 - >seq3372,superfamily,333820,111,165,8.908660000000001e-08,52.6798,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.pars.frame3,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs9_pika,pars,C-TerminusTruncated
8689,Q#51 - >seq3374,non-specific,238827,227,291,2.50233e-16,78.8722,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs9_pika.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs9_pika,marg,C-TerminusTruncated
8690,Q#51 - >seq3374,superfamily,295487,227,291,2.50233e-16,78.8722,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs9_pika.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs9_pika,marg,C-TerminusTruncated
8691,Q#51 - >seq3374,non-specific,333820,233,287,8.7402e-08,53.065,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs9_pika,marg,C-TerminusTruncated
8692,Q#51 - >seq3374,superfamily,333820,233,287,8.7402e-08,53.065,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs9_pika.marg.frame2,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC3,ORF2,hs9_pika,marg,C-TerminusTruncated
8693,Q#56 - >seq3379,non-specific,335182,1,34,0.00138324,33.4303,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs10_snmole.marg.frame1,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs10_snmole,marg,N-TerminusTruncated
8694,Q#56 - >seq3379,superfamily,335182,1,34,0.00138324,33.4303,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC3.ORF1.hs10_snmole.marg.frame1,1909130317_L1MC3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC3,ORF1,hs10_snmole,marg,N-TerminusTruncated
8695,Q#65 - >seq3388,non-specific,197310,4,218,2.22813e-26,108.59299999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8696,Q#65 - >seq3388,superfamily,351117,4,218,2.22813e-26,108.59299999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8697,Q#65 - >seq3388,non-specific,197306,4,218,7.52323e-12,65.9657,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8698,Q#65 - >seq3388,non-specific,197307,4,218,2.02985e-06,49.9789,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8699,Q#65 - >seq3388,non-specific,197320,50,231,6.98437e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
8700,Q#65 - >seq3388,non-specific,272954,4,231,1.12606e-05,47.7629,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8701,Q#65 - >seq3388,specific,335306,5,211,2.7553400000000003e-05,46.0842,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8702,Q#65 - >seq3388,non-specific,197321,2,218,0.000700208,42.153999999999996,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8703,Q#65 - >seq3388,non-specific,223780,4,219,0.00151822,41.4299,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4a.ORF2.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4a,ORF2,hs4_gibbon,marg,CompleteHit
8704,Q#67 - >seq3390,non-specific,335182,60,137,0.000663544,37.6675,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs5_gmonkey.pars.frame2,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4a,ORF1,hs5_gmonkey,pars,CompleteHit
8705,Q#67 - >seq3390,superfamily,335182,60,137,0.000663544,37.6675,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs5_gmonkey.pars.frame2,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4a,ORF1,hs5_gmonkey,pars,CompleteHit
8706,Q#68 - >seq3391,non-specific,340205,157,209,1.19686e-06,44.2492,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs5_gmonkey.pars.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,pars,CompleteHit
8707,Q#68 - >seq3391,superfamily,340205,157,209,1.19686e-06,44.2492,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs5_gmonkey.pars.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,pars,CompleteHit
8708,Q#70 - >seq3393,non-specific,340205,259,319,2.84219e-09,52.7236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,marg,CompleteHit
8709,Q#70 - >seq3393,superfamily,340205,259,319,2.84219e-09,52.7236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,marg,CompleteHit
8710,Q#70 - >seq3393,non-specific,335182,176,246,8.076699999999999e-07,46.5271,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8711,Q#70 - >seq3393,superfamily,335182,176,246,8.076699999999999e-07,46.5271,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8712,Q#70 - >seq3393,non-specific,336852,61,125,0.00385602,36.794000000000004,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8713,Q#70 - >seq3393,superfamily,336852,61,125,0.00385602,36.794000000000004,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
8714,Q#70 - >seq3393,non-specific,235175,42,139,0.00800917,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
8715,Q#70 - >seq3393,superfamily,235175,42,139,0.00800917,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
8716,Q#70 - >seq3393,non-specific,112704,3,137,0.00974159,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
8717,Q#70 - >seq3393,superfamily,112704,3,137,0.00974159,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1MC4a.ORF1.hs5_gmonkey.marg.frame1,1909130319_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
8718,Q#75 - >seq3398,non-specific,335182,156,251,2.76755e-26,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs4_gibbon,marg,CompleteHit
8719,Q#75 - >seq3398,superfamily,335182,156,251,2.76755e-26,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs4_gibbon,marg,CompleteHit
8720,Q#75 - >seq3398,non-specific,340205,278,318,7.54699e-11,56.9608,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
8721,Q#75 - >seq3398,superfamily,340205,278,318,7.54699e-11,56.9608,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
8722,Q#75 - >seq3398,non-specific,224117,42,183,0.0015761,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
8723,Q#75 - >seq3398,superfamily,224117,42,183,0.0015761,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MC4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
8724,Q#75 - >seq3398,non-specific,311007,41,223,0.00444348,38.5397,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8725,Q#75 - >seq3398,superfamily,311007,41,223,0.00444348,38.5397,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8726,Q#75 - >seq3398,non-specific,313078,50,218,0.00716303,37.397,pfam09787,Golgin_A5,C,cl25511,"Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.",L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8727,Q#75 - >seq3398,superfamily,313078,50,218,0.00716303,37.397,cl25511,Golgin_A5 superfamily,C, - ,"Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.",L1MC4a.ORF1.hs4_gibbon.marg.frame1,1909130319_L1MC4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
8728,Q#92 - >seq3415,non-specific,197310,95,184,5.192190000000001e-10,60.8281,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4a.ORF2.hs5_gmonkey.marg.frame1,1909130320_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8729,Q#92 - >seq3415,superfamily,351117,95,184,5.192190000000001e-10,60.8281,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4a.ORF2.hs5_gmonkey.marg.frame1,1909130320_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8730,Q#92 - >seq3415,non-specific,197306,95,183,0.000594693,42.4685,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4a.ORF2.hs5_gmonkey.marg.frame1,1909130320_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8731,Q#92 - >seq3415,non-specific,197320,95,180,0.00799487,39.0354,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4a.ORF2.hs5_gmonkey.marg.frame1,1909130320_L1MC4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8732,Q#98 - >seq3421,non-specific,238827,217,453,1.31592e-10,61.9234,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4a.ORF2.hs8_ctshrew.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs8_ctshrew,marg,CompleteHit
8733,Q#98 - >seq3421,superfamily,295487,217,453,1.31592e-10,61.9234,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4a.ORF2.hs8_ctshrew.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs8_ctshrew,marg,CompleteHit
8734,Q#104 - >seq3427,non-specific,238827,202,443,3.3998199999999995e-07,51.9082,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4a.ORF2.hs9_pika.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs9_pika,marg,CompleteHit
8735,Q#104 - >seq3427,superfamily,295487,202,443,3.3998199999999995e-07,51.9082,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4a.ORF2.hs9_pika.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs9_pika,marg,CompleteHit
8736,Q#106 - >seq3429,non-specific,238827,34,138,1.51976e-05,46.1302,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4a.ORF2.hs10_snmole.pars.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4a,ORF2,hs10_snmole,pars,N-TerminusTruncated
8737,Q#106 - >seq3429,superfamily,295487,34,138,1.51976e-05,46.1302,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4a.ORF2.hs10_snmole.pars.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4a,ORF2,hs10_snmole,pars,N-TerminusTruncated
8738,Q#109 - >seq3432,non-specific,238827,4,255,1.18231e-15,76.561,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4a.ORF2.hs10_snmole.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs10_snmole,marg,CompleteHit
8739,Q#109 - >seq3432,superfamily,295487,4,255,1.18231e-15,76.561,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4a.ORF2.hs10_snmole.marg.frame1,1909130321_L1MC4a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4a,ORF2,hs10_snmole,marg,CompleteHit
8740,Q#124 - >seq3447,non-specific,214395,7,115,0.000377935,42.7834,CHL00204,ycf1,NC,cl33340,Ycf1; Provisional,L1MC4a.ORF2.hs6_sqmonkey.pars.frame2,1909130321_L1MC4a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC4a,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8741,Q#124 - >seq3447,superfamily,214395,7,115,0.000377935,42.7834,cl33340,ycf1 superfamily,NC, - ,Ycf1; Provisional,L1MC4a.ORF2.hs6_sqmonkey.pars.frame2,1909130321_L1MC4a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC4a,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
8742,Q#133 - >seq3456,specific,197310,21,249,4.3351899999999994e-55,191.41099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8743,Q#133 - >seq3456,superfamily,351117,21,249,4.3351899999999994e-55,191.41099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8744,Q#133 - >seq3456,specific,238827,523,784,7.997619999999999e-50,175.942,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8745,Q#133 - >seq3456,superfamily,295487,523,784,7.997619999999999e-50,175.942,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8746,Q#133 - >seq3456,non-specific,197306,21,249,2.12863e-34,132.22,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8747,Q#133 - >seq3456,non-specific,333820,529,784,6.285880000000001e-24,100.059,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8748,Q#133 - >seq3456,superfamily,333820,529,784,6.285880000000001e-24,100.059,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8749,Q#133 - >seq3456,non-specific,223780,21,250,8.061379999999999e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8750,Q#133 - >seq3456,non-specific,197320,21,242,2.2370400000000002e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8751,Q#133 - >seq3456,non-specific,197307,21,249,2.92094e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8752,Q#133 - >seq3456,specific,335306,22,242,1.4256300000000003e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8753,Q#133 - >seq3456,non-specific,197321,19,249,1.19178e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8754,Q#133 - >seq3456,non-specific,273186,21,250,3.97992e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8755,Q#133 - >seq3456,non-specific,272954,21,249,9.20136e-11,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8756,Q#133 - >seq3456,non-specific,197319,25,249,2.2427300000000002e-10,62.2941,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8757,Q#133 - >seq3456,non-specific,197322,20,242,2.6064299999999997e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8758,Q#133 - >seq3456,non-specific,339261,121,245,7.32493e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8759,Q#133 - >seq3456,non-specific,197311,19,249,4.74055e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8760,Q#133 - >seq3456,non-specific,238828,611,749,1.86806e-06,50.2772,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,N-TerminusTruncated
8761,Q#133 - >seq3456,non-specific,274009,318,480,4.1446400000000004e-05,47.7551,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,C-TerminusTruncated
8762,Q#133 - >seq3456,superfamily,274009,318,480,4.1446400000000004e-05,47.7551,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,C-TerminusTruncated
8763,Q#133 - >seq3456,non-specific,235175,253,478,0.00018878400000000003,45.8252,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,C-TerminusTruncated
8764,Q#133 - >seq3456,superfamily,235175,253,478,0.00018878400000000003,45.8252,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,C-TerminusTruncated
8765,Q#133 - >seq3456,non-specific,238185,668,784,0.00141341,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,CompleteHit
8766,Q#133 - >seq3456,non-specific,275209,610,802,0.00244694,41.6744,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,N-TerminusTruncated
8767,Q#133 - >seq3456,superfamily,275209,610,802,0.00244694,41.6744,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs1_chimp,marg,N-TerminusTruncated
8768,Q#133 - >seq3456,non-specific,224117,242,514,0.00264178,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,N-TerminusTruncated
8769,Q#133 - >seq3456,superfamily,224117,242,514,0.00264178,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC4,ORF2,hs1_chimp,marg,N-TerminusTruncated
8770,Q#133 - >seq3456,non-specific,235175,321,477,0.00354715,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF2.hs1_chimp.marg.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,marg,BothTerminiTruncated
8771,Q#134 - >seq3457,non-specific,340205,130,191,8.03459e-21,81.6136,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs2_gorilla.pars.frame1,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8772,Q#134 - >seq3457,superfamily,340205,130,191,8.03459e-21,81.6136,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs2_gorilla.pars.frame1,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8773,Q#136 - >seq3459,non-specific,335182,47,129,5.85844e-12,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs2_gorilla.pars.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8774,Q#136 - >seq3459,superfamily,335182,47,129,5.85844e-12,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs2_gorilla.pars.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8775,Q#136 - >seq3459,non-specific,340204,3,45,0.000305578,37.001999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs2_gorilla.pars.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8776,Q#136 - >seq3459,superfamily,340204,3,45,0.000305578,37.001999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs2_gorilla.pars.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs2_gorilla,pars,CompleteHit
8777,Q#144 - >seq3467,non-specific,238827,627,741,4.74335e-10,60.7678,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8778,Q#144 - >seq3467,superfamily,295487,627,741,4.74335e-10,60.7678,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
8779,Q#144 - >seq3467,non-specific,197310,15,182,1.38726e-08,56.5909,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
8780,Q#144 - >seq3467,superfamily,351117,15,182,1.38726e-08,56.5909,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
8781,Q#144 - >seq3467,non-specific,333820,507,713,0.000183532,43.435,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs2_gorilla,marg,CompleteHit
8782,Q#144 - >seq3467,superfamily,333820,507,713,0.000183532,43.435,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs2_gorilla,marg,CompleteHit
8783,Q#144 - >seq3467,non-specific,197306,15,202,0.00171421,41.3129,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs2_gorilla,marg,CompleteHit
8784,Q#145 - >seq3468,non-specific,340205,253,314,1.4217e-18,78.1468,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8785,Q#145 - >seq3468,superfamily,340205,253,314,1.4217e-18,78.1468,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8786,Q#145 - >seq3468,non-specific,335182,157,253,3.4318e-16,72.7207,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8787,Q#145 - >seq3468,superfamily,335182,157,253,3.4318e-16,72.7207,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8788,Q#145 - >seq3468,non-specific,340204,113,155,0.000442322,37.3872,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8789,Q#145 - >seq3468,superfamily,340204,113,155,0.000442322,37.3872,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC4,ORF1,hs2_gorilla,marg,CompleteHit
8790,Q#145 - >seq3468,non-specific,237177,44,141,0.0066426,37.8354,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC4,ORF1,hs2_gorilla,marg,C-TerminusTruncated
8791,Q#145 - >seq3468,superfamily,237177,44,141,0.0066426,37.8354,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MC4.ORF1.hs2_gorilla.marg.frame3,1909130322_L1MC4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC4,ORF1,hs2_gorilla,marg,C-TerminusTruncated
8792,Q#148 - >seq3471,non-specific,238827,454,695,1.5794300000000002e-21,94.2802,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8793,Q#148 - >seq3471,superfamily,295487,454,695,1.5794300000000002e-21,94.2802,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8794,Q#148 - >seq3471,non-specific,197310,9,59,1.6384500000000003e-09,59.2873,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8795,Q#148 - >seq3471,superfamily,351117,9,59,1.6384500000000003e-09,59.2873,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8796,Q#148 - >seq3471,non-specific,197306,9,62,1.43276e-07,53.6393,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8797,Q#148 - >seq3471,non-specific,333820,460,570,3.06239e-07,51.5242,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8798,Q#148 - >seq3471,superfamily,333820,460,570,3.06239e-07,51.5242,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8799,Q#148 - >seq3471,non-specific,197307,9,68,1.50449e-05,47.6677,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8800,Q#148 - >seq3471,non-specific,223780,9,43,2.30535e-05,47.2079,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8801,Q#148 - >seq3471,non-specific,197321,7,68,0.000117151,44.8504,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8802,Q#148 - >seq3471,specific,335306,10,74,0.000156759,44.1582,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8803,Q#148 - >seq3471,non-specific,273186,9,58,0.00129153,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8804,Q#148 - >seq3471,non-specific,197320,9,43,0.00168257,41.3466,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame2,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8805,Q#153 - >seq3476,non-specific,274009,274,426,0.000558998,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8806,Q#153 - >seq3476,superfamily,274009,274,426,0.000558998,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,pars,C-TerminusTruncated
8807,Q#153 - >seq3476,non-specific,235175,276,426,0.00095224,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF2.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,pars,BothTerminiTruncated
8808,Q#153 - >seq3476,superfamily,235175,276,426,0.00095224,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC4.ORF2.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF2,hs1_chimp,pars,BothTerminiTruncated
8809,Q#157 - >seq3480,non-specific,335182,154,251,1.6639200000000002e-36,126.649,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8810,Q#157 - >seq3480,superfamily,335182,154,251,1.6639200000000002e-36,126.649,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8811,Q#157 - >seq3480,non-specific,340205,255,315,2.04129e-23,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8812,Q#157 - >seq3480,superfamily,340205,255,315,2.04129e-23,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8813,Q#157 - >seq3480,non-specific,340204,110,152,5.97126e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8814,Q#157 - >seq3480,superfamily,340204,110,152,5.97126e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs1_chimp,pars,CompleteHit
8815,Q#157 - >seq3480,non-specific,274009,43,183,5.14445e-05,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,BothTerminiTruncated
8816,Q#157 - >seq3480,superfamily,274009,43,183,5.14445e-05,44.6735,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,BothTerminiTruncated
8817,Q#157 - >seq3480,non-specific,235175,42,183,0.000261945,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,C-TerminusTruncated
8818,Q#157 - >seq3480,superfamily,235175,42,183,0.000261945,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,C-TerminusTruncated
8819,Q#157 - >seq3480,non-specific,274091,64,143,0.0006176959999999999,41.1422,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC4,ORF1,hs1_chimp,pars,N-TerminusTruncated
8820,Q#157 - >seq3480,superfamily,274091,64,143,0.0006176959999999999,41.1422,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC4,ORF1,hs1_chimp,pars,N-TerminusTruncated
8821,Q#157 - >seq3480,non-specific,274009,33,133,0.00615758,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,BothTerminiTruncated
8822,Q#157 - >seq3480,superfamily,274009,33,133,0.00615758,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.pars.frame3,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC4,ORF1,hs1_chimp,pars,BothTerminiTruncated
8823,Q#158 - >seq3481,non-specific,335182,161,258,4.204239999999999e-37,128.96,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8824,Q#158 - >seq3481,superfamily,335182,161,258,4.204239999999999e-37,128.96,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8825,Q#158 - >seq3481,non-specific,340205,264,330,4.28897e-21,85.4656,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8826,Q#158 - >seq3481,superfamily,340205,264,330,4.28897e-21,85.4656,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8827,Q#158 - >seq3481,non-specific,340204,115,159,2.18904e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8828,Q#158 - >seq3481,superfamily,340204,115,159,2.18904e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC4,ORF1,hs1_chimp,marg,CompleteHit
8829,Q#158 - >seq3481,non-specific,237177,45,151,0.000297765,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC4,ORF1,hs1_chimp,marg,C-TerminusTruncated
8830,Q#158 - >seq3481,superfamily,237177,45,151,0.000297765,42.4578,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC4,ORF1,hs1_chimp,marg,C-TerminusTruncated
8831,Q#158 - >seq3481,non-specific,224117,56,190,0.000929712,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8832,Q#158 - >seq3481,superfamily,224117,56,190,0.000929712,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8833,Q#158 - >seq3481,non-specific,274008,48,146,0.00610268,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8834,Q#158 - >seq3481,superfamily,274008,48,146,0.00610268,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8835,Q#158 - >seq3481,non-specific,274009,36,152,0.00870359,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8836,Q#158 - >seq3481,superfamily,274009,36,152,0.00870359,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC4,ORF1,hs1_chimp,marg,BothTerminiTruncated
8837,Q#158 - >seq3481,non-specific,226447,53,130,0.00966594,35.1406,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC4,ORF1,hs1_chimp,marg,N-TerminusTruncated
8838,Q#158 - >seq3481,superfamily,352825,53,130,0.00966594,35.1406,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1MC4.ORF1.hs1_chimp.marg.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4,ORF1,hs1_chimp,marg,N-TerminusTruncated
8839,Q#161 - >seq3484,specific,197310,48,232,5.8235900000000006e-34,130.549,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8840,Q#161 - >seq3484,superfamily,351117,48,232,5.8235900000000006e-34,130.549,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8841,Q#161 - >seq3484,non-specific,197306,67,232,7.65929e-19,86.7664,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8842,Q#161 - >seq3484,non-specific,238827,608,728,1.58805e-14,73.8646,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8843,Q#161 - >seq3484,superfamily,295487,608,728,1.58805e-14,73.8646,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8844,Q#161 - >seq3484,non-specific,197320,102,225,1.30479e-11,65.9994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8845,Q#161 - >seq3484,non-specific,223780,102,233,1.90271e-10,62.6159,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8846,Q#161 - >seq3484,non-specific,197307,102,232,1.52834e-08,56.5273,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8847,Q#161 - >seq3484,non-specific,197319,102,232,8.605969999999999e-08,54.5901,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8848,Q#161 - >seq3484,non-specific,333820,614,728,9.31657e-08,53.065,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8849,Q#161 - >seq3484,superfamily,333820,614,728,9.31657e-08,53.065,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8850,Q#161 - >seq3484,non-specific,339261,104,228,1.9324899999999999e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8851,Q#161 - >seq3484,non-specific,273186,102,233,6.04315e-07,51.896,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8852,Q#161 - >seq3484,non-specific,197322,103,225,3.7829000000000002e-06,50.0082,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8853,Q#161 - >seq3484,non-specific,335306,65,225,1.41974e-05,47.2398,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8854,Q#161 - >seq3484,non-specific,197321,102,232,8.78715e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8855,Q#161 - >seq3484,non-specific,272954,87,232,0.000222542,43.9109,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8856,Q#161 - >seq3484,non-specific,197311,98,232,0.00134511,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs1_chimp,pars,N-TerminusTruncated
8857,Q#161 - >seq3484,non-specific,238185,616,728,0.00137798,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs1_chimp.pars.frame1,1909130322_L1MC4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs1_chimp,pars,CompleteHit
8858,Q#163 - >seq3486,specific,238827,460,710,1.12809e-28,114.696,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs6_sqmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs6_sqmonkey,pars,CompleteHit
8859,Q#163 - >seq3486,superfamily,295487,460,710,1.12809e-28,114.696,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs6_sqmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs6_sqmonkey,pars,CompleteHit
8860,Q#163 - >seq3486,non-specific,333820,467,651,1.78276e-11,63.8506,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs6_sqmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8861,Q#163 - >seq3486,superfamily,333820,467,651,1.78276e-11,63.8506,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs6_sqmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8862,Q#163 - >seq3486,non-specific,238828,529,651,0.00313295,39.8769,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs6_sqmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
8863,Q#165 - >seq3488,non-specific,340205,160,205,5.21688e-05,40.012,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs6_sqmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
8864,Q#165 - >seq3488,superfamily,340205,160,205,5.21688e-05,40.012,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs6_sqmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC4,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
8865,Q#168 - >seq3491,specific,197310,2,145,9.4722e-31,120.919,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8866,Q#168 - >seq3491,superfamily,351117,2,145,9.4722e-31,120.919,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8867,Q#168 - >seq3491,non-specific,197306,2,149,3.51923e-17,81.7588,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8868,Q#168 - >seq3491,specific,335306,2,185,6.79969e-10,59.9514,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,CompleteHit
8869,Q#168 - >seq3491,non-specific,223780,2,134,7.22113e-08,54.5267,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8870,Q#168 - >seq3491,non-specific,197307,2,151,3.14165e-07,52.2901,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8871,Q#168 - >seq3491,non-specific,197320,2,134,3.42907e-06,49.0506,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8872,Q#168 - >seq3491,non-specific,197319,2,149,8.40811e-05,44.9601,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8873,Q#168 - >seq3491,non-specific,272954,2,135,0.000127705,44.2961,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8874,Q#168 - >seq3491,non-specific,197321,2,134,0.000159804,44.08,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8875,Q#168 - >seq3491,non-specific,197311,18,134,0.00317475,39.5825,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8876,Q#168 - >seq3491,non-specific,197336,2,147,0.00387939,39.9031,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC4.ORF2.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8877,Q#170 - >seq3493,non-specific,340205,79,123,0.00216713,34.234,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs6_sqmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
8878,Q#170 - >seq3493,superfamily,340205,79,123,0.00216713,34.234,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs6_sqmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
8879,Q#171 - >seq3494,specific,197310,9,157,4.7070899999999994e-33,127.853,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8880,Q#171 - >seq3494,superfamily,351117,9,157,4.7070899999999994e-33,127.853,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8881,Q#171 - >seq3494,non-specific,197306,9,161,1.19626e-19,89.4628,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8882,Q#171 - >seq3494,specific,335306,10,197,2.65799e-12,67.2702,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,CompleteHit
8883,Q#171 - >seq3494,non-specific,223780,9,146,4.8165e-10,61.4603,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8884,Q#171 - >seq3494,non-specific,197307,9,163,3.71272e-09,58.4533,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8885,Q#171 - >seq3494,non-specific,197320,9,146,3.43594e-08,55.599,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8886,Q#171 - >seq3494,non-specific,272954,9,147,4.4236e-06,49.3037,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8887,Q#171 - >seq3494,non-specific,197321,9,146,4.78071e-06,49.0876,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8888,Q#171 - >seq3494,non-specific,197319,7,161,1.0411300000000001e-05,48.0417,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8889,Q#171 - >seq3494,non-specific,197336,9,159,2.0118699999999998e-05,47.2219,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8890,Q#171 - >seq3494,non-specific,273186,9,147,0.00025598900000000003,43.8068,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8891,Q#171 - >seq3494,non-specific,197311,7,146,0.00409723,39.5825,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8892,Q#171 - >seq3494,non-specific,236970,9,146,0.00652074,39.4922,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1MC4.ORF2.hs5_gmonkey.marg.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8893,Q#172 - >seq3495,non-specific,238827,473,579,1.7853799999999997e-24,102.755,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8894,Q#172 - >seq3495,superfamily,295487,473,579,1.7853799999999997e-24,102.755,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8895,Q#172 - >seq3495,non-specific,333820,491,581,6.22359e-09,56.5318,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8896,Q#172 - >seq3495,superfamily,333820,491,581,6.22359e-09,56.5318,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
8897,Q#172 - >seq3495,non-specific,235175,292,432,4.1045600000000006e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MC4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8898,Q#172 - >seq3495,superfamily,235175,292,432,4.1045600000000006e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC4.ORF2.hs5_gmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MC4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
8899,Q#173 - >seq3496,non-specific,238827,626,735,8.831990000000001e-23,97.74700000000001,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8900,Q#173 - >seq3496,superfamily,295487,626,735,8.831990000000001e-23,97.74700000000001,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8901,Q#173 - >seq3496,non-specific,197310,128,209,2.3523099999999997e-13,70.8433,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8902,Q#173 - >seq3496,superfamily,351117,128,209,2.3523099999999997e-13,70.8433,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8903,Q#173 - >seq3496,non-specific,333820,626,735,2.37279e-08,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8904,Q#173 - >seq3496,superfamily,333820,626,735,2.37279e-08,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
8905,Q#173 - >seq3496,non-specific,238185,625,735,0.00560928,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,marg,CompleteHit
8906,Q#176 - >seq3499,non-specific,237177,241,353,0.00546023,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MC4.ORF2.hs6_sqmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MC4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8907,Q#176 - >seq3499,superfamily,237177,241,353,0.00546023,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MC4.ORF2.hs6_sqmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MC4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
8908,Q#177 - >seq3500,non-specific,340205,93,139,1.42092e-07,45.79,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs7_bushaby,marg,N-TerminusTruncated
8909,Q#177 - >seq3500,superfamily,340205,93,139,1.42092e-07,45.79,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs7_bushaby,marg,N-TerminusTruncated
8910,Q#178 - >seq3501,non-specific,197310,36,245,0.00018535,44.2645,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs6_sqmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC4,ORF2,hs6_sqmonkey,marg,CompleteHit
8911,Q#178 - >seq3501,superfamily,351117,36,245,0.00018535,44.2645,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs6_sqmonkey.marg.frame2,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MC4,ORF2,hs6_sqmonkey,marg,CompleteHit
8912,Q#186 - >seq3509,non-specific,238827,366,418,1.4151e-08,56.1454,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs7_bushaby.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8913,Q#186 - >seq3509,superfamily,295487,366,418,1.4151e-08,56.1454,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs7_bushaby.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs7_bushaby,pars,C-TerminusTruncated
8914,Q#187 - >seq3510,non-specific,197310,7,172,0.00485564,39.6421,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs7_bushaby.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs7_bushaby,pars,CompleteHit
8915,Q#187 - >seq3510,superfamily,351117,7,172,0.00485564,39.6421,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs7_bushaby.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs7_bushaby,pars,CompleteHit
8916,Q#188 - >seq3511,non-specific,197310,10,228,2.4706599999999997e-10,61.9837,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs7_bushaby,marg,CompleteHit
8917,Q#188 - >seq3511,superfamily,351117,10,228,2.4706599999999997e-10,61.9837,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs7_bushaby,marg,CompleteHit
8918,Q#188 - >seq3511,non-specific,238827,572,625,1.9317e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
8919,Q#188 - >seq3511,superfamily,295487,572,625,1.9317e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs7_bushaby,marg,C-TerminusTruncated
8920,Q#188 - >seq3511,non-specific,197306,10,228,0.000293392,44.0093,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs7_bushaby.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs7_bushaby,marg,CompleteHit
8921,Q#190 - >seq3513,non-specific,238827,455,561,1.07176e-24,103.14,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8922,Q#190 - >seq3513,superfamily,295487,455,561,1.07176e-24,103.14,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8923,Q#190 - >seq3513,non-specific,333820,473,563,4.01016e-09,56.917,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8924,Q#190 - >seq3513,superfamily,333820,473,563,4.01016e-09,56.917,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
8925,Q#190 - >seq3513,non-specific,235175,280,414,0.00236904,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8926,Q#190 - >seq3513,superfamily,235175,280,414,0.00236904,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC4.ORF2.hs5_gmonkey.pars.frame2,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
8927,Q#191 - >seq3514,non-specific,238827,512,755,6.788739999999999e-26,106.60700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs6_sqmonkey,marg,CompleteHit
8928,Q#191 - >seq3514,superfamily,295487,512,755,6.788739999999999e-26,106.60700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs6_sqmonkey,marg,CompleteHit
8929,Q#191 - >seq3514,non-specific,333820,530,713,4.986759999999999e-10,59.6134,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8930,Q#191 - >seq3514,superfamily,333820,530,713,4.986759999999999e-10,59.6134,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8931,Q#191 - >seq3514,non-specific,238828,585,713,3.22725e-05,46.4253,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
8932,Q#191 - >seq3514,non-specific,223542,226,407,0.00405851,41.0046,COG0466,Lon,C,cl33893,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8933,Q#191 - >seq3514,superfamily,223542,226,407,0.00405851,41.0046,cl33893,Lon superfamily,C, - ,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MC4.ORF2.hs6_sqmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
8934,Q#192 - >seq3515,non-specific,238827,611,720,5.54282e-23,98.1322,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8935,Q#192 - >seq3515,superfamily,295487,611,720,5.54282e-23,98.1322,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8936,Q#192 - >seq3515,non-specific,197310,120,201,1.38473e-13,71.2285,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8937,Q#192 - >seq3515,superfamily,351117,120,201,1.38473e-13,71.2285,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8938,Q#192 - >seq3515,non-specific,333820,611,720,1.55264e-08,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8939,Q#192 - >seq3515,superfamily,333820,611,720,1.55264e-08,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
8940,Q#192 - >seq3515,non-specific,238185,610,720,0.00324156,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs5_gmonkey,pars,CompleteHit
8941,Q#197 - >seq3520,non-specific,340205,137,184,1.36429e-11,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs3_orang.pars.frame2,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs3_orang,pars,CompleteHit
8942,Q#197 - >seq3520,superfamily,340205,137,184,1.36429e-11,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs3_orang.pars.frame2,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs3_orang,pars,CompleteHit
8943,Q#197 - >seq3520,non-specific,335182,59,113,3.94103e-09,51.9199,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs3_orang.pars.frame2,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs3_orang,pars,N-TerminusTruncated
8944,Q#197 - >seq3520,superfamily,335182,59,113,3.94103e-09,51.9199,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs3_orang.pars.frame2,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs3_orang,pars,N-TerminusTruncated
8945,Q#198 - >seq3521,non-specific,335182,170,246,2.452e-13,65.0167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs3_orang.marg.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs3_orang,marg,CompleteHit
8946,Q#198 - >seq3521,superfamily,335182,170,246,2.452e-13,65.0167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs3_orang.marg.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs3_orang,marg,CompleteHit
8947,Q#198 - >seq3521,non-specific,340205,269,332,1.75768e-09,53.1088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs3_orang.marg.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs3_orang,marg,CompleteHit
8948,Q#198 - >seq3521,superfamily,340205,269,332,1.75768e-09,53.1088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs3_orang.marg.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs3_orang,marg,CompleteHit
8949,Q#201 - >seq3524,non-specific,238827,435,518,3.74615e-09,58.0714,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs3_orang.pars.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs3_orang,pars,C-TerminusTruncated
8950,Q#201 - >seq3524,superfamily,295487,435,518,3.74615e-09,58.0714,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs3_orang.pars.frame1,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs3_orang,pars,C-TerminusTruncated
8951,Q#203 - >seq3526,specific,197310,9,228,1.1691599999999998e-48,172.921,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8952,Q#203 - >seq3526,superfamily,351117,9,228,1.1691599999999998e-48,172.921,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8953,Q#203 - >seq3526,non-specific,197306,9,228,8.67982e-30,118.738,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8954,Q#203 - >seq3526,specific,238827,543,698,1.11757e-28,114.696,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8955,Q#203 - >seq3526,superfamily,295487,543,698,1.11757e-28,114.696,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8956,Q#203 - >seq3526,non-specific,333820,532,698,3.6861700000000005e-17,80.4142,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8957,Q#203 - >seq3526,superfamily,333820,532,698,3.6861700000000005e-17,80.4142,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8958,Q#203 - >seq3526,non-specific,223780,9,229,5.94805e-17,81.8759,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8959,Q#203 - >seq3526,non-specific,197307,9,228,1.33851e-14,74.6317,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8960,Q#203 - >seq3526,non-specific,197320,8,206,1.49878e-14,74.4737,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8961,Q#203 - >seq3526,specific,335306,10,221,9.417360000000001e-14,71.5073,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8962,Q#203 - >seq3526,non-specific,197321,7,228,9.07397e-11,63.34,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8963,Q#203 - >seq3526,non-specific,273186,9,229,4.0011300000000005e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8964,Q#203 - >seq3526,non-specific,272954,9,228,6.224149999999999e-09,57.7781,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8965,Q#203 - >seq3526,non-specific,197319,8,228,1.05705e-08,57.2865,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8966,Q#203 - >seq3526,non-specific,238828,538,663,2.1291500000000002e-08,55.67,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8967,Q#203 - >seq3526,non-specific,197336,7,192,1.11136e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8968,Q#203 - >seq3526,non-specific,238185,581,698,1.32262e-06,47.7308,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8969,Q#203 - >seq3526,non-specific,339261,108,224,1.8499e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8970,Q#203 - >seq3526,non-specific,275209,579,705,3.0972399999999995e-05,47.4524,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8971,Q#203 - >seq3526,superfamily,275209,579,705,3.0972399999999995e-05,47.4524,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8972,Q#203 - >seq3526,non-specific,197311,72,228,0.00022128799999999999,43.4345,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8973,Q#203 - >seq3526,non-specific,139971,7,200,0.000222537,43.9143,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8974,Q#203 - >seq3526,non-specific,197317,124,221,0.000422296,42.9744,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8975,Q#203 - >seq3526,non-specific,197314,7,221,0.000427364,43.1011,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MC4,ORF2,hs3_orang,pars,CompleteHit
8976,Q#203 - >seq3526,non-specific,225565,105,222,0.00294178,40.8876,COG3021,YafD,N,cl00490,"Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only]; Uncharacterized protein conserved in bacteria [Function unknown].",L1MC4.ORF2.hs3_orang.pars.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC4,ORF2,hs3_orang,pars,N-TerminusTruncated
8977,Q#206 - >seq3529,specific,197310,9,235,5.40731e-53,185.63299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8978,Q#206 - >seq3529,superfamily,351117,9,235,5.40731e-53,185.63299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8979,Q#206 - >seq3529,specific,238827,514,784,2.6977299999999998e-45,162.846,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8980,Q#206 - >seq3529,superfamily,295487,514,784,2.6977299999999998e-45,162.846,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8981,Q#206 - >seq3529,non-specific,197306,9,235,3.52078e-33,128.753,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8982,Q#206 - >seq3529,non-specific,333820,533,784,5.78461e-23,97.3629,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8983,Q#206 - >seq3529,superfamily,333820,533,784,5.78461e-23,97.3629,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8984,Q#206 - >seq3529,non-specific,223780,9,236,1.94385e-17,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8985,Q#206 - >seq3529,non-specific,197307,9,235,8.77711e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8986,Q#206 - >seq3529,non-specific,197320,8,228,5.53959e-16,79.0961,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8987,Q#206 - >seq3529,specific,335306,10,228,4.53166e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8988,Q#206 - >seq3529,non-specific,197321,7,235,3.12883e-12,67.9624,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8989,Q#206 - >seq3529,non-specific,273186,9,236,4.25004e-11,64.6076,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8990,Q#206 - >seq3529,non-specific,238828,591,749,1.05448e-09,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
8991,Q#206 - >seq3529,non-specific,197319,8,235,1.27957e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8992,Q#206 - >seq3529,non-specific,272954,9,235,4.60258e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8993,Q#206 - >seq3529,non-specific,339261,108,231,1.3574000000000002e-07,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8994,Q#206 - >seq3529,non-specific,197336,7,193,9.28132e-07,51.4591,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8995,Q#206 - >seq3529,non-specific,197311,72,235,6.05868e-06,48.4421,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
8996,Q#206 - >seq3529,non-specific,238185,667,784,8.534110000000001e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8997,Q#206 - >seq3529,non-specific,139971,7,235,9.41584e-06,48.5367,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC4,ORF2,hs3_orang,marg,CompleteHit
8998,Q#206 - >seq3529,non-specific,275209,611,791,1.28084e-05,48.608000000000004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
8999,Q#206 - >seq3529,superfamily,275209,611,791,1.28084e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
9000,Q#206 - >seq3529,non-specific,197314,7,228,4.9454e-05,46.1827,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MC4,ORF2,hs3_orang,marg,CompleteHit
9001,Q#206 - >seq3529,non-specific,197322,108,228,5.14867e-05,46.5414,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
9002,Q#206 - >seq3529,non-specific,197317,124,228,0.000595404,42.9744,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,marg,N-TerminusTruncated
9003,Q#206 - >seq3529,non-specific,236970,9,214,0.00128975,41.8034,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs3_orang,marg,CompleteHit
9004,Q#206 - >seq3529,non-specific,197318,9,148,0.00712402,39.5871,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC4.ORF2.hs3_orang.marg.frame3,1909130323_L1MC4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs3_orang,marg,C-TerminusTruncated
9005,Q#209 - >seq3532,non-specific,340205,125,164,1.27473e-05,41.1676,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs4_gibbon.pars.frame3,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs4_gibbon,pars,C-TerminusTruncated
9006,Q#209 - >seq3532,superfamily,340205,125,164,1.27473e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs4_gibbon.pars.frame3,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs4_gibbon,pars,C-TerminusTruncated
9007,Q#210 - >seq3533,non-specific,340205,158,221,8.042369999999999e-20,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,marg,CompleteHit
9008,Q#210 - >seq3533,superfamily,340205,158,221,8.042369999999999e-20,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,marg,CompleteHit
9009,Q#210 - >seq3533,non-specific,335182,55,155,1.37078e-16,72.3355,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,marg,CompleteHit
9010,Q#210 - >seq3533,superfamily,335182,55,155,1.37078e-16,72.3355,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs5_gmonkey.marg.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,marg,CompleteHit
9011,Q#211 - >seq3534,non-specific,335182,48,116,2.99038e-16,69.6391,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs4_gibbon.pars.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,pars,CompleteHit
9012,Q#211 - >seq3534,superfamily,335182,48,116,2.99038e-16,69.6391,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs4_gibbon.pars.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,pars,CompleteHit
9013,Q#212 - >seq3535,non-specific,340205,126,169,6.35393e-11,55.0348,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
9014,Q#212 - >seq3535,superfamily,340205,126,169,6.35393e-11,55.0348,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs5_gmonkey.pars.frame3,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
9015,Q#213 - >seq3536,non-specific,335182,65,113,1.2557800000000001e-07,47.2975,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
9016,Q#213 - >seq3536,superfamily,335182,65,113,1.2557800000000001e-07,47.2975,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs5_gmonkey.pars.frame1,1909130323_L1MC4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
9017,Q#217 - >seq3540,non-specific,238827,99,207,6.1751e-11,62.3086,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs4_gibbon.pars.frame3,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9018,Q#217 - >seq3540,superfamily,295487,99,207,6.1751e-11,62.3086,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs4_gibbon.pars.frame3,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9019,Q#221 - >seq3544,non-specific,335182,66,148,1.4094100000000002e-24,92.751,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs4_gibbon.marg.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,marg,CompleteHit
9020,Q#221 - >seq3544,superfamily,335182,66,148,1.4094100000000002e-24,92.751,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs4_gibbon.marg.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,marg,CompleteHit
9021,Q#221 - >seq3544,non-specific,340205,152,214,1.43844e-17,73.5244,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs4_gibbon.marg.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,marg,CompleteHit
9022,Q#221 - >seq3544,superfamily,340205,152,214,1.43844e-17,73.5244,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs4_gibbon.marg.frame2,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC4,ORF1,hs4_gibbon,marg,CompleteHit
9023,Q#222 - >seq3545,specific,197310,258,459,2.0587700000000002e-31,123.616,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9024,Q#222 - >seq3545,superfamily,351117,258,459,2.0587700000000002e-31,123.616,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9025,Q#222 - >seq3545,non-specific,238827,743,1019,1.36264e-18,86.191,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9026,Q#222 - >seq3545,superfamily,295487,743,1019,1.36264e-18,86.191,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9027,Q#222 - >seq3545,non-specific,197306,252,459,4.0666699999999996e-16,79.4476,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9028,Q#222 - >seq3545,non-specific,197307,244,459,2.5049899999999996e-09,59.6089,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9029,Q#222 - >seq3545,specific,335306,252,452,4.44612e-09,58.4106,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9030,Q#222 - >seq3545,non-specific,197320,253,452,1.35179e-08,57.1398,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9031,Q#222 - >seq3545,non-specific,223780,252,460,8.009730000000001e-08,54.9119,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9032,Q#222 - >seq3545,non-specific,197321,252,459,5.8078900000000004e-05,46.3912,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9033,Q#222 - >seq3545,non-specific,273186,253,460,8.20117e-05,45.7328,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs4_gibbon,marg,CompleteHit
9034,Q#222 - >seq3545,non-specific,197319,330,459,0.00020674200000000002,44.5749,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9035,Q#222 - >seq3545,non-specific,272954,314,459,0.0006788019999999999,43.1405,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC4.ORF2.hs4_gibbon.marg.frame1,1909130323_L1MC4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9036,Q#223 - >seq3546,non-specific,197310,12,202,3.5769800000000003e-20,90.4885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC4,ORF2,hs0_human,pars,CompleteHit
9037,Q#223 - >seq3546,superfamily,351117,12,202,3.5769800000000003e-20,90.4885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,pars,CompleteHit
9038,Q#223 - >seq3546,non-specific,197306,9,215,1.02002e-05,47.8613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,pars,CompleteHit
9039,Q#223 - >seq3546,specific,335306,12,221,0.00203611,40.6914,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,pars,CompleteHit
9040,Q#226 - >seq3549,specific,238827,468,726,7.10987e-51,178.639,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,CompleteHit
9041,Q#226 - >seq3549,superfamily,295487,468,726,7.10987e-51,178.639,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,CompleteHit
9042,Q#226 - >seq3549,non-specific,333820,474,696,3.97669e-23,97.7481,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,CompleteHit
9043,Q#226 - >seq3549,superfamily,333820,474,696,3.97669e-23,97.7481,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,CompleteHit
9044,Q#226 - >seq3549,non-specific,238828,539,703,1.36152e-08,56.4404,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,N-TerminusTruncated
9045,Q#226 - >seq3549,non-specific,275209,556,755,7.448680000000001e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,N-TerminusTruncated
9046,Q#226 - >seq3549,superfamily,275209,556,755,7.448680000000001e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,N-TerminusTruncated
9047,Q#226 - >seq3549,non-specific,238185,615,731,0.00141087,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs0_human.marg.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC4,ORF2,hs0_human,marg,CompleteHit
9048,Q#227 - >seq3550,specific,197310,12,231,3.84051e-43,157.128,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9049,Q#227 - >seq3550,superfamily,351117,12,231,3.84051e-43,157.128,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9050,Q#227 - >seq3550,non-specific,197306,9,224,9.55517e-19,86.7664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9051,Q#227 - >seq3550,non-specific,223780,13,226,3.0415e-07,52.9859,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9052,Q#227 - >seq3550,non-specific,197307,9,230,9.168890000000001e-07,51.5197,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9053,Q#227 - >seq3550,specific,335306,12,230,1.29766e-05,47.625,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC4,ORF2,hs0_human,marg,CompleteHit
9054,Q#227 - >seq3550,non-specific,274009,322,454,0.00205336,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs0_human,marg,C-TerminusTruncated
9055,Q#227 - >seq3550,superfamily,274009,322,454,0.00205336,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC4.ORF2.hs0_human.marg.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC4,ORF2,hs0_human,marg,C-TerminusTruncated
9056,Q#228 - >seq3551,non-specific,335182,76,169,2.38822e-34,118.945,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs1_chimp.pars.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,pars,CompleteHit
9057,Q#228 - >seq3551,superfamily,335182,76,169,2.38822e-34,118.945,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs1_chimp.pars.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,pars,CompleteHit
9058,Q#228 - >seq3551,non-specific,340205,172,235,3.10383e-27,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs1_chimp.pars.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,pars,CompleteHit
9059,Q#228 - >seq3551,superfamily,340205,172,235,3.10383e-27,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs1_chimp.pars.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,pars,CompleteHit
9060,Q#231 - >seq3554,non-specific,335182,156,253,2.1718999999999997e-38,133.967,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9061,Q#231 - >seq3554,superfamily,335182,156,253,2.1718999999999997e-38,133.967,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9062,Q#231 - >seq3554,non-specific,340205,256,319,4.5482299999999996e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9063,Q#231 - >seq3554,superfamily,340205,256,319,4.5482299999999996e-27,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9064,Q#231 - >seq3554,non-specific,340204,114,153,9.307750000000001e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9065,Q#231 - >seq3554,superfamily,340204,114,153,9.307750000000001e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC5a,ORF1,hs1_chimp,marg,CompleteHit
9066,Q#231 - >seq3554,non-specific,235175,56,156,3.2815700000000005e-05,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9067,Q#231 - >seq3554,superfamily,235175,56,156,3.2815700000000005e-05,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9068,Q#231 - >seq3554,non-specific,274009,57,208,0.000265123,43.1327,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,N-TerminusTruncated
9069,Q#231 - >seq3554,superfamily,274009,57,208,0.000265123,43.1327,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,N-TerminusTruncated
9070,Q#231 - >seq3554,non-specific,274765,6,131,0.000311017,42.707,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9071,Q#231 - >seq3554,superfamily,274765,6,131,0.000311017,42.707,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9072,Q#231 - >seq3554,non-specific,197310,367,425,0.000371284,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9073,Q#231 - >seq3554,superfamily,351117,367,425,0.000371284,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9074,Q#231 - >seq3554,non-specific,235175,55,181,0.001218,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9075,Q#231 - >seq3554,non-specific,274009,48,241,0.00175077,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9076,Q#231 - >seq3554,non-specific,235505,56,183,0.00206284,40.239000000000004,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9077,Q#231 - >seq3554,superfamily,235505,56,183,0.00206284,40.239000000000004,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9078,Q#231 - >seq3554,non-specific,224117,55,240,0.00214238,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9079,Q#231 - >seq3554,superfamily,224117,55,240,0.00214238,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9080,Q#231 - >seq3554,non-specific,274008,2,139,0.00245196,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9081,Q#231 - >seq3554,superfamily,274008,2,139,0.00245196,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9082,Q#231 - >seq3554,non-specific,274008,48,258,0.00281416,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9083,Q#231 - >seq3554,superfamily,274008,48,258,0.00281416,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9084,Q#231 - >seq3554,non-specific,224117,54,252,0.00408672,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9085,Q#231 - >seq3554,non-specific,224495,55,133,0.00619682,37.7303,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9086,Q#231 - >seq3554,superfamily,224495,55,133,0.00619682,37.7303,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9087,Q#231 - >seq3554,non-specific,275320,47,195,0.00666863,37.769,TIGR04527,mycoplas_twoTM,C,cl24124,"two transmembrane protein; Members of this family are uncharacterized proteins from the genus Mycoplasma, typically about 260 amino acids long, with a hydrophobic predicted transmembrane alpha helix toward each end. Often two family members are encoded in tandem, e.g. MG_279 and MG_280 from Mycoplasma genitalium.",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9088,Q#231 - >seq3554,superfamily,275320,47,195,0.00666863,37.769,cl24124,mycoplas_twoTM superfamily,C, - ,"two transmembrane protein; Members of this family are uncharacterized proteins from the genus Mycoplasma, typically about 260 amino acids long, with a hydrophobic predicted transmembrane alpha helix toward each end. Often two family members are encoded in tandem, e.g. MG_279 and MG_280 from Mycoplasma genitalium.",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF1,hs1_chimp,marg,C-TerminusTruncated
9089,Q#231 - >seq3554,non-specific,274009,57,150,0.00891077,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs1_chimp.marg.frame1,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF1,hs1_chimp,marg,BothTerminiTruncated
9090,Q#233 - >seq3556,non-specific,340205,157,220,2.2630100000000005e-25,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs2_gorilla,pars,CompleteHit
9091,Q#233 - >seq3556,superfamily,340205,157,220,2.2630100000000005e-25,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs2_gorilla,pars,CompleteHit
9092,Q#233 - >seq3556,non-specific,335182,59,154,5.21908e-23,88.899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs2_gorilla,pars,CompleteHit
9093,Q#233 - >seq3556,superfamily,335182,59,154,5.21908e-23,88.899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs2_gorilla,pars,CompleteHit
9094,Q#233 - >seq3556,non-specific,224556,77,184,0.00261966,38.093,COG1641,COG1641,N,cl03398,"Uncharacterized conserved protein, DUF111 family [Function unknown]; Uncharacterized conserved protein [Function unknown].",L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
9095,Q#233 - >seq3556,superfamily,351986,77,184,0.00261966,38.093,cl03398,DUF111 superfamily,N, - ,Protein of unknown function DUF111; This prokaryotic family has no known function.,L1MC5a.ORF1.hs2_gorilla.pars.frame1,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
9096,Q#235 - >seq3558,specific,238827,510,772,5.861709999999999e-66,221.78099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9097,Q#235 - >seq3558,superfamily,295487,510,772,5.861709999999999e-66,221.78099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9098,Q#235 - >seq3558,non-specific,238827,510,772,5.861709999999999e-66,221.78099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9099,Q#235 - >seq3558,specific,197310,9,236,2.2838099999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9100,Q#235 - >seq3558,superfamily,351117,9,236,2.2838099999999997e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9101,Q#235 - >seq3558,non-specific,197310,9,236,2.2838099999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9102,Q#235 - >seq3558,non-specific,197306,9,236,3.02836e-53,186.533,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9103,Q#235 - >seq3558,non-specific,197306,9,236,3.02836e-53,186.533,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9104,Q#235 - >seq3558,specific,333820,516,772,8.836409999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9105,Q#235 - >seq3558,superfamily,333820,516,772,8.836409999999999e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9106,Q#235 - >seq3558,non-specific,333820,516,772,8.836409999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9107,Q#235 - >seq3558,non-specific,197307,9,236,6.230639999999999e-26,108.14399999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9108,Q#235 - >seq3558,non-specific,197307,9,236,6.230639999999999e-26,108.14399999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9109,Q#235 - >seq3558,non-specific,223780,9,238,1.8459700000000003e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9110,Q#235 - >seq3558,non-specific,223780,9,238,1.8459700000000003e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9111,Q#235 - >seq3558,non-specific,197320,8,236,1.1810799999999998e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9112,Q#235 - >seq3558,non-specific,197320,8,236,1.1810799999999998e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9113,Q#235 - >seq3558,non-specific,197321,7,236,7.168110000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9114,Q#235 - >seq3558,non-specific,197321,7,236,7.168110000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9115,Q#235 - >seq3558,specific,335306,10,229,1.09889e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9116,Q#235 - >seq3558,non-specific,335306,10,229,1.09889e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9117,Q#235 - >seq3558,non-specific,273186,9,237,2.51891e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9118,Q#235 - >seq3558,non-specific,273186,9,237,2.51891e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9119,Q#235 - >seq3558,non-specific,272954,9,236,2.1626100000000002e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9120,Q#235 - >seq3558,non-specific,272954,9,236,2.1626100000000002e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9121,Q#235 - >seq3558,non-specific,197319,8,236,6.79824e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9122,Q#235 - >seq3558,non-specific,197319,8,236,6.79824e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9123,Q#235 - >seq3558,non-specific,197336,7,235,9.91671e-13,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9124,Q#235 - >seq3558,non-specific,197336,7,235,9.91671e-13,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9125,Q#235 - >seq3558,non-specific,238828,516,738,1.0191e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9126,Q#235 - >seq3558,non-specific,238828,516,738,1.0191e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9127,Q#235 - >seq3558,non-specific,197322,9,236,1.1724000000000001e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9128,Q#235 - >seq3558,non-specific,197322,9,236,1.1724000000000001e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9129,Q#235 - >seq3558,non-specific,275209,467,800,5.70699e-11,65.5568,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9130,Q#235 - >seq3558,superfamily,275209,467,800,5.70699e-11,65.5568,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9131,Q#235 - >seq3558,non-specific,275209,467,800,5.70699e-11,65.5568,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9132,Q#235 - >seq3558,non-specific,236970,9,238,9.962760000000002e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9133,Q#235 - >seq3558,non-specific,236970,9,238,9.962760000000002e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9134,Q#235 - >seq3558,non-specific,339261,108,232,2.14105e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9135,Q#235 - >seq3558,non-specific,339261,108,232,2.14105e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9136,Q#235 - >seq3558,non-specific,197311,7,236,1.116e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9137,Q#235 - >seq3558,non-specific,197311,7,236,1.116e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9138,Q#235 - >seq3558,non-specific,197317,139,229,5.4895699999999995e-06,49.1376,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9139,Q#235 - >seq3558,non-specific,197317,139,229,5.4895699999999995e-06,49.1376,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9140,Q#235 - >seq3558,non-specific,274009,305,458,0.00033138,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9141,Q#235 - >seq3558,superfamily,274009,305,458,0.00033138,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9142,Q#235 - >seq3558,non-specific,274009,305,458,0.00033138,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9143,Q#235 - >seq3558,non-specific,274009,303,458,0.00037620599999999997,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9144,Q#235 - >seq3558,non-specific,274009,303,458,0.00037620599999999997,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9145,Q#235 - >seq3558,non-specific,223496,305,464,0.00041565199999999997,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9146,Q#235 - >seq3558,superfamily,223496,305,464,0.00041565199999999997,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9147,Q#235 - >seq3558,non-specific,223496,305,464,0.00041565199999999997,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9148,Q#235 - >seq3558,non-specific,238185,656,772,0.00046634599999999997,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9149,Q#235 - >seq3558,non-specific,238185,656,772,0.00046634599999999997,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9150,Q#235 - >seq3558,non-specific,226098,138,239,0.00120682,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9151,Q#235 - >seq3558,non-specific,226098,138,239,0.00120682,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9152,Q#235 - >seq3558,non-specific,235175,301,469,0.00284435,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9153,Q#235 - >seq3558,superfamily,235175,301,469,0.00284435,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9154,Q#235 - >seq3558,non-specific,235175,301,469,0.00284435,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,BothTerminiTruncated
9155,Q#235 - >seq3558,non-specific,312723,270,464,0.00330895,40.6771,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9156,Q#235 - >seq3558,superfamily,312723,270,464,0.00330895,40.6771,cl25728,DUF1978 superfamily, - , - ,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9157,Q#235 - >seq3558,non-specific,312723,270,464,0.00330895,40.6771,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9158,Q#235 - >seq3558,non-specific,197314,7,192,0.00357641,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9159,Q#235 - >seq3558,non-specific,197314,7,192,0.00357641,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9160,Q#235 - >seq3558,non-specific,224117,311,459,0.00594524,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9161,Q#235 - >seq3558,superfamily,224117,311,459,0.00594524,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9162,Q#235 - >seq3558,non-specific,224117,311,459,0.00594524,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,C-TerminusTruncated
9163,Q#235 - >seq3558,non-specific,274008,299,500,0.0075819,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9164,Q#235 - >seq3558,superfamily,274008,299,500,0.0075819,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9165,Q#235 - >seq3558,non-specific,274008,299,500,0.0075819,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,pars,N-TerminusTruncated
9166,Q#235 - >seq3558,non-specific,239569,525,748,0.0078137,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9167,Q#235 - >seq3558,non-specific,239569,525,748,0.0078137,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC5a.ORF2.hs1_chimp.pars.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,pars,CompleteHit
9168,Q#237 - >seq3560,specific,238827,510,772,5.861709999999999e-66,221.78099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9169,Q#237 - >seq3560,superfamily,295487,510,772,5.861709999999999e-66,221.78099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9170,Q#237 - >seq3560,non-specific,238827,510,772,5.861709999999999e-66,221.78099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9171,Q#237 - >seq3560,specific,197310,9,236,2.2838099999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9172,Q#237 - >seq3560,superfamily,351117,9,236,2.2838099999999997e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9173,Q#237 - >seq3560,non-specific,197310,9,236,2.2838099999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9174,Q#237 - >seq3560,non-specific,197306,9,236,3.02836e-53,186.533,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9175,Q#237 - >seq3560,non-specific,197306,9,236,3.02836e-53,186.533,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9176,Q#237 - >seq3560,specific,333820,516,772,8.836409999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9177,Q#237 - >seq3560,superfamily,333820,516,772,8.836409999999999e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9178,Q#237 - >seq3560,non-specific,333820,516,772,8.836409999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9179,Q#237 - >seq3560,non-specific,197307,9,236,6.230639999999999e-26,108.14399999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9180,Q#237 - >seq3560,non-specific,197307,9,236,6.230639999999999e-26,108.14399999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9181,Q#237 - >seq3560,non-specific,223780,9,238,1.8459700000000003e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9182,Q#237 - >seq3560,non-specific,223780,9,238,1.8459700000000003e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9183,Q#237 - >seq3560,non-specific,197320,8,236,1.1810799999999998e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9184,Q#237 - >seq3560,non-specific,197320,8,236,1.1810799999999998e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9185,Q#237 - >seq3560,non-specific,197321,7,236,7.168110000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9186,Q#237 - >seq3560,non-specific,197321,7,236,7.168110000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9187,Q#237 - >seq3560,specific,335306,10,229,1.09889e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9188,Q#237 - >seq3560,non-specific,335306,10,229,1.09889e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9189,Q#237 - >seq3560,non-specific,273186,9,237,2.51891e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9190,Q#237 - >seq3560,non-specific,273186,9,237,2.51891e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9191,Q#237 - >seq3560,non-specific,272954,9,236,2.1626100000000002e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9192,Q#237 - >seq3560,non-specific,272954,9,236,2.1626100000000002e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9193,Q#237 - >seq3560,non-specific,197319,8,236,6.79824e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9194,Q#237 - >seq3560,non-specific,197319,8,236,6.79824e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9195,Q#237 - >seq3560,non-specific,197336,7,235,9.91671e-13,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9196,Q#237 - >seq3560,non-specific,197336,7,235,9.91671e-13,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9197,Q#237 - >seq3560,non-specific,238828,516,738,1.0191e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9198,Q#237 - >seq3560,non-specific,238828,516,738,1.0191e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9199,Q#237 - >seq3560,non-specific,197322,9,236,1.1724000000000001e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9200,Q#237 - >seq3560,non-specific,197322,9,236,1.1724000000000001e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9201,Q#237 - >seq3560,non-specific,275209,467,800,5.70699e-11,65.5568,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9202,Q#237 - >seq3560,superfamily,275209,467,800,5.70699e-11,65.5568,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9203,Q#237 - >seq3560,non-specific,275209,467,800,5.70699e-11,65.5568,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9204,Q#237 - >seq3560,non-specific,236970,9,238,9.962760000000002e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9205,Q#237 - >seq3560,non-specific,236970,9,238,9.962760000000002e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9206,Q#237 - >seq3560,non-specific,339261,108,232,2.14105e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9207,Q#237 - >seq3560,non-specific,339261,108,232,2.14105e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9208,Q#237 - >seq3560,non-specific,197311,7,236,1.116e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9209,Q#237 - >seq3560,non-specific,197311,7,236,1.116e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9210,Q#237 - >seq3560,non-specific,197317,139,229,5.4895699999999995e-06,49.1376,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9211,Q#237 - >seq3560,non-specific,197317,139,229,5.4895699999999995e-06,49.1376,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9212,Q#237 - >seq3560,non-specific,274009,305,458,0.00033138,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9213,Q#237 - >seq3560,superfamily,274009,305,458,0.00033138,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9214,Q#237 - >seq3560,non-specific,274009,305,458,0.00033138,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9215,Q#237 - >seq3560,non-specific,274009,303,458,0.00037620599999999997,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9216,Q#237 - >seq3560,non-specific,274009,303,458,0.00037620599999999997,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9217,Q#237 - >seq3560,non-specific,223496,305,464,0.00041565199999999997,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9218,Q#237 - >seq3560,superfamily,223496,305,464,0.00041565199999999997,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9219,Q#237 - >seq3560,non-specific,223496,305,464,0.00041565199999999997,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9220,Q#237 - >seq3560,non-specific,238185,656,772,0.00046634599999999997,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9221,Q#237 - >seq3560,non-specific,238185,656,772,0.00046634599999999997,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9222,Q#237 - >seq3560,non-specific,226098,138,239,0.00120682,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9223,Q#237 - >seq3560,non-specific,226098,138,239,0.00120682,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9224,Q#237 - >seq3560,non-specific,235175,301,469,0.00284435,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9225,Q#237 - >seq3560,superfamily,235175,301,469,0.00284435,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9226,Q#237 - >seq3560,non-specific,235175,301,469,0.00284435,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,BothTerminiTruncated
9227,Q#237 - >seq3560,non-specific,312723,270,464,0.00330895,40.6771,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9228,Q#237 - >seq3560,superfamily,312723,270,464,0.00330895,40.6771,cl25728,DUF1978 superfamily, - , - ,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9229,Q#237 - >seq3560,non-specific,312723,270,464,0.00330895,40.6771,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9230,Q#237 - >seq3560,non-specific,197314,7,192,0.00357641,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9231,Q#237 - >seq3560,non-specific,197314,7,192,0.00357641,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9232,Q#237 - >seq3560,non-specific,224117,311,459,0.00594524,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9233,Q#237 - >seq3560,superfamily,224117,311,459,0.00594524,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9234,Q#237 - >seq3560,non-specific,224117,311,459,0.00594524,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,C-TerminusTruncated
9235,Q#237 - >seq3560,non-specific,274008,299,500,0.0075819,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9236,Q#237 - >seq3560,superfamily,274008,299,500,0.0075819,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9237,Q#237 - >seq3560,non-specific,274008,299,500,0.0075819,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs1_chimp,marg,N-TerminusTruncated
9238,Q#237 - >seq3560,non-specific,239569,525,748,0.0078137,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9239,Q#237 - >seq3560,non-specific,239569,525,748,0.0078137,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC5a.ORF2.hs1_chimp.marg.frame3,1909130325_L1MC5a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs1_chimp,marg,CompleteHit
9240,Q#242 - >seq3565,non-specific,340205,236,299,1.15795e-25,98.5624,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs2_gorilla,marg,CompleteHit
9241,Q#242 - >seq3565,superfamily,340205,236,299,1.15795e-25,98.5624,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs2_gorilla,marg,CompleteHit
9242,Q#242 - >seq3565,non-specific,335182,138,233,9.210530000000001e-23,91.5954,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs2_gorilla,marg,CompleteHit
9243,Q#242 - >seq3565,superfamily,335182,138,233,9.210530000000001e-23,91.5954,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs2_gorilla,marg,CompleteHit
9244,Q#242 - >seq3565,non-specific,197310,347,405,0.00035322800000000003,41.5681,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF1,hs2_gorilla,marg,C-TerminusTruncated
9245,Q#242 - >seq3565,superfamily,351117,347,405,0.00035322800000000003,41.5681,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF1,hs2_gorilla,marg,C-TerminusTruncated
9246,Q#242 - >seq3565,non-specific,224556,156,263,0.000619456,41.5598,COG1641,COG1641,N,cl03398,"Uncharacterized conserved protein, DUF111 family [Function unknown]; Uncharacterized conserved protein [Function unknown].",L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
9247,Q#242 - >seq3565,superfamily,351986,156,263,0.000619456,41.5598,cl03398,DUF111 superfamily,N, - ,Protein of unknown function DUF111; This prokaryotic family has no known function.,L1MC5a.ORF1.hs2_gorilla.marg.frame3,1909130325_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
9248,Q#243 - >seq3566,non-specific,238827,461,521,4.9558e-17,80.7982,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs0_human.pars.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs0_human,pars,C-TerminusTruncated
9249,Q#243 - >seq3566,superfamily,295487,461,521,4.9558e-17,80.7982,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs0_human.pars.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs0_human,pars,C-TerminusTruncated
9250,Q#243 - >seq3566,non-specific,333820,467,521,6.06755e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.pars.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs0_human,pars,C-TerminusTruncated
9251,Q#243 - >seq3566,superfamily,333820,467,521,6.06755e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.pars.frame2,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC4,ORF2,hs0_human,pars,C-TerminusTruncated
9252,Q#245 - >seq3568,non-specific,238827,549,703,1.88046e-19,88.117,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC4.ORF2.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs0_human,pars,N-TerminusTruncated
9253,Q#245 - >seq3568,superfamily,295487,549,703,1.88046e-19,88.117,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC4.ORF2.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs0_human,pars,N-TerminusTruncated
9254,Q#245 - >seq3568,non-specific,333820,539,701,4.80763e-12,65.7766,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs0_human,pars,CompleteHit
9255,Q#245 - >seq3568,superfamily,333820,539,701,4.80763e-12,65.7766,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC4.ORF2.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs0_human,pars,CompleteHit
9256,Q#245 - >seq3568,non-specific,238828,552,692,5.1555e-08,54.5144,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC4.ORF2.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC4,ORF2,hs0_human,pars,N-TerminusTruncated
9257,Q#256 - >seq3579,non-specific,197310,13,129,6.85429e-07,49.6573,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs8_ctshrew.pars.frame2,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
9258,Q#256 - >seq3579,superfamily,351117,13,129,6.85429e-07,49.6573,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs8_ctshrew.pars.frame2,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
9259,Q#256 - >seq3579,non-specific,197311,50,129,0.0021777,38.8121,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs8_ctshrew.pars.frame2,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC4,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
9260,Q#258 - >seq3581,non-specific,197310,4,239,3.70158e-13,68.9173,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs8_ctshrew.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs8_ctshrew,marg,CompleteHit
9261,Q#258 - >seq3581,superfamily,351117,4,239,3.70158e-13,68.9173,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs8_ctshrew.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs8_ctshrew,marg,CompleteHit
9262,Q#258 - >seq3581,non-specific,197306,2,240,1.49649e-11,64.0397,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs8_ctshrew.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs8_ctshrew,marg,CompleteHit
9263,Q#264 - >seq3587,non-specific,197310,4,201,2.28884e-07,51.9685,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC4.ORF2.hs10_snmole.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC4,ORF2,hs10_snmole,marg,CompleteHit
9264,Q#264 - >seq3587,superfamily,351117,4,201,2.28884e-07,51.9685,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs10_snmole.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs10_snmole,marg,CompleteHit
9265,Q#264 - >seq3587,non-specific,197306,2,151,0.00511412,39.0017,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC4.ORF2.hs10_snmole.marg.frame1,1909130325_L1MC4.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC4,ORF2,hs10_snmole,marg,C-TerminusTruncated
9266,Q#267 - >seq3590,non-specific,340205,233,284,4.2161500000000004e-20,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,pars,CompleteHit
9267,Q#267 - >seq3590,superfamily,340205,233,284,4.2161500000000004e-20,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.pars.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,pars,CompleteHit
9268,Q#269 - >seq3592,non-specific,335182,147,234,4.694609999999999e-41,138.205,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs0_human,pars,CompleteHit
9269,Q#269 - >seq3592,superfamily,335182,147,234,4.694609999999999e-41,138.205,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs0_human,pars,CompleteHit
9270,Q#269 - >seq3592,non-specific,340204,96,133,1.30007e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs0_human,pars,CompleteHit
9271,Q#269 - >seq3592,superfamily,340204,96,133,1.30007e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC4,ORF1,hs0_human,pars,CompleteHit
9272,Q#269 - >seq3592,non-specific,340205,237,269,0.000331444,38.086,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs0_human,pars,C-TerminusTruncated
9273,Q#269 - >seq3592,superfamily,340205,237,269,0.000331444,38.086,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.pars.frame3,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC4,ORF1,hs0_human,pars,C-TerminusTruncated
9274,Q#270 - >seq3593,non-specific,335182,161,258,3.3583599999999997e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,marg,CompleteHit
9275,Q#270 - >seq3593,superfamily,335182,161,258,3.3583599999999997e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,marg,CompleteHit
9276,Q#270 - >seq3593,non-specific,340205,261,325,5.404029999999999e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,marg,CompleteHit
9277,Q#270 - >seq3593,superfamily,340205,261,325,5.404029999999999e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC4,ORF1,hs0_human,marg,CompleteHit
9278,Q#270 - >seq3593,non-specific,340204,114,158,2.9805599999999997e-10,54.7212,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC4,ORF1,hs0_human,marg,CompleteHit
9279,Q#270 - >seq3593,superfamily,340204,114,158,2.9805599999999997e-10,54.7212,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC4.ORF1.hs0_human.marg.frame1,1909130325_L1MC4.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC4,ORF1,hs0_human,marg,CompleteHit
9280,Q#271 - >seq3594,specific,197310,83,253,4.0372199999999996e-38,142.876,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9281,Q#271 - >seq3594,superfamily,351117,83,253,4.0372199999999996e-38,142.876,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9282,Q#271 - >seq3594,non-specific,197306,83,232,3.89411e-23,99.478,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9283,Q#271 - >seq3594,non-specific,223780,83,252,1.68613e-16,80.7203,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9284,Q#271 - >seq3594,non-specific,197307,83,227,1.6843800000000002e-15,77.7133,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9285,Q#271 - >seq3594,non-specific,197320,83,227,6.7244699999999994e-15,75.6293,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9286,Q#271 - >seq3594,non-specific,197321,81,237,2.52063e-13,71.044,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9287,Q#271 - >seq3594,specific,335306,84,221,2.45483e-12,67.6554,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9288,Q#271 - >seq3594,non-specific,272954,83,237,9.84195e-12,66.6377,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9289,Q#271 - >seq3594,non-specific,197319,83,227,4.11594e-10,61.5237,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9290,Q#271 - >seq3594,non-specific,273186,83,237,7.83953e-10,60.7556,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9291,Q#271 - >seq3594,non-specific,197336,83,227,1.72822e-09,59.5483,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9292,Q#271 - >seq3594,non-specific,236970,83,220,3.5840899999999996e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9293,Q#271 - >seq3594,non-specific,197322,82,227,6.56825e-05,46.1562,cd09088,Ape2-like_AP-endo,C,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9294,Q#271 - >seq3594,non-specific,197311,104,220,0.00010097,44.5901,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9295,Q#271 - >seq3594,non-specific,197318,83,150,0.00153042,41.5131,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9296,Q#271 - >seq3594,specific,311990,1238,1255,0.00163384,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9297,Q#271 - >seq3594,superfamily,311990,1238,1255,0.00163384,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs2_gorilla.marg.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9298,Q#272 - >seq3595,non-specific,340205,1,36,5.3686199999999994e-06,45.0196,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF2.hs2_gorilla.marg.frame1,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
9299,Q#272 - >seq3595,superfamily,340205,1,36,5.3686199999999994e-06,45.0196,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF2.hs2_gorilla.marg.frame1,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
9300,Q#273 - >seq3596,specific,238827,572,832,4.01168e-59,202.521,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9301,Q#273 - >seq3596,superfamily,295487,572,832,4.01168e-59,202.521,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9302,Q#273 - >seq3596,non-specific,333820,578,802,5.48068e-27,108.919,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9303,Q#273 - >seq3596,superfamily,333820,578,802,5.48068e-27,108.919,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9304,Q#273 - >seq3596,non-specific,197310,220,298,1.36375e-11,65.8357,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC5a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
9305,Q#273 - >seq3596,superfamily,351117,220,298,1.36375e-11,65.8357,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
9306,Q#273 - >seq3596,non-specific,238828,578,799,1.4673200000000001e-08,56.4404,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9307,Q#273 - >seq3596,non-specific,275209,530,908,3.14521e-05,47.4524,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9308,Q#273 - >seq3596,superfamily,275209,530,908,3.14521e-05,47.4524,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9309,Q#273 - >seq3596,non-specific,238185,722,803,0.00464641,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs2_gorilla.marg.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,marg,CompleteHit
9310,Q#274 - >seq3597,non-specific,238827,500,582,4.4877800000000005e-20,89.2726,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9311,Q#274 - >seq3597,superfamily,295487,500,582,4.4877800000000005e-20,89.2726,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9312,Q#274 - >seq3597,non-specific,197310,148,226,1.36472e-11,65.0653,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9313,Q#274 - >seq3597,superfamily,351117,148,226,1.36472e-11,65.0653,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9314,Q#274 - >seq3597,non-specific,333820,506,558,1.2195599999999999e-09,58.0726,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9315,Q#274 - >seq3597,superfamily,333820,506,558,1.2195599999999999e-09,58.0726,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9316,Q#274 - >seq3597,non-specific,235175,295,460,0.00535616,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC5a,ORF2,hs2_gorilla,pars,BothTerminiTruncated
9317,Q#274 - >seq3597,superfamily,235175,295,460,0.00535616,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs2_gorilla.pars.frame2,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC5a,ORF2,hs2_gorilla,pars,BothTerminiTruncated
9318,Q#276 - >seq3599,specific,197310,8,178,7.54506e-38,140.95,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9319,Q#276 - >seq3599,superfamily,351117,8,178,7.54506e-38,140.95,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9320,Q#276 - >seq3599,non-specific,197306,8,157,3.88038e-23,98.7076,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9321,Q#276 - >seq3599,non-specific,238827,605,714,4.2464099999999997e-23,98.1322,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9322,Q#276 - >seq3599,superfamily,295487,605,714,4.2464099999999997e-23,98.1322,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9323,Q#276 - >seq3599,non-specific,223780,8,177,9.40926e-17,80.7203,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9324,Q#276 - >seq3599,non-specific,197307,8,152,1.3153700000000001e-15,76.9429,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9325,Q#276 - >seq3599,non-specific,197320,8,152,3.77317e-15,75.6293,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9326,Q#276 - >seq3599,non-specific,197321,6,162,1.0026399999999999e-13,71.4292,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9327,Q#276 - >seq3599,specific,335306,9,146,1.4048399999999999e-12,67.6554,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9328,Q#276 - >seq3599,non-specific,333820,534,714,2.70268e-12,65.7766,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9329,Q#276 - >seq3599,superfamily,333820,534,714,2.70268e-12,65.7766,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9330,Q#276 - >seq3599,non-specific,272954,8,162,6.43964e-12,66.2525,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9331,Q#276 - >seq3599,non-specific,197319,8,152,2.2653900000000002e-10,61.5237,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9332,Q#276 - >seq3599,non-specific,273186,8,162,4.4355e-10,60.7556,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9333,Q#276 - >seq3599,non-specific,197336,8,152,9.78935e-10,59.5483,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9334,Q#276 - >seq3599,non-specific,236970,8,145,2.59878e-07,52.589,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9335,Q#276 - >seq3599,non-specific,197322,7,152,3.73441e-05,46.1562,cd09088,Ape2-like_AP-endo,C,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9336,Q#276 - >seq3599,non-specific,197311,29,145,5.88687e-05,44.5901,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9337,Q#276 - >seq3599,non-specific,238828,547,680,8.450579999999999e-05,44.4993,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
9338,Q#276 - >seq3599,non-specific,197318,8,75,0.00137791,41.1279,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs2_gorilla.pars.frame3,1909130326_L1MC5a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
9339,Q#278 - >seq3601,non-specific,197310,21,106,2.57877e-09,58.5169,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9340,Q#278 - >seq3601,superfamily,351117,21,106,2.57877e-09,58.5169,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9341,Q#278 - >seq3601,non-specific,223496,276,412,7.866150000000001e-06,49.7587,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9342,Q#278 - >seq3601,superfamily,223496,276,412,7.866150000000001e-06,49.7587,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9343,Q#278 - >seq3601,non-specific,274008,258,406,0.00017967099999999998,45.4327,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9344,Q#278 - >seq3601,superfamily,274008,258,406,0.00017967099999999998,45.4327,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9345,Q#278 - >seq3601,non-specific,235175,258,410,0.0006430569999999999,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9346,Q#278 - >seq3601,superfamily,235175,258,410,0.0006430569999999999,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9347,Q#278 - >seq3601,non-specific,235175,250,451,0.000822535,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9348,Q#278 - >seq3601,non-specific,274009,274,408,0.00264795,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9349,Q#278 - >seq3601,superfamily,274009,274,408,0.00264795,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9350,Q#278 - >seq3601,non-specific,224241,282,473,0.00949085,39.6824,COG1322,RmuC,C,cl34228,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9351,Q#278 - >seq3601,superfamily,224241,282,473,0.00949085,39.6824,cl34228,RmuC superfamily,C, - ,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
9352,Q#278 - >seq3601,non-specific,240271,279,520,0.00970864,40.0296,PTZ00108,PTZ00108,N,cl36510,DNA topoisomerase 2-like protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9353,Q#278 - >seq3601,superfamily,240271,279,520,0.00970864,40.0296,cl36510,PTZ00108 superfamily,N, - ,DNA topoisomerase 2-like protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9354,Q#279 - >seq3602,non-specific,339134,969,1098,0.00848901,39.1585,pfam14254,DUF4348,NC,cl16750,"Domain of unknown function (DUF4348); Two structures have been solved form this DUF, Structure 4mjf and Structure 3sbu. TOPSAN records that both proteins are the only structural representatives of Pfam PF14254, DUF4348. There are no other significant hits in FFAS. DUF4348 has ~200 proteins, all from Bacteroidetes, and all with a single domain architecture with just one DUF4348 domain. There appears to be a possible gene duplication in the protein as the N-terminal domain (approx residues 25-174) and C-terminal domain (approx residues 175-286) superimpose quite well with ~1.9A r.m.s.d. and ~30% sequence identity.",L1MC5a.ORF2.hs5_gmonkey.pars.frame2,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9355,Q#279 - >seq3602,superfamily,339134,969,1098,0.00848901,39.1585,cl16750,DUF4348 superfamily,NC, - ,"Domain of unknown function (DUF4348); Two structures have been solved form this DUF, Structure 4mjf and Structure 3sbu. TOPSAN records that both proteins are the only structural representatives of Pfam PF14254, DUF4348. There are no other significant hits in FFAS. DUF4348 has ~200 proteins, all from Bacteroidetes, and all with a single domain architecture with just one DUF4348 domain. There appears to be a possible gene duplication in the protein as the N-terminal domain (approx residues 25-174) and C-terminal domain (approx residues 175-286) superimpose quite well with ~1.9A r.m.s.d. and ~30% sequence identity.",L1MC5a.ORF2.hs5_gmonkey.pars.frame2,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MC5a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9356,Q#280 - >seq3603,specific,238827,482,725,2.54817e-49,174.016,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9357,Q#280 - >seq3603,superfamily,295487,482,725,2.54817e-49,174.016,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9358,Q#280 - >seq3603,specific,197310,3,227,1.06942e-36,138.638,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9359,Q#280 - >seq3603,superfamily,351117,3,227,1.06942e-36,138.638,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9360,Q#280 - >seq3603,non-specific,333820,494,711,5.71414e-28,111.615,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9361,Q#280 - >seq3603,superfamily,333820,494,711,5.71414e-28,111.615,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9362,Q#280 - >seq3603,non-specific,197306,3,227,2.84777e-27,111.419,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9363,Q#280 - >seq3603,non-specific,197307,3,227,1.8882800000000002e-10,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9364,Q#280 - >seq3603,non-specific,223780,3,228,3.4938199999999995e-10,61.8455,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9365,Q#280 - >seq3603,specific,335306,4,220,6.04576e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9366,Q#280 - >seq3603,non-specific,197320,3,220,1.5631999999999999e-07,53.673,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9367,Q#280 - >seq3603,non-specific,238828,553,708,2.75314e-06,49.5068,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9368,Q#280 - >seq3603,non-specific,197336,3,185,5.925130000000001e-06,48.7627,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9369,Q#280 - >seq3603,non-specific,272954,3,227,6.14607e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9370,Q#280 - >seq3603,non-specific,339261,104,223,0.00039083699999999994,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9371,Q#280 - >seq3603,non-specific,197319,7,227,0.000725776,42.2637,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs5_gmonkey.pars.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,pars,CompleteHit
9372,Q#281 - >seq3604,specific,238827,512,773,1.95925e-45,163.231,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9373,Q#281 - >seq3604,superfamily,295487,512,773,1.95925e-45,163.231,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9374,Q#281 - >seq3604,specific,197310,79,237,3.59829e-27,111.289,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9375,Q#281 - >seq3604,superfamily,351117,79,237,3.59829e-27,111.289,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9376,Q#281 - >seq3604,non-specific,333820,524,745,8.457149999999999e-21,91.1997,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9377,Q#281 - >seq3604,superfamily,333820,524,745,8.457149999999999e-21,91.1997,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9378,Q#281 - >seq3604,non-specific,197306,81,237,1.1492499999999999e-18,86.3812,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9379,Q#281 - >seq3604,non-specific,197320,104,230,3.06932e-06,49.821000000000005,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9380,Q#281 - >seq3604,specific,335306,70,230,4.35326e-06,49.1658,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9381,Q#281 - >seq3604,non-specific,197307,101,237,5.804429999999999e-06,48.8233,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9382,Q#281 - >seq3604,non-specific,223496,311,534,1.02765e-05,49.7587,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9383,Q#281 - >seq3604,superfamily,223496,311,534,1.02765e-05,49.7587,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9384,Q#281 - >seq3604,non-specific,339261,104,233,1.68436e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9385,Q#281 - >seq3604,non-specific,223780,81,238,7.93471e-05,45.6671,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9386,Q#281 - >seq3604,non-specific,274008,293,441,0.000284189,45.0475,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9387,Q#281 - >seq3604,superfamily,274008,293,441,0.000284189,45.0475,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9388,Q#281 - >seq3604,non-specific,235175,293,445,0.000600767,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9389,Q#281 - >seq3604,superfamily,235175,293,445,0.000600767,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9390,Q#281 - >seq3604,non-specific,308206,304,802,0.00151711,42.6517,pfam02463,SMC_N,NC,cl37666,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9391,Q#281 - >seq3604,superfamily,308206,304,802,0.00151711,42.6517,cl37666,SMC_N superfamily,NC, - ,"RecF/RecN/SMC N terminal domain; This domain is found at the N-terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9392,Q#281 - >seq3604,non-specific,289056,283,477,0.00155267,42.9495,pfam12252,SidE,N,cl26680,Dot/Icm substrate protein; This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 1543 amino acids in length. This family is the SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.,L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9393,Q#281 - >seq3604,superfamily,289056,283,477,0.00155267,42.9495,cl26680,SidE superfamily,N, - ,Dot/Icm substrate protein; This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 1543 amino acids in length. This family is the SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.,L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MC5a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9394,Q#281 - >seq3604,non-specific,188306,313,392,0.00250389,41.835,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9395,Q#281 - >seq3604,superfamily,188306,313,392,0.00250389,41.835,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9396,Q#281 - >seq3604,non-specific,274009,309,443,0.00407182,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9397,Q#281 - >seq3604,superfamily,274009,309,443,0.00407182,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9398,Q#281 - >seq3604,non-specific,274009,313,439,0.00486298,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9399,Q#281 - >seq3604,non-specific,224117,308,490,0.00684232,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9400,Q#281 - >seq3604,superfamily,224117,308,490,0.00684232,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9401,Q#283 - >seq3606,non-specific,197310,3,83,1.2376900000000002e-13,71.6137,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9402,Q#283 - >seq3606,superfamily,351117,3,83,1.2376900000000002e-13,71.6137,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9403,Q#283 - >seq3606,non-specific,197306,3,110,1.20852e-09,59.8025,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9404,Q#283 - >seq3606,specific,335306,4,119,3.03152e-06,49.551,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9405,Q#283 - >seq3606,non-specific,197321,1,44,3.39382e-05,46.7764,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9406,Q#283 - >seq3606,non-specific,223780,3,38,4.2131499999999995e-05,46.4375,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9407,Q#283 - >seq3606,specific,311990,1189,1206,0.00012441200000000001,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9408,Q#283 - >seq3606,superfamily,311990,1189,1206,0.00012441200000000001,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs5_gmonkey,marg,CompleteHit
9409,Q#283 - >seq3606,non-specific,273186,3,38,0.0017170999999999998,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9410,Q#283 - >seq3606,non-specific,197307,3,38,0.00213591,41.1193,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9411,Q#283 - >seq3606,non-specific,197320,3,38,0.00240261,40.9614,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs5_gmonkey.marg.frame3,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9412,Q#285 - >seq3608,non-specific,340205,88,121,0.000198227,36.9304,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs6_sqmonkey.pars.frame2,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
9413,Q#285 - >seq3608,superfamily,340205,88,121,0.000198227,36.9304,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs6_sqmonkey.pars.frame2,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
9414,Q#287 - >seq3610,non-specific,340205,283,322,1.39139e-08,50.7976,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs6_sqmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
9415,Q#287 - >seq3610,superfamily,340205,283,322,1.39139e-08,50.7976,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs6_sqmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
9416,Q#288 - >seq3611,non-specific,335182,174,235,3.66544e-05,41.9047,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs6_sqmonkey.marg.frame2,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
9417,Q#288 - >seq3611,superfamily,335182,174,235,3.66544e-05,41.9047,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs6_sqmonkey.marg.frame2,1909130327_L1MC5a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
9418,Q#303 - >seq3626,non-specific,335182,161,261,2.4484099999999996e-36,126.649,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,marg,CompleteHit
9419,Q#303 - >seq3626,superfamily,335182,161,261,2.4484099999999996e-36,126.649,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,marg,CompleteHit
9420,Q#303 - >seq3626,non-specific,340205,264,309,9.571319999999999e-19,78.9172,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
9421,Q#303 - >seq3626,superfamily,340205,264,309,9.571319999999999e-19,78.9172,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs5_gmonkey.marg.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
9422,Q#304 - >seq3627,non-specific,335182,55,140,1.0069799999999998e-26,98.529,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,pars,CompleteHit
9423,Q#304 - >seq3627,superfamily,335182,55,140,1.0069799999999998e-26,98.529,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,pars,CompleteHit
9424,Q#307 - >seq3630,non-specific,340205,57,111,1.1752700000000001e-26,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs3_orang.pars.frame2,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs3_orang,pars,CompleteHit
9425,Q#307 - >seq3630,superfamily,340205,57,111,1.1752700000000001e-26,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs3_orang.pars.frame2,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs3_orang,pars,CompleteHit
9426,Q#308 - >seq3631,non-specific,335182,1,48,3.0085e-09,50.3791,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,pars,N-TerminusTruncated
9427,Q#308 - >seq3631,superfamily,335182,1,48,3.0085e-09,50.3791,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,pars,N-TerminusTruncated
9428,Q#311 - >seq3634,non-specific,335182,158,255,1.1451799999999999e-36,127.419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9429,Q#311 - >seq3634,superfamily,335182,158,255,1.1451799999999999e-36,127.419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9430,Q#311 - >seq3634,non-specific,340205,258,321,9.18791e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9431,Q#311 - >seq3634,superfamily,340205,258,321,9.18791e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9432,Q#311 - >seq3634,non-specific,340204,113,155,9.67042e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9433,Q#311 - >seq3634,superfamily,340204,113,155,9.67042e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9434,Q#311 - >seq3634,non-specific,274765,17,127,8.0907e-05,43.8626,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MC5a,ORF1,hs3_orang,marg,C-TerminusTruncated
9435,Q#311 - >seq3634,superfamily,274765,17,127,8.0907e-05,43.8626,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MC5a,ORF1,hs3_orang,marg,C-TerminusTruncated
9436,Q#311 - >seq3634,non-specific,274008,48,245,0.00207227,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9437,Q#311 - >seq3634,superfamily,274008,48,245,0.00207227,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9438,Q#311 - >seq3634,non-specific,273690,69,158,0.0023818000000000003,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1MC5a,ORF1,hs3_orang,marg,C-TerminusTruncated
9439,Q#311 - >seq3634,superfamily,355611,69,158,0.0023818000000000003,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Viral,L1MC5a,ORF1,hs3_orang,marg,C-TerminusTruncated
9440,Q#311 - >seq3634,non-specific,179385,60,147,0.00262661,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9441,Q#311 - >seq3634,superfamily,179385,60,147,0.00262661,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9442,Q#311 - >seq3634,non-specific,224117,67,216,0.00369185,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9443,Q#311 - >seq3634,superfamily,224117,67,216,0.00369185,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9444,Q#311 - >seq3634,non-specific,335555,67,133,0.00410724,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5a,ORF1,hs3_orang,marg,N-TerminusTruncated
9445,Q#311 - >seq3634,superfamily,354396,67,133,0.00410724,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1MC5a,ORF1,hs3_orang,marg,N-TerminusTruncated
9446,Q#311 - >seq3634,non-specific,224117,67,152,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9447,Q#311 - >seq3634,superfamily,224117,67,152,0.00470962,38.542,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9448,Q#311 - >seq3634,non-specific,334921,54,131,0.00502784,36.0256,pfam02403,Seryl_tRNA_N, - ,cl38070,Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9449,Q#311 - >seq3634,superfamily,334921,54,131,0.00502784,36.0256,cl38070,Seryl_tRNA_N superfamily, - , - ,Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF1,hs3_orang,marg,CompleteHit
9450,Q#311 - >seq3634,non-specific,224117,56,199,0.00536563,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9451,Q#311 - >seq3634,non-specific,197874,58,133,0.0061707,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MC5a,ORF1,hs3_orang,marg,N-TerminusTruncated
9452,Q#311 - >seq3634,superfamily,197874,58,133,0.0061707,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MC5a,ORF1,hs3_orang,marg,N-TerminusTruncated
9453,Q#311 - >seq3634,non-specific,274008,40,151,0.00688085,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9454,Q#311 - >seq3634,superfamily,274008,40,151,0.00688085,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF1.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF1,hs3_orang,marg,BothTerminiTruncated
9455,Q#314 - >seq3637,specific,238827,504,766,2.6627399999999994e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9456,Q#314 - >seq3637,superfamily,295487,504,766,2.6627399999999994e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9457,Q#314 - >seq3637,specific,197310,3,230,1.0677099999999999e-60,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9458,Q#314 - >seq3637,superfamily,351117,3,230,1.0677099999999999e-60,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9459,Q#314 - >seq3637,non-specific,197306,3,230,6.8396699999999995e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9460,Q#314 - >seq3637,specific,333820,510,766,7.27181e-35,131.64600000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9461,Q#314 - >seq3637,superfamily,333820,510,766,7.27181e-35,131.64600000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9462,Q#314 - >seq3637,non-specific,197307,3,230,1.6656699999999998e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9463,Q#314 - >seq3637,non-specific,223780,3,232,5.65736e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9464,Q#314 - >seq3637,non-specific,197320,2,230,2.1553299999999998e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9465,Q#314 - >seq3637,specific,335306,4,223,1.06846e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9466,Q#314 - >seq3637,non-specific,273186,3,231,2.80563e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9467,Q#314 - >seq3637,non-specific,197321,1,230,1.2393e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9468,Q#314 - >seq3637,non-specific,272954,3,230,7.93418e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9469,Q#314 - >seq3637,non-specific,197319,2,230,1.54202e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9470,Q#314 - >seq3637,non-specific,197336,1,188,1.39323e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9471,Q#314 - >seq3637,non-specific,238828,510,731,4.73419e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9472,Q#314 - >seq3637,non-specific,236970,3,232,2.1303400000000005e-10,62.6042,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9473,Q#314 - >seq3637,non-specific,197322,3,230,7.805670000000001e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9474,Q#314 - >seq3637,non-specific,339261,102,226,1.6625299999999998e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9475,Q#314 - >seq3637,non-specific,275209,461,794,1.71978e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9476,Q#314 - >seq3637,superfamily,275209,461,794,1.71978e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9477,Q#314 - >seq3637,non-specific,197311,1,230,1.63337e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9478,Q#314 - >seq3637,non-specific,274009,295,472,0.000160557,45.8291,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9479,Q#314 - >seq3637,superfamily,274009,295,472,0.000160557,45.8291,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9480,Q#314 - >seq3637,non-specific,238185,650,766,0.000256055,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,pars,CompleteHit
9481,Q#314 - >seq3637,non-specific,274009,301,452,0.000470064,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,C-TerminusTruncated
9482,Q#314 - >seq3637,non-specific,224117,260,385,0.00109872,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9483,Q#314 - >seq3637,superfamily,224117,260,385,0.00109872,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9484,Q#314 - >seq3637,non-specific,197314,1,186,0.00120191,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs3_orang,pars,C-TerminusTruncated
9485,Q#314 - >seq3637,non-specific,197317,133,223,0.00228116,41.0484,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,pars,N-TerminusTruncated
9486,Q#314 - >seq3637,non-specific,224117,300,453,0.00231262,42.0088,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,C-TerminusTruncated
9487,Q#314 - >seq3637,non-specific,235175,257,458,0.00236722,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9488,Q#314 - >seq3637,superfamily,235175,257,458,0.00236722,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs3_orang.pars.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,pars,BothTerminiTruncated
9489,Q#318 - >seq3641,specific,238827,510,772,2.4722499999999996e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9490,Q#318 - >seq3641,superfamily,295487,510,772,2.4722499999999996e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9491,Q#318 - >seq3641,specific,197310,9,236,1.0914599999999999e-60,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9492,Q#318 - >seq3641,superfamily,351117,9,236,1.0914599999999999e-60,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9493,Q#318 - >seq3641,non-specific,197306,9,236,5.79834e-49,174.207,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9494,Q#318 - >seq3641,specific,333820,516,772,6.27002e-35,131.64600000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9495,Q#318 - >seq3641,superfamily,333820,516,772,6.27002e-35,131.64600000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9496,Q#318 - >seq3641,non-specific,197307,9,236,1.32374e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9497,Q#318 - >seq3641,non-specific,223780,9,238,4.29403e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9498,Q#318 - >seq3641,non-specific,197320,8,236,1.5898700000000002e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9499,Q#318 - >seq3641,specific,335306,10,229,1.10791e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9500,Q#318 - >seq3641,non-specific,273186,9,237,2.433e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9501,Q#318 - >seq3641,non-specific,197321,7,236,1.0747999999999999e-17,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9502,Q#318 - >seq3641,non-specific,272954,9,236,6.092399999999999e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9503,Q#318 - >seq3641,non-specific,197319,8,236,1.2308e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9504,Q#318 - >seq3641,non-specific,197336,7,194,1.29225e-12,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9505,Q#318 - >seq3641,non-specific,238828,516,737,4.42653e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9506,Q#318 - >seq3641,non-specific,236970,9,238,2.0724200000000002e-10,62.6042,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9507,Q#318 - >seq3641,non-specific,197322,9,236,8.10488e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9508,Q#318 - >seq3641,non-specific,339261,108,232,1.9503900000000003e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9509,Q#318 - >seq3641,non-specific,275209,467,800,1.5641e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9510,Q#318 - >seq3641,superfamily,275209,467,800,1.5641e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9511,Q#318 - >seq3641,non-specific,197311,7,236,1.6764600000000002e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9512,Q#318 - >seq3641,non-specific,274009,301,478,0.000148033,46.2143,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9513,Q#318 - >seq3641,superfamily,274009,301,478,0.000148033,46.2143,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9514,Q#318 - >seq3641,non-specific,238185,656,772,0.000247221,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9515,Q#318 - >seq3641,non-specific,274009,307,458,0.000426026,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,C-TerminusTruncated
9516,Q#318 - >seq3641,non-specific,224117,266,391,0.00109264,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9517,Q#318 - >seq3641,superfamily,224117,266,391,0.00109264,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9518,Q#318 - >seq3641,non-specific,197314,7,192,0.00124532,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs3_orang,marg,C-TerminusTruncated
9519,Q#318 - >seq3641,specific,311990,1241,1258,0.00182399,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9520,Q#318 - >seq3641,superfamily,311990,1241,1258,0.00182399,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,DUF1725,L1MC5a,ORF2,hs3_orang,marg,CompleteHit
9521,Q#318 - >seq3641,non-specific,235175,263,464,0.00218044,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9522,Q#318 - >seq3641,superfamily,235175,263,464,0.00218044,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,BothTerminiTruncated
9523,Q#318 - >seq3641,non-specific,224117,306,459,0.00222296,42.394,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs3_orang,marg,C-TerminusTruncated
9524,Q#318 - >seq3641,non-specific,197317,139,229,0.00228037,41.0484,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs3_orang.marg.frame3,1909130327_L1MC5a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs3_orang,marg,N-TerminusTruncated
9525,Q#319 - >seq3642,non-specific,340205,167,207,4.1120600000000004e-13,61.9684,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
9526,Q#319 - >seq3642,superfamily,340205,167,207,4.1120600000000004e-13,61.9684,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
9527,Q#320 - >seq3643,non-specific,335182,158,249,1.6138099999999998e-29,108.929,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,marg,CompleteHit
9528,Q#320 - >seq3643,superfamily,335182,158,249,1.6138099999999998e-29,108.929,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,marg,CompleteHit
9529,Q#320 - >seq3643,non-specific,340205,267,325,6.4063199999999995e-15,68.5168,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,marg,CompleteHit
9530,Q#320 - >seq3643,superfamily,340205,267,325,6.4063199999999995e-15,68.5168,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5a,ORF1,hs4_gibbon,marg,CompleteHit
9531,Q#323 - >seq3646,specific,238827,411,672,2.9959299999999993e-63,214.077,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9532,Q#323 - >seq3646,superfamily,295487,411,672,2.9959299999999993e-63,214.077,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9533,Q#323 - >seq3646,specific,333820,417,672,4.5527899999999995e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9534,Q#323 - >seq3646,superfamily,333820,417,672,4.5527899999999995e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9535,Q#323 - >seq3646,non-specific,238828,417,637,1.84908e-09,59.1368,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9536,Q#323 - >seq3646,non-specific,275209,368,700,1.25166e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9537,Q#323 - >seq3646,superfamily,275209,368,700,1.25166e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9538,Q#323 - >seq3646,non-specific,238185,559,672,0.00018827400000000002,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs4_gibbon.pars.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs4_gibbon,pars,CompleteHit
9539,Q#324 - >seq3647,non-specific,197310,88,158,5.5478699999999995e-14,72.3841,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9540,Q#324 - >seq3647,superfamily,351117,88,158,5.5478699999999995e-14,72.3841,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9541,Q#324 - >seq3647,non-specific,197306,57,158,5.19707e-12,66.7361,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9542,Q#324 - >seq3647,non-specific,197307,98,158,1.12869e-06,51.1345,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9543,Q#324 - >seq3647,non-specific,223780,92,160,6.0703e-06,48.7487,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9544,Q#324 - >seq3647,non-specific,197321,91,158,1.5093499999999999e-05,47.5468,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9545,Q#324 - >seq3647,non-specific,273186,91,159,0.000132299,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9546,Q#324 - >seq3647,non-specific,197320,92,143,0.00770913,39.0354,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.pars.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
9547,Q#325 - >seq3648,non-specific,197310,1,95,1.0773299999999999e-14,74.6953,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
9548,Q#325 - >seq3648,superfamily,351117,1,95,1.0773299999999999e-14,74.6953,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
9549,Q#325 - >seq3648,non-specific,197306,1,87,1.36965e-10,62.4989,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
9550,Q#325 - >seq3648,non-specific,197311,1,75,0.00184865,40.7381,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.pars.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
9551,Q#326 - >seq3649,specific,311990,1109,1126,0.000740605,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9552,Q#326 - >seq3649,superfamily,311990,1109,1126,0.000740605,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5a.ORF2.hs4_gibbon.marg.frame1,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,DUF1725,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9553,Q#327 - >seq3650,non-specific,197310,88,158,1.0519e-13,71.6137,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9554,Q#327 - >seq3650,superfamily,351117,88,158,1.0519e-13,71.6137,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9555,Q#327 - >seq3650,non-specific,197306,57,158,6.68704e-12,66.3509,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9556,Q#327 - >seq3650,non-specific,197307,98,158,1.18137e-06,51.1345,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9557,Q#327 - >seq3650,non-specific,223780,92,160,6.3537199999999995e-06,48.7487,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9558,Q#327 - >seq3650,non-specific,197321,91,158,1.6082899999999998e-05,47.5468,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9559,Q#327 - >seq3650,non-specific,273186,91,159,0.000138401,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9560,Q#327 - >seq3650,non-specific,197320,92,143,0.0080597,39.0354,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs4_gibbon.marg.frame2,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
9561,Q#328 - >seq3651,specific,238827,418,679,1.0934999999999999e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9562,Q#328 - >seq3651,superfamily,295487,418,679,1.0934999999999999e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9563,Q#328 - >seq3651,specific,333820,424,679,3.49309e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9564,Q#328 - >seq3651,superfamily,333820,424,679,3.49309e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9565,Q#328 - >seq3651,non-specific,197310,1,95,1.01366e-14,74.6953,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
9566,Q#328 - >seq3651,superfamily,351117,1,95,1.01366e-14,74.6953,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
9567,Q#328 - >seq3651,non-specific,197306,1,87,2.69349e-10,61.7285,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
9568,Q#328 - >seq3651,non-specific,238828,424,644,6.32269e-10,60.2924,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9569,Q#328 - >seq3651,non-specific,275209,375,703,3.59942e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9570,Q#328 - >seq3651,superfamily,275209,375,703,3.59942e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9571,Q#328 - >seq3651,non-specific,238185,566,679,3.84256e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs4_gibbon,marg,CompleteHit
9572,Q#328 - >seq3651,non-specific,197311,1,75,0.00194266,40.7381,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs4_gibbon.marg.frame3,1909130327_L1MC5a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
9573,Q#329 - >seq3652,non-specific,335182,124,221,1.06716e-40,136.664,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,pars,CompleteHit
9574,Q#329 - >seq3652,superfamily,335182,124,221,1.06716e-40,136.664,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,pars,CompleteHit
9575,Q#329 - >seq3652,non-specific,340205,224,288,2.05094e-28,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,pars,CompleteHit
9576,Q#329 - >seq3652,superfamily,340205,224,288,2.05094e-28,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs5_gmonkey.pars.frame1,1909130327_L1MC5a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs5_gmonkey,pars,CompleteHit
9577,Q#338 - >seq3661,non-specific,335182,87,155,7.42621e-12,59.6239,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs9_pika.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs9_pika,marg,N-TerminusTruncated
9578,Q#338 - >seq3661,superfamily,335182,87,155,7.42621e-12,59.6239,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs9_pika.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs9_pika,marg,N-TerminusTruncated
9579,Q#338 - >seq3661,non-specific,340205,161,224,1.52838e-06,44.2492,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs9_pika.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs9_pika,marg,CompleteHit
9580,Q#338 - >seq3661,superfamily,340205,161,224,1.52838e-06,44.2492,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs9_pika.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs9_pika,marg,CompleteHit
9581,Q#342 - >seq3665,non-specific,238827,564,600,1.07196e-07,53.0638,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs9_pika.marg.frame1,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs9_pika,marg,C-TerminusTruncated
9582,Q#342 - >seq3665,superfamily,295487,564,600,1.07196e-07,53.0638,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs9_pika.marg.frame1,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs9_pika,marg,C-TerminusTruncated
9583,Q#342 - >seq3665,non-specific,197310,198,303,0.00023114900000000002,43.1089,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs9_pika.marg.frame1,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5a,ORF2,hs9_pika,marg,N-TerminusTruncated
9584,Q#342 - >seq3665,superfamily,351117,198,303,0.00023114900000000002,43.1089,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs9_pika.marg.frame1,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5a,ORF2,hs9_pika,marg,N-TerminusTruncated
9585,Q#346 - >seq3669,non-specific,340205,15,52,1.37514e-11,52.7236,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs10_snmole.pars.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs10_snmole,pars,C-TerminusTruncated
9586,Q#346 - >seq3669,superfamily,340205,15,52,1.37514e-11,52.7236,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs10_snmole.pars.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs10_snmole,pars,C-TerminusTruncated
9587,Q#349 - >seq3672,non-specific,340205,1,15,0.000921385,31.1524,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs10_snmole.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs10_snmole,marg,BothTerminiTruncated
9588,Q#349 - >seq3672,superfamily,340205,1,15,0.000921385,31.1524,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs10_snmole.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs10_snmole,marg,BothTerminiTruncated
9589,Q#353 - >seq3676,non-specific,335182,24,90,3.0622900000000003e-10,53.8459,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs9_pika.pars.frame2,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs9_pika,pars,N-TerminusTruncated
9590,Q#353 - >seq3676,superfamily,335182,24,90,3.0622900000000003e-10,53.8459,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs9_pika.pars.frame2,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs9_pika,pars,N-TerminusTruncated
9591,Q#353 - >seq3676,non-specific,340205,96,148,2.2367e-09,50.7976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs9_pika.pars.frame2,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs9_pika,pars,CompleteHit
9592,Q#353 - >seq3676,superfamily,340205,96,148,2.2367e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs9_pika.pars.frame2,1909130329_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5a,ORF1,hs9_pika,pars,CompleteHit
9593,Q#356 - >seq3679,non-specific,340205,32,94,1.77782e-20,77.3764,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs8_ctshrew.pars.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs8_ctshrew,pars,CompleteHit
9594,Q#356 - >seq3679,superfamily,340205,32,94,1.77782e-20,77.3764,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs8_ctshrew.pars.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5a,ORF1,hs8_ctshrew,pars,CompleteHit
9595,Q#359 - >seq3682,non-specific,340205,1,15,0.000921385,31.1524,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs8_ctshrew.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs8_ctshrew,marg,BothTerminiTruncated
9596,Q#359 - >seq3682,superfamily,340205,1,15,0.000921385,31.1524,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs8_ctshrew.marg.frame3,1909130329_L1MC5a.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs8_ctshrew,marg,BothTerminiTruncated
9597,Q#367 - >seq3690,non-specific,340204,105,146,0.00330966,34.6908,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9598,Q#367 - >seq3690,superfamily,340204,105,146,0.00330966,34.6908,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9599,Q#370 - >seq3693,non-specific,335182,160,257,5.8443299999999996e-36,125.493,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9600,Q#370 - >seq3693,superfamily,335182,160,257,5.8443299999999996e-36,125.493,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9601,Q#370 - >seq3693,non-specific,340205,260,323,5.9152399999999995e-27,100.874,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9602,Q#370 - >seq3693,superfamily,340205,260,323,5.9152399999999995e-27,100.874,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9603,Q#370 - >seq3693,non-specific,340204,114,156,3.32782e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9604,Q#370 - >seq3693,superfamily,340204,114,156,3.32782e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5a.ORF1.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5a,ORF1,hs0_human,marg,CompleteHit
9605,Q#371 - >seq3694,specific,197310,9,236,4.234669999999999e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9606,Q#371 - >seq3694,superfamily,351117,9,236,4.234669999999999e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9607,Q#371 - >seq3694,non-specific,197306,9,236,4.29726e-53,185.763,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9608,Q#371 - >seq3694,non-specific,197307,9,236,3.2702099999999997e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9609,Q#371 - >seq3694,non-specific,223780,9,238,1.22877e-25,107.29899999999999,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9610,Q#371 - >seq3694,non-specific,238827,511,762,6.2797500000000005e-24,101.214,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9611,Q#371 - >seq3694,superfamily,295487,511,762,6.2797500000000005e-24,101.214,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9612,Q#371 - >seq3694,non-specific,197321,7,236,3.02557e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9613,Q#371 - >seq3694,non-specific,197320,8,236,4.76949e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9614,Q#371 - >seq3694,specific,335306,10,229,1.0237200000000001e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9615,Q#371 - >seq3694,non-specific,273186,9,237,1.25889e-19,89.6456,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9616,Q#371 - >seq3694,non-specific,272954,9,236,1.96995e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9617,Q#371 - >seq3694,non-specific,197319,8,236,5.346880000000001e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9618,Q#371 - >seq3694,non-specific,197336,7,235,3.59457e-13,70.7191,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9619,Q#371 - >seq3694,non-specific,197322,9,236,1.47572e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9620,Q#371 - >seq3694,non-specific,236970,9,238,2.95408e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9621,Q#371 - >seq3694,non-specific,339261,108,232,1.25473e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9622,Q#371 - >seq3694,non-specific,197311,7,236,1.24349e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,pars,CompleteHit
9623,Q#371 - >seq3694,non-specific,333820,517,571,6.8826800000000005e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs0_human,pars,C-TerminusTruncated
9624,Q#371 - >seq3694,superfamily,333820,517,571,6.8826800000000005e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5a,ORF2,hs0_human,pars,C-TerminusTruncated
9625,Q#371 - >seq3694,non-specific,197317,139,229,8.60125e-06,48.3672,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9626,Q#371 - >seq3694,non-specific,226098,138,239,0.00033382,43.5432,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9627,Q#371 - >seq3694,non-specific,197314,7,192,0.000540215,42.7159,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs0_human,pars,C-TerminusTruncated
9628,Q#371 - >seq3694,non-specific,274009,303,459,0.000740555,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,pars,BothTerminiTruncated
9629,Q#371 - >seq3694,superfamily,274009,303,459,0.000740555,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,pars,BothTerminiTruncated
9630,Q#371 - >seq3694,non-specific,274009,305,459,0.00131634,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.pars.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,pars,C-TerminusTruncated
9631,Q#373 - >seq3696,non-specific,238827,533,711,6.812510000000001e-18,83.4946,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9632,Q#373 - >seq3696,superfamily,295487,533,711,6.812510000000001e-18,83.4946,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9633,Q#373 - >seq3696,non-specific,333820,532,711,1.74438e-11,64.2358,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9634,Q#373 - >seq3696,superfamily,333820,532,711,1.74438e-11,64.2358,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9635,Q#373 - >seq3696,non-specific,238828,532,640,3.16909e-05,46.4253,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,BothTerminiTruncated
9636,Q#373 - >seq3696,non-specific,275209,533,616,0.00769022,39.7484,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,BothTerminiTruncated
9637,Q#373 - >seq3696,superfamily,275209,533,616,0.00769022,39.7484,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5a.ORF2.hs0_human.marg.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5a,ORF2,hs0_human,marg,BothTerminiTruncated
9638,Q#376 - >seq3699,non-specific,238827,533,705,4.06763e-14,72.709,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9639,Q#376 - >seq3699,superfamily,295487,533,705,4.06763e-14,72.709,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9640,Q#376 - >seq3699,non-specific,333820,532,676,2.20974e-09,58.0726,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9641,Q#376 - >seq3699,superfamily,333820,532,676,2.20974e-09,58.0726,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs0_human,pars,N-TerminusTruncated
9642,Q#376 - >seq3699,non-specific,238828,532,640,3.28106e-05,46.4253,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5a.ORF2.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC5a,ORF2,hs0_human,pars,BothTerminiTruncated
9643,Q#377 - >seq3700,non-specific,335182,148,240,2.64202e-32,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9644,Q#377 - >seq3700,superfamily,335182,148,240,2.64202e-32,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5a.ORF1.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9645,Q#377 - >seq3700,non-specific,340205,243,306,2.55674e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9646,Q#377 - >seq3700,superfamily,340205,243,306,2.55674e-27,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5a.ORF1.hs0_human.pars.frame1,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MC5a,ORF1,hs0_human,pars,CompleteHit
9647,Q#378 - >seq3701,specific,197310,9,236,1.4599499999999997e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9648,Q#378 - >seq3701,superfamily,351117,9,236,1.4599499999999997e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9649,Q#378 - >seq3701,non-specific,197306,9,236,5.64286e-53,185.763,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9650,Q#378 - >seq3701,non-specific,197307,9,236,1.06021e-25,107.374,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9651,Q#378 - >seq3701,non-specific,223780,9,238,2.0398699999999998e-25,106.529,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9652,Q#378 - >seq3701,non-specific,197320,8,236,4.7788e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9653,Q#378 - >seq3701,non-specific,238827,511,766,6.7498399999999996e-21,92.3542,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9654,Q#378 - >seq3701,superfamily,295487,511,766,6.7498399999999996e-21,92.3542,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9655,Q#378 - >seq3701,non-specific,197321,7,236,1.0318e-20,92.6152,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9656,Q#378 - >seq3701,specific,335306,10,229,1.0256600000000001e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9657,Q#378 - >seq3701,non-specific,273186,9,237,2.5667e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9658,Q#378 - >seq3701,non-specific,272954,9,236,4.4370500000000003e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9659,Q#378 - >seq3701,non-specific,197319,8,236,2.158e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9660,Q#378 - >seq3701,non-specific,197336,7,235,3.60151e-13,70.7191,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9661,Q#378 - >seq3701,non-specific,197322,9,236,1.47865e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9662,Q#378 - >seq3701,non-specific,236970,9,238,4.68094e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9663,Q#378 - >seq3701,non-specific,339261,108,232,1.0454399999999999e-08,54.2655,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9664,Q#378 - >seq3701,non-specific,197311,7,236,9.773899999999999e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9665,Q#378 - >seq3701,non-specific,333820,517,664,4.269469999999999e-06,48.4426,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9666,Q#378 - >seq3701,superfamily,333820,517,664,4.269469999999999e-06,48.4426,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5a,ORF2,hs0_human,marg,CompleteHit
9667,Q#378 - >seq3701,non-specific,197317,139,229,8.85538e-06,48.3672,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9668,Q#378 - >seq3701,non-specific,274009,303,459,0.000266595,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,marg,BothTerminiTruncated
9669,Q#378 - >seq3701,superfamily,274009,303,459,0.000266595,45.0587,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,marg,BothTerminiTruncated
9670,Q#378 - >seq3701,non-specific,226098,138,239,0.000334443,43.5432,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5a,ORF2,hs0_human,marg,N-TerminusTruncated
9671,Q#378 - >seq3701,non-specific,197314,7,192,0.000541219,42.7159,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MC5a,ORF2,hs0_human,marg,C-TerminusTruncated
9672,Q#378 - >seq3701,non-specific,274009,305,459,0.0006056519999999999,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5a,ORF2,hs0_human,marg,C-TerminusTruncated
9673,Q#378 - >seq3701,non-specific,287038,311,361,0.00749473,38.5795,pfam10018,Med4,C,cl10818,"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF2,hs0_human,marg,C-TerminusTruncated
9674,Q#378 - >seq3701,superfamily,287038,311,361,0.00749473,38.5795,cl10818,Med4 superfamily,C, - ,"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.",L1MC5a.ORF2.hs0_human.marg.frame3,1909130330_L1MC5a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5a,ORF2,hs0_human,marg,C-TerminusTruncated
9675,Q#386 - >seq3709,non-specific,317481,137,201,0.000625379,40.5611,pfam15066,CAGE1,N,cl25929,Cancer-associated gene protein 1 family; CAGE-1 is a family of proteins overexpressed in tumor tissues compared with surrounding tissues. CAGE-1 gene showed testis-specific expression among normal tissues and displayed wide expression in a variety of cancer cell lines and cancer tissues. CAGE-1 is predominantly expressed during post-meiotic stages. It localizes to the acrosomal matrix and acrosomal granule showing it to be a component of the acrosome of mammalian spermatids and spermatozoa.,L1MC5a.ORF2.hs11_armadillo.pars.frame1,1909130330_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs11_armadillo,pars,N-TerminusTruncated
9676,Q#386 - >seq3709,superfamily,317481,137,201,0.000625379,40.5611,cl25929,CAGE1 superfamily,N, - ,Cancer-associated gene protein 1 family; CAGE-1 is a family of proteins overexpressed in tumor tissues compared with surrounding tissues. CAGE-1 gene showed testis-specific expression among normal tissues and displayed wide expression in a variety of cancer cell lines and cancer tissues. CAGE-1 is predominantly expressed during post-meiotic stages. It localizes to the acrosomal matrix and acrosomal granule showing it to be a component of the acrosome of mammalian spermatids and spermatozoa.,L1MC5a.ORF2.hs11_armadillo.pars.frame1,1909130330_L1MC5a.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5a,ORF2,hs11_armadillo,pars,N-TerminusTruncated
9677,Q#396 - >seq3719,non-specific,238827,568,664,4.13597e-05,45.745,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5.ORF2.hs6_sqmonkey.marg.frame3,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9678,Q#396 - >seq3719,superfamily,295487,568,664,4.13597e-05,45.745,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5.ORF2.hs6_sqmonkey.marg.frame3,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9679,Q#402 - >seq3725,non-specific,335182,163,220,2.02591e-09,53.8459,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
9680,Q#402 - >seq3725,superfamily,335182,163,220,2.02591e-09,53.8459,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
9681,Q#402 - >seq3725,non-specific,340205,245,304,8.12878e-09,51.1828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5,ORF1,hs6_sqmonkey,marg,CompleteHit
9682,Q#402 - >seq3725,superfamily,340205,245,304,8.12878e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MC5,ORF1,hs6_sqmonkey,marg,CompleteHit
9683,Q#402 - >seq3725,non-specific,340204,95,137,7.54688e-05,39.3132,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC5,ORF1,hs6_sqmonkey,marg,CompleteHit
9684,Q#402 - >seq3725,superfamily,340204,95,137,7.54688e-05,39.3132,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MC5,ORF1,hs6_sqmonkey,marg,CompleteHit
9685,Q#402 - >seq3725,non-specific,237177,24,133,0.00225119,39.3762,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC5,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
9686,Q#402 - >seq3725,superfamily,237177,24,133,0.00225119,39.3762,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MC5.ORF1.hs6_sqmonkey.marg.frame1,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MC5,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
9687,Q#404 - >seq3727,non-specific,340205,62,125,5.17674e-09,48.8716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs6_sqmonkey.pars.frame2,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5,ORF1,hs6_sqmonkey,pars,CompleteHit
9688,Q#404 - >seq3727,superfamily,340205,62,125,5.17674e-09,48.8716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs6_sqmonkey.pars.frame2,1909130331_L1MC5.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MC5,ORF1,hs6_sqmonkey,pars,CompleteHit
9689,Q#438 - >seq3761,non-specific,197310,1,229,0.00172707,41.1829,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5.ORF2.hs2_gorilla.marg.frame1,1909130331_L1MC5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC5,ORF2,hs2_gorilla,marg,CompleteHit
9690,Q#438 - >seq3761,superfamily,351117,1,229,0.00172707,41.1829,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs2_gorilla.marg.frame1,1909130331_L1MC5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC5,ORF2,hs2_gorilla,marg,CompleteHit
9691,Q#438 - >seq3761,non-specific,238827,559,673,0.00302051,40.3522,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5.ORF2.hs2_gorilla.marg.frame1,1909130331_L1MC5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9692,Q#438 - >seq3761,superfamily,295487,559,673,0.00302051,40.3522,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5.ORF2.hs2_gorilla.marg.frame1,1909130331_L1MC5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MC5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
9693,Q#451 - >seq3774,non-specific,340205,46,70,0.000997734,33.4636,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs4_gibbon.pars.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
9694,Q#451 - >seq3774,superfamily,340205,46,70,0.000997734,33.4636,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs4_gibbon.pars.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
9695,Q#455 - >seq3778,non-specific,335182,167,248,2.77452e-23,91.9806,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9696,Q#455 - >seq3778,superfamily,335182,167,248,2.77452e-23,91.9806,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9697,Q#455 - >seq3778,non-specific,340205,251,314,2.31111e-16,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9698,Q#455 - >seq3778,superfamily,340205,251,314,2.31111e-16,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9699,Q#455 - >seq3778,non-specific,340204,106,148,0.000266576,37.7724,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Trimerization,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9700,Q#455 - >seq3778,superfamily,340204,106,148,0.000266576,37.7724,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs5_gmonkey.marg.frame2,1909130331_L1MC5.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Trimerization,L1MC5,ORF1,hs5_gmonkey,marg,CompleteHit
9701,Q#466 - >seq3789,non-specific,335182,148,229,3.35602e-26,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9702,Q#466 - >seq3789,superfamily,335182,148,229,3.35602e-26,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9703,Q#466 - >seq3789,non-specific,340205,232,295,8.321180000000001e-22,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9704,Q#466 - >seq3789,superfamily,340205,232,295,8.321180000000001e-22,86.6212,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9705,Q#466 - >seq3789,non-specific,340204,90,129,8.83211e-05,39.3132,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9706,Q#466 - >seq3789,superfamily,340204,90,129,8.83211e-05,39.3132,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs4_gibbon.marg.frame3,1909130331_L1MC5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5,ORF1,hs4_gibbon,marg,CompleteHit
9707,Q#470 - >seq3793,non-specific,238827,457,538,1.2356900000000001e-09,59.227,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs6_sqmonkey.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
9708,Q#470 - >seq3793,superfamily,295487,457,538,1.2356900000000001e-09,59.227,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs6_sqmonkey.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
9709,Q#470 - >seq3793,non-specific,333820,463,496,0.00944901,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs6_sqmonkey.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
9710,Q#470 - >seq3793,superfamily,333820,463,496,0.00944901,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs6_sqmonkey.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
9711,Q#471 - >seq3794,specific,197310,9,236,3.9815e-32,125.156,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9712,Q#471 - >seq3794,superfamily,351117,9,236,3.9815e-32,125.156,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9713,Q#471 - >seq3794,non-specific,197306,9,236,1.0225299999999999e-12,69.0473,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9714,Q#471 - >seq3794,non-specific,197307,9,236,1.08445e-08,56.9125,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9715,Q#471 - >seq3794,non-specific,197320,62,229,2.1943200000000004e-08,56.3694,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9716,Q#471 - >seq3794,non-specific,197322,106,236,4.2647199999999996e-08,55.7862,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9717,Q#471 - >seq3794,non-specific,223780,62,229,4.9521699999999995e-08,55.2971,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9718,Q#471 - >seq3794,specific,335306,58,229,1.46685e-06,50.3214,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9719,Q#471 - >seq3794,non-specific,273186,7,237,4.89439e-06,49.1996,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9720,Q#471 - >seq3794,non-specific,197321,7,236,7.65717e-05,45.2356,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9721,Q#471 - >seq3794,non-specific,339261,108,232,0.000308492,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs6_sqmonkey,marg,CompleteHit
9722,Q#471 - >seq3794,non-specific,197319,106,236,0.00106741,41.8785,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9723,Q#471 - >seq3794,non-specific,197311,72,236,0.00318105,39.9677,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs6_sqmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
9724,Q#473 - >seq3796,non-specific,340205,154,218,3.2317100000000005e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs7_bushaby,pars,CompleteHit
9725,Q#473 - >seq3796,superfamily,340205,154,218,3.2317100000000005e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs7_bushaby,pars,CompleteHit
9726,Q#475 - >seq3798,non-specific,340205,219,261,8.22693e-11,56.1904,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,N-TerminusTruncated
9727,Q#475 - >seq3798,superfamily,340205,219,261,8.22693e-11,56.1904,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,N-TerminusTruncated
9728,Q#475 - >seq3798,non-specific,335182,96,190,2.6112600000000003e-09,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,CompleteHit
9729,Q#475 - >seq3798,superfamily,335182,96,190,2.6112600000000003e-09,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,CompleteHit
9730,Q#476 - >seq3799,non-specific,340205,184,204,0.00195229,35.7748,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,C-TerminusTruncated
9731,Q#476 - >seq3799,superfamily,340205,184,204,0.00195229,35.7748,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs7_bushaby.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs7_bushaby,marg,C-TerminusTruncated
9732,Q#479 - >seq3802,non-specific,238827,443,488,6.38152e-05,44.5894,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs7_bushaby.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
9733,Q#479 - >seq3802,superfamily,295487,443,488,6.38152e-05,44.5894,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs7_bushaby.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
9734,Q#480 - >seq3803,specific,197310,1,221,1.08887e-42,154.817,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9735,Q#480 - >seq3803,superfamily,351117,1,221,1.08887e-42,154.817,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9736,Q#480 - >seq3803,non-specific,197306,1,221,3.8548e-20,90.2332,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9737,Q#480 - >seq3803,non-specific,223780,1,214,7.809520000000001e-13,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9738,Q#480 - >seq3803,non-specific,197320,1,214,2.18873e-12,67.5402,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9739,Q#480 - >seq3803,specific,335306,1,214,3.41633e-11,63.4182,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9740,Q#480 - >seq3803,non-specific,273186,1,222,5.16448e-10,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9741,Q#480 - >seq3803,non-specific,197307,3,221,3.5822600000000004e-09,58.0681,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9742,Q#480 - >seq3803,non-specific,197322,93,221,1.61279e-08,56.5566,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
9743,Q#480 - >seq3803,non-specific,197321,3,221,2.0354e-08,55.636,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9744,Q#480 - >seq3803,non-specific,339261,94,217,7.24605e-08,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9745,Q#480 - >seq3803,non-specific,197311,2,221,5.83694e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9746,Q#480 - >seq3803,non-specific,272954,1,192,0.000254587,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs7_bushaby,pars,CompleteHit
9747,Q#481 - >seq3804,non-specific,335182,60,154,1.65599e-09,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs7_bushaby,pars,CompleteHit
9748,Q#481 - >seq3804,superfamily,335182,60,154,1.65599e-09,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs7_bushaby.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs7_bushaby,pars,CompleteHit
9749,Q#482 - >seq3805,specific,197310,24,226,2.16743e-32,125.927,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9750,Q#482 - >seq3805,superfamily,351117,24,226,2.16743e-32,125.927,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9751,Q#482 - >seq3805,non-specific,197306,24,226,4.82031e-12,66.7361,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9752,Q#482 - >seq3805,non-specific,197320,51,219,8.68208e-09,57.1398,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9753,Q#482 - >seq3805,non-specific,223780,51,219,1.22041e-08,56.8379,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9754,Q#482 - >seq3805,non-specific,197322,96,226,3.6741199999999996e-08,55.7862,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9755,Q#482 - >seq3805,non-specific,197307,24,226,6.30013e-08,54.6013,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9756,Q#482 - >seq3805,non-specific,273186,24,227,4.76505e-07,51.896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9757,Q#482 - >seq3805,specific,335306,47,219,2.1179499999999998e-06,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9758,Q#482 - >seq3805,non-specific,197321,51,226,9.11207e-05,44.8504,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9759,Q#482 - >seq3805,non-specific,339261,98,222,0.000250462,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs6_sqmonkey,pars,CompleteHit
9760,Q#482 - >seq3805,non-specific,197311,61,226,0.00029701099999999997,43.0493,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9761,Q#482 - >seq3805,non-specific,272954,80,226,0.00867109,38.9033,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
9762,Q#483 - >seq3806,specific,197310,5,222,2.13176e-42,154.817,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9763,Q#483 - >seq3806,superfamily,351117,5,222,2.13176e-42,154.817,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9764,Q#483 - >seq3806,non-specific,197306,5,222,1.74292e-19,88.6924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9765,Q#483 - >seq3806,non-specific,223780,5,215,1.27978e-13,71.8607,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9766,Q#483 - >seq3806,non-specific,238827,494,699,9.23443e-12,65.7754,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9767,Q#483 - >seq3806,superfamily,295487,494,699,9.23443e-12,65.7754,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
9768,Q#483 - >seq3806,non-specific,197307,5,222,7.91261e-11,63.4609,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9769,Q#483 - >seq3806,non-specific,197320,4,215,1.40898e-10,62.9178,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9770,Q#483 - >seq3806,specific,335306,6,215,2.7109699999999995e-10,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9771,Q#483 - >seq3806,non-specific,197322,68,222,6.08619e-10,61.5642,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9772,Q#483 - >seq3806,non-specific,333820,601,722,1.90392e-08,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9773,Q#483 - >seq3806,superfamily,333820,601,722,1.90392e-08,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9774,Q#483 - >seq3806,non-specific,197321,3,222,5.6187e-08,54.8656,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9775,Q#483 - >seq3806,non-specific,273186,5,223,8.235250000000001e-08,54.5924,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9776,Q#483 - >seq3806,non-specific,339261,94,218,5.20946e-07,49.2579,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9777,Q#483 - >seq3806,non-specific,238828,597,704,2.40669e-06,49.5068,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
9778,Q#483 - >seq3806,non-specific,197319,4,222,8.389520000000001e-05,45.3453,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9779,Q#483 - >seq3806,non-specific,272954,5,193,0.00018942099999999997,44.2961,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9780,Q#483 - >seq3806,non-specific,197311,39,222,0.00258426,40.3529,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,marg,CompleteHit
9781,Q#483 - >seq3806,non-specific,235175,293,474,0.00548674,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MCa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9782,Q#483 - >seq3806,superfamily,235175,293,474,0.00548674,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MCa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9783,Q#483 - >seq3806,non-specific,214368,433,862,0.0060558,40.6927,CHL00117,rpoC2,NC,cl33332,RNA polymerase beta'' subunit; Reviewed,L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MCa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9784,Q#483 - >seq3806,superfamily,214368,433,862,0.0060558,40.6927,cl33332,rpoC2 superfamily,NC, - ,RNA polymerase beta'' subunit; Reviewed,L1MCa.ORF2.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MCa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
9785,Q#486 - >seq3809,non-specific,335182,90,186,8.013130000000001e-17,73.4911,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs6_sqmonkey.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs6_sqmonkey,marg,CompleteHit
9786,Q#486 - >seq3809,superfamily,335182,90,186,8.013130000000001e-17,73.4911,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs6_sqmonkey.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs6_sqmonkey,marg,CompleteHit
9787,Q#486 - >seq3809,non-specific,340205,189,256,8.898520000000001e-17,72.3688,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs6_sqmonkey.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs6_sqmonkey,marg,CompleteHit
9788,Q#486 - >seq3809,superfamily,340205,189,256,8.898520000000001e-17,72.3688,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs6_sqmonkey.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs6_sqmonkey,marg,CompleteHit
9789,Q#488 - >seq3811,non-specific,340205,166,233,7.47166e-17,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs6_sqmonkey,pars,CompleteHit
9790,Q#488 - >seq3811,superfamily,340205,166,233,7.47166e-17,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs6_sqmonkey,pars,CompleteHit
9791,Q#488 - >seq3811,non-specific,335182,67,163,7.87389e-17,73.1059,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs6_sqmonkey,pars,CompleteHit
9792,Q#488 - >seq3811,superfamily,335182,67,163,7.87389e-17,73.1059,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs6_sqmonkey.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs6_sqmonkey,pars,CompleteHit
9793,Q#492 - >seq3815,specific,197310,5,223,7.808439999999999e-42,153.276,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9794,Q#492 - >seq3815,superfamily,351117,5,223,7.808439999999999e-42,153.276,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9795,Q#492 - >seq3815,non-specific,197306,5,223,5.387450000000001e-19,87.1516,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9796,Q#492 - >seq3815,non-specific,223780,5,216,4.05846e-13,70.3199,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9797,Q#492 - >seq3815,non-specific,238827,495,751,2.03964e-12,67.3162,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9798,Q#492 - >seq3815,superfamily,295487,495,751,2.03964e-12,67.3162,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9799,Q#492 - >seq3815,non-specific,197320,4,216,1.90794e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9800,Q#492 - >seq3815,non-specific,197307,5,223,2.0346900000000001e-10,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9801,Q#492 - >seq3815,specific,335306,6,216,2.1425599999999996e-10,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9802,Q#492 - >seq3815,non-specific,197322,69,223,5.7302e-10,61.5642,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9803,Q#492 - >seq3815,non-specific,333820,602,755,1.05565e-09,58.843,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9804,Q#492 - >seq3815,superfamily,333820,602,755,1.05565e-09,58.843,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9805,Q#492 - >seq3815,non-specific,273186,5,224,1.37163e-07,53.821999999999996,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9806,Q#492 - >seq3815,non-specific,339261,95,219,4.847059999999999e-07,49.2579,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9807,Q#492 - >seq3815,non-specific,238828,598,705,4.93203e-06,48.7364,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9808,Q#492 - >seq3815,non-specific,197319,93,223,0.000149056,44.5749,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
9809,Q#492 - >seq3815,non-specific,272954,5,194,0.000854295,41.9849,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9810,Q#492 - >seq3815,non-specific,197311,40,223,0.00235746,40.3529,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs5_gmonkey,pars,CompleteHit
9811,Q#492 - >seq3815,non-specific,235175,294,475,0.00970572,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MCa,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9812,Q#492 - >seq3815,superfamily,235175,294,475,0.00970572,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MCa.ORF2.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MCa,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
9813,Q#495 - >seq3818,specific,197310,11,234,1.10366e-40,149.424,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9814,Q#495 - >seq3818,superfamily,351117,11,234,1.10366e-40,149.424,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9815,Q#495 - >seq3818,non-specific,197306,11,234,1.57445e-20,91.3888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9816,Q#495 - >seq3818,non-specific,223780,11,227,7.596610000000001e-14,72.2459,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9817,Q#495 - >seq3818,non-specific,197320,11,227,7.77474e-13,69.081,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9818,Q#495 - >seq3818,specific,335306,12,227,3.34989e-12,66.4998,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9819,Q#495 - >seq3818,non-specific,273186,11,235,2.94309e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9820,Q#495 - >seq3818,non-specific,197321,10,234,2.93945e-10,61.413999999999994,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9821,Q#495 - >seq3818,non-specific,197307,11,234,4.2676e-10,60.7645,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9822,Q#495 - >seq3818,non-specific,197322,106,234,1.8810799999999998e-08,56.5566,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,N-TerminusTruncated
9823,Q#495 - >seq3818,non-specific,339261,107,230,4.95165e-07,48.8727,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9824,Q#495 - >seq3818,non-specific,197311,11,234,7.583839999999999e-07,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9825,Q#495 - >seq3818,non-specific,272954,11,205,0.000123699,44.2961,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9826,Q#495 - >seq3818,non-specific,197336,11,227,0.0044174,39.5179,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs7_bushaby.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9827,Q#496 - >seq3819,non-specific,340205,170,235,2.36581e-21,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,marg,CompleteHit
9828,Q#496 - >seq3819,superfamily,340205,170,235,2.36581e-21,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,marg,CompleteHit
9829,Q#496 - >seq3819,non-specific,335182,92,167,1.33207e-10,56.5423,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
9830,Q#496 - >seq3819,superfamily,335182,92,167,1.33207e-10,56.5423,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs5_gmonkey.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
9831,Q#497 - >seq3820,non-specific,238827,452,539,1.7356799999999998e-10,61.5382,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs6_sqmonkey.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
9832,Q#497 - >seq3820,superfamily,295487,452,539,1.7356799999999998e-10,61.5382,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs6_sqmonkey.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
9833,Q#497 - >seq3820,non-specific,333820,458,491,0.00810786,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs6_sqmonkey.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
9834,Q#497 - >seq3820,superfamily,333820,458,491,0.00810786,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs6_sqmonkey.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
9835,Q#498 - >seq3821,non-specific,238827,478,743,6.8623e-11,62.6938,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs7_bushaby.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9836,Q#498 - >seq3821,superfamily,295487,478,743,6.8623e-11,62.6938,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs7_bushaby.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs7_bushaby,marg,CompleteHit
9837,Q#504 - >seq3827,non-specific,340205,188,252,2.86844e-21,84.31,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs10_snmole.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs10_snmole,marg,CompleteHit
9838,Q#504 - >seq3827,superfamily,340205,188,252,2.86844e-21,84.31,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs10_snmole.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs10_snmole,marg,CompleteHit
9839,Q#504 - >seq3827,non-specific,335182,111,185,4.945019999999999e-10,55.0015,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs10_snmole.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs10_snmole,marg,N-TerminusTruncated
9840,Q#504 - >seq3827,superfamily,335182,111,185,4.945019999999999e-10,55.0015,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs10_snmole.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs10_snmole,marg,N-TerminusTruncated
9841,Q#505 - >seq3828,non-specific,340205,175,238,1.4249600000000002e-20,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs10_snmole.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs10_snmole,pars,CompleteHit
9842,Q#505 - >seq3828,superfamily,340205,175,238,1.4249600000000002e-20,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs10_snmole.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs10_snmole,pars,CompleteHit
9843,Q#505 - >seq3828,non-specific,335182,97,172,1.41888e-10,56.1571,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs10_snmole.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs10_snmole,pars,N-TerminusTruncated
9844,Q#505 - >seq3828,superfamily,335182,97,172,1.41888e-10,56.1571,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs10_snmole.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs10_snmole,pars,N-TerminusTruncated
9845,Q#508 - >seq3831,specific,197310,9,235,3.1613599999999993e-54,187.94400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9846,Q#508 - >seq3831,superfamily,351117,9,235,3.1613599999999993e-54,187.94400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9847,Q#508 - >seq3831,non-specific,197306,9,235,1.34422e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9848,Q#508 - >seq3831,non-specific,223780,9,228,6.21552e-18,84.5723,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9849,Q#508 - >seq3831,non-specific,197307,9,235,2.18087e-16,79.6393,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9850,Q#508 - >seq3831,specific,335306,10,228,3.83066e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9851,Q#508 - >seq3831,non-specific,197320,9,228,5.19269e-14,72.5478,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9852,Q#508 - >seq3831,non-specific,273186,9,236,1.38797e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9853,Q#508 - >seq3831,non-specific,197321,7,235,1.8958e-12,67.9624,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9854,Q#508 - >seq3831,non-specific,272954,9,206,2.12531e-09,58.9337,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9855,Q#508 - >seq3831,non-specific,197322,81,235,2.3851900000000002e-08,56.5566,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,N-TerminusTruncated
9856,Q#508 - >seq3831,non-specific,197319,9,235,7.808710000000001e-08,54.2049,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9857,Q#508 - >seq3831,non-specific,339261,107,231,2.5463299999999996e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9858,Q#508 - >seq3831,non-specific,197336,9,228,9.04909e-06,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,marg,CompleteHit
9859,Q#510 - >seq3833,non-specific,238827,473,665,3.0333999999999995e-22,95.821,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs9_pika.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs9_pika,marg,C-TerminusTruncated
9860,Q#510 - >seq3833,superfamily,295487,473,665,3.0333999999999995e-22,95.821,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs9_pika.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs9_pika,marg,C-TerminusTruncated
9861,Q#510 - >seq3833,non-specific,333820,482,661,2.76413e-11,63.0802,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs9_pika.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs9_pika,marg,C-TerminusTruncated
9862,Q#510 - >seq3833,superfamily,333820,482,661,2.76413e-11,63.0802,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs9_pika.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs9_pika,marg,C-TerminusTruncated
9863,Q#510 - >seq3833,non-specific,238828,518,672,0.0005262719999999999,42.1881,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs9_pika.marg.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs9_pika,marg,N-TerminusTruncated
9864,Q#511 - >seq3834,specific,197310,5,230,1.4157999999999997e-53,179.855,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9865,Q#511 - >seq3834,superfamily,351117,5,230,1.4157999999999997e-53,179.855,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9866,Q#511 - >seq3834,non-specific,197306,5,230,1.1405200000000002e-26,107.56700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9867,Q#511 - >seq3834,non-specific,223780,5,223,4.7579400000000004e-18,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9868,Q#511 - >seq3834,specific,335306,6,223,2.7313e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9869,Q#511 - >seq3834,non-specific,197307,5,230,1.93927e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9870,Q#511 - >seq3834,non-specific,273186,5,231,3.21569e-15,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9871,Q#511 - >seq3834,non-specific,197320,5,223,2.55037e-14,72.5478,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9872,Q#511 - >seq3834,non-specific,197321,3,230,6.292479999999999e-13,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9873,Q#511 - >seq3834,non-specific,272954,5,201,2.61865e-10,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9874,Q#511 - >seq3834,non-specific,197322,4,230,3.33091e-10,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9875,Q#511 - >seq3834,non-specific,197319,5,230,2.9624500000000002e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9876,Q#511 - >seq3834,non-specific,197336,5,223,2.85622e-07,51.4591,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9877,Q#511 - >seq3834,non-specific,339261,102,226,2.69947e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs9_pika.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs9_pika,pars,CompleteHit
9878,Q#513 - >seq3836,non-specific,340205,161,220,1.14057e-13,63.5092,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs9_pika,marg,CompleteHit
9879,Q#513 - >seq3836,superfamily,340205,161,220,1.14057e-13,63.5092,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs9_pika,marg,CompleteHit
9880,Q#513 - >seq3836,non-specific,335182,78,158,5.22501e-10,54.6163,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs9_pika,marg,CompleteHit
9881,Q#513 - >seq3836,superfamily,335182,78,158,5.22501e-10,54.6163,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs9_pika.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs9_pika,marg,CompleteHit
9882,Q#517 - >seq3840,non-specific,340205,148,190,2.70143e-11,56.5756,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs9_pika.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs9_pika,pars,N-TerminusTruncated
9883,Q#517 - >seq3840,superfamily,340205,148,190,2.70143e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs9_pika.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs9_pika,pars,N-TerminusTruncated
9884,Q#518 - >seq3841,non-specific,335182,50,141,1.42811e-10,55.7719,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs9_pika.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs9_pika,pars,CompleteHit
9885,Q#518 - >seq3841,superfamily,335182,50,141,1.42811e-10,55.7719,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs9_pika.pars.frame1,1909130332_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs9_pika,pars,CompleteHit
9886,Q#519 - >seq3842,specific,197310,5,228,5.700999999999999e-43,156.358,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9887,Q#519 - >seq3842,superfamily,351117,5,228,5.700999999999999e-43,156.358,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9888,Q#519 - >seq3842,non-specific,197306,5,228,3.13022e-21,93.7,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9889,Q#519 - >seq3842,non-specific,223780,5,221,1.63264e-11,65.3123,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9890,Q#519 - >seq3842,non-specific,197307,5,228,6.10158e-11,63.4609,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9891,Q#519 - >seq3842,specific,335306,6,221,1.3387399999999998e-10,61.8774,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9892,Q#519 - >seq3842,non-specific,197320,60,221,3.58647e-09,58.2954,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
9893,Q#519 - >seq3842,non-specific,197322,74,228,2.7242000000000003e-08,56.1714,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
9894,Q#519 - >seq3842,non-specific,197321,3,228,2.95349e-08,55.636,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9895,Q#519 - >seq3842,non-specific,273186,5,229,6.42679e-08,54.5924,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9896,Q#519 - >seq3842,non-specific,339261,100,224,8.092539999999999e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9897,Q#519 - >seq3842,non-specific,272954,5,199,8.653540000000001e-05,45.0665,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs8_ctshrew,marg,CompleteHit
9898,Q#519 - >seq3842,non-specific,238827,654,689,0.000159452,43.818999999999996,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
9899,Q#519 - >seq3842,superfamily,295487,654,689,0.000159452,43.818999999999996,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
9900,Q#519 - >seq3842,non-specific,238828,610,670,0.00981311,38.3361,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
9901,Q#519 - >seq3842,superfamily,295487,610,670,0.00981311,38.3361,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
9902,Q#520 - >seq3843,non-specific,238827,481,546,1.33466e-10,61.9234,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs8_ctshrew.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
9903,Q#520 - >seq3843,superfamily,295487,481,546,1.33466e-10,61.9234,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs8_ctshrew.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
9904,Q#520 - >seq3843,non-specific,333820,480,523,7.6053100000000005e-06,47.287,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs8_ctshrew.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
9905,Q#520 - >seq3843,superfamily,333820,480,523,7.6053100000000005e-06,47.287,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs8_ctshrew.marg.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
9906,Q#523 - >seq3846,specific,197310,41,230,5.1631199999999994e-36,135.942,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs8_ctshrew,pars,CompleteHit
9907,Q#523 - >seq3846,superfamily,351117,41,230,5.1631199999999994e-36,135.942,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,CompleteHit
9908,Q#523 - >seq3846,non-specific,197306,55,230,8.07204e-18,83.6848,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9909,Q#523 - >seq3846,non-specific,223780,58,223,1.51547e-10,62.2307,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9910,Q#523 - >seq3846,non-specific,197320,62,223,3.2894099999999997e-09,58.2954,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9911,Q#523 - >seq3846,specific,335306,60,223,1.41412e-08,56.0994,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9912,Q#523 - >seq3846,non-specific,197322,76,230,2.49199e-08,56.1714,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9913,Q#523 - >seq3846,non-specific,197307,85,230,5.18385e-08,54.6013,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9914,Q#523 - >seq3846,non-specific,273186,100,231,9.338339999999999e-07,50.7404,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9915,Q#523 - >seq3846,non-specific,339261,102,226,8.66789e-06,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs8_ctshrew,pars,CompleteHit
9916,Q#523 - >seq3846,non-specific,272954,85,201,0.000189011,43.9109,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
9917,Q#523 - >seq3846,non-specific,238827,622,661,0.000622712,41.893,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
9918,Q#523 - >seq3846,superfamily,295487,622,661,0.000622712,41.893,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
9919,Q#523 - >seq3846,non-specific,238828,577,663,0.00261922,40.2621,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
9920,Q#525 - >seq3848,non-specific,340205,188,246,2.70373e-13,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,marg,CompleteHit
9921,Q#525 - >seq3848,superfamily,340205,188,246,2.70373e-13,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,marg,CompleteHit
9922,Q#525 - >seq3848,non-specific,335182,110,185,3.79842e-09,52.6903,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
9923,Q#525 - >seq3848,superfamily,335182,110,185,3.79842e-09,52.6903,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs8_ctshrew.marg.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
9924,Q#528 - >seq3851,non-specific,335182,107,156,2.81375e-07,47.2975,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs8_ctshrew.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
9925,Q#528 - >seq3851,superfamily,335182,107,156,2.81375e-07,47.2975,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs8_ctshrew.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
9926,Q#529 - >seq3852,non-specific,340205,184,242,5.14e-14,64.6648,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs8_ctshrew,pars,CompleteHit
9927,Q#529 - >seq3852,superfamily,340205,184,242,5.14e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs8_ctshrew.pars.frame2,1909130332_L1MCa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs8_ctshrew,pars,CompleteHit
9928,Q#536 - >seq3859,non-specific,340205,192,260,1.9085499999999998e-18,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs2_gorilla,pars,CompleteHit
9929,Q#536 - >seq3859,superfamily,340205,192,260,1.9085499999999998e-18,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs2_gorilla,pars,CompleteHit
9930,Q#536 - >seq3859,non-specific,335182,89,188,4.4551599999999994e-10,55.3867,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs2_gorilla,pars,CompleteHit
9931,Q#536 - >seq3859,superfamily,335182,89,188,4.4551599999999994e-10,55.3867,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCa,ORF1,hs2_gorilla,pars,CompleteHit
9932,Q#539 - >seq3862,specific,197310,49,276,6.95413e-57,196.418,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9933,Q#539 - >seq3862,superfamily,351117,49,276,6.95413e-57,196.418,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9934,Q#539 - >seq3862,specific,238827,551,752,7.64659e-39,143.971,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,C-TerminusTruncated
9935,Q#539 - >seq3862,superfamily,295487,551,752,7.64659e-39,143.971,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,C-TerminusTruncated
9936,Q#539 - >seq3862,non-specific,197306,49,276,2.42076e-28,114.501,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9937,Q#539 - >seq3862,non-specific,333820,557,777,7.490510000000001e-23,96.9777,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9938,Q#539 - >seq3862,superfamily,333820,557,777,7.490510000000001e-23,96.9777,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9939,Q#539 - >seq3862,non-specific,223780,49,269,4.73639e-18,84.9575,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9940,Q#539 - >seq3862,specific,335306,50,269,6.57793e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9941,Q#539 - >seq3862,non-specific,197307,49,276,1.23651e-16,80.7949,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9942,Q#539 - >seq3862,non-specific,273186,49,277,1.1574299999999999e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9943,Q#539 - >seq3862,non-specific,197320,49,269,1.1620399999999999e-13,72.1626,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9944,Q#539 - >seq3862,non-specific,197321,47,276,3.20989e-13,70.6588,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9945,Q#539 - >seq3862,non-specific,238828,623,770,5.58397e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,N-TerminusTruncated
9946,Q#539 - >seq3862,non-specific,197322,48,276,1.0937200000000001e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9947,Q#539 - >seq3862,non-specific,272954,49,247,4.50008e-10,61.2449,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9948,Q#539 - >seq3862,non-specific,197319,49,276,3.5765500000000004e-08,55.7457,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9949,Q#539 - >seq3862,non-specific,275209,628,752,6.590689999999999e-08,55.9268,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,BothTerminiTruncated
9950,Q#539 - >seq3862,superfamily,275209,628,752,6.590689999999999e-08,55.9268,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,marg,BothTerminiTruncated
9951,Q#539 - >seq3862,non-specific,339261,148,272,3.3597500000000003e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9952,Q#539 - >seq3862,non-specific,197336,49,234,2.5417199999999998e-05,46.8367,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9953,Q#539 - >seq3862,non-specific,197311,66,276,4.31856e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9954,Q#539 - >seq3862,non-specific,236970,49,269,5.6551099999999995e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MCa.ORF2.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,marg,CompleteHit
9955,Q#541 - >seq3864,specific,197310,49,276,5.29793e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9956,Q#541 - >seq3864,superfamily,351117,49,276,5.29793e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9957,Q#541 - >seq3864,specific,238827,551,804,1.3443599999999999e-45,163.616,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9958,Q#541 - >seq3864,superfamily,295487,551,804,1.3443599999999999e-45,163.616,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9959,Q#541 - >seq3864,non-specific,197306,49,276,9.73088e-28,112.575,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9960,Q#541 - >seq3864,non-specific,333820,557,778,1.3068600000000001e-24,101.985,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9961,Q#541 - >seq3864,superfamily,333820,557,778,1.3068600000000001e-24,101.985,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9962,Q#541 - >seq3864,specific,335306,50,269,6.06247e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9963,Q#541 - >seq3864,non-specific,223780,49,269,1.58432e-17,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9964,Q#541 - >seq3864,non-specific,197307,49,276,5.92246e-16,78.4837,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9965,Q#541 - >seq3864,non-specific,273186,49,277,3.04498e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9966,Q#541 - >seq3864,non-specific,197320,49,261,2.1776799999999997e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9967,Q#541 - >seq3864,non-specific,197321,47,276,8.18472e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9968,Q#541 - >seq3864,non-specific,238828,627,791,5.65562e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,N-TerminusTruncated
9969,Q#541 - >seq3864,non-specific,197322,48,276,1.0040999999999999e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9970,Q#541 - >seq3864,non-specific,272954,49,247,1.13534e-09,60.0893,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9971,Q#541 - >seq3864,non-specific,275209,628,778,2.6122e-08,57.0824,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,BothTerminiTruncated
9972,Q#541 - >seq3864,superfamily,275209,628,778,2.6122e-08,57.0824,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,BothTerminiTruncated
9973,Q#541 - >seq3864,non-specific,197319,49,276,1.1912100000000001e-07,53.8197,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9974,Q#541 - >seq3864,non-specific,339261,148,272,7.167589999999999e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9975,Q#541 - >seq3864,non-specific,197336,49,234,2.34454e-05,46.8367,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9976,Q#541 - >seq3864,non-specific,197311,66,276,8.9281e-05,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9977,Q#541 - >seq3864,non-specific,236970,49,269,0.000104965,45.2702,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9978,Q#541 - >seq3864,non-specific,238185,697,791,0.000769021,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs1_chimp.pars.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs1_chimp,pars,CompleteHit
9979,Q#543 - >seq3866,non-specific,335182,121,194,1.3043700000000002e-10,56.5423,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs1_chimp.marg.frame3,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs1_chimp,marg,N-TerminusTruncated
9980,Q#543 - >seq3866,superfamily,335182,121,194,1.3043700000000002e-10,56.5423,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs1_chimp.marg.frame3,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs1_chimp,marg,N-TerminusTruncated
9981,Q#544 - >seq3867,non-specific,340205,196,248,3.6007900000000004e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MCa,ORF1,hs1_chimp,marg,CompleteHit
9982,Q#544 - >seq3867,superfamily,340205,196,248,3.6007900000000004e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs1_chimp.marg.frame2,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MCa,ORF1,hs1_chimp,marg,CompleteHit
9983,Q#549 - >seq3872,specific,238827,508,757,1.4897099999999997e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
9984,Q#549 - >seq3872,superfamily,295487,508,757,1.4897099999999997e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
9985,Q#549 - >seq3872,specific,197310,9,237,1.4348499999999998e-59,204.50799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9986,Q#549 - >seq3872,superfamily,351117,9,237,1.4348499999999998e-59,204.50799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9987,Q#549 - >seq3872,non-specific,197306,9,237,3.7673499999999996e-35,134.531,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9988,Q#549 - >seq3872,specific,333820,514,723,6.82353e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
9989,Q#549 - >seq3872,superfamily,333820,514,723,6.82353e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
9990,Q#549 - >seq3872,non-specific,197320,9,230,9.879600000000001e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9991,Q#549 - >seq3872,non-specific,223780,9,238,5.869380000000001e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9992,Q#549 - >seq3872,non-specific,197307,9,237,4.17177e-18,85.0321,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9993,Q#549 - >seq3872,specific,335306,10,230,2.7970500000000004e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9994,Q#549 - >seq3872,non-specific,197319,9,237,9.053780000000001e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9995,Q#549 - >seq3872,non-specific,273186,9,238,4.56638e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9996,Q#549 - >seq3872,non-specific,197321,7,237,7.53898e-13,69.8884,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9997,Q#549 - >seq3872,non-specific,272954,9,237,7.58343e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
9998,Q#549 - >seq3872,non-specific,238828,514,720,8.391710000000001e-10,60.2924,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
9999,Q#549 - >seq3872,non-specific,197336,9,195,4.2168100000000003e-07,52.6147,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
10000,Q#549 - >seq3872,non-specific,235175,263,499,3.8174e-06,51.218,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,BothTerminiTruncated
10001,Q#549 - >seq3872,superfamily,235175,263,499,3.8174e-06,51.218,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,BothTerminiTruncated
10002,Q#549 - >seq3872,non-specific,274009,304,457,1.3466199999999998e-05,49.2959,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,C-TerminusTruncated
10003,Q#549 - >seq3872,superfamily,274009,304,457,1.3466199999999998e-05,49.2959,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,C-TerminusTruncated
10004,Q#549 - >seq3872,non-specific,275209,466,654,8.43673e-05,45.9116,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,C-TerminusTruncated
10005,Q#549 - >seq3872,superfamily,275209,466,654,8.43673e-05,45.9116,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC5,ORF2,hs0_human,marg,C-TerminusTruncated
10006,Q#549 - >seq3872,non-specific,339261,110,233,0.0006683980000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC5,ORF2,hs0_human,marg,CompleteHit
10007,Q#549 - >seq3872,non-specific,274009,304,457,0.00119153,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,BothTerminiTruncated
10008,Q#549 - >seq3872,non-specific,197311,38,205,0.00167966,41.1233,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,marg,CompleteHit
10009,Q#549 - >seq3872,non-specific,235175,293,468,0.00226813,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF2,hs0_human,marg,BothTerminiTruncated
10010,Q#550 - >seq3873,specific,311990,1164,1182,0.000494788,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5.ORF2.hs0_human.marg.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MC5,ORF2,hs0_human,marg,CompleteHit
10011,Q#550 - >seq3873,superfamily,311990,1164,1182,0.000494788,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MC5.ORF2.hs0_human.marg.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,DUF1725,L1MC5,ORF2,hs0_human,marg,CompleteHit
10012,Q#552 - >seq3875,non-specific,197310,1,110,1.20947e-17,83.1697,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC5,ORF2,hs0_human,pars,C-TerminusTruncated
10013,Q#552 - >seq3875,superfamily,351117,1,110,1.20947e-17,83.1697,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,pars,C-TerminusTruncated
10014,Q#552 - >seq3875,non-specific,197306,1,122,1.3873e-08,56.3357,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,pars,C-TerminusTruncated
10015,Q#552 - >seq3875,non-specific,238827,569,616,7.46884e-08,53.8342,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10016,Q#552 - >seq3875,superfamily,295487,569,616,7.46884e-08,53.8342,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10017,Q#552 - >seq3875,non-specific,333820,532,594,1.61843e-05,46.5166,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10018,Q#552 - >seq3875,superfamily,333820,532,594,1.61843e-05,46.5166,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10019,Q#552 - >seq3875,non-specific,238828,562,608,0.00155181,41.0325,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC5.ORF2.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10020,Q#553 - >seq3876,specific,238827,457,694,1.5239399999999997e-44,160.534,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC5.ORF2.hs0_human.pars.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5,ORF2,hs0_human,pars,CompleteHit
10021,Q#553 - >seq3876,superfamily,295487,457,694,1.5239399999999997e-44,160.534,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC5.ORF2.hs0_human.pars.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5,ORF2,hs0_human,pars,CompleteHit
10022,Q#553 - >seq3876,non-specific,333820,463,688,1.2695600000000002e-23,98.9037,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.pars.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5,ORF2,hs0_human,pars,CompleteHit
10023,Q#553 - >seq3876,superfamily,333820,463,688,1.2695600000000002e-23,98.9037,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC5.ORF2.hs0_human.pars.frame2,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC5,ORF2,hs0_human,pars,CompleteHit
10024,Q#554 - >seq3877,non-specific,197310,13,204,3.14339e-22,96.6517,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC5,ORF2,hs0_human,pars,CompleteHit
10025,Q#554 - >seq3877,superfamily,351117,13,204,3.14339e-22,96.6517,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,pars,CompleteHit
10026,Q#554 - >seq3877,non-specific,197306,13,204,3.850630000000001e-10,61.3433,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,pars,CompleteHit
10027,Q#554 - >seq3877,non-specific,197320,105,197,6.76795e-08,54.8286,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10028,Q#554 - >seq3877,non-specific,197307,78,204,4.7483600000000003e-07,51.9049,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10029,Q#554 - >seq3877,non-specific,235175,230,430,7.2106399999999995e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10030,Q#554 - >seq3877,superfamily,235175,230,430,7.2106399999999995e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10031,Q#554 - >seq3877,non-specific,197319,107,204,1.41581e-05,47.6565,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10032,Q#554 - >seq3877,non-specific,274009,271,424,1.5281400000000002e-05,48.9107,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,C-TerminusTruncated
10033,Q#554 - >seq3877,superfamily,274009,271,424,1.5281400000000002e-05,48.9107,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,C-TerminusTruncated
10034,Q#554 - >seq3877,non-specific,223780,102,205,2.07811e-05,47.2079,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10035,Q#554 - >seq3877,specific,335306,19,197,3.5802399999999995e-05,46.0842,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC5,ORF2,hs0_human,pars,CompleteHit
10036,Q#554 - >seq3877,non-specific,235175,260,430,3.94392e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10037,Q#554 - >seq3877,non-specific,339261,85,200,0.000422424,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MC5,ORF2,hs0_human,pars,CompleteHit
10038,Q#554 - >seq3877,non-specific,274009,271,424,0.00148076,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10039,Q#554 - >seq3877,non-specific,334125,180,378,0.00351237,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10040,Q#554 - >seq3877,superfamily,334125,180,378,0.00351237,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MC5,ORF2,hs0_human,pars,N-TerminusTruncated
10041,Q#554 - >seq3877,non-specific,224212,231,331,0.00575987,40.4533,COG1293,YloA,NC,cl34220,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10042,Q#554 - >seq3877,superfamily,224212,231,331,0.00575987,40.4533,cl34220,YloA superfamily,NC, - ,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1MC5.ORF2.hs0_human.pars.frame1,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC5,ORF2,hs0_human,pars,BothTerminiTruncated
10043,Q#555 - >seq3878,non-specific,335182,164,262,3.83184e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,marg,CompleteHit
10044,Q#555 - >seq3878,superfamily,335182,164,262,3.83184e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,marg,CompleteHit
10045,Q#555 - >seq3878,non-specific,340205,265,321,2.1450299999999996e-22,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,marg,CompleteHit
10046,Q#555 - >seq3878,superfamily,340205,265,321,2.1450299999999996e-22,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,marg,CompleteHit
10047,Q#555 - >seq3878,non-specific,340204,119,161,1.3475e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5,ORF1,hs0_human,marg,CompleteHit
10048,Q#555 - >seq3878,superfamily,340204,119,161,1.3475e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MC5,ORF1,hs0_human,marg,CompleteHit
10049,Q#555 - >seq3878,non-specific,274009,50,157,0.000128476,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10050,Q#555 - >seq3878,superfamily,274009,50,157,0.000128476,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10051,Q#555 - >seq3878,non-specific,274008,58,157,0.000140315,43.5067,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10052,Q#555 - >seq3878,superfamily,274008,58,157,0.000140315,43.5067,cl37069,SMC_prok_B superfamily,C, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10053,Q#555 - >seq3878,non-specific,223542,35,195,0.0005850769999999999,41.3898,COG0466,Lon,C,cl33893,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10054,Q#555 - >seq3878,superfamily,223542,35,195,0.0005850769999999999,41.3898,cl33893,Lon superfamily,C, - ,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10055,Q#555 - >seq3878,non-specific,235175,61,157,0.00059049,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10056,Q#555 - >seq3878,superfamily,235175,61,157,0.00059049,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10057,Q#555 - >seq3878,non-specific,274008,42,212,0.000633299,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10058,Q#555 - >seq3878,non-specific,274009,50,158,0.000638296,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10059,Q#555 - >seq3878,non-specific,224117,33,158,0.000990174,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10060,Q#555 - >seq3878,superfamily,224117,33,158,0.000990174,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10061,Q#555 - >seq3878,non-specific,235505,98,157,0.00173489,39.8538,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10062,Q#555 - >seq3878,superfamily,235505,98,157,0.00173489,39.8538,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10063,Q#555 - >seq3878,non-specific,237177,42,157,0.00188602,39.7614,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10064,Q#555 - >seq3878,superfamily,237177,42,157,0.00188602,39.7614,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10065,Q#555 - >seq3878,non-specific,224117,42,189,0.00190083,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10066,Q#555 - >seq3878,non-specific,235175,34,150,0.00207129,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10067,Q#555 - >seq3878,non-specific,335555,63,142,0.00220739,39.5512,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10068,Q#555 - >seq3878,superfamily,354396,63,142,0.00220739,39.5512,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10069,Q#555 - >seq3878,non-specific,337663,63,155,0.00238396,39.3303,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10070,Q#555 - >seq3878,superfamily,337663,63,155,0.00238396,39.3303,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10071,Q#555 - >seq3878,non-specific,224117,34,157,0.00251028,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10072,Q#555 - >seq3878,non-specific,224117,33,169,0.00266771,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10073,Q#555 - >seq3878,non-specific,274008,57,158,0.00305563,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10074,Q#555 - >seq3878,non-specific,308892,11,186,0.00354371,38.9723,pfam03528,Rabaptin,C,cl25724,Rabaptin; Rabaptin.  ,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10075,Q#555 - >seq3878,superfamily,308892,11,186,0.00354371,38.9723,cl25724,Rabaptin superfamily,C, - ,Rabaptin; Rabaptin.  ,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10076,Q#555 - >seq3878,non-specific,224117,28,157,0.00374351,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10077,Q#555 - >seq3878,non-specific,274008,63,189,0.00417733,38.8843,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10078,Q#555 - >seq3878,non-specific,274008,46,157,0.0045563,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10079,Q#555 - >seq3878,non-specific,114219,61,257,0.00484146,38.5493,pfam05483,SCP-1,NC,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10080,Q#555 - >seq3878,superfamily,114219,61,257,0.00484146,38.5493,cl30946,SCP-1 superfamily,NC, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10081,Q#555 - >seq3878,non-specific,340016,9,133,0.00627383,37.4349,pfam17300,FIN1,N,cl38584,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10082,Q#555 - >seq3878,superfamily,340016,9,133,0.00627383,37.4349,cl38584,FIN1 superfamily,N, - ,"Filament protein FIN1; Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C-terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1.",L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10083,Q#555 - >seq3878,non-specific,179385,42,157,0.0070593999999999995,38.0974,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10084,Q#555 - >seq3878,superfamily,179385,42,157,0.0070593999999999995,38.0974,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,marg,BothTerminiTruncated
10085,Q#555 - >seq3878,non-specific,226400,80,157,0.00800704,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10086,Q#555 - >seq3878,superfamily,226400,80,157,0.00800704,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MC5,ORF1,hs0_human,marg,C-TerminusTruncated
10087,Q#555 - >seq3878,non-specific,197874,50,157,0.00937902,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10088,Q#555 - >seq3878,superfamily,197874,50,157,0.00937902,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MC5.ORF1.hs0_human.marg.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1MC5,ORF1,hs0_human,marg,N-TerminusTruncated
10089,Q#558 - >seq3881,non-specific,335182,153,249,4.280579999999999e-37,128.189,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,pars,CompleteHit
10090,Q#558 - >seq3881,superfamily,335182,153,249,4.280579999999999e-37,128.189,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,pars,CompleteHit
10091,Q#558 - >seq3881,non-specific,340205,252,297,7.37392e-19,78.9172,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,pars,C-TerminusTruncated
10092,Q#558 - >seq3881,superfamily,340205,252,297,7.37392e-19,78.9172,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MC5,ORF1,hs0_human,pars,C-TerminusTruncated
10093,Q#558 - >seq3881,non-specific,340204,108,150,5.53968e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC5,ORF1,hs0_human,pars,CompleteHit
10094,Q#558 - >seq3881,superfamily,340204,108,150,5.53968e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1MC5,ORF1,hs0_human,pars,CompleteHit
10095,Q#558 - >seq3881,non-specific,224117,50,146,0.000922768,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,pars,BothTerminiTruncated
10096,Q#558 - >seq3881,superfamily,224117,50,146,0.000922768,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MC5,ORF1,hs0_human,pars,BothTerminiTruncated
10097,Q#558 - >seq3881,non-specific,274009,43,146,0.00293144,39.2807,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,pars,BothTerminiTruncated
10098,Q#558 - >seq3881,superfamily,274009,43,146,0.00293144,39.2807,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC5.ORF1.hs0_human.pars.frame3,1909130332_L1MC5.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC5,ORF1,hs0_human,pars,BothTerminiTruncated
10099,Q#561 - >seq3884,non-specific,340205,173,238,2.5242700000000003e-21,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,pars,CompleteHit
10100,Q#561 - >seq3884,superfamily,340205,173,238,2.5242700000000003e-21,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,pars,CompleteHit
10101,Q#561 - >seq3884,non-specific,335182,92,170,4.2103999999999994e-09,52.3051,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
10102,Q#561 - >seq3884,superfamily,335182,92,170,4.2103999999999994e-09,52.3051,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs5_gmonkey.pars.frame3,1909130332_L1MCa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
10103,Q#562 - >seq3885,non-specific,340205,168,231,1.00653e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs1_chimp.pars.frame1,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs1_chimp,pars,CompleteHit
10104,Q#562 - >seq3885,superfamily,340205,168,231,1.00653e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs1_chimp.pars.frame1,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs1_chimp,pars,CompleteHit
10105,Q#562 - >seq3885,non-specific,335182,91,164,2.23523e-10,55.7719,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs1_chimp.pars.frame1,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs1_chimp,pars,N-TerminusTruncated
10106,Q#562 - >seq3885,superfamily,335182,91,164,2.23523e-10,55.7719,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs1_chimp.pars.frame1,1909130332_L1MCa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs1_chimp,pars,N-TerminusTruncated
10107,Q#563 - >seq3886,non-specific,340205,199,267,2.01435e-18,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs2_gorilla,marg,CompleteHit
10108,Q#563 - >seq3886,superfamily,340205,199,267,2.01435e-18,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs2_gorilla,marg,CompleteHit
10109,Q#563 - >seq3886,non-specific,335182,89,195,2.2551100000000001e-10,56.1571,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs2_gorilla,marg,CompleteHit
10110,Q#563 - >seq3886,superfamily,335182,89,195,2.2551100000000001e-10,56.1571,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs2_gorilla,marg,CompleteHit
10111,Q#565 - >seq3888,non-specific,238827,516,698,1.1863200000000002e-19,88.117,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10112,Q#565 - >seq3888,superfamily,295487,516,698,1.1863200000000002e-19,88.117,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10113,Q#565 - >seq3888,non-specific,333820,531,667,3.03404e-08,54.2206,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10114,Q#565 - >seq3888,superfamily,333820,531,667,3.03404e-08,54.2206,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10115,Q#565 - >seq3888,non-specific,238828,531,601,3.4859e-06,48.7364,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,BothTerminiTruncated
10116,Q#565 - >seq3888,superfamily,295487,531,601,3.4859e-06,48.7364,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,BothTerminiTruncated
10117,Q#565 - >seq3888,non-specific,275209,514,601,0.000151512,44.756,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,BothTerminiTruncated
10118,Q#565 - >seq3888,superfamily,275209,514,601,0.000151512,44.756,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs2_gorilla.pars.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,pars,BothTerminiTruncated
10119,Q#567 - >seq3890,specific,197310,9,235,1.05912e-49,175.618,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10120,Q#567 - >seq3890,superfamily,351117,9,235,1.05912e-49,175.618,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10121,Q#567 - >seq3890,non-specific,197306,9,235,1.02384e-23,101.01899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10122,Q#567 - >seq3890,non-specific,223780,9,228,2.0604700000000001e-16,79.9499,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10123,Q#567 - >seq3890,non-specific,197307,9,235,6.3616e-16,78.4837,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10124,Q#567 - >seq3890,non-specific,197320,8,228,5.57811e-14,72.933,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10125,Q#567 - >seq3890,non-specific,273186,9,236,6.01087e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10126,Q#567 - >seq3890,specific,335306,10,228,1.3221e-12,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10127,Q#567 - >seq3890,non-specific,197321,7,235,1.90607e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10128,Q#567 - >seq3890,non-specific,197322,81,235,5.23331e-09,58.4826,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10129,Q#567 - >seq3890,non-specific,272954,9,206,9.087719999999998e-09,57.3929,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10130,Q#567 - >seq3890,non-specific,197319,8,235,1.4514000000000001e-07,53.4345,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10131,Q#567 - >seq3890,non-specific,197336,7,228,9.60674e-06,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10132,Q#567 - >seq3890,non-specific,339261,107,231,1.32805e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs4_gibbon,marg,CompleteHit
10133,Q#567 - >seq3890,non-specific,234767,336,446,0.00878493,39.8212,PRK00448,polC,NC,cl35100,DNA polymerase III PolC; Validated,L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MCa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
10134,Q#567 - >seq3890,superfamily,234767,336,446,0.00878493,39.8212,cl35100,polC superfamily,NC, - ,DNA polymerase III PolC; Validated,L1MCa.ORF2.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MCa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
10135,Q#570 - >seq3893,specific,197310,9,235,3.2674599999999998e-49,174.077,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10136,Q#570 - >seq3893,superfamily,351117,9,235,3.2674599999999998e-49,174.077,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10137,Q#570 - >seq3893,non-specific,197306,9,235,2.34605e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10138,Q#570 - >seq3893,non-specific,223780,9,228,8.26798e-16,78.4091,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10139,Q#570 - >seq3893,non-specific,197307,9,235,1.8241599999999996e-15,76.9429,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10140,Q#570 - >seq3893,non-specific,273186,9,236,1.29393e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10141,Q#570 - >seq3893,non-specific,197320,8,228,1.34376e-13,71.7774,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10142,Q#570 - >seq3893,specific,335306,10,228,1.3085200000000002e-12,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10143,Q#570 - >seq3893,non-specific,197321,7,235,3.29561e-11,64.4956,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10144,Q#570 - >seq3893,non-specific,197322,81,235,5.17696e-09,58.4826,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10145,Q#570 - >seq3893,non-specific,272954,9,206,1.72806e-08,56.2373,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10146,Q#570 - >seq3893,non-specific,197319,8,235,3.7557899999999995e-07,52.2789,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10147,Q#570 - >seq3893,non-specific,197336,7,228,9.50839e-06,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10148,Q#570 - >seq3893,non-specific,339261,107,231,2.01384e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs4_gibbon.pars.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs4_gibbon,pars,CompleteHit
10149,Q#573 - >seq3896,non-specific,340205,254,316,1.24584e-14,67.3612,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs4_gibbon,marg,CompleteHit
10150,Q#573 - >seq3896,superfamily,340205,254,316,1.24584e-14,67.3612,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs4_gibbon.marg.frame3,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs4_gibbon,marg,CompleteHit
10151,Q#575 - >seq3898,non-specific,335182,185,257,4.90081e-11,58.4683,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs4_gibbon.marg.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
10152,Q#575 - >seq3898,superfamily,335182,185,257,4.90081e-11,58.4683,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs4_gibbon.marg.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
10153,Q#578 - >seq3901,non-specific,340205,175,222,3.2851e-15,67.3612,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs4_gibbon.pars.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10154,Q#578 - >seq3901,superfamily,340205,175,222,3.2851e-15,67.3612,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs4_gibbon.pars.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10155,Q#578 - >seq3901,non-specific,335182,88,155,5.074330000000001e-08,49.2235,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs4_gibbon.pars.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10156,Q#578 - >seq3901,superfamily,335182,88,155,5.074330000000001e-08,49.2235,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs4_gibbon.pars.frame1,1909130332_L1MCa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10157,Q#579 - >seq3902,specific,197310,2,227,4.1825e-54,188.71400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10158,Q#579 - >seq3902,superfamily,351117,2,227,4.1825e-54,188.71400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10159,Q#579 - >seq3902,specific,238827,516,746,6.17523e-36,135.882,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10160,Q#579 - >seq3902,superfamily,295487,516,746,6.17523e-36,135.882,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10161,Q#579 - >seq3902,non-specific,197306,2,227,1.18357e-27,112.575,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10162,Q#579 - >seq3902,non-specific,223780,2,220,4.60925e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10163,Q#579 - >seq3902,non-specific,333820,516,724,4.01064e-20,88.8885,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10164,Q#579 - >seq3902,superfamily,333820,516,724,4.01064e-20,88.8885,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10165,Q#579 - >seq3902,specific,335306,3,220,8.86966e-19,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10166,Q#579 - >seq3902,non-specific,197307,2,227,3.02102e-16,79.6393,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10167,Q#579 - >seq3902,non-specific,197320,1,220,8.786660000000002e-16,78.3257,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10168,Q#579 - >seq3902,non-specific,273186,2,228,3.5348100000000003e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10169,Q#579 - >seq3902,non-specific,197321,2,227,1.52485e-12,68.7328,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10170,Q#579 - >seq3902,non-specific,238828,573,737,3.86483e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,N-TerminusTruncated
10171,Q#579 - >seq3902,non-specific,197322,2,227,7.37699e-11,64.6458,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10172,Q#579 - >seq3902,non-specific,272954,2,198,8.62326e-11,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10173,Q#579 - >seq3902,non-specific,197319,1,227,1.43496e-08,56.9013,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10174,Q#579 - >seq3902,non-specific,197336,1,185,1.97684e-06,50.3035,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10175,Q#579 - >seq3902,non-specific,236970,2,220,2.2421400000000004e-06,50.2778,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10176,Q#579 - >seq3902,non-specific,339261,99,223,3.16632e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10177,Q#579 - >seq3902,non-specific,197311,2,227,7.598969999999999e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,marg,CompleteHit
10178,Q#579 - >seq3902,non-specific,275209,574,724,1.95599e-05,47.8376,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,BothTerminiTruncated
10179,Q#579 - >seq3902,superfamily,275209,574,724,1.95599e-05,47.8376,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs3_orang,marg,BothTerminiTruncated
10180,Q#582 - >seq3905,specific,197310,16,234,4.00013e-50,176.388,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10181,Q#582 - >seq3905,superfamily,351117,16,234,4.00013e-50,176.388,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10182,Q#582 - >seq3905,specific,238827,505,752,2.0962200000000002e-36,136.65200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10183,Q#582 - >seq3905,superfamily,295487,505,752,2.0962200000000002e-36,136.65200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10184,Q#582 - >seq3905,non-specific,197306,16,234,1.44635e-23,100.24799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10185,Q#582 - >seq3905,non-specific,333820,522,730,2.2797599999999998e-20,89.2737,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10186,Q#582 - >seq3905,superfamily,333820,522,730,2.2797599999999998e-20,89.2737,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10187,Q#582 - >seq3905,non-specific,223780,15,227,1.0257199999999998e-15,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10188,Q#582 - >seq3905,specific,335306,16,227,2.4537099999999998e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10189,Q#582 - >seq3905,non-specific,197307,16,234,1.79945e-12,68.0833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10190,Q#582 - >seq3905,non-specific,238828,579,743,3.38232e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,N-TerminusTruncated
10191,Q#582 - >seq3905,non-specific,197320,15,219,7.48492e-11,63.303000000000004,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10192,Q#582 - >seq3905,non-specific,273186,15,235,1.1999700000000003e-10,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10193,Q#582 - >seq3905,non-specific,197322,80,234,8.597319999999999e-09,57.7122,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,N-TerminusTruncated
10194,Q#582 - >seq3905,non-specific,197321,15,234,9.87124e-09,56.7916,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10195,Q#582 - >seq3905,non-specific,272954,15,205,9.80196e-07,50.8445,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10196,Q#582 - >seq3905,non-specific,339261,106,230,3.23237e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10197,Q#582 - >seq3905,non-specific,197319,22,234,1.0744e-05,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10198,Q#582 - >seq3905,non-specific,275209,580,730,1.34052e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,BothTerminiTruncated
10199,Q#582 - >seq3905,superfamily,275209,580,730,1.34052e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,BothTerminiTruncated
10200,Q#582 - >seq3905,non-specific,197311,28,234,6.86791e-05,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10201,Q#582 - >seq3905,non-specific,238185,649,743,0.00999188,36.1748,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MCa,ORF2,hs3_orang,pars,CompleteHit
10202,Q#584 - >seq3907,non-specific,238827,518,695,4.61289e-16,78.1018,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10203,Q#584 - >seq3907,superfamily,295487,518,695,4.61289e-16,78.1018,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10204,Q#584 - >seq3907,non-specific,333820,533,669,5.30525e-08,53.8354,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10205,Q#584 - >seq3907,superfamily,333820,533,669,5.30525e-08,53.8354,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10206,Q#584 - >seq3907,non-specific,238828,533,603,7.2726699999999994e-06,48.3513,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,BothTerminiTruncated
10207,Q#584 - >seq3907,superfamily,295487,533,603,7.2726699999999994e-06,48.3513,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,BothTerminiTruncated
10208,Q#584 - >seq3907,non-specific,275209,516,603,0.000335666,43.9856,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,BothTerminiTruncated
10209,Q#584 - >seq3907,superfamily,275209,516,603,0.000335666,43.9856,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs2_gorilla.marg.frame1,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCa,ORF2,hs2_gorilla,marg,BothTerminiTruncated
10210,Q#585 - >seq3908,non-specific,197310,85,227,1.2799799999999998e-26,109.363,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10211,Q#585 - >seq3908,superfamily,351117,85,227,1.2799799999999998e-26,109.363,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10212,Q#585 - >seq3908,non-specific,197306,78,227,1.06673e-13,71.7437,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10213,Q#585 - >seq3908,non-specific,223780,97,220,1.81372e-08,56.4527,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10214,Q#585 - >seq3908,non-specific,273186,98,228,1.59212e-07,53.4368,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10215,Q#585 - >seq3908,non-specific,197320,97,212,1.67107e-07,53.673,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10216,Q#585 - >seq3908,non-specific,197322,97,227,2.5858000000000003e-07,53.475,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10217,Q#585 - >seq3908,non-specific,197307,97,227,7.61123e-07,51.5197,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10218,Q#585 - >seq3908,non-specific,339261,99,223,5.27845e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs2_gorilla,marg,CompleteHit
10219,Q#585 - >seq3908,non-specific,335306,70,220,5.98406e-06,48.3954,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10220,Q#585 - >seq3908,non-specific,238827,500,587,0.0072042,39.1966,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
10221,Q#585 - >seq3908,superfamily,295487,500,587,0.0072042,39.1966,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs2_gorilla.marg.frame2,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
10222,Q#586 - >seq3909,non-specific,197310,9,110,1.84607e-14,73.9249,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
10223,Q#586 - >seq3909,superfamily,351117,9,110,1.84607e-14,73.9249,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
10224,Q#586 - >seq3909,non-specific,197306,9,80,0.00154837,41.3129,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.marg.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
10225,Q#589 - >seq3912,specific,197310,9,235,2.34284e-49,174.077,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10226,Q#589 - >seq3912,superfamily,351117,9,235,2.34284e-49,174.077,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10227,Q#589 - >seq3912,non-specific,197306,9,235,1.53007e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10228,Q#589 - >seq3912,non-specific,197307,9,235,8.53159e-13,68.8537,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10229,Q#589 - >seq3912,non-specific,223780,9,228,1.0899600000000001e-12,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10230,Q#589 - >seq3912,specific,335306,10,228,1.8924599999999998e-12,67.2702,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10231,Q#589 - >seq3912,non-specific,273186,9,236,4.09225e-11,63.8372,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10232,Q#589 - >seq3912,non-specific,197321,7,235,3.15066e-09,58.3324,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10233,Q#589 - >seq3912,non-specific,197320,9,220,3.6530999999999997e-09,58.2954,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10234,Q#589 - >seq3912,non-specific,197322,82,235,1.2160299999999999e-08,57.327,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10235,Q#589 - >seq3912,non-specific,272954,9,206,2.6726499999999997e-06,49.3037,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10236,Q#589 - >seq3912,non-specific,339261,108,231,1.7364200000000002e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10237,Q#589 - >seq3912,non-specific,197319,9,235,8.55651e-05,44.9601,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs2_gorilla.pars.frame3,1909130332_L1MCa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs2_gorilla,pars,CompleteHit
10238,Q#591 - >seq3914,non-specific,340205,172,235,2.65065e-17,73.1392,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,marg,CompleteHit
10239,Q#591 - >seq3914,superfamily,340205,172,235,2.65065e-17,73.1392,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,marg,CompleteHit
10240,Q#591 - >seq3914,non-specific,335182,68,167,5.258770000000001e-13,62.7055,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,marg,CompleteHit
10241,Q#591 - >seq3914,superfamily,335182,68,167,5.258770000000001e-13,62.7055,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs3_orang.marg.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,marg,CompleteHit
10242,Q#594 - >seq3917,non-specific,340205,170,233,2.25005e-17,73.5244,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,pars,CompleteHit
10243,Q#594 - >seq3917,superfamily,340205,170,233,2.25005e-17,73.5244,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,pars,CompleteHit
10244,Q#594 - >seq3917,non-specific,335182,66,165,5.37416e-13,62.7055,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,pars,CompleteHit
10245,Q#594 - >seq3917,superfamily,335182,66,165,5.37416e-13,62.7055,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs3_orang.pars.frame3,1909130332_L1MCa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs3_orang,pars,CompleteHit
10246,Q#599 - >seq3922,non-specific,197310,49,174,1.6890799999999997e-10,61.2133,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs1_chimp.pars.frame3,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs1_chimp,pars,N-TerminusTruncated
10247,Q#599 - >seq3922,superfamily,351117,49,174,1.6890799999999997e-10,61.2133,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs1_chimp.pars.frame3,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs1_chimp,pars,N-TerminusTruncated
10248,Q#599 - >seq3922,non-specific,197306,26,174,0.00010842399999999999,44.0093,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs1_chimp.pars.frame3,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs1_chimp,pars,N-TerminusTruncated
10249,Q#600 - >seq3923,non-specific,197310,11,243,2.1253900000000003e-16,78.9325,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs1_chimp.marg.frame1,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs1_chimp,marg,CompleteHit
10250,Q#600 - >seq3923,superfamily,351117,11,243,2.1253900000000003e-16,78.9325,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs1_chimp.marg.frame1,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs1_chimp,marg,CompleteHit
10251,Q#600 - >seq3923,non-specific,197306,11,243,1.50641e-06,49.7873,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs1_chimp.marg.frame1,1909130333_L1MCb.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs1_chimp,marg,CompleteHit
10252,Q#610 - >seq3933,non-specific,197310,1,151,1.38954e-08,54.6649,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs3_orang,pars,CompleteHit
10253,Q#610 - >seq3933,superfamily,351117,1,151,1.38954e-08,54.6649,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs3_orang,pars,CompleteHit
10254,Q#610 - >seq3933,non-specific,197320,63,148,6.29199e-05,44.043,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs3_orang,pars,BothTerminiTruncated
10255,Q#610 - >seq3933,non-specific,197322,94,150,0.00043756800000000005,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs3_orang,pars,N-TerminusTruncated
10256,Q#610 - >seq3933,non-specific,223780,2,148,0.000438267,41.4299,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs3_orang,pars,C-TerminusTruncated
10257,Q#610 - >seq3933,non-specific,197306,3,151,0.000653226,40.9277,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs3_orang.pars.frame3,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs3_orang,pars,CompleteHit
10258,Q#611 - >seq3934,non-specific,197310,139,281,1.8458e-09,58.9021,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs3_orang.marg.frame1,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs3_orang,marg,N-TerminusTruncated
10259,Q#611 - >seq3934,superfamily,351117,139,281,1.8458e-09,58.9021,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs3_orang.marg.frame1,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs3_orang,marg,N-TerminusTruncated
10260,Q#611 - >seq3934,non-specific,197320,162,239,0.000451569,42.5022,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs3_orang.marg.frame1,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCb,ORF2,hs3_orang,marg,BothTerminiTruncated
10261,Q#611 - >seq3934,non-specific,197306,139,281,0.000682132,42.0833,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs3_orang.marg.frame1,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs3_orang,marg,N-TerminusTruncated
10262,Q#611 - >seq3934,non-specific,197322,185,241,0.00117023,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs3_orang.marg.frame1,1909130333_L1MCb.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs3_orang,marg,N-TerminusTruncated
10263,Q#620 - >seq3943,specific,197310,20,226,1.1847399999999999e-48,168.299,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10264,Q#620 - >seq3943,superfamily,351117,20,226,1.1847399999999999e-48,168.299,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10265,Q#620 - >seq3943,non-specific,197306,27,226,3.7416199999999995e-22,95.2408,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10266,Q#620 - >seq3943,specific,335306,20,219,5.620529999999999e-13,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10267,Q#620 - >seq3943,non-specific,223780,27,219,1.94811e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10268,Q#620 - >seq3943,non-specific,197320,20,219,1.27137e-11,64.8438,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10269,Q#620 - >seq3943,non-specific,197307,20,226,2.58214e-11,63.8461,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10270,Q#620 - >seq3943,non-specific,197321,20,226,2.1899e-09,57.9472,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10271,Q#620 - >seq3943,non-specific,197322,72,226,2.24765e-09,58.8678,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,N-TerminusTruncated
10272,Q#620 - >seq3943,non-specific,273186,20,227,6.03127e-09,56.9036,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10273,Q#620 - >seq3943,non-specific,272954,20,197,2.09525e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10274,Q#620 - >seq3943,non-specific,339261,98,222,4.90288e-06,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10275,Q#620 - >seq3943,non-specific,197319,20,226,3.89165e-05,45.3453,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10276,Q#620 - >seq3943,non-specific,197311,27,226,0.0005906,41.1233,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs10_snmole.pars.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,pars,CompleteHit
10277,Q#622 - >seq3945,non-specific,238827,479,562,2.7507599999999996e-10,60.7678,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs10_snmole.marg.frame3,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs10_snmole,marg,C-TerminusTruncated
10278,Q#622 - >seq3945,superfamily,295487,479,562,2.7507599999999996e-10,60.7678,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs10_snmole.marg.frame3,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs10_snmole,marg,C-TerminusTruncated
10279,Q#625 - >seq3948,non-specific,340205,201,265,3.43183e-17,73.5244,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs0_human.pars.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,pars,CompleteHit
10280,Q#625 - >seq3948,superfamily,340205,201,265,3.43183e-17,73.5244,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs0_human.pars.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,pars,CompleteHit
10281,Q#625 - >seq3948,non-specific,335182,124,196,1.11734e-08,51.5347,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs0_human.pars.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,pars,N-TerminusTruncated
10282,Q#625 - >seq3948,superfamily,335182,124,196,1.11734e-08,51.5347,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs0_human.pars.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,pars,N-TerminusTruncated
10283,Q#627 - >seq3950,specific,197310,29,235,1.5908499999999999e-47,168.68400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10284,Q#627 - >seq3950,superfamily,351117,29,235,1.5908499999999999e-47,168.68400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10285,Q#627 - >seq3950,non-specific,197306,36,235,1.47724e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10286,Q#627 - >seq3950,specific,335306,29,228,9.107010000000001e-13,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10287,Q#627 - >seq3950,non-specific,223780,36,228,1.30248e-12,68.3939,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10288,Q#627 - >seq3950,non-specific,197320,29,228,2.10158e-11,64.8438,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10289,Q#627 - >seq3950,non-specific,197307,29,235,3.16008e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10290,Q#627 - >seq3950,non-specific,197321,29,235,2.9595100000000003e-09,58.3324,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10291,Q#627 - >seq3950,non-specific,197322,81,235,3.79563e-09,58.8678,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,N-TerminusTruncated
10292,Q#627 - >seq3950,non-specific,273186,29,236,4.7294999999999994e-09,57.674,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10293,Q#627 - >seq3950,non-specific,238827,572,705,8.97667e-09,56.1454,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,BothTerminiTruncated
10294,Q#627 - >seq3950,superfamily,295487,572,705,8.97667e-09,56.1454,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,BothTerminiTruncated
10295,Q#627 - >seq3950,non-specific,238828,589,712,1.6676e-08,55.67,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,N-TerminusTruncated
10296,Q#627 - >seq3950,non-specific,339261,107,231,1.51924e-06,47.7171,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10297,Q#627 - >seq3950,non-specific,272954,29,206,2.02035e-06,49.6889,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10298,Q#627 - >seq3950,non-specific,333820,593,751,1.6981e-05,46.1314,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,N-TerminusTruncated
10299,Q#627 - >seq3950,superfamily,333820,593,751,1.6981e-05,46.1314,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,N-TerminusTruncated
10300,Q#627 - >seq3950,non-specific,275209,594,661,0.00011793,44.756,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,BothTerminiTruncated
10301,Q#627 - >seq3950,superfamily,275209,594,661,0.00011793,44.756,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs10_snmole,marg,BothTerminiTruncated
10302,Q#627 - >seq3950,non-specific,197311,36,235,0.000299171,42.6641,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs10_snmole.marg.frame2,1909130333_L1MCa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCa,ORF2,hs10_snmole,marg,CompleteHit
10303,Q#628 - >seq3951,non-specific,340205,204,271,1.04758e-14,66.976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs0_human.marg.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,marg,CompleteHit
10304,Q#628 - >seq3951,superfamily,340205,204,271,1.04758e-14,66.976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCa.ORF1.hs0_human.marg.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,marg,CompleteHit
10305,Q#628 - >seq3951,non-specific,335182,126,199,3.2431e-13,63.8611,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs0_human.marg.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,marg,N-TerminusTruncated
10306,Q#628 - >seq3951,superfamily,335182,126,199,3.2431e-13,63.8611,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MCa.ORF1.hs0_human.marg.frame3,1909130333_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCa,ORF1,hs0_human,marg,N-TerminusTruncated
10307,Q#632 - >seq3955,non-specific,340205,126,187,8.976180000000001e-12,57.7312,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs7_bushaby.pars.frame2,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs7_bushaby,pars,CompleteHit
10308,Q#632 - >seq3955,superfamily,340205,126,187,8.976180000000001e-12,57.7312,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs7_bushaby.pars.frame2,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs7_bushaby,pars,CompleteHit
10309,Q#634 - >seq3957,specific,197310,9,239,8.859419999999999e-30,117.838,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10310,Q#634 - >seq3957,superfamily,351117,9,239,8.859419999999999e-30,117.838,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10311,Q#634 - >seq3957,non-specific,197306,9,239,1.0489799999999999e-10,62.4989,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10312,Q#634 - >seq3957,non-specific,197307,9,239,8.48214e-08,53.8309,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10313,Q#634 - >seq3957,non-specific,223780,9,224,1.35635e-05,47.2079,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10314,Q#634 - >seq3957,non-specific,272954,9,210,9.00294e-05,44.6813,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10315,Q#634 - >seq3957,non-specific,197321,7,239,0.00010202,44.4652,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10316,Q#634 - >seq3957,non-specific,273186,9,240,0.000109785,44.5772,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10317,Q#634 - >seq3957,specific,335306,10,231,0.001036,41.0766,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10318,Q#634 - >seq3957,non-specific,197320,9,224,0.00244685,40.191,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs6_sqmonkey.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,marg,CompleteHit
10319,Q#638 - >seq3961,non-specific,197310,151,221,1.6835999999999998e-11,63.9097,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs6_sqmonkey.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10320,Q#638 - >seq3961,superfamily,351117,151,221,1.6835999999999998e-11,63.9097,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs6_sqmonkey.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10321,Q#638 - >seq3961,non-specific,197320,158,206,0.00169297,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs6_sqmonkey.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10322,Q#638 - >seq3961,non-specific,197307,158,221,0.00251606,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs6_sqmonkey.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10323,Q#638 - >seq3961,non-specific,223780,161,206,0.00397089,39.1187,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs6_sqmonkey.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10324,Q#644 - >seq3967,specific,197310,25,219,1.08542e-30,118.223,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs7_bushaby.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs7_bushaby,pars,CompleteHit
10325,Q#644 - >seq3967,superfamily,351117,25,219,1.08542e-30,118.223,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs7_bushaby.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs7_bushaby,pars,CompleteHit
10326,Q#644 - >seq3967,non-specific,197306,21,217,9.15812e-12,64.4249,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs7_bushaby.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs7_bushaby,pars,CompleteHit
10327,Q#644 - >seq3967,non-specific,197321,25,188,0.000101919,43.6948,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs7_bushaby.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs7_bushaby,pars,CompleteHit
10328,Q#648 - >seq3971,non-specific,197310,43,239,3.50438e-20,89.3329,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs7_bushaby.marg.frame2,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs7_bushaby,marg,CompleteHit
10329,Q#648 - >seq3971,superfamily,351117,43,239,3.50438e-20,89.3329,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs7_bushaby.marg.frame2,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs7_bushaby,marg,CompleteHit
10330,Q#648 - >seq3971,non-specific,197306,57,220,8.694210000000001e-06,47.0909,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs7_bushaby.marg.frame2,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs7_bushaby,marg,CompleteHit
10331,Q#650 - >seq3973,non-specific,340205,151,193,1.89578e-13,62.3536,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs8_ctshrew.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCb,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10332,Q#650 - >seq3973,superfamily,340205,151,193,1.89578e-13,62.3536,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs8_ctshrew.pars.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCb,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10333,Q#652 - >seq3975,non-specific,340205,188,230,9.713450000000001e-14,64.2796,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs8_ctshrew.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
10334,Q#652 - >seq3975,superfamily,340205,188,230,9.713450000000001e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs8_ctshrew.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
10335,Q#656 - >seq3979,non-specific,340205,28,89,1.97984e-11,53.8792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs7_bushaby.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCb,ORF1,hs7_bushaby,marg,CompleteHit
10336,Q#656 - >seq3979,superfamily,340205,28,89,1.97984e-11,53.8792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs7_bushaby.marg.frame3,1909130335_L1MCb.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCb,ORF1,hs7_bushaby,marg,CompleteHit
10337,Q#663 - >seq3986,non-specific,340205,192,217,0.00159083,35.7748,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs4_gibbon,marg,N-TerminusTruncated
10338,Q#663 - >seq3986,superfamily,340205,192,217,0.00159083,35.7748,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs4_gibbon,marg,N-TerminusTruncated
10339,Q#666 - >seq3989,non-specific,340205,1,51,3.9657800000000005e-05,36.5452,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs6_sqmonkey.pars.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCb,ORF1,hs6_sqmonkey,pars,CompleteHit
10340,Q#666 - >seq3989,superfamily,340205,1,51,3.9657800000000005e-05,36.5452,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs6_sqmonkey.pars.frame3,1909130335_L1MCb.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MCb,ORF1,hs6_sqmonkey,pars,CompleteHit
10341,Q#669 - >seq3992,non-specific,197310,21,232,3.7455599999999996e-10,60.8281,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs4_gibbon,marg,CompleteHit
10342,Q#669 - >seq3992,superfamily,351117,21,232,3.7455599999999996e-10,60.8281,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs4_gibbon,marg,CompleteHit
10343,Q#669 - >seq3992,non-specific,197306,49,232,0.000172221,44.0093,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10344,Q#669 - >seq3992,non-specific,223780,98,184,0.00115492,41.4299,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs4_gibbon.marg.frame1,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCb,ORF2,hs4_gibbon,marg,BothTerminiTruncated
10345,Q#671 - >seq3994,non-specific,238827,472,518,1.7305099999999998e-06,49.597,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCb.ORF2.hs4_gibbon.marg.frame3,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCb,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10346,Q#671 - >seq3994,superfamily,295487,472,518,1.7305099999999998e-06,49.597,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCb.ORF2.hs4_gibbon.marg.frame3,1909130335_L1MCb.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MCb,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10347,Q#679 - >seq4002,non-specific,197310,10,252,2.14207e-07,52.3537,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs5_gmonkey,marg,CompleteHit
10348,Q#679 - >seq4002,superfamily,351117,10,252,2.14207e-07,52.3537,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs5_gmonkey,marg,CompleteHit
10349,Q#679 - >seq4002,non-specific,333820,548,645,0.00210532,39.9682,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCb.ORF2.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCb,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10350,Q#679 - >seq4002,superfamily,333820,548,645,0.00210532,39.9682,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCb.ORF2.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MCb,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10351,Q#682 - >seq4005,non-specific,340205,44,100,5.12259e-05,37.7008,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs5_gmonkey,marg,CompleteHit
10352,Q#682 - >seq4005,superfamily,340205,44,100,5.12259e-05,37.7008,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs5_gmonkey.marg.frame1,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs5_gmonkey,marg,CompleteHit
10353,Q#684 - >seq4007,non-specific,197310,37,185,6.2851e-05,43.8793,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs5_gmonkey.pars.frame2,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
10354,Q#684 - >seq4007,superfamily,351117,37,185,6.2851e-05,43.8793,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs5_gmonkey.pars.frame2,1909130335_L1MCb.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
10355,Q#696 - >seq4019,non-specific,238827,208,259,7.63189e-09,56.1454,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs3_orang.pars.frame1,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs3_orang,pars,BothTerminiTruncated
10356,Q#696 - >seq4019,superfamily,295487,208,259,7.63189e-09,56.1454,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs3_orang.pars.frame1,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs3_orang,pars,BothTerminiTruncated
10357,Q#696 - >seq4019,non-specific,333820,163,259,0.000149245,43.0498,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs3_orang.pars.frame1,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs3_orang,pars,BothTerminiTruncated
10358,Q#696 - >seq4019,superfamily,333820,163,259,0.000149245,43.0498,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs3_orang.pars.frame1,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs3_orang,pars,BothTerminiTruncated
10359,Q#696 - >seq4019,non-specific,238828,160,270,0.00118642,40.6473,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC.ORF2.hs3_orang.pars.frame1,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs3_orang,pars,N-TerminusTruncated
10360,Q#710 - >seq4033,non-specific,238827,69,169,2.42457e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs3_orang.pars.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC,ORF2,hs3_orang,pars,C-TerminusTruncated
10361,Q#710 - >seq4033,superfamily,295487,69,169,2.42457e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs3_orang.pars.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC,ORF2,hs3_orang,pars,C-TerminusTruncated
10362,Q#717 - >seq4040,non-specific,238827,492,617,3.2893499999999995e-17,81.5686,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs3_orang.marg.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10363,Q#717 - >seq4040,superfamily,295487,492,617,3.2893499999999995e-17,81.5686,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs3_orang.marg.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10364,Q#717 - >seq4040,non-specific,333820,437,617,1.91612e-10,60.769,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs3_orang.marg.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10365,Q#717 - >seq4040,superfamily,333820,437,617,1.91612e-10,60.769,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs3_orang.marg.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10366,Q#717 - >seq4040,non-specific,238828,493,553,0.00313565,40.2621,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC.ORF2.hs3_orang.marg.frame2,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10367,Q#720 - >seq4043,non-specific,340205,249,308,1.67927e-15,69.6724,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs3_orang.marg.frame1,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs3_orang,marg,CompleteHit
10368,Q#720 - >seq4043,superfamily,340205,249,308,1.67927e-15,69.6724,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs3_orang.marg.frame1,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs3_orang,marg,CompleteHit
10369,Q#720 - >seq4043,non-specific,335182,174,246,1.41912e-13,65.4019,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs3_orang.marg.frame1,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs3_orang,marg,N-TerminusTruncated
10370,Q#720 - >seq4043,superfamily,335182,174,246,1.41912e-13,65.4019,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs3_orang.marg.frame1,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs3_orang,marg,N-TerminusTruncated
10371,Q#721 - >seq4044,non-specific,340205,179,238,1.6169000000000001e-15,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs3_orang.pars.frame3,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs3_orang,pars,CompleteHit
10372,Q#721 - >seq4044,superfamily,340205,179,238,1.6169000000000001e-15,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs3_orang.pars.frame3,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs3_orang,pars,CompleteHit
10373,Q#721 - >seq4044,non-specific,335182,104,176,5.90134e-13,62.7055,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs3_orang.pars.frame3,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs3_orang,pars,N-TerminusTruncated
10374,Q#721 - >seq4044,superfamily,335182,104,176,5.90134e-13,62.7055,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs3_orang.pars.frame3,1909130336_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs3_orang,pars,N-TerminusTruncated
10375,Q#725 - >seq4048,non-specific,340205,185,247,4.6424199999999995e-18,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs2_gorilla.marg.frame2,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs2_gorilla,marg,CompleteHit
10376,Q#725 - >seq4048,superfamily,340205,185,247,4.6424199999999995e-18,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs2_gorilla.marg.frame2,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs2_gorilla,marg,CompleteHit
10377,Q#725 - >seq4048,non-specific,335182,110,156,7.39548e-09,51.9199,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs2_gorilla.marg.frame2,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
10378,Q#725 - >seq4048,superfamily,335182,110,156,7.39548e-09,51.9199,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs2_gorilla.marg.frame2,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
10379,Q#729 - >seq4052,non-specific,340205,139,200,3.33598e-17,72.3688,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs2_gorilla.pars.frame1,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs2_gorilla,pars,CompleteHit
10380,Q#729 - >seq4052,superfamily,340205,139,200,3.33598e-17,72.3688,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs2_gorilla.pars.frame1,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs2_gorilla,pars,CompleteHit
10381,Q#729 - >seq4052,non-specific,335182,71,110,8.28995e-09,51.1495,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs2_gorilla.pars.frame1,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
10382,Q#729 - >seq4052,superfamily,335182,71,110,8.28995e-09,51.1495,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs2_gorilla.pars.frame1,1909130336_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
10383,Q#730 - >seq4053,non-specific,340205,200,260,6.54714e-15,67.7464,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,marg,CompleteHit
10384,Q#730 - >seq4053,superfamily,340205,200,260,6.54714e-15,67.7464,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,marg,CompleteHit
10385,Q#730 - >seq4053,non-specific,335182,122,197,6.84071e-13,63.0907,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,marg,CompleteHit
10386,Q#730 - >seq4053,superfamily,335182,122,197,6.84071e-13,63.0907,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,marg,CompleteHit
10387,Q#730 - >seq4053,non-specific,274105,107,242,0.00130364,39.650999999999996,TIGR02389,RNA_pol_rpoA2,NC,cl37098,"DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]",L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD1,ORF1,hs1_chimp,marg,BothTerminiTruncated
10388,Q#730 - >seq4053,superfamily,274105,107,242,0.00130364,39.650999999999996,cl37098,RNA_pol_rpoA2 superfamily,NC, - ,"DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]",L1MD1.ORF1.hs1_chimp.marg.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD1,ORF1,hs1_chimp,marg,BothTerminiTruncated
10389,Q#733 - >seq4056,non-specific,340205,197,257,6.8237899999999996e-15,67.3612,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,pars,CompleteHit
10390,Q#733 - >seq4056,superfamily,340205,197,257,6.8237899999999996e-15,67.3612,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,pars,CompleteHit
10391,Q#733 - >seq4056,non-specific,335182,118,194,8.42392e-14,65.4019,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,pars,CompleteHit
10392,Q#733 - >seq4056,superfamily,335182,118,194,8.42392e-14,65.4019,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs1_chimp,pars,CompleteHit
10393,Q#733 - >seq4056,non-specific,274105,103,239,0.00667883,37.3398,TIGR02389,RNA_pol_rpoA2,NC,cl37098,"DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]",L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MD1,ORF1,hs1_chimp,pars,BothTerminiTruncated
10394,Q#733 - >seq4056,superfamily,274105,103,239,0.00667883,37.3398,cl37098,RNA_pol_rpoA2 superfamily,NC, - ,"DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]",L1MD1.ORF1.hs1_chimp.pars.frame3,1909130336_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MD1,ORF1,hs1_chimp,pars,BothTerminiTruncated
10395,Q#736 - >seq4059,non-specific,238827,448,731,1.26002e-16,80.0278,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs4_gibbon.marg.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,marg,CompleteHit
10396,Q#736 - >seq4059,superfamily,295487,448,731,1.26002e-16,80.0278,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs4_gibbon.marg.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,marg,CompleteHit
10397,Q#736 - >seq4059,non-specific,333820,571,690,0.000843711,41.50899999999999,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs4_gibbon.marg.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10398,Q#736 - >seq4059,superfamily,333820,571,690,0.000843711,41.50899999999999,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs4_gibbon.marg.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10399,Q#739 - >seq4062,non-specific,238827,330,435,6.44385e-08,53.8342,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs4_gibbon.pars.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10400,Q#739 - >seq4062,superfamily,295487,330,435,6.44385e-08,53.8342,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs4_gibbon.pars.frame2,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10401,Q#740 - >seq4063,non-specific,238827,458,546,9.731489999999999e-14,71.1682,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10402,Q#740 - >seq4063,superfamily,295487,458,546,9.731489999999999e-14,71.1682,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10403,Q#740 - >seq4063,non-specific,333820,413,541,1.91966e-09,57.6874,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10404,Q#740 - >seq4063,superfamily,333820,413,541,1.91966e-09,57.6874,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10405,Q#740 - >seq4063,non-specific,197310,2,73,7.837779999999999e-07,50.8129,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10406,Q#740 - >seq4063,superfamily,351117,2,73,7.837779999999999e-07,50.8129,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10407,Q#740 - >seq4063,non-specific,238828,410,541,0.00587713,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC.ORF2.hs4_gibbon.pars.frame1,1909130336_L1MC.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10408,Q#747 - >seq4070,non-specific,238827,367,470,3.9460100000000005e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs3_orang.marg.frame3,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs3_orang,marg,C-TerminusTruncated
10409,Q#747 - >seq4070,superfamily,295487,367,470,3.9460100000000005e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs3_orang.marg.frame3,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs3_orang,marg,C-TerminusTruncated
10410,Q#747 - >seq4070,non-specific,197310,12,79,0.0005391080000000001,42.7237,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC.ORF2.hs3_orang.marg.frame3,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10411,Q#747 - >seq4070,superfamily,351117,12,79,0.0005391080000000001,42.7237,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC.ORF2.hs3_orang.marg.frame3,1909130336_L1MC.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC,ORF2,hs3_orang,marg,N-TerminusTruncated
10412,Q#753 - >seq4076,non-specific,197310,49,240,2.75139e-21,93.5701,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs10_snmole,marg,CompleteHit
10413,Q#753 - >seq4076,superfamily,351117,49,240,2.75139e-21,93.5701,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs10_snmole,marg,CompleteHit
10414,Q#753 - >seq4076,non-specific,197306,93,240,1.4310799999999998e-09,59.0321,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10415,Q#753 - >seq4076,non-specific,197322,102,233,5.4248699999999995e-08,55.401,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10416,Q#753 - >seq4076,non-specific,223780,102,241,7.062659999999999e-07,51.4451,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10417,Q#753 - >seq4076,specific,335306,60,233,2.15572e-06,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10418,Q#753 - >seq4076,non-specific,197307,102,240,2.18046e-06,49.5937,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10419,Q#753 - >seq4076,non-specific,197320,104,233,4.5886899999999996e-05,45.5838,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10420,Q#753 - >seq4076,non-specific,273186,104,241,0.000116846,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs10_snmole,marg,N-TerminusTruncated
10421,Q#753 - >seq4076,non-specific,339261,130,236,0.0077548,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCb.ORF2.hs10_snmole.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MCb,ORF2,hs10_snmole,marg,CompleteHit
10422,Q#756 - >seq4079,non-specific,197310,58,131,0.000179948,42.7237,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs10_snmole.pars.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MCb,ORF2,hs10_snmole,pars,BothTerminiTruncated
10423,Q#756 - >seq4079,superfamily,351117,58,131,0.000179948,42.7237,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs10_snmole.pars.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs10_snmole,pars,BothTerminiTruncated
10424,Q#757 - >seq4080,non-specific,197310,148,208,5.82187e-07,50.4277,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs10_snmole.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs10_snmole,pars,N-TerminusTruncated
10425,Q#757 - >seq4080,superfamily,351117,148,208,5.82187e-07,50.4277,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs10_snmole.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs10_snmole,pars,N-TerminusTruncated
10426,Q#760 - >seq4083,non-specific,340205,197,252,2.1397200000000003e-10,55.0348,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs10_snmole.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs10_snmole,marg,CompleteHit
10427,Q#760 - >seq4083,superfamily,340205,197,252,2.1397200000000003e-10,55.0348,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs10_snmole.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MCb,ORF1,hs10_snmole,marg,CompleteHit
10428,Q#762 - >seq4085,non-specific,340205,152,203,3.78551e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs10_snmole.pars.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs10_snmole,pars,CompleteHit
10429,Q#762 - >seq4085,superfamily,340205,152,203,3.78551e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs10_snmole.pars.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs10_snmole,pars,CompleteHit
10430,Q#767 - >seq4090,non-specific,197310,48,291,1.71629e-16,79.3177,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs9_pika.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs9_pika,marg,CompleteHit
10431,Q#767 - >seq4090,superfamily,351117,48,291,1.71629e-16,79.3177,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs9_pika.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,marg,CompleteHit
10432,Q#767 - >seq4090,non-specific,197306,48,291,1.1765499999999999e-07,53.2541,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs9_pika.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,marg,CompleteHit
10433,Q#767 - >seq4090,specific,335306,49,284,0.00035452199999999996,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCb.ORF2.hs9_pika.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,marg,CompleteHit
10434,Q#767 - >seq4090,non-specific,197322,190,284,0.00963249,38.8375,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs9_pika.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs9_pika,marg,N-TerminusTruncated
10435,Q#769 - >seq4092,non-specific,340205,150,171,0.0085812,33.4636,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs9_pika.marg.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCb,ORF1,hs9_pika,marg,C-TerminusTruncated
10436,Q#769 - >seq4092,superfamily,340205,150,171,0.0085812,33.4636,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs9_pika.marg.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MCb,ORF1,hs9_pika,marg,C-TerminusTruncated
10437,Q#774 - >seq4097,non-specific,340205,148,190,1.3584700000000003e-10,54.6496,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs9_pika.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCb,ORF1,hs9_pika,pars,C-TerminusTruncated
10438,Q#774 - >seq4097,superfamily,340205,148,190,1.3584700000000003e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs9_pika.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MCb,ORF1,hs9_pika,pars,C-TerminusTruncated
10439,Q#776 - >seq4099,non-specific,197310,94,223,5.47781e-12,65.4505,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10440,Q#776 - >seq4099,superfamily,351117,94,223,5.47781e-12,65.4505,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10441,Q#776 - >seq4099,non-specific,197307,159,223,0.000223585,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10442,Q#776 - >seq4099,non-specific,273186,159,223,0.00276111,39.5696,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10443,Q#776 - >seq4099,non-specific,197320,159,193,0.00492166,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10444,Q#776 - >seq4099,non-specific,223780,160,216,0.00524054,38.7335,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs8_ctshrew.marg.frame2,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10445,Q#777 - >seq4100,non-specific,197310,10,57,2.962e-05,45.4201,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs8_ctshrew.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10446,Q#777 - >seq4100,superfamily,351117,10,57,2.962e-05,45.4201,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10447,Q#777 - >seq4100,non-specific,197321,10,85,0.00435663,38.6872,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MCb,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10448,Q#777 - >seq4100,non-specific,197307,10,43,0.00483454,38.8081,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10449,Q#777 - >seq4100,non-specific,197306,10,43,0.00566371,38.2313,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.marg.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10450,Q#778 - >seq4101,non-specific,197310,2,43,0.000244268,41.1829,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10451,Q#778 - >seq4101,superfamily,351117,2,43,0.000244268,41.1829,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10452,Q#778 - >seq4101,non-specific,223780,2,29,0.00114633,39.5039,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10453,Q#778 - >seq4101,non-specific,197321,2,96,0.00187904,38.6872,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10454,Q#778 - >seq4101,non-specific,197336,2,29,0.00609095,37.2067,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10455,Q#778 - >seq4101,non-specific,197307,2,29,0.00754701,36.8821,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10456,Q#780 - >seq4103,non-specific,197310,134,205,7.004239999999999e-12,63.5245,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10457,Q#780 - >seq4103,superfamily,351117,134,205,7.004239999999999e-12,63.5245,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10458,Q#780 - >seq4103,non-specific,197307,141,205,4.86724e-05,43.4305,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10459,Q#780 - >seq4103,non-specific,273186,141,205,0.000947433,39.5696,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10460,Q#780 - >seq4103,non-specific,223780,142,198,0.00167751,38.7335,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10461,Q#780 - >seq4103,non-specific,197320,141,175,0.00179627,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10462,Q#780 - >seq4103,non-specific,197306,141,205,0.00656646,37.0757,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs8_ctshrew.pars.frame1,1909130336_L1MCb.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MCb,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10463,Q#782 - >seq4105,non-specific,197310,9,226,5.7757799999999995e-18,82.7845,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs9_pika,pars,CompleteHit
10464,Q#782 - >seq4105,superfamily,351117,9,226,5.7757799999999995e-18,82.7845,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,pars,CompleteHit
10465,Q#782 - >seq4105,non-specific,197306,9,226,2.50412e-12,66.3509,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,pars,CompleteHit
10466,Q#782 - >seq4105,non-specific,197307,9,226,1.13135e-08,55.7569,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs9_pika,pars,CompleteHit
10467,Q#782 - >seq4105,specific,335306,10,219,3.57083e-06,48.0102,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs9_pika,pars,CompleteHit
10468,Q#782 - >seq4105,non-specific,223780,119,227,6.23269e-06,47.5931,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs9_pika,pars,N-TerminusTruncated
10469,Q#782 - >seq4105,non-specific,197322,131,219,7.669939999999999e-05,44.6154,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs9_pika,pars,N-TerminusTruncated
10470,Q#782 - >seq4105,non-specific,273186,119,227,0.00010698200000000001,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs9_pika,pars,N-TerminusTruncated
10471,Q#782 - >seq4105,non-specific,197320,127,197,0.00023350400000000002,42.8874,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs9_pika,pars,N-TerminusTruncated
10472,Q#782 - >seq4105,non-specific,197321,119,226,0.00154078,40.228,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs9_pika.pars.frame3,1909130336_L1MCb.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs9_pika,pars,N-TerminusTruncated
10473,Q#807 - >seq4130,non-specific,197310,9,217,4.9357900000000003e-14,71.9989,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs0_human.pars.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs0_human,pars,CompleteHit
10474,Q#807 - >seq4130,superfamily,351117,9,217,4.9357900000000003e-14,71.9989,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs0_human.pars.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs0_human,pars,CompleteHit
10475,Q#807 - >seq4130,non-specific,197306,76,217,4.66793e-06,48.2465,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs0_human.pars.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs0_human,pars,N-TerminusTruncated
10476,Q#807 - >seq4130,non-specific,223780,124,207,0.00190783,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs0_human.pars.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCb,ORF2,hs0_human,pars,N-TerminusTruncated
10477,Q#807 - >seq4130,non-specific,197322,140,199,0.00629604,39.2227,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs0_human.pars.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCb,ORF2,hs0_human,pars,N-TerminusTruncated
10478,Q#815 - >seq4138,non-specific,197310,9,237,4.1561699999999996e-19,87.0217,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs0_human,marg,CompleteHit
10479,Q#815 - >seq4138,superfamily,351117,9,237,4.1561699999999996e-19,87.0217,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs0_human,marg,CompleteHit
10480,Q#815 - >seq4138,non-specific,197306,76,237,1.19559e-08,56.3357,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10481,Q#815 - >seq4138,non-specific,223780,125,230,0.000104974,44.5115,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10482,Q#815 - >seq4138,non-specific,197307,137,237,0.000443849,42.6601,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10483,Q#815 - >seq4138,non-specific,197322,141,237,0.000885484,41.919,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10484,Q#815 - >seq4138,non-specific,273186,141,238,0.00742961,38.7992,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10485,Q#815 - >seq4138,non-specific,197320,127,230,0.00823829,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCb.ORF2.hs0_human.marg.frame3,1909130336_L1MCb.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCb,ORF2,hs0_human,marg,N-TerminusTruncated
10486,Q#817 - >seq4140,specific,197310,7,230,6.24202e-38,142.105,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10487,Q#817 - >seq4140,superfamily,351117,7,230,6.24202e-38,142.105,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10488,Q#817 - >seq4140,non-specific,197306,7,230,8.02361e-20,89.848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10489,Q#817 - >seq4140,non-specific,238827,495,599,2.91348e-18,84.6502,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10490,Q#817 - >seq4140,superfamily,295487,495,599,2.91348e-18,84.6502,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10491,Q#817 - >seq4140,non-specific,223780,7,219,3.758019999999999e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10492,Q#817 - >seq4140,non-specific,197307,7,230,8.17745e-11,63.4609,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10493,Q#817 - >seq4140,non-specific,333820,513,693,4.09229e-09,57.3022,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10494,Q#817 - >seq4140,superfamily,333820,513,693,4.09229e-09,57.3022,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10495,Q#817 - >seq4140,non-specific,197320,7,215,7.33611e-09,57.9102,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10496,Q#817 - >seq4140,specific,335306,8,223,9.48775e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10497,Q#817 - >seq4140,non-specific,197321,5,230,1.49307e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10498,Q#817 - >seq4140,non-specific,273186,7,231,7.29855e-07,51.896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10499,Q#817 - >seq4140,non-specific,272954,7,201,3.76091e-06,49.6889,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10500,Q#817 - >seq4140,non-specific,197319,7,230,1.41884e-05,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,CompleteHit
10501,Q#817 - >seq4140,non-specific,197322,103,230,0.00447658,40.3782,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10502,Q#820 - >seq4143,specific,197310,4,222,3.35897e-35,134.401,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10503,Q#820 - >seq4143,superfamily,351117,4,222,3.35897e-35,134.401,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10504,Q#820 - >seq4143,non-specific,197306,4,222,1.0805900000000001e-18,86.3812,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10505,Q#820 - >seq4143,non-specific,238827,487,591,2.8531400000000004e-18,84.6502,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10506,Q#820 - >seq4143,superfamily,295487,487,591,2.8531400000000004e-18,84.6502,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10507,Q#820 - >seq4143,non-specific,223780,4,211,6.92115e-12,66.8531,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10508,Q#820 - >seq4143,non-specific,197307,4,222,1.19371e-10,63.0757,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10509,Q#820 - >seq4143,non-specific,333820,505,685,3.82448e-09,57.3022,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10510,Q#820 - >seq4143,superfamily,333820,505,685,3.82448e-09,57.3022,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
10511,Q#820 - >seq4143,non-specific,197320,4,207,3.79558e-08,55.599,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10512,Q#820 - >seq4143,non-specific,197321,2,222,4.30398e-07,52.5544,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10513,Q#820 - >seq4143,specific,335306,5,215,4.50191e-07,51.8622,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10514,Q#820 - >seq4143,non-specific,272954,4,193,9.640239999999999e-06,48.1481,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10515,Q#820 - >seq4143,non-specific,197319,4,222,3.1690700000000005e-05,46.5009,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,marg,CompleteHit
10516,Q#820 - >seq4143,non-specific,197322,96,222,0.00254597,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10517,Q#822 - >seq4145,non-specific,335182,17,87,2.45202e-08,49.2235,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs5_gmonkey.pars.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
10518,Q#822 - >seq4145,superfamily,335182,17,87,2.45202e-08,49.2235,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs5_gmonkey.pars.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
10519,Q#825 - >seq4148,non-specific,335182,44,102,2.53761e-08,49.6087,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs5_gmonkey.marg.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
10520,Q#825 - >seq4148,superfamily,335182,44,102,2.53761e-08,49.6087,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs5_gmonkey.marg.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
10521,Q#825 - >seq4148,non-specific,340205,151,197,1.5956099999999998e-05,41.1676,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs5_gmonkey.marg.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
10522,Q#825 - >seq4148,superfamily,340205,151,197,1.5956099999999998e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs5_gmonkey.marg.frame3,1909130337_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
10523,Q#831 - >seq4154,non-specific,335182,45,127,1.3307100000000001e-07,47.6827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs4_gibbon,marg,CompleteHit
10524,Q#831 - >seq4154,superfamily,335182,45,127,1.3307100000000001e-07,47.6827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs4_gibbon.marg.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs4_gibbon,marg,CompleteHit
10525,Q#833 - >seq4156,specific,197310,9,235,1.4171499999999998e-50,178.31400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10526,Q#833 - >seq4156,superfamily,351117,9,235,1.4171499999999998e-50,178.31400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10527,Q#833 - >seq4156,non-specific,197306,9,235,1.0209500000000001e-25,106.79700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10528,Q#833 - >seq4156,non-specific,223780,9,224,2.1918299999999998e-17,83.0315,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10529,Q#833 - >seq4156,non-specific,197307,9,235,1.5982e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10530,Q#833 - >seq4156,non-specific,197320,9,220,2.3563000000000003e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10531,Q#833 - >seq4156,specific,335306,10,228,7.67869e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10532,Q#833 - >seq4156,non-specific,197321,7,235,7.19413e-11,63.7252,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10533,Q#833 - >seq4156,non-specific,273186,9,236,3.4184399999999996e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10534,Q#833 - >seq4156,non-specific,272954,9,206,2.34103e-08,56.2373,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10535,Q#833 - >seq4156,non-specific,197319,9,235,4.4391e-08,55.3605,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10536,Q#833 - >seq4156,non-specific,197322,91,235,6.49311e-06,49.2378,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,N-TerminusTruncated
10537,Q#833 - >seq4156,non-specific,197311,7,146,0.000297254,43.0493,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,C-TerminusTruncated
10538,Q#833 - >seq4156,non-specific,339261,108,231,0.00046278300000000003,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10539,Q#833 - >seq4156,non-specific,197336,9,193,0.0007233060000000001,42.5995,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10540,Q#833 - >seq4156,non-specific,139971,7,235,0.00215749,40.8328,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1MD1.ORF2.hs3_orang.pars.frame3,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10541,Q#834 - >seq4157,specific,197310,9,234,3.82398e-47,168.68400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10542,Q#834 - >seq4157,superfamily,351117,9,234,3.82398e-47,168.68400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10543,Q#834 - >seq4157,non-specific,197306,9,234,6.79169e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10544,Q#834 - >seq4157,non-specific,238827,515,735,1.00998e-20,91.969,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10545,Q#834 - >seq4157,superfamily,295487,515,735,1.00998e-20,91.969,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10546,Q#834 - >seq4157,non-specific,223780,9,223,2.7363000000000005e-17,83.0315,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10547,Q#834 - >seq4157,non-specific,197307,9,234,5.146e-14,73.0909,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10548,Q#834 - >seq4157,non-specific,197320,9,219,1.62806e-13,71.7774,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10549,Q#834 - >seq4157,specific,335306,10,227,4.2392399999999996e-13,69.9666,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10550,Q#834 - >seq4157,non-specific,197321,7,234,1.20443e-10,62.9548,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10551,Q#834 - >seq4157,non-specific,273186,9,235,1.8295e-10,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10552,Q#834 - >seq4157,non-specific,197319,9,234,8.67209e-09,57.6717,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10553,Q#834 - >seq4157,non-specific,272954,9,205,1.62888e-08,56.6225,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10554,Q#834 - >seq4157,non-specific,197322,8,234,3.33659e-06,50.3934,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10555,Q#834 - >seq4157,non-specific,333820,515,725,1.36984e-05,46.9018,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10556,Q#834 - >seq4157,superfamily,333820,515,725,1.36984e-05,46.9018,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10557,Q#834 - >seq4157,non-specific,197336,9,192,6.62944e-05,45.6811,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10558,Q#834 - >seq4157,non-specific,197311,7,145,0.00045433,42.6641,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs3_orang,marg,C-TerminusTruncated
10559,Q#834 - >seq4157,non-specific,339261,107,230,0.00136534,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD1.ORF2.hs3_orang.marg.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MD1,ORF2,hs3_orang,marg,CompleteHit
10560,Q#835 - >seq4158,non-specific,238827,483,694,2.47059e-20,90.8134,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs3_orang.pars.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10561,Q#835 - >seq4158,superfamily,295487,483,694,2.47059e-20,90.8134,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs3_orang.pars.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10562,Q#835 - >seq4158,non-specific,333820,483,689,2.7896e-05,45.7462,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs3_orang.pars.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10563,Q#835 - >seq4158,superfamily,333820,483,689,2.7896e-05,45.7462,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs3_orang.pars.frame2,1909130337_L1MD1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs3_orang,pars,CompleteHit
10564,Q#837 - >seq4160,non-specific,340205,76,139,2.20444e-21,81.2284,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs4_gibbon.pars.frame2,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs4_gibbon,pars,CompleteHit
10565,Q#837 - >seq4160,superfamily,340205,76,139,2.20444e-21,81.2284,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs4_gibbon.pars.frame2,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs4_gibbon,pars,CompleteHit
10566,Q#838 - >seq4161,non-specific,335182,1,42,0.00023031900000000002,37.6675,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
10567,Q#838 - >seq4161,superfamily,335182,1,42,0.00023031900000000002,37.6675,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs4_gibbon.pars.frame3,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
10568,Q#839 - >seq4162,non-specific,340205,134,197,1.75036e-20,80.8432,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs4_gibbon.marg.frame1,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs4_gibbon,marg,CompleteHit
10569,Q#839 - >seq4162,superfamily,340205,134,197,1.75036e-20,80.8432,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs4_gibbon.marg.frame1,1909130337_L1MD1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs4_gibbon,marg,CompleteHit
10570,Q#842 - >seq4165,specific,197310,9,234,6.0592599999999995e-31,122.075,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10571,Q#842 - >seq4165,superfamily,351117,9,234,6.0592599999999995e-31,122.075,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10572,Q#842 - >seq4165,non-specific,197306,9,234,7.42172e-17,81.3736,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10573,Q#842 - >seq4165,non-specific,238827,488,593,2.50765e-13,70.3978,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10574,Q#842 - >seq4165,superfamily,295487,488,593,2.50765e-13,70.3978,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10575,Q#842 - >seq4165,specific,335306,10,227,2.93771e-08,55.32899999999999,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10576,Q#842 - >seq4165,non-specific,197307,9,234,5.4220000000000005e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10577,Q#842 - >seq4165,non-specific,223780,9,223,5.71359e-07,52.2155,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10578,Q#842 - >seq4165,non-specific,197320,9,219,5.3765e-06,49.0506,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,CompleteHit
10579,Q#842 - >seq4165,non-specific,197322,138,234,0.000660656,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10580,Q#843 - >seq4166,non-specific,340205,169,202,7.75815e-05,39.6268,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,C-TerminusTruncated
10581,Q#843 - >seq4166,superfamily,340205,169,202,7.75815e-05,39.6268,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,C-TerminusTruncated
10582,Q#845 - >seq4168,non-specific,335182,91,172,4.94828e-18,76.5727,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,CompleteHit
10583,Q#845 - >seq4168,superfamily,335182,91,172,4.94828e-18,76.5727,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,CompleteHit
10584,Q#845 - >seq4168,non-specific,340205,188,246,1.4394899999999999e-08,50.0272,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,CompleteHit
10585,Q#845 - >seq4168,superfamily,340205,188,246,1.4394899999999999e-08,50.0272,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs7_bushaby,pars,CompleteHit
10586,Q#846 - >seq4169,non-specific,335182,110,194,5.71329e-17,74.2615,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,CompleteHit
10587,Q#846 - >seq4169,superfamily,335182,110,194,5.71329e-17,74.2615,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,CompleteHit
10588,Q#846 - >seq4169,non-specific,340205,230,268,5.05715e-07,45.79,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
10589,Q#846 - >seq4169,superfamily,340205,230,268,5.05715e-07,45.79,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
10590,Q#847 - >seq4170,non-specific,197310,4,236,2.0006799999999998e-26,108.978,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10591,Q#847 - >seq4170,superfamily,351117,4,236,2.0006799999999998e-26,108.978,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10592,Q#847 - >seq4170,non-specific,197306,4,236,5.34956e-10,60.9581,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10593,Q#847 - >seq4170,non-specific,223780,4,225,4.06066e-09,58.7639,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10594,Q#847 - >seq4170,non-specific,197320,8,221,6.2887599999999996e-06,48.6654,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10595,Q#847 - >seq4170,non-specific,273186,4,237,0.000310349,43.8068,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10596,Q#847 - >seq4170,non-specific,197307,4,236,0.0007041360000000001,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10597,Q#847 - >seq4170,non-specific,272954,4,207,0.00110937,41.9849,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10598,Q#847 - >seq4170,non-specific,197321,2,236,0.00623771,39.4576,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs7_bushaby.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10599,Q#849 - >seq4172,non-specific,197310,63,205,9.599139999999999e-17,80.4733,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10600,Q#849 - >seq4172,superfamily,351117,63,205,9.599139999999999e-17,80.4733,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10601,Q#849 - >seq4172,non-specific,238827,511,552,0.000203358,43.818999999999996,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs7_bushaby,pars,BothTerminiTruncated
10602,Q#849 - >seq4172,superfamily,295487,511,552,0.000203358,43.818999999999996,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs7_bushaby,pars,BothTerminiTruncated
10603,Q#849 - >seq4172,non-specific,197306,64,205,0.000368577,43.2389,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10604,Q#849 - >seq4172,non-specific,223780,75,194,0.00165861,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10605,Q#849 - >seq4172,non-specific,197320,75,190,0.00186583,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10606,Q#849 - >seq4172,non-specific,333820,507,566,0.00752217,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
10607,Q#849 - >seq4172,superfamily,333820,507,566,0.00752217,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.pars.frame1,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs7_bushaby,pars,C-TerminusTruncated
10608,Q#851 - >seq4174,non-specific,238827,473,708,8.468510000000001e-22,95.0506,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,CompleteHit
10609,Q#851 - >seq4174,superfamily,295487,473,708,8.468510000000001e-22,95.0506,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,CompleteHit
10610,Q#851 - >seq4174,non-specific,333820,470,675,1.27715e-11,64.62100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,CompleteHit
10611,Q#851 - >seq4174,superfamily,333820,470,675,1.27715e-11,64.62100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,CompleteHit
10612,Q#851 - >seq4174,non-specific,238828,601,663,5.5099700000000004e-05,45.6549,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
10613,Q#851 - >seq4174,non-specific,238185,597,676,0.000120948,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,pars,CompleteHit
10614,Q#852 - >seq4175,non-specific,238827,507,566,9.47997e-10,59.9974,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
10615,Q#852 - >seq4175,superfamily,295487,507,566,9.47997e-10,59.9974,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs7_bushaby,marg,C-TerminusTruncated
10616,Q#852 - >seq4175,non-specific,338612,129,329,7.50446e-05,46.9655,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD1.ORF2.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other,L1MD1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
10617,Q#852 - >seq4175,superfamily,338612,129,329,7.50446e-05,46.9655,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD1.ORF2.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MD1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
10618,Q#853 - >seq4176,non-specific,238827,493,731,1.34133e-23,100.05799999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10619,Q#853 - >seq4176,superfamily,295487,493,731,1.34133e-23,100.05799999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10620,Q#853 - >seq4176,non-specific,333820,490,698,3.31196e-11,63.4654,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10621,Q#853 - >seq4176,superfamily,333820,490,698,3.31196e-11,63.4654,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10622,Q#853 - >seq4176,non-specific,238185,619,699,0.00019443599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,CompleteHit
10623,Q#853 - >seq4176,non-specific,238828,623,686,0.00101205,41.8029,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs7_bushaby.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
10624,Q#854 - >seq4177,non-specific,340205,188,249,4.26792e-06,43.0936,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,CompleteHit
10625,Q#854 - >seq4177,superfamily,340205,188,249,4.26792e-06,43.0936,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs7_bushaby.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs7_bushaby,marg,CompleteHit
10626,Q#855 - >seq4178,non-specific,238827,584,679,5.99012e-12,66.1606,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10627,Q#855 - >seq4178,superfamily,295487,584,679,5.99012e-12,66.1606,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10628,Q#855 - >seq4178,non-specific,333820,584,662,0.000175256,43.435,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10629,Q#855 - >seq4178,superfamily,333820,584,662,0.000175256,43.435,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10630,Q#855 - >seq4178,non-specific,238828,584,665,0.00124049,41.4177,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10631,Q#858 - >seq4181,specific,197310,1,221,7.852389999999998e-30,118.60799999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10632,Q#858 - >seq4181,superfamily,351117,1,221,7.852389999999998e-30,118.60799999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10633,Q#858 - >seq4181,non-specific,238827,470,702,7.662170000000001e-22,95.0506,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10634,Q#858 - >seq4181,superfamily,295487,470,702,7.662170000000001e-22,95.0506,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10635,Q#858 - >seq4181,non-specific,197306,1,221,1.0976800000000001e-15,77.9068,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10636,Q#858 - >seq4181,specific,335306,1,214,2.7087299999999997e-07,52.6326,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10637,Q#858 - >seq4181,non-specific,333820,493,685,2.784e-06,48.8278,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10638,Q#858 - >seq4181,superfamily,333820,493,685,2.784e-06,48.8278,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10639,Q#858 - >seq4181,non-specific,197307,1,221,6.275650000000001e-06,48.8233,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10640,Q#858 - >seq4181,non-specific,223780,1,210,1.25652e-05,47.9783,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10641,Q#858 - >seq4181,non-specific,197320,1,206,2.01862e-05,47.1246,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,CompleteHit
10642,Q#858 - >seq4181,non-specific,197322,125,221,0.00064228,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10643,Q#858 - >seq4181,non-specific,238828,607,688,0.00221871,40.6473,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs6_sqmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10644,Q#860 - >seq4183,specific,197310,9,237,5.9571799999999995e-40,147.88299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10645,Q#860 - >seq4183,superfamily,351117,9,237,5.9571799999999995e-40,147.88299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10646,Q#860 - >seq4183,non-specific,197306,9,237,7.8442e-20,89.848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10647,Q#860 - >seq4183,specific,335306,10,230,1.43537e-09,59.181000000000004,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10648,Q#860 - >seq4183,non-specific,223780,9,208,4.22259e-09,58.3787,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10649,Q#860 - >seq4183,non-specific,197320,9,209,9.54211e-09,57.525,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10650,Q#860 - >seq4183,non-specific,197307,9,237,4.0606e-08,55.3717,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10651,Q#860 - >seq4183,non-specific,272954,9,208,0.000227039,43.9109,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10652,Q#860 - >seq4183,non-specific,197321,7,237,0.000297142,43.6948,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.pars.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10653,Q#861 - >seq4184,non-specific,238827,518,704,2.7013799999999997e-14,73.0942,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs5_gmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10654,Q#861 - >seq4184,superfamily,295487,518,704,2.7013799999999997e-14,73.0942,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs5_gmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10655,Q#861 - >seq4184,non-specific,333820,524,704,1.53428e-06,49.5982,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10656,Q#861 - >seq4184,superfamily,333820,524,704,1.53428e-06,49.5982,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10657,Q#862 - >seq4185,non-specific,238827,486,543,4.26962e-14,72.709,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs5_gmonkey.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10658,Q#862 - >seq4185,superfamily,295487,486,543,4.26962e-14,72.709,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs5_gmonkey.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10659,Q#862 - >seq4185,non-specific,333820,503,543,4.75868e-06,48.0574,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10660,Q#862 - >seq4185,superfamily,333820,503,543,4.75868e-06,48.0574,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.marg.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
10661,Q#863 - >seq4186,specific,197310,9,236,9.384219999999997e-40,147.498,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10662,Q#863 - >seq4186,superfamily,351117,9,236,9.384219999999997e-40,147.498,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10663,Q#863 - >seq4186,non-specific,197306,9,236,2.9799900000000004e-20,91.0036,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10664,Q#863 - >seq4186,non-specific,197320,9,208,4.62765e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10665,Q#863 - >seq4186,non-specific,223780,9,207,1.1664e-09,60.3047,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10666,Q#863 - >seq4186,specific,335306,10,229,1.6548399999999998e-09,59.181000000000004,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10667,Q#863 - >seq4186,non-specific,197307,9,236,2.1176e-08,56.1421,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10668,Q#863 - >seq4186,non-specific,272954,9,207,9.75776e-05,45.0665,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10669,Q#863 - >seq4186,non-specific,197321,7,236,0.000446176,43.3096,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs5_gmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs5_gmonkey,marg,CompleteHit
10670,Q#864 - >seq4187,specific,238827,486,756,6.34992e-30,118.54799999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs5_gmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10671,Q#864 - >seq4187,superfamily,295487,486,756,6.34992e-30,118.54799999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs5_gmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10672,Q#864 - >seq4187,non-specific,333820,503,756,2.94653e-14,72.325,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10673,Q#864 - >seq4187,superfamily,333820,503,756,2.94653e-14,72.325,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs5_gmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs5_gmonkey,pars,CompleteHit
10674,Q#865 - >seq4188,non-specific,335182,73,146,1.1290600000000001e-14,66.5575,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs6_sqmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs6_sqmonkey,pars,CompleteHit
10675,Q#865 - >seq4188,superfamily,335182,73,146,1.1290600000000001e-14,66.5575,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs6_sqmonkey.pars.frame2,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs6_sqmonkey,pars,CompleteHit
10676,Q#866 - >seq4189,non-specific,340205,177,216,4.55858e-08,48.4864,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
10677,Q#866 - >seq4189,superfamily,340205,177,216,4.55858e-08,48.4864,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs6_sqmonkey.marg.frame1,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
10678,Q#868 - >seq4191,non-specific,335182,86,159,9.18446e-15,67.3279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs6_sqmonkey,marg,CompleteHit
10679,Q#868 - >seq4191,superfamily,335182,86,159,9.18446e-15,67.3279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs6_sqmonkey.marg.frame3,1909130339_L1MD1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs6_sqmonkey,marg,CompleteHit
10680,Q#871 - >seq4194,non-specific,238827,533,717,2.14813e-19,88.117,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10681,Q#871 - >seq4194,superfamily,295487,533,717,2.14813e-19,88.117,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10682,Q#871 - >seq4194,non-specific,333820,522,717,3.62129e-10,60.3838,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs10_snmole,marg,CompleteHit
10683,Q#871 - >seq4194,superfamily,333820,522,717,3.62129e-10,60.3838,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs10_snmole,marg,CompleteHit
10684,Q#871 - >seq4194,non-specific,238828,532,611,0.00547153,39.4917,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs10_snmole,marg,BothTerminiTruncated
10685,Q#873 - >seq4196,non-specific,335182,91,159,8.323989999999999e-14,65.0167,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs10_snmole,marg,N-TerminusTruncated
10686,Q#873 - >seq4196,superfamily,335182,91,159,8.323989999999999e-14,65.0167,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs10_snmole,marg,N-TerminusTruncated
10687,Q#874 - >seq4197,non-specific,340205,163,192,2.33212e-07,46.5604,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs10_snmole,marg,C-TerminusTruncated
10688,Q#874 - >seq4197,superfamily,340205,163,192,2.33212e-07,46.5604,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs10_snmole,marg,C-TerminusTruncated
10689,Q#875 - >seq4198,non-specific,340205,180,228,6.036669999999999e-06,42.7084,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs10_snmole,marg,N-TerminusTruncated
10690,Q#875 - >seq4198,superfamily,340205,180,228,6.036669999999999e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs10_snmole,marg,N-TerminusTruncated
10691,Q#876 - >seq4199,non-specific,238827,247,426,2.16867e-17,81.5686,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,pars,N-TerminusTruncated
10692,Q#876 - >seq4199,superfamily,295487,247,426,2.16867e-17,81.5686,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,pars,N-TerminusTruncated
10693,Q#876 - >seq4199,non-specific,333820,248,426,7.37679e-07,49.9834,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,pars,N-TerminusTruncated
10694,Q#876 - >seq4199,superfamily,333820,248,426,7.37679e-07,49.9834,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,pars,N-TerminusTruncated
10695,Q#878 - >seq4201,specific,197310,44,227,4.4641599999999996e-33,128.238,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs10_snmole,marg,CompleteHit
10696,Q#878 - >seq4201,superfamily,351117,44,227,4.4641599999999996e-33,128.238,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs10_snmole,marg,CompleteHit
10697,Q#878 - >seq4201,non-specific,238827,502,585,1.14677e-16,80.0278,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,marg,C-TerminusTruncated
10698,Q#878 - >seq4201,superfamily,295487,502,585,1.14677e-16,80.0278,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,marg,C-TerminusTruncated
10699,Q#878 - >seq4201,non-specific,197306,63,227,1.70159e-11,65.5805,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10700,Q#878 - >seq4201,non-specific,197322,69,227,8.962210000000001e-08,55.0158,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10701,Q#878 - >seq4201,non-specific,197307,81,227,2.04078e-06,50.3641,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10702,Q#878 - >seq4201,non-specific,223780,81,220,3.28033e-06,49.9043,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10703,Q#878 - >seq4201,non-specific,333820,508,562,1.17922e-05,46.9018,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,marg,C-TerminusTruncated
10704,Q#878 - >seq4201,superfamily,333820,508,562,1.17922e-05,46.9018,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs10_snmole,marg,C-TerminusTruncated
10705,Q#878 - >seq4201,non-specific,197319,81,227,0.0007967860000000001,42.2637,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10706,Q#878 - >seq4201,specific,335306,63,220,0.00245551,40.6914,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10707,Q#878 - >seq4201,non-specific,197320,96,220,0.00263858,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs10_snmole,marg,N-TerminusTruncated
10708,Q#878 - >seq4201,non-specific,339261,98,223,0.00988843,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD1.ORF2.hs10_snmole.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MD1,ORF2,hs10_snmole,marg,CompleteHit
10709,Q#881 - >seq4204,non-specific,340205,105,168,7.70524e-19,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs1_chimp.pars.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,pars,CompleteHit
10710,Q#881 - >seq4204,superfamily,340205,105,168,7.70524e-19,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs1_chimp.pars.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,pars,CompleteHit
10711,Q#881 - >seq4204,non-specific,335182,8,102,5.59011e-14,63.8611,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs1_chimp.pars.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,pars,CompleteHit
10712,Q#881 - >seq4204,superfamily,335182,8,102,5.59011e-14,63.8611,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs1_chimp.pars.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,pars,CompleteHit
10713,Q#882 - >seq4205,non-specific,340205,158,220,8.0115e-13,61.198,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs0_human.pars.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,pars,CompleteHit
10714,Q#882 - >seq4205,superfamily,340205,158,220,8.0115e-13,61.198,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs0_human.pars.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,pars,CompleteHit
10715,Q#882 - >seq4205,non-specific,335182,73,154,2.2486799999999997e-09,52.6903,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs0_human.pars.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,pars,CompleteHit
10716,Q#882 - >seq4205,superfamily,335182,73,154,2.2486799999999997e-09,52.6903,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs0_human.pars.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,pars,CompleteHit
10717,Q#885 - >seq4208,non-specific,340205,155,217,1.1960700000000002e-12,60.8128,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs0_human.marg.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,marg,CompleteHit
10718,Q#885 - >seq4208,superfamily,340205,155,217,1.1960700000000002e-12,60.8128,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs0_human.marg.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,marg,CompleteHit
10719,Q#885 - >seq4208,non-specific,335182,74,151,2.37926e-10,55.3867,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs0_human.marg.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,marg,CompleteHit
10720,Q#885 - >seq4208,superfamily,335182,74,151,2.37926e-10,55.3867,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs0_human.marg.frame3,1909130340_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs0_human,marg,CompleteHit
10721,Q#886 - >seq4209,non-specific,340205,92,154,4.984829999999999e-22,83.1544,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs10_snmole,pars,CompleteHit
10722,Q#886 - >seq4209,superfamily,340205,92,154,4.984829999999999e-22,83.1544,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs10_snmole,pars,CompleteHit
10723,Q#889 - >seq4212,non-specific,340205,254,317,1.44915e-17,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10724,Q#889 - >seq4212,superfamily,340205,254,317,1.44915e-17,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10725,Q#889 - >seq4212,non-specific,335182,157,251,1.66053e-12,62.7055,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10726,Q#889 - >seq4212,superfamily,335182,157,251,1.66053e-12,62.7055,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10727,Q#889 - >seq4212,non-specific,340204,110,151,0.00017521599999999998,38.5428,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10728,Q#889 - >seq4212,superfamily,340204,110,151,0.00017521599999999998,38.5428,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MD2.ORF1.hs1_chimp.marg.frame1,1909130340_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1MD2,ORF1,hs1_chimp,marg,CompleteHit
10729,Q#893 - >seq4216,non-specific,335182,31,84,1.2875799999999998e-09,52.3051,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs10_snmole,pars,N-TerminusTruncated
10730,Q#893 - >seq4216,superfamily,335182,31,84,1.2875799999999998e-09,52.3051,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs10_snmole.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs10_snmole,pars,N-TerminusTruncated
10731,Q#894 - >seq4217,non-specific,238827,199,279,4.84354e-15,75.0202,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs10_snmole,pars,C-TerminusTruncated
10732,Q#894 - >seq4217,superfamily,295487,199,279,4.84354e-15,75.0202,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs10_snmole,pars,C-TerminusTruncated
10733,Q#894 - >seq4217,non-specific,333820,205,258,0.000645112,41.50899999999999,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs10_snmole,pars,C-TerminusTruncated
10734,Q#894 - >seq4217,superfamily,333820,205,258,0.000645112,41.50899999999999,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs10_snmole.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs10_snmole,pars,C-TerminusTruncated
10735,Q#895 - >seq4218,non-specific,238827,388,470,3.69944e-16,78.487,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs9_pika,marg,C-TerminusTruncated
10736,Q#895 - >seq4218,superfamily,295487,388,470,3.69944e-16,78.487,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs9_pika,marg,C-TerminusTruncated
10737,Q#895 - >seq4218,non-specific,197310,60,184,1.1298e-09,59.6725,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10738,Q#895 - >seq4218,superfamily,351117,60,184,1.1298e-09,59.6725,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10739,Q#895 - >seq4218,non-specific,333820,394,448,5.9349700000000005e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs9_pika,marg,C-TerminusTruncated
10740,Q#895 - >seq4218,superfamily,333820,394,448,5.9349700000000005e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs9_pika,marg,C-TerminusTruncated
10741,Q#896 - >seq4219,non-specific,340205,99,145,3.6408e-17,71.2132,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs8_ctshrew.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10742,Q#896 - >seq4219,superfamily,340205,99,145,3.6408e-17,71.2132,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs8_ctshrew.pars.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10743,Q#898 - >seq4221,non-specific,335182,8,58,0.000813573,36.8971,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10744,Q#898 - >seq4221,superfamily,335182,8,58,0.000813573,36.8971,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
10745,Q#899 - >seq4222,non-specific,340205,100,164,5.686100000000001e-22,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,CompleteHit
10746,Q#899 - >seq4222,superfamily,340205,100,164,5.686100000000001e-22,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,CompleteHit
10747,Q#900 - >seq4223,non-specific,335182,42,82,0.000690576,36.8971,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
10748,Q#900 - >seq4223,superfamily,335182,42,82,0.000690576,36.8971,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
10749,Q#901 - >seq4224,non-specific,335182,8,58,0.00128945,36.1267,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
10750,Q#901 - >seq4224,superfamily,335182,8,58,0.00128945,36.1267,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs8_ctshrew.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
10751,Q#903 - >seq4226,non-specific,238827,332,464,9.67554e-19,85.8058,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10752,Q#903 - >seq4226,superfamily,295487,332,464,9.67554e-19,85.8058,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10753,Q#903 - >seq4226,non-specific,333820,337,463,1.9365299999999998e-14,72.325,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10754,Q#903 - >seq4226,superfamily,333820,337,463,1.9365299999999998e-14,72.325,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10755,Q#903 - >seq4226,non-specific,238828,337,463,1.00368e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
10756,Q#903 - >seq4226,non-specific,275209,338,463,2.4404799999999998e-08,56.6972,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10757,Q#903 - >seq4226,superfamily,275209,338,463,2.4404799999999998e-08,56.6972,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs8_ctshrew.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
10758,Q#904 - >seq4227,non-specific,238827,285,350,2.16547e-19,87.7318,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10759,Q#904 - >seq4227,superfamily,295487,285,350,2.16547e-19,87.7318,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10760,Q#904 - >seq4227,non-specific,333820,291,345,1.6964000000000003e-07,52.2946,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10761,Q#904 - >seq4227,superfamily,333820,291,345,1.6964000000000003e-07,52.2946,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
10762,Q#905 - >seq4228,non-specific,238827,466,531,2.54363e-19,87.7318,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10763,Q#905 - >seq4228,superfamily,295487,466,531,2.54363e-19,87.7318,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10764,Q#905 - >seq4228,non-specific,333820,472,526,1.95704e-07,52.2946,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10765,Q#905 - >seq4228,superfamily,333820,472,526,1.95704e-07,52.2946,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.marg.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD1,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
10766,Q#906 - >seq4229,specific,197310,5,237,4.1418e-37,139.79399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10767,Q#906 - >seq4229,superfamily,351117,5,237,4.1418e-37,139.79399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10768,Q#906 - >seq4229,non-specific,197306,5,237,2.1291700000000002e-19,88.6924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10769,Q#906 - >seq4229,non-specific,238827,569,701,2.0222e-18,85.0354,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10770,Q#906 - >seq4229,superfamily,295487,569,701,2.0222e-18,85.0354,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10771,Q#906 - >seq4229,non-specific,333820,574,700,3.5524400000000006e-14,71.9398,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10772,Q#906 - >seq4229,superfamily,333820,574,700,3.5524400000000006e-14,71.9398,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10773,Q#906 - >seq4229,non-specific,197321,3,237,3.2556900000000002e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10774,Q#906 - >seq4229,non-specific,197320,5,209,4.9229599999999995e-12,67.155,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10775,Q#906 - >seq4229,non-specific,197307,5,237,6.54239e-12,66.9277,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10776,Q#906 - >seq4229,non-specific,223780,5,230,7.59419e-12,66.8531,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10777,Q#906 - >seq4229,non-specific,238828,574,700,3.08851e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10778,Q#906 - >seq4229,non-specific,275209,575,700,3.31717e-08,56.6972,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10779,Q#906 - >seq4229,superfamily,275209,575,700,3.31717e-08,56.6972,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10780,Q#906 - >seq4229,specific,335306,6,230,2.18247e-07,53.0178,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD1,ORF2,hs8_ctshrew,marg,CompleteHit
10781,Q#906 - >seq4229,non-specific,197322,107,237,0.000136098,45.0006,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs8_ctshrew.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
10782,Q#908 - >seq4231,non-specific,340205,146,193,3.96234e-11,56.5756,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs9_pika,pars,C-TerminusTruncated
10783,Q#908 - >seq4231,superfamily,340205,146,193,3.96234e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD1,ORF1,hs9_pika,pars,C-TerminusTruncated
10784,Q#909 - >seq4232,non-specific,335182,64,122,0.000127376,39.5935,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs9_pika.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs9_pika,pars,C-TerminusTruncated
10785,Q#909 - >seq4232,superfamily,335182,64,122,0.000127376,39.5935,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs9_pika.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD1,ORF1,hs9_pika,pars,C-TerminusTruncated
10786,Q#910 - >seq4233,non-specific,335182,113,208,4.4413900000000004e-08,49.9939,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs9_pika,marg,CompleteHit
10787,Q#910 - >seq4233,superfamily,335182,113,208,4.4413900000000004e-08,49.9939,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD1.ORF1.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD1,ORF1,hs9_pika,marg,CompleteHit
10788,Q#912 - >seq4235,non-specific,340205,213,243,7.08385e-06,42.7084,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs9_pika.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs9_pika,marg,BothTerminiTruncated
10789,Q#912 - >seq4235,superfamily,340205,213,243,7.08385e-06,42.7084,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD1.ORF1.hs9_pika.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD1,ORF1,hs9_pika,marg,BothTerminiTruncated
10790,Q#914 - >seq4237,non-specific,238827,426,601,1.7433900000000002e-22,96.9766,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10791,Q#914 - >seq4237,superfamily,295487,426,601,1.7433900000000002e-22,96.9766,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10792,Q#914 - >seq4237,non-specific,333820,418,601,3.93781e-17,80.4142,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10793,Q#914 - >seq4237,superfamily,333820,418,601,3.93781e-17,80.4142,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10794,Q#914 - >seq4237,non-specific,275209,426,629,3.95622e-11,65.5568,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10795,Q#914 - >seq4237,superfamily,275209,426,629,3.95622e-11,65.5568,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10796,Q#914 - >seq4237,non-specific,238828,425,572,4.95936e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,N-TerminusTruncated
10797,Q#914 - >seq4237,non-specific,238185,496,601,0.00520318,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs9_pika.pars.frame2,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD1,ORF2,hs9_pika,pars,CompleteHit
10798,Q#915 - >seq4238,non-specific,238827,367,431,9.15993e-09,56.5306,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs9_pika.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs9_pika,pars,C-TerminusTruncated
10799,Q#915 - >seq4238,superfamily,295487,367,431,9.15993e-09,56.5306,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs9_pika.pars.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs9_pika,pars,C-TerminusTruncated
10800,Q#916 - >seq4239,non-specific,238827,439,627,1.4008900000000002e-21,94.2802,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10801,Q#916 - >seq4239,superfamily,295487,439,627,1.4008900000000002e-21,94.2802,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10802,Q#916 - >seq4239,non-specific,333820,431,594,4.10689e-15,74.6362,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10803,Q#916 - >seq4239,superfamily,333820,431,594,4.10689e-15,74.6362,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10804,Q#916 - >seq4239,non-specific,238828,438,597,5.75386e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,N-TerminusTruncated
10805,Q#916 - >seq4239,non-specific,275209,439,594,4.0003599999999997e-07,53.2304,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,BothTerminiTruncated
10806,Q#916 - >seq4239,superfamily,275209,439,594,4.0003599999999997e-07,53.2304,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD1.ORF2.hs9_pika.marg.frame1,1909130340_L1MD1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs9_pika,marg,BothTerminiTruncated
10807,Q#917 - >seq4240,non-specific,312868,190,353,0.00530316,40.5753,pfam09507,CDC27,NC,cl25760,"DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.",L1MD1.ORF2.hs8_ctshrew.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10808,Q#917 - >seq4240,superfamily,312868,190,353,0.00530316,40.5753,cl25760,CDC27 superfamily,NC, - ,"DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.",L1MD1.ORF2.hs8_ctshrew.marg.frame3,1909130340_L1MD1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
10809,Q#920 - >seq4243,specific,197310,9,236,7.684099999999999e-44,159.054,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10810,Q#920 - >seq4243,superfamily,351117,9,236,7.684099999999999e-44,159.054,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10811,Q#920 - >seq4243,non-specific,197306,9,236,9.11236e-27,110.264,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10812,Q#920 - >seq4243,non-specific,238827,530,770,2.71421e-24,102.369,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10813,Q#920 - >seq4243,superfamily,295487,530,770,2.71421e-24,102.369,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10814,Q#920 - >seq4243,non-specific,223780,9,229,1.06247e-16,81.1055,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10815,Q#920 - >seq4243,specific,335306,12,229,1.84815e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10816,Q#920 - >seq4243,non-specific,197320,13,229,2.9672899999999997e-15,76.7849,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10817,Q#920 - >seq4243,non-specific,197307,9,236,8.253279999999999e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10818,Q#920 - >seq4243,non-specific,197321,7,236,8.339120000000001e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10819,Q#920 - >seq4243,non-specific,273186,9,237,5.20804e-12,67.304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10820,Q#920 - >seq4243,non-specific,197319,8,236,1.3324800000000001e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10821,Q#920 - >seq4243,non-specific,272954,9,208,3.94864e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10822,Q#920 - >seq4243,non-specific,333820,530,737,2.9052799999999998e-08,54.6058,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10823,Q#920 - >seq4243,superfamily,333820,530,737,2.9052799999999998e-08,54.6058,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10824,Q#920 - >seq4243,non-specific,197336,7,229,5.75179e-06,49.1479,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10825,Q#920 - >seq4243,non-specific,339261,108,232,0.00040519300000000004,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MD2,ORF2,hs1_chimp,marg,CompleteHit
10826,Q#920 - >seq4243,non-specific,197322,106,236,0.000562876,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,marg,N-TerminusTruncated
10827,Q#920 - >seq4243,non-specific,238828,582,667,0.00699322,39.1065,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs1_chimp.marg.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,marg,BothTerminiTruncated
10828,Q#922 - >seq4245,specific,197310,9,233,3.07165e-40,148.654,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10829,Q#922 - >seq4245,superfamily,351117,9,233,3.07165e-40,148.654,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10830,Q#922 - >seq4245,non-specific,197306,9,233,2.93527e-25,105.641,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10831,Q#922 - >seq4245,non-specific,238827,528,770,3.7670999999999997e-22,96.2062,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10832,Q#922 - >seq4245,superfamily,295487,528,770,3.7670999999999997e-22,96.2062,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10833,Q#922 - >seq4245,non-specific,223780,9,226,6.1189e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10834,Q#922 - >seq4245,non-specific,197320,13,226,2.60624e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10835,Q#922 - >seq4245,specific,335306,12,226,3.19798e-13,70.3517,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10836,Q#922 - >seq4245,non-specific,197307,9,233,6.471569999999999e-13,70.0093,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10837,Q#922 - >seq4245,non-specific,197321,7,233,1.41052e-11,66.0364,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10838,Q#922 - >seq4245,non-specific,273186,9,234,1.3138000000000002e-10,63.0668,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10839,Q#922 - >seq4245,non-specific,197319,8,233,3.1233699999999997e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10840,Q#922 - >seq4245,non-specific,272954,9,205,7.54032e-09,57.7781,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10841,Q#922 - >seq4245,non-specific,333820,528,770,1.83615e-07,52.2946,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10842,Q#922 - >seq4245,superfamily,333820,528,770,1.83615e-07,52.2946,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10843,Q#922 - >seq4245,non-specific,339261,107,229,0.000264065,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10844,Q#922 - >seq4245,non-specific,197336,7,226,0.00151977,41.4439,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,CompleteHit
10845,Q#922 - >seq4245,non-specific,197322,126,233,0.00289227,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs1_chimp,pars,N-TerminusTruncated
10846,Q#922 - >seq4245,non-specific,197317,117,226,0.0055669,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MD2.ORF2.hs1_chimp.pars.frame3,1909130341_L1MD2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs1_chimp,pars,N-TerminusTruncated
10847,Q#925 - >seq4248,non-specific,197310,70,169,2.26431e-14,73.5397,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10848,Q#925 - >seq4248,superfamily,351117,70,169,2.26431e-14,73.5397,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10849,Q#925 - >seq4248,non-specific,223780,60,162,6.254869999999999e-05,45.6671,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10850,Q#925 - >seq4248,non-specific,197306,52,169,0.000130961,44.3945,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10851,Q#925 - >seq4248,non-specific,197322,60,169,0.00324356,40.3782,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10852,Q#925 - >seq4248,non-specific,238827,548,659,0.00386793,39.5818,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10853,Q#925 - >seq4248,superfamily,295487,548,659,0.00386793,39.5818,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10854,Q#925 - >seq4248,non-specific,197307,60,169,0.00979056,38.8081,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
10855,Q#927 - >seq4250,non-specific,197310,29,128,2.33921e-14,73.1545,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10856,Q#927 - >seq4250,superfamily,351117,29,128,2.33921e-14,73.1545,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10857,Q#927 - >seq4250,non-specific,223780,19,121,7.23935e-05,45.2819,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10858,Q#927 - >seq4250,non-specific,197306,11,128,0.000131475,44.3945,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10859,Q#927 - >seq4250,non-specific,197322,19,128,0.00297244,40.3782,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
10860,Q#933 - >seq4256,non-specific,340205,85,150,2.25294e-15,66.2056,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,pars,CompleteHit
10861,Q#933 - >seq4256,superfamily,340205,85,150,2.25294e-15,66.2056,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,pars,CompleteHit
10862,Q#933 - >seq4256,non-specific,335182,5,82,7.543290000000001e-07,44.6011,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
10863,Q#933 - >seq4256,superfamily,335182,5,82,7.543290000000001e-07,44.6011,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs2_gorilla.pars.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
10864,Q#936 - >seq4259,non-specific,340205,117,182,9.311899999999999e-17,70.828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,marg,CompleteHit
10865,Q#936 - >seq4259,superfamily,340205,117,182,9.311899999999999e-17,70.828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,marg,CompleteHit
10866,Q#936 - >seq4259,non-specific,335182,37,114,3.58006e-07,46.5271,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
10867,Q#936 - >seq4259,superfamily,335182,37,114,3.58006e-07,46.5271,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs2_gorilla.marg.frame3,1909130343_L1MD2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
10868,Q#938 - >seq4261,non-specific,340205,155,219,2.1591e-08,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,marg,CompleteHit
10869,Q#938 - >seq4261,superfamily,340205,155,219,2.1591e-08,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,marg,CompleteHit
10870,Q#938 - >seq4261,non-specific,335182,70,152,1.52131e-05,42.2899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,marg,CompleteHit
10871,Q#938 - >seq4261,superfamily,335182,70,152,1.52131e-05,42.2899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,marg,CompleteHit
10872,Q#941 - >seq4264,non-specific,197310,18,198,6.460739999999999e-17,81.2437,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs4_gibbon.pars.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs4_gibbon,pars,CompleteHit
10873,Q#941 - >seq4264,superfamily,351117,18,198,6.460739999999999e-17,81.2437,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs4_gibbon.pars.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,pars,CompleteHit
10874,Q#941 - >seq4264,non-specific,197306,13,198,1.0263299999999999e-07,54.0245,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs4_gibbon.pars.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,pars,CompleteHit
10875,Q#941 - >seq4264,specific,335306,104,191,0.00142004,41.4618,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs4_gibbon.pars.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10876,Q#942 - >seq4265,non-specific,238827,453,536,1.6421700000000002e-06,49.9822,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs4_gibbon.pars.frame2,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10877,Q#942 - >seq4265,superfamily,295487,453,536,1.6421700000000002e-06,49.9822,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs4_gibbon.pars.frame2,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
10878,Q#943 - >seq4266,non-specific,197310,44,227,5.141359999999999e-22,96.2665,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10879,Q#943 - >seq4266,superfamily,351117,44,227,5.141359999999999e-22,96.2665,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10880,Q#943 - >seq4266,non-specific,197306,3,227,1.5715700000000003e-10,62.4989,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10881,Q#943 - >seq4266,non-specific,223780,103,228,0.000191914,44.5115,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10882,Q#943 - >seq4266,non-specific,197320,55,199,0.00154536,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10883,Q#943 - >seq4266,specific,335306,49,220,0.00337905,40.3062,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs4_gibbon.marg.frame3,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
10884,Q#946 - >seq4269,non-specific,238827,539,629,0.00151794,41.1226,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10885,Q#946 - >seq4269,superfamily,295487,539,629,0.00151794,41.1226,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
10886,Q#947 - >seq4270,non-specific,340205,110,173,1.6898e-06,43.4788,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,pars,CompleteHit
10887,Q#947 - >seq4270,superfamily,340205,110,173,1.6898e-06,43.4788,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,pars,CompleteHit
10888,Q#947 - >seq4270,non-specific,335182,40,107,0.000514815,37.2823,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10889,Q#947 - >seq4270,superfamily,335182,40,107,0.000514815,37.2823,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs4_gibbon.pars.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
10890,Q#948 - >seq4271,non-specific,238827,463,656,9.957530000000001e-09,56.5306,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10891,Q#948 - >seq4271,superfamily,295487,463,656,9.957530000000001e-09,56.5306,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10892,Q#948 - >seq4271,non-specific,333820,486,649,0.0006707639999999999,41.8942,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10893,Q#948 - >seq4271,superfamily,333820,486,649,0.0006707639999999999,41.8942,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs4_gibbon.marg.frame1,1909130344_L1MD2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs4_gibbon,marg,CompleteHit
10894,Q#953 - >seq4276,non-specific,340205,124,188,1.64305e-10,54.6496,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs3_orang,marg,CompleteHit
10895,Q#953 - >seq4276,superfamily,340205,124,188,1.64305e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs3_orang,marg,CompleteHit
10896,Q#953 - >seq4276,non-specific,335182,20,120,0.00018904,39.2083,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs3_orang,marg,CompleteHit
10897,Q#953 - >seq4276,superfamily,335182,20,120,0.00018904,39.2083,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs3_orang,marg,CompleteHit
10898,Q#955 - >seq4278,non-specific,340205,74,134,2.4659999999999997e-08,47.3308,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs3_orang.pars.frame3,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs3_orang,pars,CompleteHit
10899,Q#955 - >seq4278,superfamily,340205,74,134,2.4659999999999997e-08,47.3308,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs3_orang.pars.frame3,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs3_orang,pars,CompleteHit
10900,Q#957 - >seq4280,non-specific,197310,8,235,2.75711e-26,107.822,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MD2,ORF2,hs3_orang,pars,CompleteHit
10901,Q#957 - >seq4280,superfamily,351117,8,235,2.75711e-26,107.822,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,pars,CompleteHit
10902,Q#957 - >seq4280,non-specific,197306,8,235,1.70366e-13,70.9733,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,pars,CompleteHit
10903,Q#957 - >seq4280,specific,335306,9,228,6.561560000000001e-08,53.7882,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,pars,CompleteHit
10904,Q#957 - >seq4280,non-specific,223780,128,228,4.110680000000001e-06,49.1339,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs3_orang,pars,N-TerminusTruncated
10905,Q#957 - >seq4280,non-specific,197307,8,235,6.50452e-05,45.3565,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs3_orang,pars,CompleteHit
10906,Q#957 - >seq4280,non-specific,197320,126,228,0.00078353,41.7318,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs3_orang,pars,N-TerminusTruncated
10907,Q#957 - >seq4280,non-specific,197317,121,228,0.00292669,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,pars,N-TerminusTruncated
10908,Q#957 - >seq4280,non-specific,197322,140,235,0.00325264,40.3782,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs3_orang.pars.frame2,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MD2,ORF2,hs3_orang,pars,N-TerminusTruncated
10909,Q#959 - >seq4282,non-specific,197310,113,347,6.47053e-24,101.274,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD2,ORF2,hs3_orang,marg,CompleteHit
10910,Q#959 - >seq4282,superfamily,351117,113,347,6.47053e-24,101.274,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,marg,CompleteHit
10911,Q#959 - >seq4282,non-specific,197306,113,347,2.58952e-12,67.5065,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,marg,CompleteHit
10912,Q#959 - >seq4282,specific,335306,114,340,7.704910000000001e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,marg,CompleteHit
10913,Q#959 - >seq4282,non-specific,223780,241,340,0.00159147,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD2,ORF2,hs3_orang,marg,N-TerminusTruncated
10914,Q#959 - >seq4282,non-specific,197307,113,347,0.00359494,40.3489,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD2,ORF2,hs3_orang,marg,CompleteHit
10915,Q#959 - >seq4282,non-specific,197317,234,340,0.00478977,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MD2.ORF2.hs3_orang.marg.frame1,1909130344_L1MD2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs3_orang,marg,N-TerminusTruncated
10916,Q#961 - >seq4284,non-specific,238827,535,738,6.09363e-21,92.3542,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10917,Q#961 - >seq4284,superfamily,295487,535,738,6.09363e-21,92.3542,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10918,Q#961 - >seq4284,non-specific,197310,119,216,1.61118e-17,83.1697,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10919,Q#961 - >seq4284,superfamily,351117,119,216,1.61118e-17,83.1697,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10920,Q#961 - >seq4284,non-specific,333820,554,738,1.86201e-13,69.6286,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10921,Q#961 - >seq4284,superfamily,333820,554,738,1.86201e-13,69.6286,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10922,Q#961 - >seq4284,non-specific,197306,3,216,6.00429e-10,60.9581,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,CompleteHit
10923,Q#961 - >seq4284,non-specific,238828,554,722,1.7869300000000002e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10924,Q#961 - >seq4284,specific,335306,7,209,1.14676e-06,50.7066,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,CompleteHit
10925,Q#961 - >seq4284,non-specific,223780,118,209,1.05629e-05,48.3635,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10926,Q#961 - >seq4284,non-specific,197320,118,209,2.08908e-05,47.1246,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10927,Q#961 - >seq4284,non-specific,197322,120,216,7.39875e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10928,Q#961 - >seq4284,non-specific,275209,556,705,0.00012098700000000001,45.5264,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
10929,Q#961 - >seq4284,superfamily,275209,556,705,0.00012098700000000001,45.5264,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
10930,Q#961 - >seq4284,non-specific,197307,120,216,0.00032328799999999997,43.4305,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10931,Q#961 - >seq4284,non-specific,197317,107,209,0.00526193,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10932,Q#961 - >seq4284,non-specific,197321,108,216,0.00768741,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
10933,Q#963 - >seq4286,non-specific,197310,102,214,3.62264e-18,84.7105,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10934,Q#963 - >seq4286,superfamily,351117,102,214,3.62264e-18,84.7105,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10935,Q#963 - >seq4286,non-specific,197306,40,214,9.445e-10,60.1877,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10936,Q#963 - >seq4286,non-specific,197320,103,207,2.5598400000000003e-06,49.821000000000005,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10937,Q#963 - >seq4286,non-specific,223780,107,207,3.99953e-06,49.5191,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10938,Q#963 - >seq4286,non-specific,197307,107,214,4.63366e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10939,Q#963 - >seq4286,non-specific,197322,118,214,7.177569999999999e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10940,Q#963 - >seq4286,specific,335306,41,207,0.000119231,44.5434,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10941,Q#963 - >seq4286,non-specific,197321,98,214,0.00124833,41.7688,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10942,Q#963 - >seq4286,non-specific,273186,106,215,0.00221339,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10943,Q#964 - >seq4287,non-specific,238827,484,674,4.55338e-21,92.7394,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10944,Q#964 - >seq4287,superfamily,295487,484,674,4.55338e-21,92.7394,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10945,Q#964 - >seq4287,non-specific,333820,490,674,5.01519e-14,71.1694,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10946,Q#964 - >seq4287,superfamily,333820,490,674,5.01519e-14,71.1694,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10947,Q#964 - >seq4287,non-specific,238828,486,658,2.35411e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
10948,Q#964 - >seq4287,non-specific,275209,492,641,4.1826199999999996e-05,46.681999999999995,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
10949,Q#964 - >seq4287,superfamily,275209,492,641,4.1826199999999996e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs6_sqmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
10950,Q#965 - >seq4288,non-specific,238827,422,480,1.4632499999999998e-14,73.8646,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
10951,Q#965 - >seq4288,superfamily,295487,422,480,1.4632499999999998e-14,73.8646,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
10952,Q#965 - >seq4288,non-specific,333820,428,480,0.000125801,43.8202,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
10953,Q#965 - >seq4288,superfamily,333820,428,480,0.000125801,43.8202,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
10954,Q#967 - >seq4290,non-specific,340205,117,181,8.50782e-22,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs7_bushaby.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,marg,CompleteHit
10955,Q#967 - >seq4290,superfamily,340205,117,181,8.50782e-22,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs7_bushaby.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,marg,CompleteHit
10956,Q#967 - >seq4290,non-specific,335182,18,114,7.63141e-18,74.2615,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs7_bushaby.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,marg,CompleteHit
10957,Q#967 - >seq4290,superfamily,335182,18,114,7.63141e-18,74.2615,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs7_bushaby.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,marg,CompleteHit
10958,Q#973 - >seq4296,non-specific,238827,438,496,9.07151e-15,74.2498,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs6_sqmonkey.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10959,Q#973 - >seq4296,superfamily,295487,438,496,9.07151e-15,74.2498,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs6_sqmonkey.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10960,Q#973 - >seq4296,non-specific,333820,444,496,8.779770000000001e-05,44.2054,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10961,Q#973 - >seq4296,superfamily,333820,444,496,8.779770000000001e-05,44.2054,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs6_sqmonkey.marg.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
10962,Q#974 - >seq4297,non-specific,335182,31,114,4.61705e-18,75.0319,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,marg,CompleteHit
10963,Q#974 - >seq4297,superfamily,335182,31,114,4.61705e-18,75.0319,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,marg,CompleteHit
10964,Q#974 - >seq4297,non-specific,340205,118,180,5.044670000000001e-13,60.8128,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,marg,CompleteHit
10965,Q#974 - >seq4297,superfamily,340205,118,180,5.044670000000001e-13,60.8128,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs6_sqmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,marg,CompleteHit
10966,Q#975 - >seq4298,non-specific,340205,117,181,7.03541e-22,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs7_bushaby.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,pars,CompleteHit
10967,Q#975 - >seq4298,superfamily,340205,117,181,7.03541e-22,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs7_bushaby.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,pars,CompleteHit
10968,Q#975 - >seq4298,non-specific,335182,18,114,6.70659e-18,74.6467,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs7_bushaby.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,pars,CompleteHit
10969,Q#975 - >seq4298,superfamily,335182,18,114,6.70659e-18,74.6467,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs7_bushaby.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs7_bushaby,pars,CompleteHit
10970,Q#978 - >seq4301,non-specific,340205,86,135,0.00542976,33.4636,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs5_gmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
10971,Q#978 - >seq4301,superfamily,340205,86,135,0.00542976,33.4636,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs5_gmonkey.pars.frame2,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
10972,Q#980 - >seq4303,non-specific,340205,96,154,1.10414e-11,56.5756,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs6_sqmonkey,pars,CompleteHit
10973,Q#980 - >seq4303,superfamily,340205,96,154,1.10414e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs6_sqmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs6_sqmonkey,pars,CompleteHit
10974,Q#981 - >seq4304,non-specific,335182,91,173,0.00040544199999999994,38.4379,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs5_gmonkey,marg,CompleteHit
10975,Q#981 - >seq4304,superfamily,335182,91,173,0.00040544199999999994,38.4379,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs5_gmonkey,marg,CompleteHit
10976,Q#981 - >seq4304,non-specific,340205,189,263,0.00546353,34.6192,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs5_gmonkey,marg,CompleteHit
10977,Q#981 - >seq4304,superfamily,340205,189,263,0.00546353,34.6192,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs5_gmonkey,marg,CompleteHit
10978,Q#985 - >seq4308,non-specific,238827,448,677,4.7788900000000006e-08,54.6046,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs5_gmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10979,Q#985 - >seq4308,superfamily,295487,448,677,4.7788900000000006e-08,54.6046,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs5_gmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10980,Q#985 - >seq4308,non-specific,333820,448,645,0.00224642,40.3534,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs5_gmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10981,Q#985 - >seq4308,superfamily,333820,448,645,0.00224642,40.3534,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs5_gmonkey.pars.frame3,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10982,Q#986 - >seq4309,non-specific,238828,406,513,0.00022710599999999998,43.7289,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
10983,Q#986 - >seq4309,superfamily,295487,406,513,0.00022710599999999998,43.7289,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs5_gmonkey.marg.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
10984,Q#987 - >seq4310,non-specific,238827,533,611,1.69106e-06,49.9822,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs5_gmonkey.marg.frame2,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10985,Q#987 - >seq4310,superfamily,295487,533,611,1.69106e-06,49.9822,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs5_gmonkey.marg.frame2,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
10986,Q#989 - >seq4312,non-specific,335182,18,96,2.53384e-17,71.9503,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,pars,CompleteHit
10987,Q#989 - >seq4312,superfamily,335182,18,96,2.53384e-17,71.9503,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs6_sqmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD2,ORF1,hs6_sqmonkey,pars,CompleteHit
10988,Q#990 - >seq4313,non-specific,197310,10,195,3.1180300000000004e-05,46.5757,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs5_gmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10989,Q#990 - >seq4313,superfamily,351117,10,195,3.1180300000000004e-05,46.5757,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs5_gmonkey.pars.frame1,1909130345_L1MD2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs5_gmonkey,pars,CompleteHit
10990,Q#992 - >seq4315,non-specific,197310,38,97,9.47941e-11,62.7541,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs7_bushaby.marg.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
10991,Q#992 - >seq4315,superfamily,351117,38,97,9.47941e-11,62.7541,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs7_bushaby.marg.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
10992,Q#993 - >seq4316,specific,238827,345,605,5.20442e-45,161.69,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
10993,Q#993 - >seq4316,superfamily,295487,345,605,5.20442e-45,161.69,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
10994,Q#993 - >seq4316,non-specific,333820,351,605,4.8630499999999994e-23,97.3629,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
10995,Q#993 - >seq4316,superfamily,333820,351,605,4.8630499999999994e-23,97.3629,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
10996,Q#993 - >seq4316,non-specific,238828,390,605,8.28553e-14,71.8484,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
10997,Q#993 - >seq4316,non-specific,275209,423,575,6.33287e-09,59.0084,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,BothTerminiTruncated
10998,Q#993 - >seq4316,superfamily,275209,423,575,6.33287e-09,59.0084,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,BothTerminiTruncated
10999,Q#993 - >seq4316,non-specific,239569,491,582,0.000393776,42.9451,cd03487,RT_Bac_retron_II,N,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11000,Q#993 - >seq4316,non-specific,238185,489,605,0.00206803,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs7_bushaby.marg.frame1,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs7_bushaby,marg,CompleteHit
11001,Q#994 - >seq4317,non-specific,238827,357,477,2.19761e-25,105.066,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11002,Q#994 - >seq4317,superfamily,295487,357,477,2.19761e-25,105.066,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11003,Q#994 - >seq4317,non-specific,333820,352,477,2.08189e-11,63.4654,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11004,Q#994 - >seq4317,superfamily,333820,352,477,2.08189e-11,63.4654,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11005,Q#994 - >seq4317,non-specific,238828,352,477,9.59182e-07,50.6624,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11006,Q#994 - >seq4317,non-specific,275209,356,501,0.000967717,42.0596,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11007,Q#994 - >seq4317,superfamily,275209,356,501,0.000967717,42.0596,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11008,Q#994 - >seq4317,non-specific,239569,360,453,0.00390093,39.4783,cd03487,RT_Bac_retron_II,N,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11009,Q#994 - >seq4317,non-specific,238185,358,477,0.00408152,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs7_bushaby.pars.frame2,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs7_bushaby,pars,CompleteHit
11010,Q#996 - >seq4319,non-specific,238827,214,315,7.58654e-18,83.1094,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs7_bushaby.pars.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11011,Q#996 - >seq4319,superfamily,295487,214,315,7.58654e-18,83.1094,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs7_bushaby.pars.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11012,Q#996 - >seq4319,non-specific,333820,220,315,1.4496500000000001e-05,46.5166,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.pars.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11013,Q#996 - >seq4319,superfamily,333820,220,315,1.4496500000000001e-05,46.5166,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs7_bushaby.pars.frame3,1909130346_L1MD2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11014,Q#998 - >seq4321,non-specific,197310,12,206,2.99779e-23,99.7332,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11015,Q#998 - >seq4321,superfamily,351117,12,206,2.99779e-23,99.7332,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11016,Q#998 - >seq4321,non-specific,197306,64,204,4.3180400000000005e-12,67.1213,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11017,Q#998 - >seq4321,non-specific,223780,69,204,2.20354e-09,59.5343,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11018,Q#998 - >seq4321,non-specific,197320,69,205,2.31426e-08,56.3694,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11019,Q#998 - >seq4321,specific,335306,64,204,3.7750500000000004e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11020,Q#998 - >seq4321,non-specific,197307,14,205,0.00067066,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11021,Q#998 - >seq4321,non-specific,272954,88,204,0.00166828,41.2145,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs9_pika.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11022,Q#999 - >seq4322,specific,238827,505,764,4.02852e-49,173.63099999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11023,Q#999 - >seq4322,superfamily,295487,505,764,4.02852e-49,173.63099999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11024,Q#999 - >seq4322,specific,333820,511,764,1.6144299999999998e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11025,Q#999 - >seq4322,superfamily,333820,511,764,1.6144299999999998e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11026,Q#999 - >seq4322,non-specific,238828,578,734,2.8975400000000004e-16,79.1672,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11027,Q#999 - >seq4322,non-specific,275209,583,819,4.00389e-12,69.0236,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11028,Q#999 - >seq4322,superfamily,275209,583,819,4.00389e-12,69.0236,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11029,Q#999 - >seq4322,non-specific,274009,252,432,0.000213057,45.4439,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11030,Q#999 - >seq4322,superfamily,274009,252,432,0.000213057,45.4439,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11031,Q#999 - >seq4322,non-specific,238185,654,764,0.00047937800000000003,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs9_pika,marg,CompleteHit
11032,Q#999 - >seq4322,non-specific,224117,250,443,0.000663941,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11033,Q#999 - >seq4322,superfamily,224117,250,443,0.000663941,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11034,Q#999 - >seq4322,non-specific,234767,222,416,0.000956355,43.288000000000004,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD2,ORF2,hs9_pika,marg,C-TerminusTruncated
11035,Q#999 - >seq4322,superfamily,234767,222,416,0.000956355,43.288000000000004,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD2,ORF2,hs9_pika,marg,C-TerminusTruncated
11036,Q#999 - >seq4322,non-specific,274009,251,394,0.0034428000000000006,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11037,Q#999 - >seq4322,non-specific,274008,259,412,0.00433137,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11038,Q#999 - >seq4322,superfamily,274008,259,412,0.00433137,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11039,Q#999 - >seq4322,non-specific,338612,290,361,0.00488064,40.8023,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11040,Q#999 - >seq4322,superfamily,338612,290,361,0.00488064,40.8023,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD2,ORF2,hs9_pika,marg,BothTerminiTruncated
11041,Q#999 - >seq4322,non-specific,225288,252,404,0.00568833,40.8432,COG2433,COG2433,N,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11042,Q#999 - >seq4322,superfamily,331991,252,404,0.00568833,40.8432,cl27170,DUF460 superfamily,N, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11043,Q#999 - >seq4322,non-specific,274008,251,390,0.00844723,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11044,Q#999 - >seq4322,non-specific,224117,252,425,0.00952839,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs9_pika,marg,C-TerminusTruncated
11045,Q#1000 - >seq4323,non-specific,274009,188,324,9.31041e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11046,Q#1000 - >seq4323,superfamily,274009,188,324,9.31041e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11047,Q#1000 - >seq4323,non-specific,225288,189,317,0.000367704,44.31,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11048,Q#1000 - >seq4323,superfamily,331991,189,317,0.000367704,44.31,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11049,Q#1000 - >seq4323,non-specific,338612,227,333,0.00105125,43.1135,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11050,Q#1000 - >seq4323,superfamily,338612,227,333,0.00105125,43.1135,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11051,Q#1000 - >seq4323,non-specific,274009,189,325,0.0017562,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11052,Q#1000 - >seq4323,non-specific,235175,193,315,0.00244738,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11053,Q#1000 - >seq4323,superfamily,235175,193,315,0.00244738,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11054,Q#1000 - >seq4323,non-specific,224117,187,320,0.00269015,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11055,Q#1000 - >seq4323,superfamily,224117,187,320,0.00269015,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11056,Q#1000 - >seq4323,non-specific,237177,207,327,0.00303359,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11057,Q#1000 - >seq4323,superfamily,237177,207,327,0.00303359,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11058,Q#1000 - >seq4323,non-specific,274008,198,327,0.0035497,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11059,Q#1000 - >seq4323,superfamily,274008,198,327,0.0035497,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11060,Q#1000 - >seq4323,non-specific,224117,189,327,0.004142100000000001,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11061,Q#1000 - >seq4323,non-specific,234767,134,303,0.00542136,40.9768,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11062,Q#1000 - >seq4323,superfamily,234767,134,303,0.00542136,40.9768,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MD2.ORF2.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11063,Q#1001 - >seq4324,non-specific,197310,34,164,5.02455e-15,75.4657,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11064,Q#1001 - >seq4324,superfamily,351117,34,164,5.02455e-15,75.4657,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11065,Q#1001 - >seq4324,non-specific,197320,52,161,5.64907e-08,54.8286,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11066,Q#1001 - >seq4324,non-specific,223780,52,161,1.53706e-07,53.7563,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11067,Q#1001 - >seq4324,non-specific,197306,49,161,8.127889999999999e-07,51.3281,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11068,Q#1001 - >seq4324,specific,335306,73,159,0.000101893,44.9286,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11069,Q#1001 - >seq4324,non-specific,197307,52,161,0.000228282,43.8157,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11070,Q#1001 - >seq4324,non-specific,114219,52,313,0.00107936,42.7865,pfam05483,SCP-1,N,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11071,Q#1001 - >seq4324,superfamily,114219,52,313,0.00107936,42.7865,cl30946,SCP-1 superfamily,N, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11072,Q#1001 - >seq4324,non-specific,272954,52,161,0.00492757,39.6737,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11073,Q#1001 - >seq4324,non-specific,313469,201,322,0.00867332,39.8436,pfam10243,MIP-T3,C,cl25761,"Microtubule-binding protein MIP-T3; This protein, which interacts with both microtubules and TRAF3 (tumor necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11074,Q#1001 - >seq4324,superfamily,313469,201,322,0.00867332,39.8436,cl25761,MIP-T3 superfamily,C, - ,"Microtubule-binding protein MIP-T3; This protein, which interacts with both microtubules and TRAF3 (tumor necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.",L1MD2.ORF2.hs9_pika.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11075,Q#1002 - >seq4325,non-specific,114219,59,301,0.00448066,40.8605,pfam05483,SCP-1,N,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MD2.ORF2.hs9_pika.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11076,Q#1002 - >seq4325,superfamily,114219,59,301,0.00448066,40.8605,cl30946,SCP-1 superfamily,N, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1MD2.ORF2.hs9_pika.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MD2,ORF2,hs9_pika,marg,N-TerminusTruncated
11077,Q#1003 - >seq4326,specific,238827,435,690,5.108649999999999e-48,170.55,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,CompleteHit
11078,Q#1003 - >seq4326,superfamily,295487,435,690,5.108649999999999e-48,170.55,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,CompleteHit
11079,Q#1003 - >seq4326,specific,333820,441,661,3.20418e-29,115.08200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,CompleteHit
11080,Q#1003 - >seq4326,superfamily,333820,441,661,3.20418e-29,115.08200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,CompleteHit
11081,Q#1003 - >seq4326,non-specific,238828,507,664,1.59595e-16,79.9376,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11082,Q#1003 - >seq4326,non-specific,275209,512,665,5.64716e-11,65.1716,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11083,Q#1003 - >seq4326,superfamily,275209,512,665,5.64716e-11,65.1716,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,BothTerminiTruncated
11084,Q#1003 - >seq4326,non-specific,238185,583,650,0.000161278,41.5676,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,C-TerminusTruncated
11085,Q#1003 - >seq4326,non-specific,239569,583,664,0.00208513,40.6339,cd03487,RT_Bac_retron_II,N,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MD2.ORF2.hs9_pika.pars.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs9_pika,pars,N-TerminusTruncated
11086,Q#1006 - >seq4329,non-specific,335182,29,101,1.95076e-07,46.9123,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs9_pika,marg,CompleteHit
11087,Q#1006 - >seq4329,superfamily,335182,29,101,1.95076e-07,46.9123,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs9_pika,marg,CompleteHit
11088,Q#1006 - >seq4329,non-specific,340205,114,181,3.26336e-07,45.4048,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs9_pika,marg,CompleteHit
11089,Q#1006 - >seq4329,superfamily,340205,114,181,3.26336e-07,45.4048,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs9_pika.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs9_pika,marg,CompleteHit
11090,Q#1007 - >seq4330,non-specific,335182,24,80,0.00137207,36.1267,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs9_pika,pars,N-TerminusTruncated
11091,Q#1007 - >seq4330,superfamily,335182,24,80,0.00137207,36.1267,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs9_pika.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs9_pika,pars,N-TerminusTruncated
11092,Q#1010 - >seq4333,non-specific,238827,445,640,2.21365e-14,73.4794,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs8_ctshrew.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11093,Q#1010 - >seq4333,superfamily,295487,445,640,2.21365e-14,73.4794,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs8_ctshrew.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11094,Q#1010 - >seq4333,non-specific,333820,449,608,7.16539e-07,50.3686,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11095,Q#1010 - >seq4333,superfamily,333820,449,608,7.16539e-07,50.3686,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11096,Q#1010 - >seq4333,non-specific,238828,449,611,0.00858756,38.7213,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs8_ctshrew.marg.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11097,Q#1012 - >seq4335,non-specific,238827,393,439,1.91745e-10,61.5382,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs8_ctshrew.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11098,Q#1012 - >seq4335,superfamily,295487,393,439,1.91745e-10,61.5382,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs8_ctshrew.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11099,Q#1012 - >seq4335,non-specific,333820,391,431,0.00185832,40.3534,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11100,Q#1012 - >seq4335,superfamily,333820,391,431,0.00185832,40.3534,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.marg.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11101,Q#1013 - >seq4336,non-specific,340205,111,170,2.2912e-14,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs8_ctshrew,pars,CompleteHit
11102,Q#1013 - >seq4336,superfamily,340205,111,170,2.2912e-14,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs8_ctshrew,pars,CompleteHit
11103,Q#1013 - >seq4336,non-specific,335182,41,89,4.104959999999999e-06,43.0603,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
11104,Q#1013 - >seq4336,superfamily,335182,41,89,4.104959999999999e-06,43.0603,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
11105,Q#1014 - >seq4337,non-specific,340205,164,226,6.419069999999999e-13,61.5832,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs8_ctshrew,marg,CompleteHit
11106,Q#1014 - >seq4337,superfamily,340205,164,226,6.419069999999999e-13,61.5832,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs8_ctshrew,marg,CompleteHit
11107,Q#1014 - >seq4337,non-specific,335182,79,142,7.2164e-08,48.8383,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
11108,Q#1014 - >seq4337,superfamily,335182,79,142,7.2164e-08,48.8383,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
11109,Q#1017 - >seq4340,non-specific,238827,436,624,2.68895e-16,78.8722,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11110,Q#1017 - >seq4340,superfamily,295487,436,624,2.68895e-16,78.8722,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11111,Q#1017 - >seq4340,non-specific,333820,440,592,3.34278e-08,54.2206,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11112,Q#1017 - >seq4340,superfamily,333820,440,592,3.34278e-08,54.2206,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11113,Q#1017 - >seq4340,non-specific,238828,440,595,0.00025252099999999996,43.3437,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11114,Q#1017 - >seq4340,non-specific,172774,557,595,0.0005589,43.4395,PRK14286,PRK14286,N,cl31697,chaperone protein DnaJ; Provisional,L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11115,Q#1017 - >seq4340,superfamily,172774,557,595,0.0005589,43.4395,cl31697,PRK14286 superfamily,N, - ,chaperone protein DnaJ; Provisional,L1MD2.ORF2.hs8_ctshrew.pars.frame2,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MD2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11116,Q#1018 - >seq4341,non-specific,238827,385,431,2.0543000000000003e-10,61.5382,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11117,Q#1018 - >seq4341,superfamily,295487,385,431,2.0543000000000003e-10,61.5382,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11118,Q#1018 - >seq4341,non-specific,333820,383,423,0.0019183,40.3534,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11119,Q#1018 - >seq4341,superfamily,333820,383,423,0.0019183,40.3534,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs8_ctshrew.pars.frame3,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11120,Q#1019 - >seq4342,non-specific,338612,151,250,0.0047494,40.8023,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD2,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
11121,Q#1019 - >seq4342,superfamily,338612,151,250,0.0047494,40.8023,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MD2.ORF2.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD2,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
11122,Q#1019 - >seq4342,non-specific,274009,190,386,0.00599894,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11123,Q#1019 - >seq4342,superfamily,274009,190,386,0.00599894,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD2.ORF2.hs8_ctshrew.marg.frame1,1909130350_L1MD2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11124,Q#1024 - >seq4347,non-specific,275318,45,180,0.000872567,42.9828,TIGR04525,prot_M_MG281,N,cl22766,"IgG-blocking protein M; Members of this family, including MG_281 of Mycoplasma genitalium, bind conserved regions of the IgG light chain sequences, blocking IgG's normal function of antigen-specific binding. It is therefore an important virulence protein. Members of this family are found also in Mycoplasma pneumoniae, M. penetrans, M. gallisepticum, and M. iowae. Model TIGR04524 describes a region within this protein that is shared by many additional Mycoplasma and Ureaplasma proteins. [Cellular processes, Pathogenesis]",L1MD2.ORF2.hs11_armadillo.marg.frame1,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD2,ORF2,hs11_armadillo,marg,N-TerminusTruncated
11125,Q#1024 - >seq4347,superfamily,276720,45,180,0.000872567,42.9828,cl22766,mycoplas_M_dom superfamily,N, - ,"IgG-blocking virulence domain; This model defines a domain restricted to Mycoplasma and Ureaplasma proteins. Members include protein M of Mycoplasma genitalium, MG_281, a virulence protein that binds the IgG light chain to block the binding of antibody to antigen. The crystal structure of the protein M antibody-binding region is solved (PDB|4NZR), and includes this homology domain. Full-length homologs to MG_281 are known in a few other Mycoplasma species, but this model's seed alignment demonstrates distant homology to many additional proteins with a much wider distribution across the Mollicutes. Member proteins include paralogous families in some species, such as MCAP_0345, MCAP_0347, MCAP_0349, and MCAP_0351 in Mycoplasma capricolum. [Cellular processes, Pathogenesis]",L1MD2.ORF2.hs11_armadillo.marg.frame1,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD2,ORF2,hs11_armadillo,marg,N-TerminusTruncated
11126,Q#1030 - >seq4353,non-specific,340205,52,111,1.53153e-14,62.7388,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs11_armadillo.pars.frame2,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD2,ORF1,hs11_armadillo,pars,CompleteHit
11127,Q#1030 - >seq4353,superfamily,340205,52,111,1.53153e-14,62.7388,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs11_armadillo.pars.frame2,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MD2,ORF1,hs11_armadillo,pars,CompleteHit
11128,Q#1032 - >seq4355,non-specific,340205,164,225,1.6882799999999999e-15,68.5168,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs11_armadillo.marg.frame3,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs11_armadillo,marg,CompleteHit
11129,Q#1032 - >seq4355,superfamily,340205,164,225,1.6882799999999999e-15,68.5168,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs11_armadillo.marg.frame3,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs11_armadillo,marg,CompleteHit
11130,Q#1032 - >seq4355,non-specific,335182,92,160,0.000614881,37.6675,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs11_armadillo.marg.frame3,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs11_armadillo,marg,N-TerminusTruncated
11131,Q#1032 - >seq4355,superfamily,335182,92,160,0.000614881,37.6675,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs11_armadillo.marg.frame3,1909130352_L1MD2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs11_armadillo,marg,N-TerminusTruncated
11132,Q#1034 - >seq4357,non-specific,238827,403,634,9.720809999999998e-21,91.969,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs0_human.pars.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs0_human,pars,CompleteHit
11133,Q#1034 - >seq4357,superfamily,295487,403,634,9.720809999999998e-21,91.969,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs0_human.pars.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs0_human,pars,CompleteHit
11134,Q#1034 - >seq4357,non-specific,333820,455,634,3.05077e-09,57.3022,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs0_human.pars.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11135,Q#1034 - >seq4357,superfamily,333820,455,634,3.05077e-09,57.3022,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs0_human.pars.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11136,Q#1034 - >seq4357,non-specific,238828,451,602,6.0957e-05,45.2697,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs0_human.pars.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11137,Q#1036 - >seq4359,non-specific,197310,70,166,4.3676300000000006e-14,72.7693,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11138,Q#1036 - >seq4359,superfamily,351117,70,166,4.3676300000000006e-14,72.7693,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11139,Q#1036 - >seq4359,non-specific,197306,58,166,2.52831e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11140,Q#1036 - >seq4359,non-specific,223780,57,167,0.000315897,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11141,Q#1036 - >seq4359,specific,335306,55,159,0.00050432,42.6174,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11142,Q#1036 - >seq4359,non-specific,197307,65,166,0.000505117,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11143,Q#1036 - >seq4359,non-specific,197321,103,166,0.0094052,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs0_human.pars.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD2,ORF2,hs0_human,pars,N-TerminusTruncated
11144,Q#1037 - >seq4360,non-specific,238827,402,632,1.4832900000000001e-18,85.4206,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD2.ORF2.hs0_human.marg.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs0_human,marg,CompleteHit
11145,Q#1037 - >seq4360,superfamily,295487,402,632,1.4832900000000001e-18,85.4206,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD2.ORF2.hs0_human.marg.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs0_human,marg,CompleteHit
11146,Q#1037 - >seq4360,non-specific,333820,454,598,2.0617400000000004e-08,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs0_human.marg.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11147,Q#1037 - >seq4360,superfamily,333820,454,598,2.0617400000000004e-08,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD2.ORF2.hs0_human.marg.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11148,Q#1037 - >seq4360,non-specific,238828,450,601,0.00010904,44.4993,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD2.ORF2.hs0_human.marg.frame1,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11149,Q#1038 - >seq4361,non-specific,197310,73,168,4.8380800000000005e-14,72.7693,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11150,Q#1038 - >seq4361,superfamily,351117,73,168,4.8380800000000005e-14,72.7693,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11151,Q#1038 - >seq4361,non-specific,223780,60,169,2.32762e-05,47.2079,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11152,Q#1038 - >seq4361,non-specific,197306,57,168,6.04426e-05,45.5501,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11153,Q#1038 - >seq4361,non-specific,197307,68,168,0.00042544400000000003,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11154,Q#1038 - >seq4361,specific,335306,61,161,0.000503566,42.6174,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11155,Q#1038 - >seq4361,non-specific,197321,105,168,0.00844376,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD2.ORF2.hs0_human.marg.frame3,1909130353_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD2,ORF2,hs0_human,marg,N-TerminusTruncated
11156,Q#1040 - >seq4363,non-specific,335182,147,239,1.8986000000000002e-16,73.4911,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs3_orang.marg.frame2,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD3,ORF1,hs3_orang,marg,CompleteHit
11157,Q#1040 - >seq4363,superfamily,335182,147,239,1.8986000000000002e-16,73.4911,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs3_orang.marg.frame2,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD3,ORF1,hs3_orang,marg,CompleteHit
11158,Q#1040 - >seq4363,non-specific,340205,254,307,2.17067e-16,72.3688,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs3_orang.marg.frame2,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD3,ORF1,hs3_orang,marg,CompleteHit
11159,Q#1040 - >seq4363,superfamily,340205,254,307,2.17067e-16,72.3688,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs3_orang.marg.frame2,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MD3,ORF1,hs3_orang,marg,CompleteHit
11160,Q#1041 - >seq4364,non-specific,337766,56,140,1.67848e-05,45.6815,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1MD3,ORF1,hs3_orang,marg,N-TerminusTruncated
11161,Q#1041 - >seq4364,superfamily,337766,56,140,1.67848e-05,45.6815,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1MD3,ORF1,hs3_orang,marg,N-TerminusTruncated
11162,Q#1041 - >seq4364,non-specific,274765,49,132,0.000328015,41.9366,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11163,Q#1041 - >seq4364,superfamily,274765,49,132,0.000328015,41.9366,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11164,Q#1041 - >seq4364,non-specific,273690,55,171,0.00116619,40.0217,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Viral,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11165,Q#1041 - >seq4364,superfamily,355611,55,171,0.00116619,40.0217,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Viral,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11166,Q#1041 - >seq4364,non-specific,274009,48,134,0.00152155,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11167,Q#1041 - >seq4364,superfamily,274009,48,134,0.00152155,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11168,Q#1041 - >seq4364,non-specific,337715,60,154,0.00395015,38.3637,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11169,Q#1041 - >seq4364,superfamily,337715,60,154,0.00395015,38.3637,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11170,Q#1041 - >seq4364,non-specific,235175,55,143,0.00399435,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11171,Q#1041 - >seq4364,superfamily,235175,55,143,0.00399435,38.8916,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11172,Q#1041 - >seq4364,non-specific,335555,44,138,0.00500242,38.0104,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD3,ORF1,hs3_orang,marg,N-TerminusTruncated
11173,Q#1041 - >seq4364,superfamily,354396,44,138,0.00500242,38.0104,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1MD3,ORF1,hs3_orang,marg,N-TerminusTruncated
11174,Q#1041 - >seq4364,non-specific,224117,56,142,0.00522705,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11175,Q#1041 - >seq4364,superfamily,224117,56,142,0.00522705,38.542,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1MD3,ORF1,hs3_orang,marg,BothTerminiTruncated
11176,Q#1041 - >seq4364,non-specific,226400,59,130,0.00665277,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11177,Q#1041 - >seq4364,superfamily,226400,59,130,0.00665277,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11178,Q#1041 - >seq4364,non-specific,235175,36,140,0.00964762,37.3508,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MD3.ORF1.hs3_orang.marg.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MD3,ORF1,hs3_orang,marg,C-TerminusTruncated
11179,Q#1043 - >seq4366,non-specific,340205,142,200,6.94676e-16,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs3_orang.pars.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD3,ORF1,hs3_orang,pars,CompleteHit
11180,Q#1043 - >seq4366,superfamily,340205,142,200,6.94676e-16,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs3_orang.pars.frame1,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MD3,ORF1,hs3_orang,pars,CompleteHit
11181,Q#1046 - >seq4369,non-specific,335182,63,154,4.08477e-18,76.1875,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs3_orang.pars.frame3,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD3,ORF1,hs3_orang,pars,CompleteHit
11182,Q#1046 - >seq4369,superfamily,335182,63,154,4.08477e-18,76.1875,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs3_orang.pars.frame3,1909130354_L1MD3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD3,ORF1,hs3_orang,pars,CompleteHit
11183,Q#1056 - >seq4379,non-specific,235689,28,88,0.00597323,34.6471,PRK06069,sdhA,NC,cl35423,succinate dehydrogenase flavoprotein subunit; Reviewed,L1MD3.ORF1.hs4_gibbon.marg.frame2,1909130354_L1MD3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MD3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
11184,Q#1056 - >seq4379,superfamily,235689,28,88,0.00597323,34.6471,cl35423,sdhA superfamily,NC, - ,succinate dehydrogenase flavoprotein subunit; Reviewed,L1MD3.ORF1.hs4_gibbon.marg.frame2,1909130354_L1MD3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MD3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
11185,Q#1070 - >seq4393,non-specific,197310,1,174,0.00138039,41.5681,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD3.ORF2.hs1_chimp.marg.frame1,1909130354_L1MD3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MD3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11186,Q#1070 - >seq4393,superfamily,351117,1,174,0.00138039,41.5681,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD3.ORF2.hs1_chimp.marg.frame1,1909130354_L1MD3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MD3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11187,Q#1078 - >seq4401,non-specific,335182,1,33,1.4568e-05,39.9787,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs2_gorilla.marg.frame3,1909130354_L1MD3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
11188,Q#1078 - >seq4401,superfamily,335182,1,33,1.4568e-05,39.9787,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs2_gorilla.marg.frame3,1909130354_L1MD3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
11189,Q#1082 - >seq4405,specific,197310,6,233,5.655e-32,125.156,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,CompleteHit
11190,Q#1082 - >seq4405,superfamily,351117,6,233,5.655e-32,125.156,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,CompleteHit
11191,Q#1082 - >seq4405,non-specific,238827,521,711,7.76778e-18,83.4946,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11192,Q#1082 - >seq4405,superfamily,295487,521,711,7.76778e-18,83.4946,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11193,Q#1082 - >seq4405,non-specific,197306,3,233,1.75595e-16,80.218,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,CompleteHit
11194,Q#1082 - >seq4405,specific,335306,6,226,3.67198e-08,55.32899999999999,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,CompleteHit
11195,Q#1082 - >seq4405,non-specific,197320,7,149,1.57892e-07,53.673,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11196,Q#1082 - >seq4405,non-specific,272954,7,156,2.18322e-06,50.4593,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11197,Q#1082 - >seq4405,non-specific,223780,7,149,1.8084200000000002e-05,47.5931,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11198,Q#1082 - >seq4405,non-specific,197307,3,158,5.5906099999999997e-05,46.1269,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11199,Q#1082 - >seq4405,non-specific,333820,564,713,7.83187e-05,44.5906,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11200,Q#1082 - >seq4405,superfamily,333820,564,713,7.83187e-05,44.5906,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11201,Q#1082 - >seq4405,non-specific,238828,590,673,0.00403628,40.2621,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD3.ORF2.hs6_sqmonkey.marg.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
11202,Q#1088 - >seq4411,non-specific,238827,161,317,8.975799999999999e-17,79.6426,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD3.ORF2.hs6_sqmonkey.pars.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
11203,Q#1088 - >seq4411,superfamily,295487,161,317,8.975799999999999e-17,79.6426,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD3.ORF2.hs6_sqmonkey.pars.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
11204,Q#1088 - >seq4411,non-specific,333820,170,319,9.173510000000001e-05,43.8202,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs6_sqmonkey.pars.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
11205,Q#1088 - >seq4411,superfamily,333820,170,319,9.173510000000001e-05,43.8202,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs6_sqmonkey.pars.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
11206,Q#1088 - >seq4411,non-specific,238828,196,279,0.00271714,39.8769,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MD3.ORF2.hs6_sqmonkey.pars.frame3,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
11207,Q#1091 - >seq4414,non-specific,340205,209,257,7.03401e-08,48.1012,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs7_bushaby.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs7_bushaby,marg,CompleteHit
11208,Q#1091 - >seq4414,superfamily,340205,209,257,7.03401e-08,48.1012,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs7_bushaby.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs7_bushaby,marg,CompleteHit
11209,Q#1091 - >seq4414,non-specific,335182,141,207,0.0014239,36.8971,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs7_bushaby.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs7_bushaby,marg,N-TerminusTruncated
11210,Q#1091 - >seq4414,superfamily,335182,141,207,0.0014239,36.8971,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs7_bushaby.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs7_bushaby,marg,N-TerminusTruncated
11211,Q#1101 - >seq4424,non-specific,340205,177,231,2.85333e-17,73.1392,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs6_sqmonkey.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs6_sqmonkey,marg,CompleteHit
11212,Q#1101 - >seq4424,superfamily,340205,177,231,2.85333e-17,73.1392,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs6_sqmonkey.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs6_sqmonkey,marg,CompleteHit
11213,Q#1101 - >seq4424,non-specific,335182,77,174,6.42255e-07,46.1419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs6_sqmonkey.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs6_sqmonkey,marg,CompleteHit
11214,Q#1101 - >seq4424,superfamily,335182,77,174,6.42255e-07,46.1419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs6_sqmonkey.marg.frame1,1909130355_L1MD3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs6_sqmonkey,marg,CompleteHit
11215,Q#1134 - >seq4457,non-specific,238827,282,560,8.82007e-07,50.7526,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD3.ORF2.hs11_armadillo.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD3,ORF2,hs11_armadillo,marg,CompleteHit
11216,Q#1134 - >seq4457,superfamily,295487,282,560,8.82007e-07,50.7526,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD3.ORF2.hs11_armadillo.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MD3,ORF2,hs11_armadillo,marg,CompleteHit
11217,Q#1135 - >seq4458,non-specific,252088,97,157,0.00195289,39.1751,pfam03656,Pam16,C,cl02542,"Pam16; The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM). In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel. Pam18 stimulates the ATPase activity of mtHsp70.",L1MD3.ORF2.hs11_armadillo.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MD3,ORF2,hs11_armadillo,marg,C-TerminusTruncated
11218,Q#1135 - >seq4458,superfamily,351794,97,157,0.00195289,39.1751,cl02542,DnaJ superfamily,C, - ,"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.",L1MD3.ORF2.hs11_armadillo.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Unusual,L1MD3,ORF2,hs11_armadillo,marg,C-TerminusTruncated
11219,Q#1138 - >seq4461,non-specific,238827,296,380,5.73102e-11,63.07899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD3.ORF2.hs10_snmole.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs10_snmole,marg,C-TerminusTruncated
11220,Q#1138 - >seq4461,superfamily,295487,296,380,5.73102e-11,63.07899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD3.ORF2.hs10_snmole.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs10_snmole,marg,C-TerminusTruncated
11221,Q#1138 - >seq4461,non-specific,333820,296,394,2.8175700000000002e-05,45.7462,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs10_snmole.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs10_snmole,marg,C-TerminusTruncated
11222,Q#1138 - >seq4461,superfamily,333820,296,394,2.8175700000000002e-05,45.7462,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD3.ORF2.hs10_snmole.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs10_snmole,marg,C-TerminusTruncated
11223,Q#1140 - >seq4463,non-specific,238827,299,362,2.47537e-10,61.153,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD3.ORF2.hs9_pika.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs9_pika,marg,C-TerminusTruncated
11224,Q#1140 - >seq4463,superfamily,295487,299,362,2.47537e-10,61.153,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD3.ORF2.hs9_pika.marg.frame2,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MD3,ORF2,hs9_pika,marg,C-TerminusTruncated
11225,Q#1145 - >seq4468,non-specific,340205,208,256,1.1865999999999998e-09,53.1088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs8_ctshrew.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs8_ctshrew,marg,CompleteHit
11226,Q#1145 - >seq4468,superfamily,340205,208,256,1.1865999999999998e-09,53.1088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs8_ctshrew.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs8_ctshrew,marg,CompleteHit
11227,Q#1158 - >seq4481,non-specific,340205,187,235,1.4728700000000001e-08,49.641999999999996,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs9_pika.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs9_pika,marg,CompleteHit
11228,Q#1158 - >seq4481,superfamily,340205,187,235,1.4728700000000001e-08,49.641999999999996,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs9_pika.marg.frame1,1909130357_L1MD3.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs9_pika,marg,CompleteHit
11229,Q#1159 - >seq4482,specific,197310,39,262,6.65545e-46,164.447,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11230,Q#1159 - >seq4482,superfamily,351117,39,262,6.65545e-46,164.447,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11231,Q#1159 - >seq4482,non-specific,197306,39,262,7.80726e-23,98.3224,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11232,Q#1159 - >seq4482,non-specific,223780,39,263,2.4994299999999998e-14,73.7867,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11233,Q#1159 - >seq4482,non-specific,197307,39,262,2.85982e-14,73.4761,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11234,Q#1159 - >seq4482,non-specific,197321,37,262,1.27196e-12,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11235,Q#1159 - >seq4482,specific,335306,40,255,1.3634399999999999e-12,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11236,Q#1159 - >seq4482,non-specific,197320,39,255,1.83638e-12,67.9254,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11237,Q#1159 - >seq4482,non-specific,197319,39,262,9.87739e-11,63.0645,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11238,Q#1159 - >seq4482,non-specific,273186,39,263,1.85169e-09,59.2148,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11239,Q#1159 - >seq4482,non-specific,272954,39,262,7.91359e-08,54.3113,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11240,Q#1159 - >seq4482,non-specific,197322,136,255,8.12466e-07,51.549,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,N-TerminusTruncated
11241,Q#1159 - >seq4482,non-specific,197336,39,221,1.14849e-05,47.6071,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,CompleteHit
11242,Q#1159 - >seq4482,non-specific,197317,148,255,0.0047075,39.5076,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,pars,N-TerminusTruncated
11243,Q#1159 - >seq4482,non-specific,197311,37,173,0.00577926,38.8121,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs3_orang,pars,C-TerminusTruncated
11244,Q#1161 - >seq4484,non-specific,335182,58,155,6.169239999999999e-18,75.4171,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs3_orang,marg,CompleteHit
11245,Q#1161 - >seq4484,superfamily,335182,58,155,6.169239999999999e-18,75.4171,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs3_orang,marg,CompleteHit
11246,Q#1161 - >seq4484,non-specific,340205,158,219,1.10399e-14,65.8204,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs3_orang,marg,CompleteHit
11247,Q#1161 - >seq4484,superfamily,340205,158,219,1.10399e-14,65.8204,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs3_orang,marg,CompleteHit
11248,Q#1165 - >seq4488,specific,197310,9,233,2.34109e-29,117.06700000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs2_gorilla,marg,CompleteHit
11249,Q#1165 - >seq4488,superfamily,351117,9,233,2.34109e-29,117.06700000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,CompleteHit
11250,Q#1165 - >seq4488,non-specific,197306,9,233,6.765260000000001e-10,60.5729,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,CompleteHit
11251,Q#1165 - >seq4488,non-specific,197307,9,233,0.00020359599999999998,43.8157,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,CompleteHit
11252,Q#1165 - >seq4488,non-specific,223780,127,218,0.000222563,44.1263,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
11253,Q#1165 - >seq4488,non-specific,197322,137,233,0.000813224,42.6894,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
11254,Q#1165 - >seq4488,specific,335306,10,226,0.0018250999999999999,40.6914,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,CompleteHit
11255,Q#1165 - >seq4488,non-specific,197320,127,218,0.00196156,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,marg,N-TerminusTruncated
11256,Q#1167 - >seq4490,non-specific,238827,485,570,6.0007e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs2_gorilla.marg.frame2,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MDa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
11257,Q#1167 - >seq4490,superfamily,295487,485,570,6.0007e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs2_gorilla.marg.frame2,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1MDa,ORF2,hs2_gorilla,marg,C-TerminusTruncated
11258,Q#1170 - >seq4493,specific,197310,9,233,4.03655e-29,116.29700000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs2_gorilla,pars,CompleteHit
11259,Q#1170 - >seq4493,superfamily,351117,9,233,4.03655e-29,116.29700000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,CompleteHit
11260,Q#1170 - >seq4493,non-specific,197306,9,233,9.158919999999999e-10,59.8025,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,CompleteHit
11261,Q#1170 - >seq4493,non-specific,223780,127,218,0.000191602,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
11262,Q#1170 - >seq4493,non-specific,197307,9,233,0.000219754,43.8157,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,CompleteHit
11263,Q#1170 - >seq4493,non-specific,197322,137,233,0.00068062,42.6894,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
11264,Q#1170 - >seq4493,specific,335306,10,226,0.00153644,40.6914,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,CompleteHit
11265,Q#1170 - >seq4493,non-specific,197320,127,218,0.00164709,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs2_gorilla,pars,N-TerminusTruncated
11266,Q#1171 - >seq4494,non-specific,335182,56,153,7.29618e-18,75.4171,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs3_orang,pars,CompleteHit
11267,Q#1171 - >seq4494,superfamily,335182,56,153,7.29618e-18,75.4171,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs3_orang,pars,CompleteHit
11268,Q#1171 - >seq4494,non-specific,340205,156,221,2.75199e-15,67.7464,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs3_orang,pars,CompleteHit
11269,Q#1171 - >seq4494,superfamily,340205,156,221,2.75199e-15,67.7464,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs3_orang.pars.frame2,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs3_orang,pars,CompleteHit
11270,Q#1173 - >seq4496,non-specific,238827,500,571,7.09489e-11,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs4_gibbon.pars.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MDa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
11271,Q#1173 - >seq4496,superfamily,295487,500,571,7.09489e-11,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs4_gibbon.pars.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MDa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
11272,Q#1174 - >seq4497,specific,197310,44,269,1.3923899999999999e-46,167.143,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11273,Q#1174 - >seq4497,superfamily,351117,44,269,1.3923899999999999e-46,167.143,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11274,Q#1174 - >seq4497,non-specific,197306,44,269,7.984380000000001e-24,101.404,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11275,Q#1174 - >seq4497,non-specific,223780,44,270,6.88868e-16,78.7943,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11276,Q#1174 - >seq4497,non-specific,197307,44,269,2.59282e-14,73.8613,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11277,Q#1174 - >seq4497,specific,335306,45,262,5.8788e-14,72.2777,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11278,Q#1174 - >seq4497,non-specific,197321,42,269,4.84224e-13,70.2736,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11279,Q#1174 - >seq4497,non-specific,197320,44,262,1.8313099999999998e-12,68.3106,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11280,Q#1174 - >seq4497,non-specific,197319,44,269,1.12735e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11281,Q#1174 - >seq4497,non-specific,273186,44,270,2.85223e-10,61.9112,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11282,Q#1174 - >seq4497,non-specific,272954,44,269,7.941040000000001e-09,57.7781,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11283,Q#1174 - >seq4497,non-specific,197322,141,262,1.01884e-06,51.9342,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,N-TerminusTruncated
11284,Q#1174 - >seq4497,non-specific,197336,44,228,1.73699e-05,47.6071,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,CompleteHit
11285,Q#1174 - >seq4497,non-specific,197311,42,180,0.00143577,41.1233,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs3_orang,marg,C-TerminusTruncated
11286,Q#1174 - >seq4497,non-specific,197317,153,262,0.00595986,39.5076,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs3_orang.marg.frame3,1909130358_L1MDa.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs3_orang,marg,N-TerminusTruncated
11287,Q#1176 - >seq4499,non-specific,335182,62,143,1.04935e-11,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs4_gibbon,pars,CompleteHit
11288,Q#1176 - >seq4499,superfamily,335182,62,143,1.04935e-11,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs4_gibbon,pars,CompleteHit
11289,Q#1176 - >seq4499,non-specific,340205,180,226,1.96492e-11,57.7312,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
11290,Q#1176 - >seq4499,superfamily,340205,180,226,1.96492e-11,57.7312,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
11291,Q#1176 - >seq4499,non-specific,340204,17,59,0.00439191,33.9204,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1MDa,ORF1,hs4_gibbon,pars,CompleteHit
11292,Q#1176 - >seq4499,superfamily,340204,17,59,0.00439191,33.9204,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MDa.ORF1.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1MDa,ORF1,hs4_gibbon,pars,CompleteHit
11293,Q#1180 - >seq4503,non-specific,335182,73,154,9.02442e-12,59.6239,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs4_gibbon,marg,CompleteHit
11294,Q#1180 - >seq4503,superfamily,335182,73,154,9.02442e-12,59.6239,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs4_gibbon,marg,CompleteHit
11295,Q#1180 - >seq4503,non-specific,340205,191,237,2.13972e-11,57.7312,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
11296,Q#1180 - >seq4503,superfamily,340205,191,237,2.13972e-11,57.7312,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
11297,Q#1180 - >seq4503,non-specific,340204,28,70,0.00514164,33.9204,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MDa,ORF1,hs4_gibbon,marg,CompleteHit
11298,Q#1180 - >seq4503,superfamily,340204,28,70,0.00514164,33.9204,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1MDa.ORF1.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Trimerization,L1MDa,ORF1,hs4_gibbon,marg,CompleteHit
11299,Q#1181 - >seq4504,non-specific,197310,117,211,9.68163e-15,74.3101,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11300,Q#1181 - >seq4504,superfamily,351117,117,211,9.68163e-15,74.3101,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11301,Q#1181 - >seq4504,non-specific,197306,97,211,7.11774e-08,54.0245,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11302,Q#1181 - >seq4504,specific,335306,117,204,0.000447364,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11303,Q#1181 - >seq4504,non-specific,197320,112,186,0.00258238,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11304,Q#1181 - >seq4504,non-specific,197307,102,211,0.00292677,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11305,Q#1181 - >seq4504,non-specific,223780,101,212,0.00435118,39.5039,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs4_gibbon.pars.frame2,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
11306,Q#1182 - >seq4505,non-specific,197310,3,90,9.175100000000001e-07,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs4_gibbon.pars.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
11307,Q#1182 - >seq4505,superfamily,351117,3,90,9.175100000000001e-07,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.pars.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
11308,Q#1183 - >seq4506,non-specific,238827,496,567,1.55615e-10,61.9234,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs4_gibbon.marg.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
11309,Q#1183 - >seq4506,superfamily,295487,496,567,1.55615e-10,61.9234,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs4_gibbon.marg.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
11310,Q#1183 - >seq4506,non-specific,197310,4,89,1.8785399999999998e-05,47.3461,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs4_gibbon.marg.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MDa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
11311,Q#1183 - >seq4506,superfamily,351117,4,89,1.8785399999999998e-05,47.3461,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.marg.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
11312,Q#1183 - >seq4506,non-specific,197306,4,93,0.00446393,40.1573,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.marg.frame1,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
11313,Q#1185 - >seq4508,non-specific,197310,115,209,5.56158e-15,75.4657,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11314,Q#1185 - >seq4508,superfamily,351117,115,209,5.56158e-15,75.4657,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11315,Q#1185 - >seq4508,non-specific,197306,95,209,3.29879e-07,52.4837,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11316,Q#1185 - >seq4508,specific,335306,115,202,0.000625338,42.2322,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11317,Q#1185 - >seq4508,non-specific,197320,110,184,0.00362025,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11318,Q#1185 - >seq4508,non-specific,197307,100,209,0.00591488,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs4_gibbon.marg.frame3,1909130358_L1MDa.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs4_gibbon,marg,N-TerminusTruncated
11319,Q#1186 - >seq4509,non-specific,238827,483,568,5.58161e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs2_gorilla.pars.frame2,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs2_gorilla,pars,C-TerminusTruncated
11320,Q#1186 - >seq4509,superfamily,295487,483,568,5.58161e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs2_gorilla.pars.frame2,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs2_gorilla,pars,C-TerminusTruncated
11321,Q#1194 - >seq4517,non-specific,340205,166,227,2.40183e-08,49.2568,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs0_human.marg.frame1,1909130358_L1MD3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs0_human,marg,CompleteHit
11322,Q#1194 - >seq4517,superfamily,340205,166,227,2.40183e-08,49.2568,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD3.ORF1.hs0_human.marg.frame1,1909130358_L1MD3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs0_human,marg,CompleteHit
11323,Q#1194 - >seq4517,non-specific,335182,87,134,0.00047988800000000004,38.0527,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs0_human.marg.frame1,1909130358_L1MD3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs0_human,marg,BothTerminiTruncated
11324,Q#1194 - >seq4517,superfamily,335182,87,134,0.00047988800000000004,38.0527,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD3.ORF1.hs0_human.marg.frame1,1909130358_L1MD3.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD3,ORF1,hs0_human,marg,BothTerminiTruncated
11325,Q#1204 - >seq4527,non-specific,340205,160,220,1.64888e-22,86.6212,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs1_chimp.pars.frame2,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs1_chimp,pars,CompleteHit
11326,Q#1204 - >seq4527,superfamily,340205,160,220,1.64888e-22,86.6212,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs1_chimp.pars.frame2,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs1_chimp,pars,CompleteHit
11327,Q#1204 - >seq4527,non-specific,335182,62,157,1.37882e-17,74.6467,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs1_chimp.pars.frame2,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs1_chimp,pars,CompleteHit
11328,Q#1204 - >seq4527,superfamily,335182,62,157,1.37882e-17,74.6467,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs1_chimp.pars.frame2,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs1_chimp,pars,CompleteHit
11329,Q#1207 - >seq4530,non-specific,340205,176,236,7.22589e-20,80.0728,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,pars,CompleteHit
11330,Q#1207 - >seq4530,superfamily,340205,176,236,7.22589e-20,80.0728,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,pars,CompleteHit
11331,Q#1207 - >seq4530,non-specific,335182,77,173,1.3529399999999999e-18,77.7283,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,pars,CompleteHit
11332,Q#1207 - >seq4530,superfamily,335182,77,173,1.3529399999999999e-18,77.7283,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs2_gorilla.pars.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,pars,CompleteHit
11333,Q#1210 - >seq4533,specific,197310,3,229,1.08066e-30,120.919,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs1_chimp,marg,CompleteHit
11334,Q#1210 - >seq4533,superfamily,351117,3,229,1.08066e-30,120.919,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,marg,CompleteHit
11335,Q#1210 - >seq4533,non-specific,197306,3,229,2.40129e-16,79.4476,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,marg,CompleteHit
11336,Q#1210 - >seq4533,specific,335306,4,222,5.7157e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,marg,CompleteHit
11337,Q#1210 - >seq4533,non-specific,223780,126,230,4.35867e-05,46.0523,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,marg,N-TerminusTruncated
11338,Q#1210 - >seq4533,non-specific,197307,3,229,9.00377e-05,44.9713,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,marg,CompleteHit
11339,Q#1210 - >seq4533,non-specific,197322,123,222,0.0006344640000000001,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs1_chimp,marg,N-TerminusTruncated
11340,Q#1210 - >seq4533,non-specific,197317,110,222,0.00576494,39.5076,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,marg,N-TerminusTruncated
11341,Q#1210 - >seq4533,non-specific,197320,126,222,0.00746204,39.4206,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,marg,N-TerminusTruncated
11342,Q#1212 - >seq4535,non-specific,340205,172,232,3.94839e-20,80.458,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,marg,CompleteHit
11343,Q#1212 - >seq4535,superfamily,340205,172,232,3.94839e-20,80.458,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,marg,CompleteHit
11344,Q#1212 - >seq4535,non-specific,335182,73,169,6.90054e-19,78.4987,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,marg,CompleteHit
11345,Q#1212 - >seq4535,superfamily,335182,73,169,6.90054e-19,78.4987,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs2_gorilla.marg.frame3,1909130358_L1MDa.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs2_gorilla,marg,CompleteHit
11346,Q#1213 - >seq4536,specific,197310,3,229,1.88447e-30,119.764,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs1_chimp,pars,CompleteHit
11347,Q#1213 - >seq4536,superfamily,351117,3,229,1.88447e-30,119.764,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,pars,CompleteHit
11348,Q#1213 - >seq4536,non-specific,197306,3,229,9.716700000000001e-17,80.218,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,pars,CompleteHit
11349,Q#1213 - >seq4536,specific,335306,4,222,3.66336e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,pars,CompleteHit
11350,Q#1213 - >seq4536,non-specific,223780,126,230,3.49715e-05,46.0523,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,pars,N-TerminusTruncated
11351,Q#1213 - >seq4536,non-specific,197307,3,229,0.000120301,44.2009,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,pars,CompleteHit
11352,Q#1213 - >seq4536,non-specific,197322,123,222,0.000405804,43.0746,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs1_chimp,pars,N-TerminusTruncated
11353,Q#1213 - >seq4536,non-specific,197317,110,222,0.00373279,39.5076,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs1_chimp,pars,N-TerminusTruncated
11354,Q#1213 - >seq4536,non-specific,197320,126,222,0.00483231,39.4206,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs1_chimp.pars.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs1_chimp,pars,N-TerminusTruncated
11355,Q#1215 - >seq4538,non-specific,340205,154,214,3.3554199999999996e-22,85.4656,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs1_chimp,marg,CompleteHit
11356,Q#1215 - >seq4538,superfamily,340205,154,214,3.3554199999999996e-22,85.4656,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs1_chimp,marg,CompleteHit
11357,Q#1215 - >seq4538,non-specific,335182,56,151,4.20044e-18,75.8023,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs1_chimp,marg,CompleteHit
11358,Q#1215 - >seq4538,superfamily,335182,56,151,4.20044e-18,75.8023,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs1_chimp.marg.frame3,1909130358_L1MDa.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs1_chimp,marg,CompleteHit
11359,Q#1219 - >seq4542,non-specific,335182,14,86,2.06758e-13,62.7055,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs5_gmonkey.marg.frame3,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
11360,Q#1219 - >seq4542,superfamily,335182,14,86,2.06758e-13,62.7055,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs5_gmonkey.marg.frame3,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
11361,Q#1220 - >seq4543,non-specific,340205,103,162,2.06425e-21,82.384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs5_gmonkey.marg.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,marg,CompleteHit
11362,Q#1220 - >seq4543,superfamily,340205,103,162,2.06425e-21,82.384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs5_gmonkey.marg.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,marg,CompleteHit
11363,Q#1224 - >seq4547,non-specific,340205,108,167,4.59408e-21,81.6136,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs5_gmonkey.pars.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,pars,CompleteHit
11364,Q#1224 - >seq4547,superfamily,340205,108,167,4.59408e-21,81.6136,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs5_gmonkey.pars.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,pars,CompleteHit
11365,Q#1224 - >seq4547,non-specific,335182,29,104,9.65872e-13,61.1647,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs5_gmonkey.pars.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
11366,Q#1224 - >seq4547,superfamily,335182,29,104,9.65872e-13,61.1647,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs5_gmonkey.pars.frame2,1909130402_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
11367,Q#1225 - >seq4548,non-specific,340205,171,229,3.4317300000000002e-15,67.7464,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs6_sqmonkey.marg.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,marg,CompleteHit
11368,Q#1225 - >seq4548,superfamily,340205,171,229,3.4317300000000002e-15,67.7464,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs6_sqmonkey.marg.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,marg,CompleteHit
11369,Q#1225 - >seq4548,non-specific,335182,68,155,4.2869900000000003e-14,65.7871,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs6_sqmonkey.marg.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,marg,CompleteHit
11370,Q#1225 - >seq4548,superfamily,335182,68,155,4.2869900000000003e-14,65.7871,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs6_sqmonkey.marg.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,marg,CompleteHit
11371,Q#1228 - >seq4551,non-specific,340205,158,216,2.16613e-15,67.7464,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs6_sqmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs6_sqmonkey,pars,CompleteHit
11372,Q#1228 - >seq4551,superfamily,340205,158,216,2.16613e-15,67.7464,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs6_sqmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs6_sqmonkey,pars,CompleteHit
11373,Q#1230 - >seq4553,non-specific,335182,86,146,8.2599e-12,59.2387,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs6_sqmonkey.pars.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11374,Q#1230 - >seq4553,superfamily,335182,86,146,8.2599e-12,59.2387,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs6_sqmonkey.pars.frame3,1909130403_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11375,Q#1231 - >seq4554,specific,197310,69,290,5.270109999999999e-30,118.60799999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MDa,ORF2,hs5_gmonkey,marg,CompleteHit
11376,Q#1231 - >seq4554,superfamily,351117,69,290,5.270109999999999e-30,118.60799999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs5_gmonkey,marg,CompleteHit
11377,Q#1231 - >seq4554,non-specific,197306,66,290,2.18054e-14,73.2844,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs5_gmonkey,marg,CompleteHit
11378,Q#1231 - >seq4554,non-specific,223780,226,283,0.00178981,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
11379,Q#1231 - >seq4554,non-specific,197320,231,283,0.00381218,39.4206,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
11380,Q#1231 - >seq4554,non-specific,197307,231,290,0.00420938,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.marg.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
11381,Q#1234 - >seq4557,specific,197310,4,224,1.34329e-32,125.542,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs5_gmonkey,pars,CompleteHit
11382,Q#1234 - >seq4557,superfamily,351117,4,224,1.34329e-32,125.542,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs5_gmonkey,pars,CompleteHit
11383,Q#1234 - >seq4557,non-specific,197306,1,224,5.58457e-13,68.6621,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MDa,ORF2,hs5_gmonkey,pars,CompleteHit
11384,Q#1234 - >seq4557,non-specific,197320,157,217,0.000586251,41.7318,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
11385,Q#1234 - >seq4557,non-specific,223780,164,217,0.00118739,41.0447,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
11386,Q#1234 - >seq4557,non-specific,197307,164,224,0.00300391,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MDa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
11387,Q#1234 - >seq4557,non-specific,197322,164,224,0.00605828,38.8375,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
11388,Q#1234 - >seq4557,non-specific,197321,161,224,0.00867002,38.302,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs5_gmonkey.pars.frame2,1909130403_L1MDa.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MDa,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
11389,Q#1238 - >seq4561,non-specific,340205,185,248,3.10597e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs8_ctshrew.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs8_ctshrew,marg,CompleteHit
11390,Q#1238 - >seq4561,superfamily,340205,185,248,3.10597e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs8_ctshrew.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs8_ctshrew,marg,CompleteHit
11391,Q#1238 - >seq4561,non-specific,335182,87,182,2.92843e-22,87.7434,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs8_ctshrew.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs8_ctshrew,marg,CompleteHit
11392,Q#1238 - >seq4561,superfamily,335182,87,182,2.92843e-22,87.7434,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs8_ctshrew.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs8_ctshrew,marg,CompleteHit
11393,Q#1240 - >seq4563,non-specific,335182,20,100,1.8015899999999998e-09,52.3051,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs9_pika,marg,CompleteHit
11394,Q#1240 - >seq4563,superfamily,335182,20,100,1.8015899999999998e-09,52.3051,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs9_pika,marg,CompleteHit
11395,Q#1243 - >seq4566,specific,197310,9,235,2.6299499999999995e-42,149.424,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11396,Q#1243 - >seq4566,superfamily,351117,9,235,2.6299499999999995e-42,149.424,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11397,Q#1243 - >seq4566,non-specific,197306,9,235,4.08886e-21,91.774,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11398,Q#1243 - >seq4566,specific,335306,10,228,1.7341600000000001e-09,57.6402,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11399,Q#1243 - >seq4566,non-specific,223780,9,228,9.93306e-09,55.6823,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11400,Q#1243 - >seq4566,non-specific,197320,61,228,1.4882e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11401,Q#1243 - >seq4566,non-specific,197307,9,235,2.25532e-07,51.5197,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11402,Q#1243 - >seq4566,non-specific,197322,106,235,6.33729e-07,50.7786,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11403,Q#1243 - >seq4566,non-specific,339261,107,231,0.000119019,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MDa,ORF2,hs8_ctshrew,pars,CompleteHit
11404,Q#1243 - >seq4566,non-specific,273186,105,236,0.00122423,40.34,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11405,Q#1243 - >seq4566,non-specific,197321,105,235,0.00214062,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11406,Q#1243 - >seq4566,non-specific,223542,196,359,0.00257172,39.849000000000004,COG0466,Lon,C,cl33893,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MDa,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11407,Q#1243 - >seq4566,superfamily,223542,196,359,0.00257172,39.849000000000004,cl33893,Lon superfamily,C, - ,"ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones].",L1MDa.ORF2.hs8_ctshrew.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MDa,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11408,Q#1244 - >seq4567,non-specific,340205,114,174,1.9058499999999998e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs9_pika.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs9_pika,marg,CompleteHit
11409,Q#1244 - >seq4567,superfamily,340205,114,174,1.9058499999999998e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs9_pika.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs9_pika,marg,CompleteHit
11410,Q#1246 - >seq4569,specific,197310,2,227,2.41935e-40,145.572,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11411,Q#1246 - >seq4569,superfamily,351117,2,227,2.41935e-40,145.572,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11412,Q#1246 - >seq4569,non-specific,197306,2,227,3.53835e-22,95.2408,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11413,Q#1246 - >seq4569,specific,335306,3,220,8.14668e-10,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11414,Q#1246 - >seq4569,non-specific,223780,2,220,3.6912399999999993e-09,57.2231,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11415,Q#1246 - >seq4569,non-specific,197320,53,220,6.93071e-08,53.2878,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11416,Q#1246 - >seq4569,non-specific,197307,2,227,1.0197200000000001e-07,53.0605,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11417,Q#1246 - >seq4569,non-specific,197322,98,227,8.12299e-07,50.7786,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11418,Q#1246 - >seq4569,non-specific,339261,99,223,0.00011591200000000001,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11419,Q#1246 - >seq4569,non-specific,273186,97,228,0.000819473,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11420,Q#1246 - >seq4569,non-specific,197321,1,227,0.00174468,39.8428,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs8_ctshrew,marg,CompleteHit
11421,Q#1246 - >seq4569,non-specific,274009,290,380,0.00727001,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MDa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
11422,Q#1246 - >seq4569,superfamily,274009,290,380,0.00727001,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF2.hs8_ctshrew.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MDa,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
11423,Q#1248 - >seq4571,non-specific,340205,111,171,1.73913e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs9_pika.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs9_pika,pars,CompleteHit
11424,Q#1248 - >seq4571,superfamily,340205,111,171,1.73913e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs9_pika.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs9_pika,pars,CompleteHit
11425,Q#1248 - >seq4571,non-specific,335182,61,108,0.00191945,36.1267,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs9_pika,pars,N-TerminusTruncated
11426,Q#1248 - >seq4571,superfamily,335182,61,108,0.00191945,36.1267,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs9_pika,pars,N-TerminusTruncated
11427,Q#1249 - >seq4572,non-specific,335182,20,73,6.01183e-06,43.0603,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs9_pika,pars,C-TerminusTruncated
11428,Q#1249 - >seq4572,superfamily,335182,20,73,6.01183e-06,43.0603,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs9_pika.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs9_pika,pars,C-TerminusTruncated
11429,Q#1251 - >seq4574,non-specific,340205,184,247,3.31644e-23,89.3176,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs8_ctshrew.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs8_ctshrew,pars,CompleteHit
11430,Q#1251 - >seq4574,superfamily,340205,184,247,3.31644e-23,89.3176,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs8_ctshrew.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs8_ctshrew,pars,CompleteHit
11431,Q#1251 - >seq4574,non-specific,335182,86,181,2.93823e-22,87.7434,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs8_ctshrew.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs8_ctshrew,pars,CompleteHit
11432,Q#1251 - >seq4574,superfamily,335182,86,181,2.93823e-22,87.7434,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs8_ctshrew.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs8_ctshrew,pars,CompleteHit
11433,Q#1256 - >seq4579,specific,197310,3,224,2.31926e-40,148.268,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11434,Q#1256 - >seq4579,superfamily,351117,3,224,2.31926e-40,148.268,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11435,Q#1256 - >seq4579,non-specific,197306,3,224,1.2872400000000001e-21,94.4704,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11436,Q#1256 - >seq4579,non-specific,223780,3,217,3.33891e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11437,Q#1256 - >seq4579,specific,335306,4,217,1.95602e-09,58.4106,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11438,Q#1256 - >seq4579,non-specific,197307,3,224,7.084470000000001e-09,57.2977,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11439,Q#1256 - >seq4579,non-specific,197320,3,217,2.0704599999999997e-08,55.599,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11440,Q#1256 - >seq4579,non-specific,197319,3,224,4.590669999999999e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11441,Q#1256 - >seq4579,non-specific,197321,1,224,6.21065e-07,51.3988,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11442,Q#1256 - >seq4579,non-specific,197322,81,224,5.32349e-06,48.8526,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11443,Q#1256 - >seq4579,non-specific,272954,3,195,0.000664605,41.9849,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11444,Q#1256 - >seq4579,non-specific,339261,97,220,0.000964778,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11445,Q#1256 - >seq4579,non-specific,197311,62,224,0.00396272,39.1973,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11446,Q#1256 - >seq4579,non-specific,338612,251,347,0.00574513,40.0319,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Other,L1MDa,ORF2,hs7_bushaby,marg,BothTerminiTruncated
11447,Q#1256 - >seq4579,superfamily,338612,251,347,0.00574513,40.0319,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MDa.ORF2.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Unusual,L1MDa,ORF2,hs7_bushaby,marg,BothTerminiTruncated
11448,Q#1259 - >seq4582,non-specific,197310,1,213,3.7592000000000004e-22,95.8813,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs6_sqmonkey.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,pars,CompleteHit
11449,Q#1259 - >seq4582,superfamily,351117,1,213,3.7592000000000004e-22,95.8813,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs6_sqmonkey.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,pars,CompleteHit
11450,Q#1259 - >seq4582,non-specific,197306,1,213,3.9858099999999996e-12,66.7361,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs6_sqmonkey.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,pars,CompleteHit
11451,Q#1259 - >seq4582,specific,335306,8,206,3.88269e-06,48.3954,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs6_sqmonkey.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,pars,CompleteHit
11452,Q#1261 - >seq4584,specific,197310,9,229,1.15582e-27,112.06,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11453,Q#1261 - >seq4584,superfamily,351117,9,229,1.15582e-27,112.06,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11454,Q#1261 - >seq4584,non-specific,197306,9,229,3.45649e-17,81.7588,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11455,Q#1261 - >seq4584,specific,335306,10,222,3.6012499999999997e-09,57.6402,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11456,Q#1261 - >seq4584,non-specific,197307,9,229,1.58399e-06,50.3641,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11457,Q#1261 - >seq4584,non-specific,223780,9,43,3.5223e-06,49.1339,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11458,Q#1261 - >seq4584,non-specific,197320,9,222,4.38563e-06,49.0506,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,CompleteHit
11459,Q#1261 - >seq4584,non-specific,273186,9,43,3.8826100000000004e-05,46.118,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11460,Q#1261 - >seq4584,non-specific,197321,7,43,0.000120927,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11461,Q#1261 - >seq4584,non-specific,197336,9,43,0.00137466,41.0587,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11462,Q#1261 - >seq4584,non-specific,272954,9,43,0.00637256,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs6_sqmonkey.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
11463,Q#1267 - >seq4590,non-specific,340205,164,228,3.0218099999999997e-22,86.236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,marg,CompleteHit
11464,Q#1267 - >seq4590,superfamily,340205,164,228,3.0218099999999997e-22,86.236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,marg,CompleteHit
11465,Q#1267 - >seq4590,non-specific,335182,66,161,1.86331e-21,85.04700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,marg,CompleteHit
11466,Q#1267 - >seq4590,superfamily,335182,66,161,1.86331e-21,85.04700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs7_bushaby.marg.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,marg,CompleteHit
11467,Q#1268 - >seq4591,specific,197310,41,224,1.06483e-33,129.00799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,CompleteHit
11468,Q#1268 - >seq4591,superfamily,351117,41,224,1.06483e-33,129.00799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,CompleteHit
11469,Q#1268 - >seq4591,non-specific,197306,30,224,2.0817600000000002e-17,82.14399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,CompleteHit
11470,Q#1268 - >seq4591,non-specific,223780,51,217,2.35873e-09,58.7639,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,CompleteHit
11471,Q#1268 - >seq4591,non-specific,197320,51,217,1.44624e-08,55.9842,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11472,Q#1268 - >seq4591,specific,335306,56,217,1.76849e-07,52.6326,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11473,Q#1268 - >seq4591,non-specific,197319,80,224,1.13169e-06,50.3529,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11474,Q#1268 - >seq4591,non-specific,197322,80,224,2.3189e-06,50.0082,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11475,Q#1268 - >seq4591,non-specific,197307,80,224,8.33178e-06,47.6677,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11476,Q#1268 - >seq4591,non-specific,273186,94,225,3.8256799999999996e-05,45.7328,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11477,Q#1268 - >seq4591,non-specific,197321,51,224,5.5833599999999993e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11478,Q#1268 - >seq4591,non-specific,197311,61,224,0.00123128,40.7381,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11479,Q#1268 - >seq4591,non-specific,339261,96,220,0.00197767,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MDa,ORF2,hs7_bushaby,pars,CompleteHit
11480,Q#1268 - >seq4591,non-specific,272954,51,195,0.00536015,39.2885,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11481,Q#1268 - >seq4591,non-specific,338612,251,347,0.00690293,39.6467,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF2,hs7_bushaby,pars,BothTerminiTruncated
11482,Q#1268 - >seq4591,superfamily,338612,251,347,0.00690293,39.6467,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1MDa.ORF2.hs7_bushaby.pars.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF2,hs7_bushaby,pars,BothTerminiTruncated
11483,Q#1269 - >seq4592,non-specific,238827,481,659,1.6901499999999999e-15,75.7906,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs7_bushaby.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11484,Q#1269 - >seq4592,superfamily,295487,481,659,1.6901499999999999e-15,75.7906,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs7_bushaby.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11485,Q#1269 - >seq4592,non-specific,333820,482,645,4.42127e-09,56.5318,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MDa.ORF2.hs7_bushaby.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11486,Q#1269 - >seq4592,superfamily,333820,482,645,4.42127e-09,56.5318,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MDa.ORF2.hs7_bushaby.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs7_bushaby,pars,C-TerminusTruncated
11487,Q#1269 - >seq4592,non-specific,238828,546,636,4.77341e-06,47.9661,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MDa.ORF2.hs7_bushaby.pars.frame2,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MDa,ORF2,hs7_bushaby,pars,BothTerminiTruncated
11488,Q#1271 - >seq4594,specific,238827,471,728,4.98244e-31,120.859,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs7_bushaby.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11489,Q#1271 - >seq4594,superfamily,295487,471,728,4.98244e-31,120.859,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs7_bushaby.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11490,Q#1271 - >seq4594,non-specific,333820,472,728,1.61296e-15,75.0214,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MDa.ORF2.hs7_bushaby.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11491,Q#1271 - >seq4594,superfamily,333820,472,728,1.61296e-15,75.0214,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MDa.ORF2.hs7_bushaby.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs7_bushaby,marg,CompleteHit
11492,Q#1271 - >seq4594,non-specific,238828,536,694,7.16177e-08,53.744,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MDa.ORF2.hs7_bushaby.marg.frame1,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11493,Q#1272 - >seq4595,non-specific,340205,164,228,3.2073400000000003e-22,85.8508,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs7_bushaby.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,pars,CompleteHit
11494,Q#1272 - >seq4595,superfamily,340205,164,228,3.2073400000000003e-22,85.8508,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs7_bushaby.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,pars,CompleteHit
11495,Q#1272 - >seq4595,non-specific,335182,66,161,1.26543e-21,85.4322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs7_bushaby.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,pars,CompleteHit
11496,Q#1272 - >seq4595,superfamily,335182,66,161,1.26543e-21,85.4322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs7_bushaby.pars.frame3,1909130404_L1MDa.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs7_bushaby,pars,CompleteHit
11497,Q#1273 - >seq4596,non-specific,335182,111,205,4.549639999999999e-19,79.6543,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs10_snmole,marg,CompleteHit
11498,Q#1273 - >seq4596,superfamily,335182,111,205,4.549639999999999e-19,79.6543,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs10_snmole,marg,CompleteHit
11499,Q#1273 - >seq4596,non-specific,340205,208,255,2.34536e-16,71.5984,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11500,Q#1273 - >seq4596,superfamily,340205,208,255,2.34536e-16,71.5984,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11501,Q#1273 - >seq4596,non-specific,235461,16,77,0.00039884,41.207,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_tRNAsynthetase,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11502,Q#1273 - >seq4596,superfamily,235461,16,77,0.00039884,41.207,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_tRNAsynthetase,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11503,Q#1273 - >seq4596,non-specific,235600,3,191,0.00370541,38.37,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_ATPase,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11504,Q#1273 - >seq4596,superfamily,235600,3,191,0.00370541,38.37,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Other_ATPase,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11505,Q#1273 - >seq4596,non-specific,235175,6,132,0.00470772,38.1212,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11506,Q#1273 - >seq4596,superfamily,235175,6,132,0.00470772,38.1212,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MDa,ORF1,hs10_snmole,marg,C-TerminusTruncated
11507,Q#1273 - >seq4596,non-specific,224117,5,157,0.00521044,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MDa,ORF1,hs10_snmole,marg,BothTerminiTruncated
11508,Q#1273 - >seq4596,superfamily,224117,5,157,0.00521044,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.marg.frame2,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MDa,ORF1,hs10_snmole,marg,BothTerminiTruncated
11509,Q#1274 - >seq4597,specific,197310,3,226,1.16015e-29,117.838,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs10_snmole,marg,CompleteHit
11510,Q#1274 - >seq4597,superfamily,351117,3,226,1.16015e-29,117.838,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs10_snmole,marg,CompleteHit
11511,Q#1274 - >seq4597,non-specific,197306,3,226,4.69275e-14,72.5141,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs10_snmole,marg,CompleteHit
11512,Q#1274 - >seq4597,non-specific,197320,96,184,6.34984e-05,45.1986,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,marg,BothTerminiTruncated
11513,Q#1274 - >seq4597,non-specific,223780,3,184,0.000103953,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,marg,C-TerminusTruncated
11514,Q#1274 - >seq4597,non-specific,197307,3,226,0.000439722,42.6601,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,marg,CompleteHit
11515,Q#1274 - >seq4597,non-specific,197322,96,226,0.00419121,39.993,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs10_snmole.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs10_snmole,marg,N-TerminusTruncated
11516,Q#1276 - >seq4599,non-specific,238827,502,561,5.77111e-08,53.8342,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs10_snmole.marg.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs10_snmole,marg,BothTerminiTruncated
11517,Q#1276 - >seq4599,superfamily,295487,502,561,5.77111e-08,53.8342,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs10_snmole.marg.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1MDa,ORF2,hs10_snmole,marg,BothTerminiTruncated
11518,Q#1277 - >seq4600,non-specific,197310,57,199,1.08065e-15,76.6213,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11519,Q#1277 - >seq4600,superfamily,351117,57,199,1.08065e-15,76.6213,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11520,Q#1277 - >seq4600,non-specific,197306,41,199,2.0842400000000004e-08,55.1801,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11521,Q#1277 - >seq4600,non-specific,197320,77,165,4.30439e-05,45.1986,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,pars,BothTerminiTruncated
11522,Q#1277 - >seq4600,non-specific,223780,62,165,8.0625e-05,44.5115,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,pars,BothTerminiTruncated
11523,Q#1277 - >seq4600,non-specific,197311,43,199,0.00218722,39.5825,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11524,Q#1277 - >seq4600,non-specific,197307,62,180,0.00232868,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11525,Q#1277 - >seq4600,specific,335306,38,192,0.00470362,38.7654,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs10_snmole,pars,N-TerminusTruncated
11526,Q#1283 - >seq4606,non-specific,274009,4,70,0.000223855,41.9771,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11527,Q#1283 - >seq4606,superfamily,274009,4,70,0.000223855,41.9771,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11528,Q#1283 - >seq4606,non-specific,224117,7,121,0.000342695,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11529,Q#1283 - >seq4606,superfamily,224117,7,121,0.000342695,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11530,Q#1283 - >seq4606,non-specific,224117,5,83,0.00044824599999999996,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11531,Q#1283 - >seq4606,non-specific,335555,1,66,0.00045620400000000004,40.7068,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11532,Q#1283 - >seq4606,superfamily,354396,1,66,0.00045620400000000004,40.7068,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Flagellar,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11533,Q#1283 - >seq4606,non-specific,188306,3,89,0.000593087,40.2942,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11534,Q#1283 - >seq4606,superfamily,188306,3,89,0.000593087,40.2942,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11535,Q#1283 - >seq4606,non-specific,224117,3,87,0.000618499,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11536,Q#1283 - >seq4606,non-specific,224117,7,85,0.00135718,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11537,Q#1283 - >seq4606,non-specific,179385,4,88,0.00139861,39.6382,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11538,Q#1283 - >seq4606,superfamily,179385,4,88,0.00139861,39.6382,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11539,Q#1283 - >seq4606,non-specific,237177,3,86,0.00183522,38.991,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11540,Q#1283 - >seq4606,superfamily,237177,3,86,0.00183522,38.991,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11541,Q#1283 - >seq4606,non-specific,225288,7,117,0.0019095,38.9172,COG2433,COG2433,N,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11542,Q#1283 - >seq4606,superfamily,331991,7,117,0.0019095,38.9172,cl27170,DUF460 superfamily,N, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11543,Q#1283 - >seq4606,non-specific,336997,7,82,0.00192214,38.7514,pfam08317,Spc7,N,cl38261,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11544,Q#1283 - >seq4606,superfamily,336997,7,82,0.00192214,38.7514,cl38261,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11545,Q#1283 - >seq4606,non-specific,274009,4,121,0.00192982,39.2807,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11546,Q#1283 - >seq4606,non-specific,224117,4,87,0.00199141,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11547,Q#1283 - >seq4606,non-specific,179385,4,86,0.00199898,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11548,Q#1283 - >seq4606,non-specific,274008,4,87,0.00273252,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11549,Q#1283 - >seq4606,superfamily,274008,4,87,0.00273252,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11550,Q#1283 - >seq4606,non-specific,223910,2,76,0.00273612,38.4332,COG0840,Tar,N,cl30773,"Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms]; Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11551,Q#1283 - >seq4606,superfamily,357649,2,76,0.00273612,38.4332,cl30773,MCP_signal superfamily,N, - ,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11552,Q#1283 - >seq4606,non-specific,273690,9,88,0.00297899,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Viral,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11553,Q#1283 - >seq4606,superfamily,355611,9,88,0.00297899,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Viral,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11554,Q#1283 - >seq4606,non-specific,311715,4,127,0.00514694,37.5208,pfam07888,CALCOCO1,NC,cl37761,"Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11555,Q#1283 - >seq4606,superfamily,311715,4,127,0.00514694,37.5208,cl37761,CALCOCO1 superfamily,NC, - ,"Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11556,Q#1283 - >seq4606,non-specific,309330,3,111,0.00550775,36.6791,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11557,Q#1283 - >seq4606,superfamily,309330,3,111,0.00550775,36.6791,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11558,Q#1283 - >seq4606,non-specific,224117,4,86,0.00595108,37.7716,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11559,Q#1283 - >seq4606,non-specific,224117,6,86,0.00595108,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11560,Q#1283 - >seq4606,non-specific,235600,4,97,0.00651197,37.2144,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11561,Q#1283 - >seq4606,superfamily,235600,4,97,0.00651197,37.2144,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1MDa,ORF1,hs10_snmole,pars,C-TerminusTruncated
11562,Q#1283 - >seq4606,non-specific,224117,7,116,0.00679965,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11563,Q#1283 - >seq4606,non-specific,333788,5,80,0.00681013,36.8194,pfam00038,Filament,N,cl25641,Intermediate filament protein; Intermediate filament protein.  ,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11564,Q#1283 - >seq4606,superfamily,333788,5,80,0.00681013,36.8194,cl25641,Filament superfamily,N, - ,Intermediate filament protein; Intermediate filament protein.  ,L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MDa,ORF1,hs10_snmole,pars,N-TerminusTruncated
11565,Q#1283 - >seq4606,non-specific,224117,4,87,0.00692156,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11566,Q#1283 - >seq4606,non-specific,274009,11,86,0.00815663,37.3547,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MDa.ORF1.hs10_snmole.pars.frame1,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MDa,ORF1,hs10_snmole,pars,BothTerminiTruncated
11567,Q#1284 - >seq4607,specific,197310,3,229,8.72669e-43,155.58700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11568,Q#1284 - >seq4607,superfamily,351117,3,229,8.72669e-43,155.58700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11569,Q#1284 - >seq4607,non-specific,197306,3,229,1.1845299999999999e-23,100.634,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11570,Q#1284 - >seq4607,non-specific,223780,3,222,4.972220000000001e-16,78.7943,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11571,Q#1284 - >seq4607,non-specific,197307,3,229,4.09639e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11572,Q#1284 - >seq4607,non-specific,197321,1,229,2.27512e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11573,Q#1284 - >seq4607,non-specific,197320,3,222,2.3908400000000003e-12,67.5402,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11574,Q#1284 - >seq4607,specific,335306,4,222,8.93782e-12,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11575,Q#1284 - >seq4607,non-specific,273186,3,230,4.348780000000001e-10,61.1408,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11576,Q#1284 - >seq4607,non-specific,197319,3,229,1.53291e-07,53.4345,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11577,Q#1284 - >seq4607,non-specific,197322,2,229,2.2872599999999998e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11578,Q#1284 - >seq4607,non-specific,272954,3,200,2.74233e-06,49.3037,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11579,Q#1284 - >seq4607,non-specific,197317,112,222,9.921100000000001e-05,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,marg,N-TerminusTruncated
11580,Q#1284 - >seq4607,non-specific,197311,31,139,0.000998731,41.1233,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,marg,C-TerminusTruncated
11581,Q#1284 - >seq4607,non-specific,339261,101,225,0.00144131,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MDa,ORF2,hs9_pika,marg,CompleteHit
11582,Q#1284 - >seq4607,non-specific,238827,549,619,0.00414141,39.5818,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MDa,ORF2,hs9_pika,marg,C-TerminusTruncated
11583,Q#1284 - >seq4607,superfamily,295487,549,619,0.00414141,39.5818,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MDa.ORF2.hs9_pika.marg.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1MDa,ORF2,hs9_pika,marg,C-TerminusTruncated
11584,Q#1287 - >seq4610,specific,197310,3,227,5.92676e-44,154.43200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11585,Q#1287 - >seq4610,superfamily,351117,3,227,5.92676e-44,154.43200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11586,Q#1287 - >seq4610,non-specific,197306,3,227,3.4079099999999994e-23,97.9372,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11587,Q#1287 - >seq4610,non-specific,223780,3,220,5.89975e-17,80.3351,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11588,Q#1287 - >seq4610,non-specific,197307,3,227,2.9436400000000003e-16,78.0985,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11589,Q#1287 - >seq4610,non-specific,197321,1,227,3.88339e-14,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11590,Q#1287 - >seq4610,non-specific,197320,3,220,8.129470000000001e-13,67.9254,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11591,Q#1287 - >seq4610,non-specific,273186,3,228,4.74516e-11,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11592,Q#1287 - >seq4610,specific,335306,4,220,9.94487e-11,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11593,Q#1287 - >seq4610,non-specific,197319,3,227,2.58966e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11594,Q#1287 - >seq4610,non-specific,197322,99,227,4.49607e-08,54.2454,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,N-TerminusTruncated
11595,Q#1287 - >seq4610,non-specific,272954,3,198,4.2168599999999996e-07,50.8445,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11596,Q#1287 - >seq4610,non-specific,197317,112,220,7.64455e-05,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs9_pika,pars,N-TerminusTruncated
11597,Q#1287 - >seq4610,non-specific,197311,31,137,0.0011317,39.9677,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs9_pika,pars,C-TerminusTruncated
11598,Q#1287 - >seq4610,non-specific,339261,100,223,0.00873038,36.1611,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MDa.ORF2.hs9_pika.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MDa,ORF2,hs9_pika,pars,CompleteHit
11599,Q#1290 - >seq4613,non-specific,340205,182,246,2.1034700000000002e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs10_snmole,pars,CompleteHit
11600,Q#1290 - >seq4613,superfamily,340205,182,246,2.1034700000000002e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs10_snmole,pars,CompleteHit
11601,Q#1290 - >seq4613,non-specific,335182,85,179,6.52906e-19,78.8839,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs10_snmole,pars,CompleteHit
11602,Q#1290 - >seq4613,superfamily,335182,85,179,6.52906e-19,78.8839,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs10_snmole.pars.frame3,1909130405_L1MDa.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MDa,ORF1,hs10_snmole,pars,CompleteHit
11603,Q#1291 - >seq4614,specific,197310,9,235,1.1792499999999998e-38,143.64600000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11604,Q#1291 - >seq4614,superfamily,351117,9,235,1.1792499999999998e-38,143.64600000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11605,Q#1291 - >seq4614,non-specific,197306,9,235,4.167569999999999e-18,84.4552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11606,Q#1291 - >seq4614,non-specific,197307,9,235,8.297499999999999e-11,63.0757,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11607,Q#1291 - >seq4614,non-specific,223780,9,224,1.38284e-09,59.5343,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11608,Q#1291 - >seq4614,specific,335306,10,228,2.08559e-06,49.551,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11609,Q#1291 - >seq4614,non-specific,197320,9,220,2.88282e-06,49.4358,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11610,Q#1291 - >seq4614,non-specific,197322,105,235,5.0433900000000005e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,marg,N-TerminusTruncated
11611,Q#1291 - >seq4614,non-specific,197321,7,235,0.00013093,44.4652,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11612,Q#1291 - >seq4614,non-specific,197319,9,235,0.000429083,43.0341,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,marg,CompleteHit
11613,Q#1296 - >seq4619,specific,197310,3,227,3.0341399999999995e-38,142.49,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11614,Q#1296 - >seq4619,superfamily,351117,3,227,3.0341399999999995e-38,142.49,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11615,Q#1296 - >seq4619,non-specific,197306,3,227,8.694509999999999e-18,83.2996,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11616,Q#1296 - >seq4619,non-specific,197307,3,227,8.96446e-11,62.6905,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11617,Q#1296 - >seq4619,non-specific,223780,3,216,4.49505e-09,57.9935,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11618,Q#1296 - >seq4619,non-specific,197320,3,212,2.10304e-06,49.821000000000005,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11619,Q#1296 - >seq4619,specific,335306,4,220,2.39621e-06,49.1658,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11620,Q#1296 - >seq4619,non-specific,197321,1,227,5.57621e-05,45.2356,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11621,Q#1296 - >seq4619,non-specific,197322,131,227,9.93111e-05,45.0006,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,pars,N-TerminusTruncated
11622,Q#1296 - >seq4619,non-specific,197319,3,227,0.000732581,41.8785,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11623,Q#1296 - >seq4619,non-specific,272954,3,198,0.00622367,38.9033,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MDa.ORF2.hs0_human.pars.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MDa,ORF2,hs0_human,pars,CompleteHit
11624,Q#1298 - >seq4621,non-specific,340205,174,220,1.43416e-10,55.0348,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs0_human.marg.frame1,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs0_human,marg,N-TerminusTruncated
11625,Q#1298 - >seq4621,superfamily,340205,174,220,1.43416e-10,55.0348,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs0_human.marg.frame1,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1MDa,ORF1,hs0_human,marg,N-TerminusTruncated
11626,Q#1300 - >seq4623,non-specific,335182,71,151,6.107339999999999e-16,70.4095,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs0_human.pars.frame2,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs0_human,pars,CompleteHit
11627,Q#1300 - >seq4623,superfamily,335182,71,151,6.107339999999999e-16,70.4095,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs0_human.pars.frame2,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MDa,ORF1,hs0_human,pars,CompleteHit
11628,Q#1301 - >seq4624,non-specific,340205,171,217,3.48177e-11,56.5756,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs0_human.pars.frame1,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MDa,ORF1,hs0_human,pars,N-TerminusTruncated
11629,Q#1301 - >seq4624,superfamily,340205,171,217,3.48177e-11,56.5756,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MDa.ORF1.hs0_human.pars.frame1,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MDa,ORF1,hs0_human,pars,N-TerminusTruncated
11630,Q#1302 - >seq4625,non-specific,335182,68,141,4.9695e-12,60.0091,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs0_human,marg,C-TerminusTruncated
11631,Q#1302 - >seq4625,superfamily,335182,68,141,4.9695e-12,60.0091,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MDa.ORF1.hs0_human.marg.frame3,1909130408_L1MDa.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1MDa,ORF1,hs0_human,marg,C-TerminusTruncated
11632,Q#1306 - >seq4629,non-specific,340205,28,67,5.48841e-05,36.9304,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs5_gmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
11633,Q#1306 - >seq4629,superfamily,340205,28,67,5.48841e-05,36.9304,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs5_gmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
11634,Q#1308 - >seq4631,non-specific,340205,138,177,0.000235825,38.086,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs5_gmonkey.marg.frame2,1909130410_L1ME1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
11635,Q#1308 - >seq4631,superfamily,340205,138,177,0.000235825,38.086,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs5_gmonkey.marg.frame2,1909130410_L1ME1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
11636,Q#1311 - >seq4634,non-specific,340205,110,168,6.71075e-22,83.1544,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs6_sqmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,pars,CompleteHit
11637,Q#1311 - >seq4634,superfamily,340205,110,168,6.71075e-22,83.1544,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs6_sqmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,pars,CompleteHit
11638,Q#1311 - >seq4634,non-specific,335182,36,107,1.9880499999999998e-17,72.7207,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs6_sqmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11639,Q#1311 - >seq4634,superfamily,335182,36,107,1.9880499999999998e-17,72.7207,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs6_sqmonkey.pars.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11640,Q#1314 - >seq4637,non-specific,335182,28,71,0.000633772,37.2823,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs4_gibbon.marg.frame2,1909130410_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
11641,Q#1314 - >seq4637,superfamily,335182,28,71,0.000633772,37.2823,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs4_gibbon.marg.frame2,1909130410_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
11642,Q#1317 - >seq4640,non-specific,340205,252,316,2.5685799999999997e-24,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs6_sqmonkey.marg.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,marg,CompleteHit
11643,Q#1317 - >seq4640,superfamily,340205,252,316,2.5685799999999997e-24,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs6_sqmonkey.marg.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,marg,CompleteHit
11644,Q#1317 - >seq4640,non-specific,335182,178,249,1.3622699999999999e-17,76.5727,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs6_sqmonkey.marg.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
11645,Q#1317 - >seq4640,superfamily,335182,178,249,1.3622699999999999e-17,76.5727,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs6_sqmonkey.marg.frame3,1909130410_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
11646,Q#1319 - >seq4642,non-specific,335182,23,66,0.000428714,37.2823,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs4_gibbon.pars.frame3,1909130410_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
11647,Q#1319 - >seq4642,superfamily,335182,23,66,0.000428714,37.2823,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs4_gibbon.pars.frame3,1909130410_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
11648,Q#1320 - >seq4643,non-specific,340205,174,213,2.07424e-10,54.6496,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs1_chimp.pars.frame1,1909130410_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs1_chimp,pars,N-TerminusTruncated
11649,Q#1320 - >seq4643,superfamily,340205,174,213,2.07424e-10,54.6496,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs1_chimp.pars.frame1,1909130410_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs1_chimp,pars,N-TerminusTruncated
11650,Q#1325 - >seq4648,non-specific,340205,175,214,1.86032e-10,55.0348,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs1_chimp.marg.frame1,1909130410_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs1_chimp,marg,N-TerminusTruncated
11651,Q#1325 - >seq4648,superfamily,340205,175,214,1.86032e-10,55.0348,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs1_chimp.marg.frame1,1909130410_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs1_chimp,marg,N-TerminusTruncated
11652,Q#1330 - >seq4653,non-specific,340205,136,180,2.26875e-07,45.79,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs2_gorilla.marg.frame3,1909130410_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
11653,Q#1330 - >seq4653,superfamily,340205,136,180,2.26875e-07,45.79,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs2_gorilla.marg.frame3,1909130410_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
11654,Q#1332 - >seq4655,non-specific,340205,122,166,3.06399e-07,45.4048,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs2_gorilla.pars.frame1,1909130410_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
11655,Q#1332 - >seq4655,superfamily,340205,122,166,3.06399e-07,45.4048,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs2_gorilla.pars.frame1,1909130410_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
11656,Q#1333 - >seq4656,non-specific,340205,165,228,3.31603e-26,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,pars,CompleteHit
11657,Q#1333 - >seq4656,superfamily,340205,165,228,3.31603e-26,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,pars,CompleteHit
11658,Q#1333 - >seq4656,non-specific,335182,72,159,7.36285e-08,48.8383,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,pars,CompleteHit
11659,Q#1333 - >seq4656,superfamily,335182,72,159,7.36285e-08,48.8383,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,pars,CompleteHit
11660,Q#1337 - >seq4660,specific,238827,516,710,5.178009999999999e-30,118.54799999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11661,Q#1337 - >seq4660,superfamily,295487,516,710,5.178009999999999e-30,118.54799999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11662,Q#1337 - >seq4660,non-specific,333820,509,710,1.8541899999999998e-19,87.3477,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11663,Q#1337 - >seq4660,superfamily,333820,509,710,1.8541899999999998e-19,87.3477,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11664,Q#1337 - >seq4660,non-specific,238828,522,680,1.13716e-13,71.4632,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11665,Q#1337 - >seq4660,non-specific,275209,527,704,1.4263399999999999e-09,60.9344,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11666,Q#1337 - >seq4660,superfamily,275209,527,704,1.4263399999999999e-09,60.9344,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11667,Q#1337 - >seq4660,non-specific,238185,596,710,0.00020704099999999999,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs10_snmole.marg.frame2,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11668,Q#1338 - >seq4661,non-specific,340205,166,229,3.95114e-26,96.2512,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,marg,CompleteHit
11669,Q#1338 - >seq4661,superfamily,340205,166,229,3.95114e-26,96.2512,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,marg,CompleteHit
11670,Q#1338 - >seq4661,non-specific,335182,73,160,7.81513e-08,48.8383,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,marg,CompleteHit
11671,Q#1338 - >seq4661,superfamily,335182,73,160,7.81513e-08,48.8383,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs10_snmole,marg,CompleteHit
11672,Q#1341 - >seq4664,specific,238827,405,664,4.38277e-54,187.88400000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11673,Q#1341 - >seq4664,superfamily,295487,405,664,4.38277e-54,187.88400000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11674,Q#1341 - >seq4664,non-specific,333820,411,664,9.627749999999999e-27,108.149,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11675,Q#1341 - >seq4664,superfamily,333820,411,664,9.627749999999999e-27,108.149,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11676,Q#1341 - >seq4664,non-specific,197310,3,123,5.11255e-22,95.8813,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11677,Q#1341 - >seq4664,superfamily,351117,3,123,5.11255e-22,95.8813,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11678,Q#1341 - >seq4664,non-specific,238828,411,632,1.15025e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11679,Q#1341 - >seq4664,non-specific,197306,1,121,9.71321e-11,63.2693,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11680,Q#1341 - >seq4664,non-specific,275209,480,658,6.7371e-10,62.09,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11681,Q#1341 - >seq4664,superfamily,275209,480,658,6.7371e-10,62.09,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11682,Q#1341 - >seq4664,non-specific,197320,16,118,1.4638799999999999e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11683,Q#1341 - >seq4664,non-specific,223780,1,117,2.27474e-08,56.4527,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11684,Q#1341 - >seq4664,non-specific,197322,1,118,2.6120900000000003e-05,47.3118,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11685,Q#1341 - >seq4664,non-specific,197307,1,118,5.38649e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11686,Q#1341 - >seq4664,non-specific,272954,1,117,8.46901e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11687,Q#1341 - >seq4664,non-specific,273186,16,118,0.00014028899999999998,44.5772,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11688,Q#1341 - >seq4664,non-specific,197321,16,104,0.000370394,43.3096,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11689,Q#1341 - >seq4664,specific,335306,37,120,0.0020594000000000003,40.6914,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11690,Q#1341 - >seq4664,non-specific,238185,548,629,0.00348298,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,pars,CompleteHit
11691,Q#1341 - >seq4664,non-specific,197311,12,114,0.00763719,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs10_snmole.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,pars,N-TerminusTruncated
11692,Q#1343 - >seq4666,specific,197310,9,236,8.95989e-51,179.084,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11693,Q#1343 - >seq4666,superfamily,351117,9,236,8.95989e-51,179.084,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11694,Q#1343 - >seq4666,non-specific,197306,9,236,3.69053e-23,99.478,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11695,Q#1343 - >seq4666,non-specific,223780,9,229,2.98794e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11696,Q#1343 - >seq4666,non-specific,197321,7,236,2.22201e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11697,Q#1343 - >seq4666,non-specific,238827,510,575,2.6383900000000005e-16,78.8722,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,marg,C-TerminusTruncated
11698,Q#1343 - >seq4666,superfamily,295487,510,575,2.6383900000000005e-16,78.8722,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,marg,C-TerminusTruncated
11699,Q#1343 - >seq4666,non-specific,197307,9,236,1.39852e-15,77.7133,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11700,Q#1343 - >seq4666,specific,335306,10,229,3.01009e-15,76.1297,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11701,Q#1343 - >seq4666,non-specific,197320,9,229,4.9717199999999995e-14,73.3181,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11702,Q#1343 - >seq4666,non-specific,273186,9,237,2.24466e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11703,Q#1343 - >seq4666,non-specific,272954,9,207,1.45748e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11704,Q#1343 - >seq4666,non-specific,197319,9,236,1.5631099999999998e-09,59.5977,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11705,Q#1343 - >seq4666,non-specific,197311,7,236,3.11758e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11706,Q#1343 - >seq4666,non-specific,197322,91,229,7.4211e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,N-TerminusTruncated
11707,Q#1343 - >seq4666,non-specific,339261,108,232,2.7765799999999998e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11708,Q#1343 - >seq4666,non-specific,333820,516,583,5.56772e-05,44.9758,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,marg,C-TerminusTruncated
11709,Q#1343 - >seq4666,superfamily,333820,516,583,5.56772e-05,44.9758,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs10_snmole,marg,C-TerminusTruncated
11710,Q#1343 - >seq4666,non-specific,197336,9,194,0.00613318,39.5179,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME1.ORF2.hs10_snmole.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs10_snmole,marg,CompleteHit
11711,Q#1348 - >seq4671,non-specific,340205,143,205,7.04261e-15,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs9_pika.marg.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs9_pika,marg,CompleteHit
11712,Q#1348 - >seq4671,superfamily,340205,143,205,7.04261e-15,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs9_pika.marg.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs9_pika,marg,CompleteHit
11713,Q#1351 - >seq4674,non-specific,335182,57,121,1.5435e-13,63.8611,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs7_bushaby.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
11714,Q#1351 - >seq4674,superfamily,335182,57,121,1.5435e-13,63.8611,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs7_bushaby.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,pars,N-TerminusTruncated
11715,Q#1351 - >seq4674,non-specific,340205,130,193,3.6452199999999995e-09,51.1828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs7_bushaby.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,pars,CompleteHit
11716,Q#1351 - >seq4674,superfamily,340205,130,193,3.6452199999999995e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs7_bushaby.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,pars,CompleteHit
11717,Q#1353 - >seq4676,non-specific,340205,115,178,2.2636700000000003e-09,51.568000000000005,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs7_bushaby.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,marg,CompleteHit
11718,Q#1353 - >seq4676,superfamily,340205,115,178,2.2636700000000003e-09,51.568000000000005,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs7_bushaby.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs7_bushaby,marg,CompleteHit
11719,Q#1354 - >seq4677,non-specific,335182,42,127,0.00037219,38.0527,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs8_ctshrew.pars.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs8_ctshrew,pars,CompleteHit
11720,Q#1354 - >seq4677,superfamily,335182,42,127,0.00037219,38.0527,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs8_ctshrew.pars.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs8_ctshrew,pars,CompleteHit
11721,Q#1355 - >seq4678,non-specific,335182,52,111,3.6564e-14,65.0167,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs7_bushaby.marg.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
11722,Q#1355 - >seq4678,superfamily,335182,52,111,3.6564e-14,65.0167,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs7_bushaby.marg.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME1,ORF1,hs7_bushaby,marg,N-TerminusTruncated
11723,Q#1356 - >seq4679,non-specific,340205,127,190,7.31743e-15,65.8204,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs8_ctshrew.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,pars,CompleteHit
11724,Q#1356 - >seq4679,superfamily,340205,127,190,7.31743e-15,65.8204,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs8_ctshrew.pars.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,pars,CompleteHit
11725,Q#1359 - >seq4682,non-specific,340205,174,234,1.13968e-17,74.2948,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs8_ctshrew.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,marg,CompleteHit
11726,Q#1359 - >seq4682,superfamily,340205,174,234,1.13968e-17,74.2948,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs8_ctshrew.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,marg,CompleteHit
11727,Q#1359 - >seq4682,non-specific,335182,66,152,6.094540000000001e-06,43.4455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs8_ctshrew.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,marg,CompleteHit
11728,Q#1359 - >seq4682,superfamily,335182,66,152,6.094540000000001e-06,43.4455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME1.ORF1.hs8_ctshrew.marg.frame3,1909130415_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs8_ctshrew,marg,CompleteHit
11729,Q#1360 - >seq4683,non-specific,340205,116,178,6.38499e-15,66.2056,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs9_pika.pars.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs9_pika,pars,CompleteHit
11730,Q#1360 - >seq4683,superfamily,340205,116,178,6.38499e-15,66.2056,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs9_pika.pars.frame1,1909130415_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME1,ORF1,hs9_pika,pars,CompleteHit
11731,Q#1367 - >seq4690,non-specific,335182,297,375,4.499939999999999e-29,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,CompleteHit
11732,Q#1367 - >seq4690,superfamily,335182,297,375,4.499939999999999e-29,108.544,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,CompleteHit
11733,Q#1367 - >seq4690,non-specific,340205,239,303,2.4830900000000004e-08,50.0272,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,CompleteHit
11734,Q#1367 - >seq4690,superfamily,340205,239,303,2.4830900000000004e-08,50.0272,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,CompleteHit
11735,Q#1367 - >seq4690,non-specific,340205,378,403,4.35049e-06,43.864,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,C-TerminusTruncated
11736,Q#1367 - >seq4690,superfamily,340205,378,403,4.35049e-06,43.864,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs1_chimp.marg.frame3,1909130417_L1ME2.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs1_chimp,marg,C-TerminusTruncated
11737,Q#1388 - >seq4711,non-specific,340205,1,31,4.95315e-05,36.16,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs11_armadillo.marg.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs11_armadillo,marg,C-TerminusTruncated
11738,Q#1388 - >seq4711,superfamily,340205,1,31,4.95315e-05,36.16,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME1.ORF1.hs11_armadillo.marg.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME1,ORF1,hs11_armadillo,marg,C-TerminusTruncated
11739,Q#1391 - >seq4714,non-specific,238827,40,194,2.66026e-07,51.9082,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs11_armadillo.pars.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs11_armadillo,pars,N-TerminusTruncated
11740,Q#1391 - >seq4714,superfamily,295487,40,194,2.66026e-07,51.9082,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs11_armadillo.pars.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs11_armadillo,pars,N-TerminusTruncated
11741,Q#1394 - >seq4717,non-specific,238827,73,174,1.3299799999999998e-07,53.449,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs11_armadillo.marg.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs11_armadillo,marg,C-TerminusTruncated
11742,Q#1394 - >seq4717,superfamily,295487,73,174,1.3299799999999998e-07,53.449,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs11_armadillo.marg.frame3,1909130417_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs11_armadillo,marg,C-TerminusTruncated
11743,Q#1406 - >seq4729,non-specific,340205,190,215,2.83427e-07,46.1752,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs3_orang.marg.frame1,1909130419_L1ME2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs3_orang,marg,C-TerminusTruncated
11744,Q#1406 - >seq4729,superfamily,340205,190,215,2.83427e-07,46.1752,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs3_orang.marg.frame1,1909130419_L1ME2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs3_orang,marg,C-TerminusTruncated
11745,Q#1441 - >seq4764,non-specific,340205,86,140,1.8629700000000001e-16,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs6_sqmonkey.marg.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,marg,CompleteHit
11746,Q#1441 - >seq4764,superfamily,340205,86,140,1.8629700000000001e-16,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs6_sqmonkey.marg.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,marg,CompleteHit
11747,Q#1441 - >seq4764,non-specific,335182,1,65,9.67939e-14,63.0907,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs6_sqmonkey.marg.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
11748,Q#1441 - >seq4764,superfamily,335182,1,65,9.67939e-14,63.0907,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs6_sqmonkey.marg.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
11749,Q#1444 - >seq4767,non-specific,340205,80,134,1.39088e-16,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs6_sqmonkey.pars.frame2,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2,ORF1,hs6_sqmonkey,pars,CompleteHit
11750,Q#1444 - >seq4767,superfamily,340205,80,134,1.39088e-16,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs6_sqmonkey.pars.frame2,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2,ORF1,hs6_sqmonkey,pars,CompleteHit
11751,Q#1446 - >seq4769,non-specific,335182,1,64,1.6172999999999998e-13,61.9351,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs6_sqmonkey.pars.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11752,Q#1446 - >seq4769,superfamily,335182,1,64,1.6172999999999998e-13,61.9351,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs6_sqmonkey.pars.frame3,1909130423_L1ME2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
11753,Q#1455 - >seq4778,non-specific,238827,505,608,4.55584e-09,57.6862,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs7_bushaby.marg.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
11754,Q#1455 - >seq4778,superfamily,295487,505,608,4.55584e-09,57.6862,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs7_bushaby.marg.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs7_bushaby,marg,C-TerminusTruncated
11755,Q#1455 - >seq4778,non-specific,197310,50,204,6.39096e-05,45.8053,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs7_bushaby.marg.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11756,Q#1455 - >seq4778,superfamily,351117,50,204,6.39096e-05,45.8053,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs7_bushaby.marg.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME2,ORF2,hs7_bushaby,marg,N-TerminusTruncated
11757,Q#1458 - >seq4781,non-specific,197310,44,197,2.9650599999999995e-06,49.6573,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs7_bushaby.pars.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11758,Q#1458 - >seq4781,superfamily,351117,44,197,2.9650599999999995e-06,49.6573,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs7_bushaby.pars.frame2,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME2,ORF2,hs7_bushaby,pars,N-TerminusTruncated
11759,Q#1460 - >seq4783,non-specific,335182,73,178,0.00178889,36.8971,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs7_bushaby.marg.frame1,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs7_bushaby,marg,CompleteHit
11760,Q#1460 - >seq4783,superfamily,335182,73,178,0.00178889,36.8971,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs7_bushaby.marg.frame1,1909130425_L1ME2.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs7_bushaby,marg,CompleteHit
11761,Q#1465 - >seq4788,non-specific,238827,440,550,2.22092e-18,85.0354,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs8_ctshrew.marg.frame2,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11762,Q#1465 - >seq4788,superfamily,295487,440,550,2.22092e-18,85.0354,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs8_ctshrew.marg.frame2,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11763,Q#1465 - >seq4788,non-specific,333820,446,567,5.114369999999999e-06,48.0574,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs8_ctshrew.marg.frame2,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11764,Q#1465 - >seq4788,superfamily,333820,446,567,5.114369999999999e-06,48.0574,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs8_ctshrew.marg.frame2,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11765,Q#1466 - >seq4789,non-specific,197310,12,129,0.0016899999999999999,41.1829,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs8_ctshrew.marg.frame1,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11766,Q#1466 - >seq4789,superfamily,351117,12,129,0.0016899999999999999,41.1829,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs8_ctshrew.marg.frame1,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME2,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
11767,Q#1467 - >seq4790,non-specific,238827,462,686,2.0089000000000002e-19,88.117,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11768,Q#1467 - >seq4790,superfamily,295487,462,686,2.0089000000000002e-19,88.117,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
11769,Q#1467 - >seq4790,non-specific,333820,468,684,3.6862199999999997e-06,48.4426,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs8_ctshrew,pars,CompleteHit
11770,Q#1467 - >seq4790,superfamily,333820,468,684,3.6862199999999997e-06,48.4426,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs8_ctshrew,pars,CompleteHit
11771,Q#1467 - >seq4790,non-specific,197310,110,198,0.000447515,43.1089,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11772,Q#1467 - >seq4790,superfamily,351117,110,198,0.000447515,43.1089,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME2,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
11773,Q#1470 - >seq4793,non-specific,340205,207,254,3.81191e-15,68.1316,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs8_ctshrew.marg.frame1,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
11774,Q#1470 - >seq4793,superfamily,340205,207,254,3.81191e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs8_ctshrew.marg.frame1,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
11775,Q#1472 - >seq4795,non-specific,340205,105,152,1.0833500000000001e-15,66.976,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
11776,Q#1472 - >seq4795,superfamily,340205,105,152,1.0833500000000001e-15,66.976,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs8_ctshrew.pars.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
11777,Q#1475 - >seq4798,non-specific,197310,114,210,1.90505e-08,56.2057,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs8_ctshrew.marg.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11778,Q#1475 - >seq4798,superfamily,351117,114,210,1.90505e-08,56.2057,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs8_ctshrew.marg.frame3,1909130427_L1ME2.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME2,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
11779,Q#1477 - >seq4800,non-specific,238827,535,563,0.00142073,41.1226,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs9_pika.pars.frame3,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs9_pika,pars,BothTerminiTruncated
11780,Q#1477 - >seq4800,superfamily,295487,535,563,0.00142073,41.1226,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs9_pika.pars.frame3,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs9_pika,pars,BothTerminiTruncated
11781,Q#1478 - >seq4801,non-specific,238827,442,696,1.5457799999999998e-17,82.7242,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs9_pika.pars.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs9_pika,pars,CompleteHit
11782,Q#1478 - >seq4801,superfamily,295487,442,696,1.5457799999999998e-17,82.7242,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs9_pika.pars.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs9_pika,pars,CompleteHit
11783,Q#1478 - >seq4801,non-specific,333820,458,641,7.900069999999999e-07,50.3686,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs9_pika.pars.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs9_pika,pars,C-TerminusTruncated
11784,Q#1478 - >seq4801,superfamily,333820,458,641,7.900069999999999e-07,50.3686,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs9_pika.pars.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs9_pika,pars,C-TerminusTruncated
11785,Q#1480 - >seq4803,non-specific,238827,457,560,4.31899e-17,81.1834,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11786,Q#1480 - >seq4803,superfamily,295487,457,560,4.31899e-17,81.1834,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11787,Q#1480 - >seq4803,non-specific,333820,473,560,3.13718e-05,45.7462,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11788,Q#1480 - >seq4803,superfamily,333820,473,560,3.13718e-05,45.7462,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11789,Q#1481 - >seq4804,non-specific,197310,21,185,2.3090800000000002e-07,52.7389,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs9_pika.pars.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME2,ORF2,hs9_pika,pars,CompleteHit
11790,Q#1481 - >seq4804,superfamily,351117,21,185,2.3090800000000002e-07,52.7389,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs9_pika.pars.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME2,ORF2,hs9_pika,pars,CompleteHit
11791,Q#1482 - >seq4805,non-specific,197310,26,150,1.4171200000000002e-07,53.5093,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11792,Q#1482 - >seq4805,superfamily,351117,26,150,1.4171200000000002e-07,53.5093,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME2,ORF2,hs9_pika,marg,C-TerminusTruncated
11793,Q#1482 - >seq4805,non-specific,238827,562,590,0.00156585,41.1226,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs9_pika,marg,BothTerminiTruncated
11794,Q#1482 - >seq4805,superfamily,295487,562,590,0.00156585,41.1226,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,RT,L1ME2,ORF2,hs9_pika,marg,BothTerminiTruncated
11795,Q#1483 - >seq4806,non-specific,335182,57,124,5.172949999999999e-06,43.4455,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME2,ORF1,hs9_pika,marg,N-TerminusTruncated
11796,Q#1483 - >seq4806,superfamily,335182,57,124,5.172949999999999e-06,43.4455,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs9_pika.marg.frame2,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME2,ORF1,hs9_pika,marg,N-TerminusTruncated
11797,Q#1484 - >seq4807,non-specific,340317,134,204,0.00518199,35.0894,pfam17602,DUF5498,N,cl38862,Family of unknown function (DUF5498); This is a family of unknown function found in Myoviridae.,L1ME2.ORF1.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2,ORF1,hs9_pika,marg,N-TerminusTruncated
11798,Q#1484 - >seq4807,superfamily,340317,134,204,0.00518199,35.0894,cl38862,DUF5498 superfamily,N, - ,Family of unknown function (DUF5498); This is a family of unknown function found in Myoviridae.,L1ME2.ORF1.hs9_pika.marg.frame1,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2,ORF1,hs9_pika,marg,N-TerminusTruncated
11799,Q#1485 - >seq4808,non-specific,335182,5,44,4.7262299999999996e-05,37.6675,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs9_pika.pars.frame3,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs9_pika,pars,BothTerminiTruncated
11800,Q#1485 - >seq4808,superfamily,335182,5,44,4.7262299999999996e-05,37.6675,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs9_pika.pars.frame3,1909130428_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2,ORF1,hs9_pika,pars,BothTerminiTruncated
11801,Q#1491 - >seq4814,non-specific,340205,211,269,1.31235e-19,80.0728,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs0_human.marg.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,marg,CompleteHit
11802,Q#1491 - >seq4814,superfamily,340205,211,269,1.31235e-19,80.0728,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs0_human.marg.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,marg,CompleteHit
11803,Q#1491 - >seq4814,non-specific,335182,167,208,3.89851e-05,41.5195,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs0_human.marg.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,marg,N-TerminusTruncated
11804,Q#1491 - >seq4814,superfamily,335182,167,208,3.89851e-05,41.5195,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs0_human.marg.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,marg,N-TerminusTruncated
11805,Q#1494 - >seq4817,non-specific,340205,195,233,6.685220000000001e-09,50.7976,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs0_human.pars.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,pars,N-TerminusTruncated
11806,Q#1494 - >seq4817,superfamily,340205,195,233,6.685220000000001e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs0_human.pars.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,pars,N-TerminusTruncated
11807,Q#1494 - >seq4817,non-specific,335182,147,188,9.18851e-05,39.9787,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs0_human.pars.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,pars,N-TerminusTruncated
11808,Q#1494 - >seq4817,superfamily,335182,147,188,9.18851e-05,39.9787,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs0_human.pars.frame1,1909130431_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs0_human,pars,N-TerminusTruncated
11809,Q#1497 - >seq4820,non-specific,197310,130,276,1.5281199999999997e-09,59.6725,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs10_snmole.marg.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2,ORF2,hs10_snmole,marg,N-TerminusTruncated
11810,Q#1497 - >seq4820,superfamily,351117,130,276,1.5281199999999997e-09,59.6725,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs10_snmole.marg.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME2,ORF2,hs10_snmole,marg,N-TerminusTruncated
11811,Q#1498 - >seq4821,non-specific,340205,88,142,1.08725e-12,58.8868,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs10_snmole.pars.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,pars,CompleteHit
11812,Q#1498 - >seq4821,superfamily,340205,88,142,1.08725e-12,58.8868,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs10_snmole.pars.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,pars,CompleteHit
11813,Q#1498 - >seq4821,non-specific,335182,3,72,6.643559999999999e-07,44.6011,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs10_snmole.pars.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,pars,CompleteHit
11814,Q#1498 - >seq4821,superfamily,335182,3,72,6.643559999999999e-07,44.6011,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs10_snmole.pars.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,pars,CompleteHit
11815,Q#1499 - >seq4822,non-specific,238827,399,471,0.00801004,38.8114,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs10_snmole.pars.frame2,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs10_snmole,pars,C-TerminusTruncated
11816,Q#1499 - >seq4822,superfamily,295487,399,471,0.00801004,38.8114,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs10_snmole.pars.frame2,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs10_snmole,pars,C-TerminusTruncated
11817,Q#1501 - >seq4824,non-specific,340205,146,204,4.05602e-13,61.5832,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs10_snmole.marg.frame3,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs10_snmole,marg,CompleteHit
11818,Q#1501 - >seq4824,superfamily,340205,146,204,4.05602e-13,61.5832,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2.ORF1.hs10_snmole.marg.frame3,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2,ORF1,hs10_snmole,marg,CompleteHit
11819,Q#1503 - >seq4826,non-specific,335182,82,156,1.44128e-14,66.5575,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs10_snmole.marg.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,marg,CompleteHit
11820,Q#1503 - >seq4826,superfamily,335182,82,156,1.44128e-14,66.5575,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2.ORF1.hs10_snmole.marg.frame1,1909130431_L1ME2.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2,ORF1,hs10_snmole,marg,CompleteHit
11821,Q#1507 - >seq4830,non-specific,335182,154,247,1.13886e-14,68.8687,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs1_chimp.marg.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,marg,CompleteHit
11822,Q#1507 - >seq4830,superfamily,335182,154,247,1.13886e-14,68.8687,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs1_chimp.marg.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,marg,CompleteHit
11823,Q#1507 - >seq4830,non-specific,340205,271,320,3.74551e-11,58.1164,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.marg.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,marg,CompleteHit
11824,Q#1507 - >seq4830,superfamily,340205,271,320,3.74551e-11,58.1164,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.marg.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,marg,CompleteHit
11825,Q#1514 - >seq4837,non-specific,335555,70,194,0.00188136,39.9364,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1ME2z.ORF1.hs1_chimp.marg.frame1,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other,L1ME2z,ORF1,hs1_chimp,marg,N-TerminusTruncated
11826,Q#1514 - >seq4837,superfamily,354396,70,194,0.00188136,39.9364,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1ME2z.ORF1.hs1_chimp.marg.frame1,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1ME2z,ORF1,hs1_chimp,marg,N-TerminusTruncated
11827,Q#1516 - >seq4839,non-specific,340205,190,214,0.0007796760000000001,36.5452,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame2,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,N-TerminusTruncated
11828,Q#1516 - >seq4839,superfamily,340205,190,214,0.0007796760000000001,36.5452,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame2,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,N-TerminusTruncated
11829,Q#1518 - >seq4841,non-specific,238827,502,608,5.24025e-22,95.4358,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11830,Q#1518 - >seq4841,superfamily,295487,502,608,5.24025e-22,95.4358,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11831,Q#1518 - >seq4841,non-specific,197310,102,235,1.02122e-18,86.6365,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11832,Q#1518 - >seq4841,superfamily,351117,102,235,1.02122e-18,86.6365,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11833,Q#1518 - >seq4841,non-specific,333820,508,639,1.2193000000000001e-06,49.9834,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11834,Q#1518 - >seq4841,superfamily,333820,508,639,1.2193000000000001e-06,49.9834,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,RT,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11835,Q#1518 - >seq4841,non-specific,197307,105,235,1.84078e-06,50.3641,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11836,Q#1518 - >seq4841,non-specific,197306,103,235,2.0894900000000002e-06,50.1725,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11837,Q#1518 - >seq4841,non-specific,197320,105,228,8.86998e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11838,Q#1518 - >seq4841,non-specific,273186,106,236,7.60934e-05,45.3476,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11839,Q#1518 - >seq4841,non-specific,223780,105,236,0.000275891,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11840,Q#1518 - >seq4841,non-specific,197319,105,235,0.0021296999999999996,41.1081,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME2.ORF2.hs0_human.marg.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11841,Q#1519 - >seq4842,non-specific,197310,22,109,7.66015e-09,57.3613,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs0_human.marg.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11842,Q#1519 - >seq4842,superfamily,351117,22,109,7.66015e-09,57.3613,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.marg.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,marg,C-TerminusTruncated
11843,Q#1520 - >seq4843,non-specific,238827,582,660,2.29456e-11,64.6198,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs0_human.marg.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11844,Q#1520 - >seq4843,superfamily,295487,582,660,2.29456e-11,64.6198,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs0_human.marg.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11845,Q#1520 - >seq4843,non-specific,333820,575,661,2.18811e-05,46.1314,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.marg.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11846,Q#1520 - >seq4843,superfamily,333820,575,661,2.18811e-05,46.1314,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.marg.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2,ORF2,hs0_human,marg,N-TerminusTruncated
11847,Q#1521 - >seq4844,non-specific,197310,2,89,3.72825e-09,58.1317,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11848,Q#1521 - >seq4844,superfamily,351117,2,89,3.72825e-09,58.1317,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11849,Q#1521 - >seq4844,non-specific,238827,569,640,2.1878000000000002e-08,55.7602,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11850,Q#1521 - >seq4844,superfamily,295487,569,640,2.1878000000000002e-08,55.7602,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11851,Q#1521 - >seq4844,non-specific,333820,530,640,0.00660635,38.8126,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11852,Q#1521 - >seq4844,superfamily,333820,530,640,0.00660635,38.8126,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.pars.frame3,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11853,Q#1522 - >seq4845,non-specific,238827,442,549,1.08727e-21,94.6654,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2.ORF2.hs0_human.pars.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11854,Q#1522 - >seq4845,superfamily,295487,442,549,1.08727e-21,94.6654,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2.ORF2.hs0_human.pars.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11855,Q#1522 - >seq4845,non-specific,333820,448,572,7.11049e-06,47.6722,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.pars.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11856,Q#1522 - >seq4845,superfamily,333820,448,572,7.11049e-06,47.6722,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2.ORF2.hs0_human.pars.frame2,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2,ORF2,hs0_human,pars,C-TerminusTruncated
11857,Q#1523 - >seq4846,non-specific,197310,84,220,5.9803e-18,84.3253,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11858,Q#1523 - >seq4846,superfamily,351117,84,220,5.9803e-18,84.3253,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11859,Q#1523 - >seq4846,non-specific,197306,85,220,1.00578e-05,47.8613,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11860,Q#1523 - >seq4846,non-specific,197320,87,213,1.2621600000000001e-05,47.895,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11861,Q#1523 - >seq4846,non-specific,197307,87,220,7.94829e-05,45.3565,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11862,Q#1523 - >seq4846,non-specific,273186,88,221,0.0014111,41.4956,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11863,Q#1523 - >seq4846,non-specific,223780,87,221,0.00191897,41.0447,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11864,Q#1523 - >seq4846,non-specific,197319,87,220,0.00283406,40.7229,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME2.ORF2.hs0_human.pars.frame1,1909130433_L1ME2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME2,ORF2,hs0_human,pars,N-TerminusTruncated
11865,Q#1524 - >seq4847,non-specific,335182,66,158,2.63493e-14,66.1723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,CompleteHit
11866,Q#1524 - >seq4847,superfamily,335182,66,158,2.63493e-14,66.1723,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,CompleteHit
11867,Q#1524 - >seq4847,non-specific,340205,162,203,3.59631e-05,40.3972,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,C-TerminusTruncated
11868,Q#1524 - >seq4847,superfamily,340205,162,203,3.59631e-05,40.3972,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs1_chimp.pars.frame3,1909130433_L1ME2z.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs1_chimp,pars,C-TerminusTruncated
11869,Q#1527 - >seq4850,non-specific,238827,332,581,3.4182499999999995e-07,51.9082,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs2_gorilla,marg,CompleteHit
11870,Q#1527 - >seq4850,superfamily,295487,332,581,3.4182499999999995e-07,51.9082,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs2_gorilla,marg,CompleteHit
11871,Q#1527 - >seq4850,non-specific,333820,332,497,1.67238e-05,46.5166,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs2_gorilla,marg,C-TerminusTruncated
11872,Q#1527 - >seq4850,superfamily,333820,332,497,1.67238e-05,46.5166,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs2_gorilla,marg,C-TerminusTruncated
11873,Q#1527 - >seq4850,non-specific,270921,775,820,0.00156869,41.4385,cd14019,STKc_Cdc7,NC,cl21453,"Catalytic domain of the Serine/Threonine Kinase, Cell Division Cycle 7 kinase; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Cdc7 kinase (or Hsk1 in fission yeast) is a critical regulator in the initiation of DNA replication. It forms a complex with a Dbf4-related regulatory subunit, a cyclin-like molecule that activates the kinase in late G1 phase, and is also referred to as Dbf4-dependent kinase (DDK). Its main targets are mini-chromosome maintenance (MCM) proteins. Cdc7 kinase may also have additional roles in meiosis, checkpoint responses, the maintenance and repair of chromosome structures, and cancer progression. The Cdc7 kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2z,ORF2,hs2_gorilla,marg,BothTerminiTruncated
11874,Q#1527 - >seq4850,superfamily,354810,775,820,0.00156869,41.4385,cl21453,PKc_like superfamily,NC, - ,"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins.",L1ME2z.ORF2.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2z,ORF2,hs2_gorilla,marg,BothTerminiTruncated
11875,Q#1528 - >seq4851,non-specific,238827,171,231,0.00219275,39.967,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs2_gorilla.pars.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs2_gorilla,pars,C-TerminusTruncated
11876,Q#1528 - >seq4851,superfamily,295487,171,231,0.00219275,39.967,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs2_gorilla.pars.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs2_gorilla,pars,C-TerminusTruncated
11877,Q#1529 - >seq4852,non-specific,333820,242,311,0.00766837,38.0422,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs2_gorilla.pars.frame2,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2z,ORF2,hs2_gorilla,pars,BothTerminiTruncated
11878,Q#1529 - >seq4852,superfamily,333820,242,311,0.00766837,38.0422,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs2_gorilla.pars.frame2,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME2z,ORF2,hs2_gorilla,pars,BothTerminiTruncated
11879,Q#1531 - >seq4854,non-specific,335182,93,171,2.16945e-15,69.2539,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs2_gorilla.pars.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs2_gorilla,pars,CompleteHit
11880,Q#1531 - >seq4854,superfamily,335182,93,171,2.16945e-15,69.2539,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs2_gorilla.pars.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME2z,ORF1,hs2_gorilla,pars,CompleteHit
11881,Q#1533 - >seq4856,non-specific,340204,112,155,0.00874192,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME2z,ORF1,hs2_gorilla,marg,CompleteHit
11882,Q#1533 - >seq4856,superfamily,340204,112,155,0.00874192,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs2_gorilla.marg.frame1,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME2z,ORF1,hs2_gorilla,marg,CompleteHit
11883,Q#1536 - >seq4859,non-specific,335182,148,243,4.98409e-18,78.1135,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs2_gorilla.marg.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs2_gorilla,marg,CompleteHit
11884,Q#1536 - >seq4859,superfamily,335182,148,243,4.98409e-18,78.1135,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs2_gorilla.marg.frame3,1909130434_L1ME2z.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs2_gorilla,marg,CompleteHit
11885,Q#1537 - >seq4860,non-specific,335182,154,244,8.64748e-25,96.2178,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs3_orang.marg.frame3,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs3_orang,marg,CompleteHit
11886,Q#1537 - >seq4860,superfamily,335182,154,244,8.64748e-25,96.2178,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs3_orang.marg.frame3,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs3_orang,marg,CompleteHit
11887,Q#1537 - >seq4860,non-specific,340205,248,317,2.3169e-12,61.198,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs3_orang.marg.frame3,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs3_orang,marg,CompleteHit
11888,Q#1537 - >seq4860,superfamily,340205,248,317,2.3169e-12,61.198,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs3_orang.marg.frame3,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs3_orang,marg,CompleteHit
11889,Q#1538 - >seq4861,non-specific,235505,50,151,0.00157072,39.8538,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1ME2z.ORF1.hs3_orang.marg.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1ME2z,ORF1,hs3_orang,marg,BothTerminiTruncated
11890,Q#1538 - >seq4861,superfamily,235505,50,151,0.00157072,39.8538,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1ME2z.ORF1.hs3_orang.marg.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2z,ORF1,hs3_orang,marg,BothTerminiTruncated
11891,Q#1538 - >seq4861,non-specific,129694,47,264,0.00360789,39.2597,TIGR00606,rad50,N,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1ME2z.ORF1.hs3_orang.marg.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_DNARepair,L1ME2z,ORF1,hs3_orang,marg,N-TerminusTruncated
11892,Q#1538 - >seq4861,superfamily,129694,47,264,0.00360789,39.2597,cl31018,rad50 superfamily,N, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1ME2z.ORF1.hs3_orang.marg.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_IndelAndChars_N1.frame1,Other_DNARepair,L1ME2z,ORF1,hs3_orang,marg,N-TerminusTruncated
11893,Q#1541 - >seq4864,non-specific,335182,84,161,1.09172e-16,72.3355,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs3_orang.pars.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2z,ORF1,hs3_orang,pars,CompleteHit
11894,Q#1541 - >seq4864,superfamily,335182,84,161,1.09172e-16,72.3355,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs3_orang.pars.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2z,ORF1,hs3_orang,pars,CompleteHit
11895,Q#1541 - >seq4864,non-specific,340205,165,202,2.97384e-08,48.8716,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs3_orang.pars.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2z,ORF1,hs3_orang,pars,C-TerminusTruncated
11896,Q#1541 - >seq4864,superfamily,340205,165,202,2.97384e-08,48.8716,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs3_orang.pars.frame1,1909130436_L1ME2z.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.LORF12_macse_round1.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME2z,ORF1,hs3_orang,pars,C-TerminusTruncated
11897,Q#1543 - >seq4866,specific,197310,9,231,4.042049999999999e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11898,Q#1543 - >seq4866,superfamily,351117,9,231,4.042049999999999e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11899,Q#1543 - >seq4866,non-specific,197306,9,229,1.3615699999999998e-37,141.08,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11900,Q#1543 - >seq4866,non-specific,197307,9,229,3.0861999999999997e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11901,Q#1543 - >seq4866,non-specific,197320,9,194,6.3588899999999995e-21,92.9633,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11902,Q#1543 - >seq4866,non-specific,223780,9,229,3.14019e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11903,Q#1543 - >seq4866,non-specific,197321,7,229,4.75842e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11904,Q#1543 - >seq4866,specific,335306,10,229,9.59829e-17,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11905,Q#1543 - >seq4866,non-specific,273186,9,229,4.4740499999999994e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11906,Q#1543 - >seq4866,non-specific,272954,9,194,9.913760000000001e-14,72.0305,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11907,Q#1543 - >seq4866,non-specific,197319,13,229,4.64387e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11908,Q#1543 - >seq4866,non-specific,236970,9,194,1.67283e-10,62.6042,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11909,Q#1543 - >seq4866,non-specific,238827,649,729,2.25602e-10,61.5382,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11910,Q#1543 - >seq4866,superfamily,295487,649,729,2.25602e-10,61.5382,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11911,Q#1543 - >seq4866,non-specific,197336,9,194,1.00691e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11912,Q#1543 - >seq4866,non-specific,197322,8,229,4.02411e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11913,Q#1543 - >seq4866,non-specific,339261,108,231,0.00734858,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs1_chimp.pars.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs1_chimp,pars,CompleteHit
11914,Q#1544 - >seq4867,specific,238827,492,667,7.17162e-44,158.22299999999998,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11915,Q#1544 - >seq4867,superfamily,295487,492,667,7.17162e-44,158.22299999999998,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11916,Q#1544 - >seq4867,non-specific,333820,498,667,2.49212e-24,100.83,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11917,Q#1544 - >seq4867,superfamily,333820,498,667,2.49212e-24,100.83,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11918,Q#1544 - >seq4867,non-specific,238828,498,676,7.9314e-09,56.8256,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
11919,Q#1544 - >seq4867,non-specific,275209,569,653,1.54334e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,BothTerminiTruncated
11920,Q#1544 - >seq4867,superfamily,275209,569,653,1.54334e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs1_chimp,pars,BothTerminiTruncated
11921,Q#1544 - >seq4867,non-specific,274009,222,451,0.000117605,45.8291,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs1_chimp,pars,BothTerminiTruncated
11922,Q#1544 - >seq4867,superfamily,274009,222,451,0.000117605,45.8291,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs1_chimp,pars,BothTerminiTruncated
11923,Q#1544 - >seq4867,non-specific,313357,304,446,0.00151564,40.3276,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11924,Q#1544 - >seq4867,superfamily,321788,304,446,0.00151564,40.3276,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11925,Q#1544 - >seq4867,non-specific,197874,213,382,0.008081999999999999,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11926,Q#1544 - >seq4867,superfamily,197874,213,382,0.008081999999999999,39.2305,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11927,Q#1544 - >seq4867,non-specific,224117,221,483,0.00927023,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11928,Q#1544 - >seq4867,superfamily,224117,221,483,0.00927023,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs1_chimp.pars.frame2,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1P4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
11929,Q#1546 - >seq4869,specific,197310,9,236,8.699179999999999e-60,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11930,Q#1546 - >seq4869,superfamily,351117,9,236,8.699179999999999e-60,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11931,Q#1546 - >seq4869,non-specific,197306,9,236,6.91199e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11932,Q#1546 - >seq4869,non-specific,197307,9,236,1.12792e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11933,Q#1546 - >seq4869,non-specific,223780,9,238,5.3818599999999996e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11934,Q#1546 - >seq4869,non-specific,197321,7,236,2.63552e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11935,Q#1546 - >seq4869,non-specific,197320,8,236,3.3370199999999994e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11936,Q#1546 - >seq4869,specific,335306,10,229,5.84127e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11937,Q#1546 - >seq4869,non-specific,273186,9,237,5.330149999999999e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11938,Q#1546 - >seq4869,non-specific,272954,9,236,4.35472e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11939,Q#1546 - >seq4869,non-specific,197319,8,236,1.3219299999999998e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11940,Q#1546 - >seq4869,non-specific,197336,7,235,6.069600000000001e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11941,Q#1546 - >seq4869,non-specific,197322,9,236,1.20506e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11942,Q#1546 - >seq4869,non-specific,339261,108,232,2.7713000000000006e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11943,Q#1546 - >seq4869,non-specific,236970,9,238,1.3499600000000002e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11944,Q#1546 - >seq4869,non-specific,197311,7,236,4.42038e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11945,Q#1546 - >seq4869,non-specific,274009,305,457,0.0001189,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,C-TerminusTruncated
11946,Q#1546 - >seq4869,superfamily,274009,305,457,0.0001189,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,C-TerminusTruncated
11947,Q#1546 - >seq4869,non-specific,235175,301,468,0.00024292400000000002,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,BothTerminiTruncated
11948,Q#1546 - >seq4869,superfamily,235175,301,468,0.00024292400000000002,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,BothTerminiTruncated
11949,Q#1546 - >seq4869,non-specific,197317,139,229,0.00026949900000000003,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11950,Q#1546 - >seq4869,non-specific,223496,305,499,0.00108272,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs1_chimp,marg,BothTerminiTruncated
11951,Q#1546 - >seq4869,superfamily,223496,305,499,0.00108272,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1P3,ORF2,hs1_chimp,marg,BothTerminiTruncated
11952,Q#1546 - >seq4869,non-specific,223496,263,449,0.00254945,42.0547,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs1_chimp,marg,C-TerminusTruncated
11953,Q#1546 - >seq4869,non-specific,224117,263,500,0.00541585,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11954,Q#1546 - >seq4869,superfamily,224117,263,500,0.00541585,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11955,Q#1546 - >seq4869,non-specific,274009,305,455,0.00783207,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.marg.frame3,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11956,Q#1548 - >seq4871,specific,238827,475,720,1.0554499999999998e-60,206.75799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11957,Q#1548 - >seq4871,superfamily,295487,475,720,1.0554499999999998e-60,206.75799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11958,Q#1548 - >seq4871,specific,333820,476,720,1.06379e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11959,Q#1548 - >seq4871,superfamily,333820,476,720,1.06379e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11960,Q#1548 - >seq4871,non-specific,238828,530,685,6.985489999999999e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11961,Q#1548 - >seq4871,non-specific,275209,535,748,5.465569999999999e-09,59.0084,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11962,Q#1548 - >seq4871,superfamily,275209,535,748,5.465569999999999e-09,59.0084,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,N-TerminusTruncated
11963,Q#1548 - >seq4871,non-specific,238185,604,720,1.01902e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs1_chimp.marg.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P3,ORF2,hs1_chimp,marg,CompleteHit
11964,Q#1550 - >seq4873,specific,238827,480,725,1.0178099999999999e-60,206.373,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11965,Q#1550 - >seq4873,superfamily,295487,480,725,1.0178099999999999e-60,206.373,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11966,Q#1550 - >seq4873,specific,333820,481,725,9.04231e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11967,Q#1550 - >seq4873,superfamily,333820,481,725,9.04231e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11968,Q#1550 - >seq4873,non-specific,238828,535,690,6.57675e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11969,Q#1550 - >seq4873,non-specific,275209,540,753,4.62426e-09,59.3936,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11970,Q#1550 - >seq4873,superfamily,275209,540,753,4.62426e-09,59.3936,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11971,Q#1550 - >seq4873,non-specific,238185,609,725,6.70319e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs1_chimp.pars.frame2,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11972,Q#1551 - >seq4874,specific,197310,30,229,1.7150099999999998e-49,175.232,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11973,Q#1551 - >seq4874,superfamily,351117,30,229,1.7150099999999998e-49,175.232,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11974,Q#1551 - >seq4874,non-specific,197306,25,229,1.31549e-39,146.858,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11975,Q#1551 - >seq4874,non-specific,197307,25,229,8.856669999999999e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11976,Q#1551 - >seq4874,non-specific,223780,20,231,6.66925e-16,78.7943,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11977,Q#1551 - >seq4874,non-specific,197320,13,229,8.56553e-13,69.4662,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11978,Q#1551 - >seq4874,non-specific,197321,25,229,1.7036200000000002e-12,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11979,Q#1551 - >seq4874,specific,335306,23,222,8.21028e-12,65.7294,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11980,Q#1551 - >seq4874,non-specific,273186,14,230,4.2707999999999994e-10,61.1408,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11981,Q#1551 - >seq4874,non-specific,272954,20,229,9.13529e-10,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11982,Q#1551 - >seq4874,non-specific,339261,101,225,1.11979e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11983,Q#1551 - >seq4874,non-specific,197319,20,229,2.96214e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11984,Q#1551 - >seq4874,non-specific,197322,84,229,6.29857e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11985,Q#1551 - >seq4874,non-specific,197336,20,228,1.4749200000000002e-06,50.6887,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11986,Q#1551 - >seq4874,non-specific,197311,30,229,9.79172e-06,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs1_chimp,pars,CompleteHit
11987,Q#1551 - >seq4874,non-specific,274009,298,450,0.00015936799999999998,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,C-TerminusTruncated
11988,Q#1551 - >seq4874,superfamily,274009,298,450,0.00015936799999999998,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,C-TerminusTruncated
11989,Q#1551 - >seq4874,non-specific,197317,132,222,0.00024186799999999998,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11990,Q#1551 - >seq4874,non-specific,235175,294,461,0.00038009,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,BothTerminiTruncated
11991,Q#1551 - >seq4874,superfamily,235175,294,461,0.00038009,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,BothTerminiTruncated
11992,Q#1551 - >seq4874,non-specific,236970,61,231,0.000591988,42.5738,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11993,Q#1551 - >seq4874,non-specific,223496,302,492,0.00190942,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs1_chimp,pars,BothTerminiTruncated
11994,Q#1551 - >seq4874,superfamily,223496,302,492,0.00190942,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1P3,ORF2,hs1_chimp,pars,BothTerminiTruncated
11995,Q#1551 - >seq4874,non-specific,223496,256,442,0.00416794,40.8991,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs1_chimp,pars,C-TerminusTruncated
11996,Q#1551 - >seq4874,non-specific,224117,256,493,0.00772465,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11997,Q#1551 - >seq4874,superfamily,224117,256,493,0.00772465,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11998,Q#1551 - >seq4874,non-specific,274009,298,448,0.00951371,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs1_chimp.pars.frame1,1909130924_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF2,hs1_chimp,pars,N-TerminusTruncated
11999,Q#1552 - >seq4875,specific,238827,510,772,1.8301899999999998e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12000,Q#1552 - >seq4875,superfamily,295487,510,772,1.8301899999999998e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12001,Q#1552 - >seq4875,specific,197310,9,236,6.26464e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12002,Q#1552 - >seq4875,superfamily,351117,9,236,6.26464e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12003,Q#1552 - >seq4875,non-specific,197306,9,236,3.34568e-53,186.148,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12004,Q#1552 - >seq4875,specific,333820,516,772,3.10974e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12005,Q#1552 - >seq4875,superfamily,333820,516,772,3.10974e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12006,Q#1552 - >seq4875,non-specific,197307,9,236,1.6187200000000002e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12007,Q#1552 - >seq4875,non-specific,223780,9,238,5.91478e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12008,Q#1552 - >seq4875,non-specific,197320,8,221,1.2314100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12009,Q#1552 - >seq4875,specific,335306,10,229,7.1822e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12010,Q#1552 - >seq4875,non-specific,197321,7,236,2.5619499999999997e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12011,Q#1552 - >seq4875,non-specific,273186,9,237,7.973300000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12012,Q#1552 - >seq4875,non-specific,272954,9,236,1.939e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12013,Q#1552 - >seq4875,non-specific,197319,8,236,4.35029e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12014,Q#1552 - >seq4875,non-specific,197336,7,235,1.20169e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12015,Q#1552 - >seq4875,non-specific,197322,9,236,5.88785e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12016,Q#1552 - >seq4875,non-specific,238828,516,737,1.35441e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12017,Q#1552 - >seq4875,non-specific,275209,467,800,4.5008099999999997e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12018,Q#1552 - >seq4875,superfamily,275209,467,800,4.5008099999999997e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12019,Q#1552 - >seq4875,non-specific,339261,108,232,7.77941e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12020,Q#1552 - >seq4875,non-specific,236970,9,238,1.27864e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12021,Q#1552 - >seq4875,non-specific,197311,7,236,6.05171e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,marg,CompleteHit
12022,Q#1552 - >seq4875,non-specific,197317,139,229,0.00010938,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,marg,N-TerminusTruncated
12023,Q#1552 - >seq4875,non-specific,197314,7,192,0.000123061,45.0271,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs0_human,marg,C-TerminusTruncated
12024,Q#1552 - >seq4875,non-specific,238185,656,772,0.000125865,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12025,Q#1552 - >seq4875,non-specific,226098,138,239,0.000432747,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,marg,N-TerminusTruncated
12026,Q#1552 - >seq4875,non-specific,274009,305,453,0.000900695,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,C-TerminusTruncated
12027,Q#1552 - >seq4875,superfamily,274009,305,453,0.000900695,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,C-TerminusTruncated
12028,Q#1552 - >seq4875,non-specific,235175,295,464,0.00352332,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,BothTerminiTruncated
12029,Q#1552 - >seq4875,superfamily,235175,295,464,0.00352332,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,BothTerminiTruncated
12030,Q#1552 - >seq4875,non-specific,274008,157,500,0.00357973,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,N-TerminusTruncated
12031,Q#1552 - >seq4875,superfamily,274008,157,500,0.00357973,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,marg,N-TerminusTruncated
12032,Q#1552 - >seq4875,non-specific,239569,525,748,0.00696982,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs0_human,marg,CompleteHit
12033,Q#1552 - >seq4875,non-specific,293702,337,451,0.00880753,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs0_human,marg,C-TerminusTruncated
12034,Q#1552 - >seq4875,superfamily,293702,337,451,0.00880753,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs0_human.marg.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs0_human,marg,C-TerminusTruncated
12035,Q#1557 - >seq4880,specific,238827,510,772,1.4262599999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12036,Q#1557 - >seq4880,superfamily,295487,510,772,1.4262599999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12037,Q#1557 - >seq4880,specific,197310,9,236,5.060329999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12038,Q#1557 - >seq4880,superfamily,351117,9,236,5.060329999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12039,Q#1557 - >seq4880,non-specific,197306,9,236,1.64763e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12040,Q#1557 - >seq4880,specific,333820,516,772,2.96122e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12041,Q#1557 - >seq4880,superfamily,333820,516,772,2.96122e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12042,Q#1557 - >seq4880,non-specific,197307,9,236,2.40736e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12043,Q#1557 - >seq4880,non-specific,223780,9,238,1.5604e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12044,Q#1557 - >seq4880,non-specific,197320,8,236,2.1265300000000003e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12045,Q#1557 - >seq4880,non-specific,197321,7,236,7.175050000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12046,Q#1557 - >seq4880,specific,335306,10,229,1.33537e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12047,Q#1557 - >seq4880,non-specific,273186,9,237,8.682540000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12048,Q#1557 - >seq4880,non-specific,272954,9,236,1.66827e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12049,Q#1557 - >seq4880,non-specific,197319,8,236,4.4329400000000006e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12050,Q#1557 - >seq4880,non-specific,197336,7,235,2.80585e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12051,Q#1557 - >seq4880,non-specific,238828,516,737,2.2539e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12052,Q#1557 - >seq4880,non-specific,197322,9,236,2.76928e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12053,Q#1557 - >seq4880,non-specific,275209,467,800,9.60509e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12054,Q#1557 - >seq4880,superfamily,275209,467,800,9.60509e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12055,Q#1557 - >seq4880,non-specific,236970,9,238,4.3818299999999995e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12056,Q#1557 - >seq4880,non-specific,339261,108,232,1.82405e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12057,Q#1557 - >seq4880,non-specific,197311,7,236,2.04483e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12058,Q#1557 - >seq4880,non-specific,197317,139,229,1.45838e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12059,Q#1557 - >seq4880,non-specific,238185,656,772,0.00017680299999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,marg,CompleteHit
12060,Q#1557 - >seq4880,non-specific,274009,305,453,0.00090921,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12061,Q#1557 - >seq4880,superfamily,274009,305,453,0.00090921,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12062,Q#1557 - >seq4880,non-specific,226098,138,239,0.00167039,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12063,Q#1557 - >seq4880,non-specific,197314,7,192,0.00195139,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12064,Q#1557 - >seq4880,non-specific,235175,295,464,0.00335135,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12065,Q#1557 - >seq4880,superfamily,235175,295,464,0.00335135,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12066,Q#1557 - >seq4880,non-specific,274008,263,500,0.00494052,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12067,Q#1557 - >seq4880,superfamily,274008,263,500,0.00494052,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12068,Q#1557 - >seq4880,non-specific,293702,337,451,0.00808057,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12069,Q#1557 - >seq4880,superfamily,293702,337,451,0.00808057,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12070,Q#1559 - >seq4882,specific,238827,510,772,1.8301899999999998e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12071,Q#1559 - >seq4882,superfamily,295487,510,772,1.8301899999999998e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12072,Q#1559 - >seq4882,specific,197310,9,236,6.26464e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12073,Q#1559 - >seq4882,superfamily,351117,9,236,6.26464e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12074,Q#1559 - >seq4882,non-specific,197306,9,236,3.34568e-53,186.148,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12075,Q#1559 - >seq4882,specific,333820,516,772,3.10974e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12076,Q#1559 - >seq4882,superfamily,333820,516,772,3.10974e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12077,Q#1559 - >seq4882,non-specific,197307,9,236,1.6187200000000002e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12078,Q#1559 - >seq4882,non-specific,223780,9,238,5.91478e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12079,Q#1559 - >seq4882,non-specific,197320,8,221,1.2314100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12080,Q#1559 - >seq4882,specific,335306,10,229,7.1822e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12081,Q#1559 - >seq4882,non-specific,197321,7,236,2.5619499999999997e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12082,Q#1559 - >seq4882,non-specific,273186,9,237,7.973300000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12083,Q#1559 - >seq4882,non-specific,272954,9,236,1.939e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12084,Q#1559 - >seq4882,non-specific,197319,8,236,4.35029e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12085,Q#1559 - >seq4882,non-specific,197336,7,235,1.20169e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12086,Q#1559 - >seq4882,non-specific,197322,9,236,5.88785e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12087,Q#1559 - >seq4882,non-specific,238828,516,737,1.35441e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12088,Q#1559 - >seq4882,non-specific,275209,467,800,4.5008099999999997e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12089,Q#1559 - >seq4882,superfamily,275209,467,800,4.5008099999999997e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12090,Q#1559 - >seq4882,non-specific,339261,108,232,7.77941e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12091,Q#1559 - >seq4882,non-specific,236970,9,238,1.27864e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12092,Q#1559 - >seq4882,non-specific,197311,7,236,6.05171e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs0_human,pars,CompleteHit
12093,Q#1559 - >seq4882,non-specific,197317,139,229,0.00010938,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,pars,N-TerminusTruncated
12094,Q#1559 - >seq4882,non-specific,197314,7,192,0.000123061,45.0271,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs0_human,pars,C-TerminusTruncated
12095,Q#1559 - >seq4882,non-specific,238185,656,772,0.000125865,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12096,Q#1559 - >seq4882,non-specific,226098,138,239,0.000432747,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs0_human,pars,N-TerminusTruncated
12097,Q#1559 - >seq4882,non-specific,274009,305,453,0.000900695,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,C-TerminusTruncated
12098,Q#1559 - >seq4882,superfamily,274009,305,453,0.000900695,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,C-TerminusTruncated
12099,Q#1559 - >seq4882,non-specific,235175,295,464,0.00352332,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,BothTerminiTruncated
12100,Q#1559 - >seq4882,superfamily,235175,295,464,0.00352332,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,BothTerminiTruncated
12101,Q#1559 - >seq4882,non-specific,274008,157,500,0.00357973,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,N-TerminusTruncated
12102,Q#1559 - >seq4882,superfamily,274008,157,500,0.00357973,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs0_human,pars,N-TerminusTruncated
12103,Q#1559 - >seq4882,non-specific,239569,525,748,0.00696982,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs0_human,pars,CompleteHit
12104,Q#1559 - >seq4882,non-specific,293702,337,451,0.00880753,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs0_human,pars,C-TerminusTruncated
12105,Q#1559 - >seq4882,superfamily,293702,337,451,0.00880753,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs0_human.pars.frame3,1909130924_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs0_human,pars,C-TerminusTruncated
12106,Q#1563 - >seq4886,specific,197310,9,236,6.060429999999999e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12107,Q#1563 - >seq4886,superfamily,351117,9,236,6.060429999999999e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12108,Q#1563 - >seq4886,specific,238827,509,772,1.2312999999999998e-49,175.172,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12109,Q#1563 - >seq4886,superfamily,295487,509,772,1.2312999999999998e-49,175.172,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12110,Q#1563 - >seq4886,non-specific,197306,9,236,1.2083399999999997e-39,147.243,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12111,Q#1563 - >seq4886,non-specific,333820,515,772,1.39929e-23,98.9037,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12112,Q#1563 - >seq4886,superfamily,333820,515,772,1.39929e-23,98.9037,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12113,Q#1563 - >seq4886,non-specific,197307,9,236,2.73015e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12114,Q#1563 - >seq4886,non-specific,223780,9,237,1.63069e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12115,Q#1563 - >seq4886,non-specific,197320,9,229,2.79886e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12116,Q#1563 - >seq4886,non-specific,197321,7,236,2.85559e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12117,Q#1563 - >seq4886,specific,335306,10,229,3.94988e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12118,Q#1563 - >seq4886,non-specific,273186,9,237,2.4119299999999997e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12119,Q#1563 - >seq4886,non-specific,197319,13,236,2.1711e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12120,Q#1563 - >seq4886,non-specific,272954,9,207,1.24049e-11,66.2525,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12121,Q#1563 - >seq4886,non-specific,238828,582,737,2.03832e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,N-TerminusTruncated
12122,Q#1563 - >seq4886,non-specific,197336,9,194,7.938960000000001e-10,60.7039,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12123,Q#1563 - >seq4886,non-specific,197322,8,236,9.5274e-09,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12124,Q#1563 - >seq4886,non-specific,236970,9,237,2.1429900000000002e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12125,Q#1563 - >seq4886,non-specific,275209,587,800,5.1150699999999996e-08,56.312,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,N-TerminusTruncated
12126,Q#1563 - >seq4886,superfamily,275209,587,800,5.1150699999999996e-08,56.312,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,N-TerminusTruncated
12127,Q#1563 - >seq4886,non-specific,197311,30,236,1.15949e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,marg,CompleteHit
12128,Q#1563 - >seq4886,non-specific,339261,108,232,3.69227e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12129,Q#1563 - >seq4886,non-specific,235175,291,463,8.45586e-05,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs0_human,marg,BothTerminiTruncated
12130,Q#1563 - >seq4886,superfamily,235175,291,463,8.45586e-05,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs0_human,marg,BothTerminiTruncated
12131,Q#1563 - >seq4886,non-specific,238185,656,770,0.000296424,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs0_human,marg,CompleteHit
12132,Q#1563 - >seq4886,non-specific,274009,264,467,0.000516599,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs0_human,marg,BothTerminiTruncated
12133,Q#1563 - >seq4886,superfamily,274009,264,467,0.000516599,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs0_human,marg,BothTerminiTruncated
12134,Q#1563 - >seq4886,non-specific,224117,263,466,0.0008465660000000001,43.5496,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs0_human,marg,N-TerminusTruncated
12135,Q#1563 - >seq4886,superfamily,224117,263,466,0.0008465660000000001,43.5496,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs0_human.marg.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P4a,ORF2,hs0_human,marg,N-TerminusTruncated
12136,Q#1566 - >seq4889,specific,197310,9,236,5.11991e-63,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12137,Q#1566 - >seq4889,superfamily,351117,9,236,5.11991e-63,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12138,Q#1566 - >seq4889,non-specific,197306,9,236,1.08036e-40,149.939,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12139,Q#1566 - >seq4889,non-specific,197307,9,236,7.70729e-23,98.8993,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12140,Q#1566 - >seq4889,non-specific,223780,9,237,1.64113e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12141,Q#1566 - >seq4889,non-specific,197321,7,236,2.70888e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12142,Q#1566 - >seq4889,non-specific,197320,9,229,1.00322e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12143,Q#1566 - >seq4889,specific,335306,10,229,3.40393e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12144,Q#1566 - >seq4889,non-specific,273186,9,237,5.14627e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12145,Q#1566 - >seq4889,non-specific,197319,13,236,5.18031e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12146,Q#1566 - >seq4889,non-specific,272954,9,207,6.68573e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12147,Q#1566 - >seq4889,non-specific,197336,9,194,6.83178e-10,60.7039,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12148,Q#1566 - >seq4889,non-specific,236970,9,237,2.7447399999999998e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12149,Q#1566 - >seq4889,non-specific,197322,8,236,8.16765e-09,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12150,Q#1566 - >seq4889,non-specific,197311,30,236,3.271e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs0_human,pars,CompleteHit
12151,Q#1566 - >seq4889,non-specific,339261,108,232,1.55947e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs0_human.pars.frame3,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12152,Q#1567 - >seq4890,specific,238827,480,742,1.9641599999999997e-51,180.18,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12153,Q#1567 - >seq4890,superfamily,295487,480,742,1.9641599999999997e-51,180.18,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12154,Q#1567 - >seq4890,non-specific,333820,486,742,1.3187199999999999e-25,104.682,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12155,Q#1567 - >seq4890,superfamily,333820,486,742,1.3187199999999999e-25,104.682,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12156,Q#1567 - >seq4890,non-specific,238828,552,707,5.70931e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,N-TerminusTruncated
12157,Q#1567 - >seq4890,non-specific,275209,557,770,2.58237e-08,57.0824,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,N-TerminusTruncated
12158,Q#1567 - >seq4890,superfamily,275209,557,770,2.58237e-08,57.0824,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,N-TerminusTruncated
12159,Q#1567 - >seq4890,non-specific,238185,626,740,5.1807799999999995e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs0_human,pars,CompleteHit
12160,Q#1567 - >seq4890,non-specific,235175,296,434,0.000278443,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs0_human,pars,BothTerminiTruncated
12161,Q#1567 - >seq4890,superfamily,235175,296,434,0.000278443,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs0_human.pars.frame2,1909130924_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs0_human,pars,BothTerminiTruncated
12162,Q#1569 - >seq4892,specific,197310,9,231,1.1037199999999998e-64,218.375,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12163,Q#1569 - >seq4892,superfamily,351117,9,231,1.1037199999999998e-64,218.375,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12164,Q#1569 - >seq4892,specific,238827,508,770,1.4804199999999999e-62,211.766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12165,Q#1569 - >seq4892,superfamily,295487,508,770,1.4804199999999999e-62,211.766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12166,Q#1569 - >seq4892,non-specific,197306,9,229,2.6556299999999997e-40,149.16899999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12167,Q#1569 - >seq4892,specific,333820,514,770,9.142539999999998e-32,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12168,Q#1569 - >seq4892,superfamily,333820,514,770,9.142539999999998e-32,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12169,Q#1569 - >seq4892,non-specific,197321,7,229,2.5279399999999998e-23,100.319,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12170,Q#1569 - >seq4892,non-specific,197307,9,229,8.04136e-23,98.8993,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12171,Q#1569 - >seq4892,non-specific,223780,9,229,1.1564200000000003e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12172,Q#1569 - >seq4892,non-specific,197320,9,229,1.1924200000000002e-22,98.3561,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12173,Q#1569 - >seq4892,specific,335306,10,229,7.13818e-20,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12174,Q#1569 - >seq4892,non-specific,273186,9,229,2.72999e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12175,Q#1569 - >seq4892,non-specific,272954,9,207,5.5237000000000004e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12176,Q#1569 - >seq4892,non-specific,197319,13,229,7.07423e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12177,Q#1569 - >seq4892,non-specific,236970,9,207,3.02558e-11,64.9154,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12178,Q#1569 - >seq4892,non-specific,197336,9,194,4.79395e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12179,Q#1569 - >seq4892,non-specific,238828,580,735,1.2354799999999999e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12180,Q#1569 - >seq4892,non-specific,197322,8,229,8.16321e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12181,Q#1569 - >seq4892,non-specific,275209,585,794,5.35901e-08,55.9268,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12182,Q#1569 - >seq4892,superfamily,275209,585,794,5.35901e-08,55.9268,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12183,Q#1569 - >seq4892,non-specific,197311,30,204,1.1646199999999999e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12184,Q#1569 - >seq4892,non-specific,339261,108,231,7.68504e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12185,Q#1569 - >seq4892,non-specific,235175,291,467,0.000157092,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
12186,Q#1569 - >seq4892,superfamily,235175,291,467,0.000157092,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs4_gibbon,marg,BothTerminiTruncated
12187,Q#1569 - >seq4892,non-specific,238185,654,770,0.000160445,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,marg,CompleteHit
12188,Q#1572 - >seq4895,specific,197310,9,231,7.17613e-65,218.76,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12189,Q#1572 - >seq4895,superfamily,351117,9,231,7.17613e-65,218.76,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12190,Q#1572 - >seq4895,non-specific,197306,9,229,7.932179999999999e-41,150.32399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12191,Q#1572 - >seq4895,specific,238827,509,700,8.584790000000001e-41,149.749,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12192,Q#1572 - >seq4895,superfamily,295487,509,700,8.584790000000001e-41,149.749,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12193,Q#1572 - >seq4895,non-specific,197321,7,229,3.534969999999999e-24,102.63,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12194,Q#1572 - >seq4895,non-specific,197307,9,229,9.75133e-24,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12195,Q#1572 - >seq4895,non-specific,223780,9,229,2.46682e-23,100.365,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12196,Q#1572 - >seq4895,non-specific,333820,515,685,5.2873e-23,97.3629,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12197,Q#1572 - >seq4895,superfamily,333820,515,685,5.2873e-23,97.3629,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12198,Q#1572 - >seq4895,non-specific,197320,9,229,1.13098e-22,98.3561,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12199,Q#1572 - >seq4895,specific,335306,10,229,6.781899999999999e-20,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12200,Q#1572 - >seq4895,non-specific,273186,9,229,1.31249e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12201,Q#1572 - >seq4895,non-specific,197319,13,229,9.011190000000001e-15,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12202,Q#1572 - >seq4895,non-specific,272954,9,207,1.5348e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12203,Q#1572 - >seq4895,non-specific,236970,9,207,1.94675e-11,65.6858,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12204,Q#1572 - >seq4895,non-specific,197336,9,194,4.55149e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12205,Q#1572 - >seq4895,non-specific,197322,8,229,7.73831e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12206,Q#1572 - >seq4895,non-specific,238828,581,690,9.16256e-09,56.8256,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12207,Q#1572 - >seq4895,non-specific,197311,30,204,1.10846e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12208,Q#1572 - >seq4895,non-specific,275209,586,670,1.62985e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12209,Q#1572 - >seq4895,superfamily,275209,586,670,1.62985e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12210,Q#1572 - >seq4895,non-specific,235175,291,467,2.61217e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12211,Q#1572 - >seq4895,superfamily,235175,291,467,2.61217e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12212,Q#1572 - >seq4895,non-specific,339261,108,231,0.000140187,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs4_gibbon,pars,CompleteHit
12213,Q#1573 - >seq4896,specific,238827,510,772,1.4363599999999997e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12214,Q#1573 - >seq4896,superfamily,295487,510,772,1.4363599999999997e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12215,Q#1573 - >seq4896,specific,197310,9,231,9.731999999999998e-61,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12216,Q#1573 - >seq4896,superfamily,351117,9,231,9.731999999999998e-61,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12217,Q#1573 - >seq4896,non-specific,197306,9,229,7.890159999999999e-37,139.154,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12218,Q#1573 - >seq4896,specific,333820,516,772,8.687319999999999e-31,119.705,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12219,Q#1573 - >seq4896,superfamily,333820,516,772,8.687319999999999e-31,119.705,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12220,Q#1573 - >seq4896,non-specific,197320,9,194,7.39563e-21,92.9633,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
12221,Q#1573 - >seq4896,non-specific,197307,9,229,2.8433700000000004e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12222,Q#1573 - >seq4896,non-specific,223780,9,229,9.49099e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12223,Q#1573 - >seq4896,non-specific,197321,7,229,1.09362e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12224,Q#1573 - >seq4896,specific,335306,10,229,1.1106100000000002e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12225,Q#1573 - >seq4896,non-specific,273186,9,229,6.8891499999999995e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12226,Q#1573 - >seq4896,non-specific,272954,9,194,6.93374e-13,69.7193,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
12227,Q#1573 - >seq4896,non-specific,197319,13,229,3.50221e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12228,Q#1573 - >seq4896,non-specific,238828,516,737,3.94412e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12229,Q#1573 - >seq4896,non-specific,236970,9,194,8.473480000000002e-10,60.6782,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
12230,Q#1573 - >seq4896,non-specific,197336,9,194,1.16711e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12231,Q#1573 - >seq4896,non-specific,197322,8,229,4.67997e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12232,Q#1573 - >seq4896,non-specific,275209,587,800,2.73304e-07,53.6156,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,N-TerminusTruncated
12233,Q#1573 - >seq4896,superfamily,275209,587,800,2.73304e-07,53.6156,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,N-TerminusTruncated
12234,Q#1573 - >seq4896,non-specific,235175,291,469,3.20186e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12235,Q#1573 - >seq4896,superfamily,235175,291,469,3.20186e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12236,Q#1573 - >seq4896,non-specific,223496,264,502,0.000406031,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12237,Q#1573 - >seq4896,superfamily,223496,264,502,0.000406031,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12238,Q#1573 - >seq4896,non-specific,274009,265,449,0.0025951,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12239,Q#1573 - >seq4896,superfamily,274009,265,449,0.0025951,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs1_chimp,marg,BothTerminiTruncated
12240,Q#1573 - >seq4896,non-specific,238185,656,770,0.00525493,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs1_chimp.marg.frame3,1909130924_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs1_chimp,marg,CompleteHit
12241,Q#1575 - >seq4898,specific,238827,509,770,9.643169999999998e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12242,Q#1575 - >seq4898,superfamily,295487,509,770,9.643169999999998e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12243,Q#1575 - >seq4898,specific,197310,9,235,9.918309999999997e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12244,Q#1575 - >seq4898,superfamily,351117,9,235,9.918309999999997e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12245,Q#1575 - >seq4898,non-specific,197306,9,235,2.7941199999999998e-39,146.08700000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12246,Q#1575 - >seq4898,specific,333820,515,770,5.48572e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12247,Q#1575 - >seq4898,superfamily,333820,515,770,5.48572e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12248,Q#1575 - >seq4898,non-specific,197307,9,235,2.1345300000000004e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12249,Q#1575 - >seq4898,non-specific,223780,9,236,5.58127e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12250,Q#1575 - >seq4898,non-specific,197321,7,235,8.67833e-22,95.6968,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12251,Q#1575 - >seq4898,non-specific,197320,9,228,8.23637e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12252,Q#1575 - >seq4898,specific,335306,10,228,7.668319999999999e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12253,Q#1575 - >seq4898,non-specific,273186,9,236,4.3133599999999995e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12254,Q#1575 - >seq4898,non-specific,197319,13,235,6.306990000000001e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12255,Q#1575 - >seq4898,non-specific,272954,9,206,5.07645e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12256,Q#1575 - >seq4898,non-specific,238828,515,735,8.14099e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12257,Q#1575 - >seq4898,non-specific,197322,8,235,8.183560000000001e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12258,Q#1575 - >seq4898,non-specific,197336,9,193,1.10804e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12259,Q#1575 - >seq4898,non-specific,275209,586,798,1.02903e-08,58.238,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,N-TerminusTruncated
12260,Q#1575 - >seq4898,superfamily,275209,586,798,1.02903e-08,58.238,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,N-TerminusTruncated
12261,Q#1575 - >seq4898,non-specific,236970,9,236,1.14166e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12262,Q#1575 - >seq4898,non-specific,339261,108,231,3.6336199999999995e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12263,Q#1575 - >seq4898,non-specific,197311,30,235,4.24221e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12264,Q#1575 - >seq4898,non-specific,238185,655,768,0.000172549,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs3_orang,marg,CompleteHit
12265,Q#1575 - >seq4898,non-specific,235175,290,468,0.000311647,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs3_orang,marg,BothTerminiTruncated
12266,Q#1575 - >seq4898,superfamily,235175,290,468,0.000311647,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs3_orang,marg,BothTerminiTruncated
12267,Q#1575 - >seq4898,non-specific,223496,262,443,0.0027373000000000002,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs3_orang,marg,BothTerminiTruncated
12268,Q#1575 - >seq4898,superfamily,223496,262,443,0.0027373000000000002,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.marg.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1P4a,ORF2,hs3_orang,marg,BothTerminiTruncated
12269,Q#1578 - >seq4901,specific,238827,509,771,3.0114599999999994e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12270,Q#1578 - >seq4901,superfamily,295487,509,771,3.0114599999999994e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12271,Q#1578 - >seq4901,specific,197310,9,235,1.2345299999999998e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12272,Q#1578 - >seq4901,superfamily,351117,9,235,1.2345299999999998e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12273,Q#1578 - >seq4901,non-specific,197306,9,235,3.0750199999999996e-39,145.702,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12274,Q#1578 - >seq4901,specific,333820,515,771,9.47971e-32,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12275,Q#1578 - >seq4901,superfamily,333820,515,771,9.47971e-32,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12276,Q#1578 - >seq4901,non-specific,197307,9,235,2.03132e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12277,Q#1578 - >seq4901,non-specific,223780,9,236,5.77819e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12278,Q#1578 - >seq4901,non-specific,197321,7,235,7.652289999999999e-22,95.6968,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12279,Q#1578 - >seq4901,non-specific,197320,9,228,8.53417e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12280,Q#1578 - >seq4901,specific,335306,10,228,6.850419999999999e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12281,Q#1578 - >seq4901,non-specific,273186,9,236,3.8784e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12282,Q#1578 - >seq4901,non-specific,197319,13,235,6.11618e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12283,Q#1578 - >seq4901,non-specific,272954,9,206,5.50412e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12284,Q#1578 - >seq4901,non-specific,238828,515,736,1.6150299999999999e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12285,Q#1578 - >seq4901,non-specific,197322,8,235,7.274989999999999e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12286,Q#1578 - >seq4901,non-specific,197336,9,193,9.88723e-10,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12287,Q#1578 - >seq4901,non-specific,275209,586,799,7.05787e-08,55.5416,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,N-TerminusTruncated
12288,Q#1578 - >seq4901,superfamily,275209,586,799,7.05787e-08,55.5416,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,N-TerminusTruncated
12289,Q#1578 - >seq4901,non-specific,236970,9,236,9.06122e-07,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12290,Q#1578 - >seq4901,non-specific,339261,108,231,4.09404e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12291,Q#1578 - >seq4901,non-specific,197311,30,235,4.4963e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12292,Q#1578 - >seq4901,non-specific,238185,655,769,0.000261239,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4a,ORF2,hs3_orang,pars,CompleteHit
12293,Q#1578 - >seq4901,non-specific,235175,290,468,0.000458316,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF2,hs3_orang,pars,BothTerminiTruncated
12294,Q#1578 - >seq4901,superfamily,235175,290,468,0.000458316,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF2,hs3_orang,pars,BothTerminiTruncated
12295,Q#1578 - >seq4901,non-specific,223496,262,443,0.00485876,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs3_orang,pars,BothTerminiTruncated
12296,Q#1578 - >seq4901,superfamily,223496,262,443,0.00485876,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs3_orang.pars.frame3,1909130924_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1P4a,ORF2,hs3_orang,pars,BothTerminiTruncated
12297,Q#1580 - >seq4903,specific,238827,483,711,9.761819999999998e-45,160.92,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12298,Q#1580 - >seq4903,superfamily,295487,483,711,9.761819999999998e-45,160.92,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12299,Q#1580 - >seq4903,non-specific,333820,472,711,1.82428e-21,92.7405,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12300,Q#1580 - >seq4903,superfamily,333820,472,711,1.82428e-21,92.7405,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12301,Q#1580 - >seq4903,non-specific,238828,504,676,3.80122e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12302,Q#1580 - >seq4903,non-specific,275209,527,735,2.0300699999999999e-07,54.0008,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12303,Q#1580 - >seq4903,superfamily,275209,527,735,2.0300699999999999e-07,54.0008,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12304,Q#1580 - >seq4903,non-specific,238185,596,709,0.00132979,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12305,Q#1580 - >seq4903,non-specific,223764,988,1037,0.00701216,39.1235,COG0692,Ung,NC,cl00483,"Uracil DNA glycosylase [Replication, recombination and repair]; Uracil DNA glycosylase [DNA replication, recombination, and repair].",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12306,Q#1580 - >seq4903,superfamily,351114,988,1037,0.00701216,39.1235,cl00483,UDG_like superfamily,NC, - ,"Uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. At least five UDG families have been characterized so far; these families share similar overall folds and common active site motifs. They demonstrate different substrate specificities, but often the function of one enzyme can be complemented by the other. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water interactions. Family 2 enzymes are mismatch specific and explicitly recognize the widowed guanine on the complementary strand, rather than the extrahelical scissile pyrimidine. This allows a broader specificity so that some Family 2 enzymes can excise uracil as well as 3, N(4)-ethenocytosine from mismatches with guanine. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are both thermostable. Family 4 enzymes specifically recognize uracil in a manner similar to human UDG (Family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (Family 2). These results suggest that the mechanism by which Family 4 UDGs remove uracils from DNA is similar to that of Family 1 enzyme. Although Family 5 enzymes are close relatives of Family 4, they show different substrate specificities.",L1P4a.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12307,Q#1581 - >seq4904,specific,197310,9,231,7.494059999999999e-62,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12308,Q#1581 - >seq4904,superfamily,351117,9,231,7.494059999999999e-62,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12309,Q#1581 - >seq4904,non-specific,197306,9,229,8.637399999999999e-38,141.85,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12310,Q#1581 - >seq4904,non-specific,197307,9,229,7.88364e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12311,Q#1581 - >seq4904,non-specific,223780,9,229,2.30362e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12312,Q#1581 - >seq4904,non-specific,197320,9,194,4.19126e-20,90.6521,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12313,Q#1581 - >seq4904,non-specific,197321,7,229,7.6269e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12314,Q#1581 - >seq4904,specific,335306,10,229,1.4772399999999998e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12315,Q#1581 - >seq4904,non-specific,273186,9,229,8.69962e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12316,Q#1581 - >seq4904,non-specific,272954,9,194,7.75305e-12,66.6377,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12317,Q#1581 - >seq4904,non-specific,197319,13,229,2.19643e-11,64.9905,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12318,Q#1581 - >seq4904,non-specific,197336,9,194,5.97159e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,marg,CompleteHit
12319,Q#1581 - >seq4904,non-specific,236970,9,194,7.17072e-09,57.9818,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12320,Q#1581 - >seq4904,non-specific,224117,264,467,0.00240175,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12321,Q#1581 - >seq4904,superfamily,224117,264,467,0.00240175,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12322,Q#1581 - >seq4904,non-specific,235175,268,450,0.00267833,41.588,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12323,Q#1581 - >seq4904,superfamily,235175,268,450,0.00267833,41.588,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12324,Q#1581 - >seq4904,non-specific,313357,321,464,0.00423252,39.172,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12325,Q#1581 - >seq4904,superfamily,321788,321,464,0.00423252,39.172,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs2_gorilla.marg.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4a,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12326,Q#1584 - >seq4907,specific,197310,9,231,7.546609999999998e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12327,Q#1584 - >seq4907,superfamily,351117,9,231,7.546609999999998e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12328,Q#1584 - >seq4907,specific,238827,519,748,2.4791899999999997e-44,159.764,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12329,Q#1584 - >seq4907,superfamily,295487,519,748,2.4791899999999997e-44,159.764,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12330,Q#1584 - >seq4907,non-specific,197306,9,229,9.190989999999999e-38,141.85,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12331,Q#1584 - >seq4907,non-specific,333820,508,748,5.06858e-21,91.5849,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12332,Q#1584 - >seq4907,superfamily,333820,508,748,5.06858e-21,91.5849,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12333,Q#1584 - >seq4907,non-specific,197307,9,229,1.9700900000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12334,Q#1584 - >seq4907,non-specific,223780,9,229,2.90429e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12335,Q#1584 - >seq4907,non-specific,197320,9,194,4.20991e-20,90.6521,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12336,Q#1584 - >seq4907,non-specific,197321,7,229,2.88696e-19,88.37799999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12337,Q#1584 - >seq4907,specific,335306,10,229,1.4836e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12338,Q#1584 - >seq4907,non-specific,273186,9,229,8.41596e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12339,Q#1584 - >seq4907,non-specific,272954,9,194,3.5272400000000002e-12,67.4081,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12340,Q#1584 - >seq4907,non-specific,197319,13,229,3.89091e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12341,Q#1584 - >seq4907,non-specific,238828,540,713,1.61783e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12342,Q#1584 - >seq4907,non-specific,236970,9,194,3.62273e-09,58.7522,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12343,Q#1584 - >seq4907,non-specific,197336,9,194,5.99753e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12344,Q#1584 - >seq4907,non-specific,275209,563,772,1.50727e-06,51.3044,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12345,Q#1584 - >seq4907,superfamily,275209,563,772,1.50727e-06,51.3044,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12346,Q#1584 - >seq4907,non-specific,238185,632,746,0.00369603,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs2_gorilla.pars.frame2,1909130924_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4a,ORF2,hs2_gorilla,pars,CompleteHit
12347,Q#1585 - >seq4908,non-specific,238827,610,700,4.9505e-16,78.1018,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs4_gibbon.pars.frame1,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12348,Q#1585 - >seq4908,superfamily,295487,610,700,4.9505e-16,78.1018,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs4_gibbon.pars.frame1,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12349,Q#1585 - >seq4908,non-specific,333820,617,700,0.00084753,41.1238,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.pars.frame1,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12350,Q#1585 - >seq4908,superfamily,333820,617,700,0.00084753,41.1238,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs4_gibbon.pars.frame1,1909130924_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12351,Q#1590 - >seq4913,specific,238827,510,772,5.212789999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12352,Q#1590 - >seq4913,superfamily,295487,510,772,5.212789999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12353,Q#1590 - >seq4913,specific,197310,9,236,4.22518e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12354,Q#1590 - >seq4913,superfamily,351117,9,236,4.22518e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12355,Q#1590 - >seq4913,non-specific,197306,9,236,1.2335299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12356,Q#1590 - >seq4913,specific,333820,516,772,2.93727e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12357,Q#1590 - >seq4913,superfamily,333820,516,772,2.93727e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12358,Q#1590 - >seq4913,non-specific,197307,9,236,2.1283700000000005e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12359,Q#1590 - >seq4913,non-specific,223780,9,238,1.2913099999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12360,Q#1590 - >seq4913,non-specific,197320,8,236,1.93563e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12361,Q#1590 - >seq4913,non-specific,197321,7,236,6.91411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12362,Q#1590 - >seq4913,specific,335306,10,229,1.32427e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12363,Q#1590 - >seq4913,non-specific,273186,9,237,7.54038e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12364,Q#1590 - >seq4913,non-specific,272954,9,236,1.54873e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12365,Q#1590 - >seq4913,non-specific,197319,8,236,4.39545e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12366,Q#1590 - >seq4913,non-specific,197336,7,235,2.6802599999999997e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12367,Q#1590 - >seq4913,non-specific,238828,516,737,2.25636e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12368,Q#1590 - >seq4913,non-specific,197322,9,236,2.74523e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12369,Q#1590 - >seq4913,non-specific,275209,467,800,4.3863800000000003e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12370,Q#1590 - >seq4913,superfamily,275209,467,800,4.3863800000000003e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12371,Q#1590 - >seq4913,non-specific,236970,9,238,4.07488e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12372,Q#1590 - >seq4913,non-specific,339261,108,232,1.64277e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12373,Q#1590 - >seq4913,non-specific,197311,7,236,1.9721e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12374,Q#1590 - >seq4913,non-specific,197317,139,229,1.2963999999999998e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12375,Q#1590 - >seq4913,non-specific,238185,656,772,0.00017040799999999999,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12376,Q#1590 - >seq4913,non-specific,274009,305,453,0.00093257,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12377,Q#1590 - >seq4913,superfamily,274009,305,453,0.00093257,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12378,Q#1590 - >seq4913,non-specific,226098,138,239,0.00165679,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12379,Q#1590 - >seq4913,non-specific,197314,7,192,0.00193556,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12380,Q#1590 - >seq4913,non-specific,235175,295,464,0.00371069,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
12381,Q#1590 - >seq4913,superfamily,235175,295,464,0.00371069,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
12382,Q#1590 - >seq4913,non-specific,274008,263,500,0.00590101,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12383,Q#1590 - >seq4913,superfamily,274008,263,500,0.00590101,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12384,Q#1590 - >seq4913,non-specific,239569,525,748,0.00859876,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,pars,CompleteHit
12385,Q#1590 - >seq4913,non-specific,293702,337,451,0.00889232,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12386,Q#1590 - >seq4913,superfamily,293702,337,451,0.00889232,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12387,Q#1593 - >seq4916,specific,238827,510,772,4.794359999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12388,Q#1593 - >seq4916,superfamily,295487,510,772,4.794359999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12389,Q#1593 - >seq4916,specific,197310,9,236,4.066839999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12390,Q#1593 - >seq4916,superfamily,351117,9,236,4.066839999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12391,Q#1593 - >seq4916,non-specific,197306,9,236,1.43484e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12392,Q#1593 - >seq4916,specific,333820,516,772,2.81398e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12393,Q#1593 - >seq4916,superfamily,333820,516,772,2.81398e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12394,Q#1593 - >seq4916,non-specific,197307,9,236,2.16113e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12395,Q#1593 - >seq4916,non-specific,223780,9,238,1.41481e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12396,Q#1593 - >seq4916,non-specific,197320,8,236,1.94675e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12397,Q#1593 - >seq4916,non-specific,197321,7,236,6.95376e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12398,Q#1593 - >seq4916,specific,335306,10,229,1.33167e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12399,Q#1593 - >seq4916,non-specific,273186,9,237,8.10296e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12400,Q#1593 - >seq4916,non-specific,272954,9,236,1.66355e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12401,Q#1593 - >seq4916,non-specific,197319,8,236,4.54659e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12402,Q#1593 - >seq4916,non-specific,197336,7,235,2.90436e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12403,Q#1593 - >seq4916,non-specific,238828,516,737,2.26891e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12404,Q#1593 - >seq4916,non-specific,197322,9,236,2.76126e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12405,Q#1593 - >seq4916,non-specific,275209,467,800,4.3343800000000004e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12406,Q#1593 - >seq4916,superfamily,275209,467,800,4.3343800000000004e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12407,Q#1593 - >seq4916,non-specific,236970,9,238,4.21223e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12408,Q#1593 - >seq4916,non-specific,339261,108,232,1.65125e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12409,Q#1593 - >seq4916,non-specific,197311,7,236,2.03931e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12410,Q#1593 - >seq4916,non-specific,197317,139,229,1.35204e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,marg,N-TerminusTruncated
12411,Q#1593 - >seq4916,non-specific,238185,656,772,0.000171275,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12412,Q#1593 - >seq4916,non-specific,274009,305,453,0.000937853,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,C-TerminusTruncated
12413,Q#1593 - >seq4916,superfamily,274009,305,453,0.000937853,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,C-TerminusTruncated
12414,Q#1593 - >seq4916,non-specific,226098,138,239,0.00166586,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,marg,N-TerminusTruncated
12415,Q#1593 - >seq4916,non-specific,197314,7,192,0.00196365,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P1,ORF2,hs1_chimp,marg,C-TerminusTruncated
12416,Q#1593 - >seq4916,non-specific,235175,295,464,0.00360705,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,BothTerminiTruncated
12417,Q#1593 - >seq4916,superfamily,235175,295,464,0.00360705,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,BothTerminiTruncated
12418,Q#1593 - >seq4916,non-specific,274008,263,500,0.00564051,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,N-TerminusTruncated
12419,Q#1593 - >seq4916,superfamily,274008,263,500,0.00564051,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,marg,N-TerminusTruncated
12420,Q#1593 - >seq4916,non-specific,239569,525,748,0.0083363,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs1_chimp,marg,CompleteHit
12421,Q#1593 - >seq4916,non-specific,293702,337,451,0.008864200000000001,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs1_chimp,marg,C-TerminusTruncated
12422,Q#1593 - >seq4916,superfamily,293702,337,451,0.008864200000000001,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs1_chimp.marg.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs1_chimp,marg,C-TerminusTruncated
12423,Q#1595 - >seq4918,specific,238827,510,772,1.4262599999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12424,Q#1595 - >seq4918,superfamily,295487,510,772,1.4262599999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12425,Q#1595 - >seq4918,specific,197310,9,236,5.060329999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12426,Q#1595 - >seq4918,superfamily,351117,9,236,5.060329999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12427,Q#1595 - >seq4918,non-specific,197306,9,236,1.64763e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12428,Q#1595 - >seq4918,specific,333820,516,772,2.96122e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12429,Q#1595 - >seq4918,superfamily,333820,516,772,2.96122e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12430,Q#1595 - >seq4918,non-specific,197307,9,236,2.40736e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12431,Q#1595 - >seq4918,non-specific,223780,9,238,1.5604e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12432,Q#1595 - >seq4918,non-specific,197320,8,236,2.1265300000000003e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12433,Q#1595 - >seq4918,non-specific,197321,7,236,7.175050000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12434,Q#1595 - >seq4918,specific,335306,10,229,1.33537e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12435,Q#1595 - >seq4918,non-specific,273186,9,237,8.682540000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12436,Q#1595 - >seq4918,non-specific,272954,9,236,1.66827e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12437,Q#1595 - >seq4918,non-specific,197319,8,236,4.4329400000000006e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12438,Q#1595 - >seq4918,non-specific,197336,7,235,2.80585e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12439,Q#1595 - >seq4918,non-specific,238828,516,737,2.2539e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12440,Q#1595 - >seq4918,non-specific,197322,9,236,2.76928e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12441,Q#1595 - >seq4918,non-specific,275209,467,800,9.60509e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12442,Q#1595 - >seq4918,superfamily,275209,467,800,9.60509e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12443,Q#1595 - >seq4918,non-specific,236970,9,238,4.3818299999999995e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12444,Q#1595 - >seq4918,non-specific,339261,108,232,1.82405e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12445,Q#1595 - >seq4918,non-specific,197311,7,236,2.04483e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12446,Q#1595 - >seq4918,non-specific,197317,139,229,1.45838e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12447,Q#1595 - >seq4918,non-specific,238185,656,772,0.00017680299999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs2_gorilla,pars,CompleteHit
12448,Q#1595 - >seq4918,non-specific,274009,305,453,0.00090921,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12449,Q#1595 - >seq4918,superfamily,274009,305,453,0.00090921,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12450,Q#1595 - >seq4918,non-specific,226098,138,239,0.00167039,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12451,Q#1595 - >seq4918,non-specific,197314,7,192,0.00195139,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12452,Q#1595 - >seq4918,non-specific,235175,295,464,0.00335135,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
12453,Q#1595 - >seq4918,superfamily,235175,295,464,0.00335135,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
12454,Q#1595 - >seq4918,non-specific,274008,263,500,0.00494052,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12455,Q#1595 - >seq4918,superfamily,274008,263,500,0.00494052,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
12456,Q#1595 - >seq4918,non-specific,293702,337,451,0.00808057,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12457,Q#1595 - >seq4918,superfamily,293702,337,451,0.00808057,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs2_gorilla.pars.frame3,1909130924_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
12458,Q#1597 - >seq4920,specific,238827,510,772,5.432939999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12459,Q#1597 - >seq4920,superfamily,295487,510,772,5.432939999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12460,Q#1597 - >seq4920,specific,197310,9,236,4.5744499999999994e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12461,Q#1597 - >seq4920,superfamily,351117,9,236,4.5744499999999994e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12462,Q#1597 - >seq4920,non-specific,197306,9,236,1.3211900000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12463,Q#1597 - >seq4920,specific,333820,516,772,3.05576e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12464,Q#1597 - >seq4920,superfamily,333820,516,772,3.05576e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12465,Q#1597 - >seq4920,non-specific,197307,9,236,2.15085e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12466,Q#1597 - >seq4920,non-specific,223780,9,238,1.42148e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12467,Q#1597 - >seq4920,non-specific,197320,8,236,2.05111e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12468,Q#1597 - >seq4920,non-specific,197321,7,236,6.986729999999999e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12469,Q#1597 - >seq4920,specific,335306,10,229,1.3255100000000001e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12470,Q#1597 - >seq4920,non-specific,273186,9,237,7.691800000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12471,Q#1597 - >seq4920,non-specific,272954,9,236,1.62484e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12472,Q#1597 - >seq4920,non-specific,197319,8,236,4.39962e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12473,Q#1597 - >seq4920,non-specific,197336,7,235,2.7848200000000002e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12474,Q#1597 - >seq4920,non-specific,238828,516,737,2.36711e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12475,Q#1597 - >seq4920,non-specific,197322,9,236,2.7478999999999996e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12476,Q#1597 - >seq4920,non-specific,275209,467,800,4.55008e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12477,Q#1597 - >seq4920,superfamily,275209,467,800,4.55008e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12478,Q#1597 - >seq4920,non-specific,236970,9,238,4.23105e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12479,Q#1597 - >seq4920,non-specific,339261,108,232,1.69271e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12480,Q#1597 - >seq4920,non-specific,197311,7,236,2.20851e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12481,Q#1597 - >seq4920,non-specific,197317,139,229,1.37058e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,pars,N-TerminusTruncated
12482,Q#1597 - >seq4920,non-specific,238185,656,772,0.000173909,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12483,Q#1597 - >seq4920,non-specific,274009,305,453,0.000965571,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,C-TerminusTruncated
12484,Q#1597 - >seq4920,superfamily,274009,305,453,0.000965571,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,C-TerminusTruncated
12485,Q#1597 - >seq4920,non-specific,226098,138,239,0.0016583,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs1_chimp,pars,N-TerminusTruncated
12486,Q#1597 - >seq4920,non-specific,197314,7,192,0.00200808,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P1,ORF2,hs1_chimp,pars,C-TerminusTruncated
12487,Q#1597 - >seq4920,non-specific,235175,295,464,0.00362086,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,BothTerminiTruncated
12488,Q#1597 - >seq4920,superfamily,235175,295,464,0.00362086,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,BothTerminiTruncated
12489,Q#1597 - >seq4920,non-specific,274008,263,500,0.00575857,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,N-TerminusTruncated
12490,Q#1597 - >seq4920,superfamily,274008,263,500,0.00575857,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs1_chimp,pars,N-TerminusTruncated
12491,Q#1597 - >seq4920,non-specific,239569,525,748,0.00876436,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs1_chimp,pars,CompleteHit
12492,Q#1597 - >seq4920,non-specific,293702,337,451,0.00890049,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs1_chimp,pars,C-TerminusTruncated
12493,Q#1597 - >seq4920,superfamily,293702,337,451,0.00890049,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs1_chimp.pars.frame3,1909130924_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs1_chimp,pars,C-TerminusTruncated
12494,Q#1602 - >seq4925,non-specific,197310,94,191,1.46276e-05,47.3461,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs3_orang.marg.frame1,1909130924_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEg,ORF2,hs3_orang,marg,N-TerminusTruncated
12495,Q#1602 - >seq4925,superfamily,351117,94,191,1.46276e-05,47.3461,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs3_orang.marg.frame1,1909130924_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEg,ORF2,hs3_orang,marg,N-TerminusTruncated
12496,Q#1602 - >seq4925,non-specific,238827,421,498,0.00167283,40.7374,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEg.ORF2.hs3_orang.marg.frame1,1909130924_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs3_orang,marg,C-TerminusTruncated
12497,Q#1602 - >seq4925,superfamily,295487,421,498,0.00167283,40.7374,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEg.ORF2.hs3_orang.marg.frame1,1909130924_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs3_orang,marg,C-TerminusTruncated
12498,Q#1612 - >seq4935,specific,238827,510,772,5.212789999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12499,Q#1612 - >seq4935,superfamily,295487,510,772,5.212789999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12500,Q#1612 - >seq4935,specific,197310,9,236,4.22518e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12501,Q#1612 - >seq4935,superfamily,351117,9,236,4.22518e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12502,Q#1612 - >seq4935,non-specific,197306,9,236,1.2335299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12503,Q#1612 - >seq4935,specific,333820,516,772,2.93727e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12504,Q#1612 - >seq4935,superfamily,333820,516,772,2.93727e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12505,Q#1612 - >seq4935,non-specific,197307,9,236,2.1283700000000005e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12506,Q#1612 - >seq4935,non-specific,223780,9,238,1.2913099999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12507,Q#1612 - >seq4935,non-specific,197320,8,236,1.93563e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12508,Q#1612 - >seq4935,non-specific,197321,7,236,6.91411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12509,Q#1612 - >seq4935,specific,335306,10,229,1.32427e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12510,Q#1612 - >seq4935,non-specific,273186,9,237,7.54038e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12511,Q#1612 - >seq4935,non-specific,272954,9,236,1.54873e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12512,Q#1612 - >seq4935,non-specific,197319,8,236,4.39545e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12513,Q#1612 - >seq4935,non-specific,197336,7,235,2.6802599999999997e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12514,Q#1612 - >seq4935,non-specific,238828,516,737,2.25636e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12515,Q#1612 - >seq4935,non-specific,197322,9,236,2.74523e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12516,Q#1612 - >seq4935,non-specific,275209,467,800,4.3863800000000003e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12517,Q#1612 - >seq4935,superfamily,275209,467,800,4.3863800000000003e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12518,Q#1612 - >seq4935,non-specific,236970,9,238,4.07488e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12519,Q#1612 - >seq4935,non-specific,339261,108,232,1.64277e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12520,Q#1612 - >seq4935,non-specific,197311,7,236,1.9721e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12521,Q#1612 - >seq4935,non-specific,197317,139,229,1.2963999999999998e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12522,Q#1612 - >seq4935,non-specific,238185,656,772,0.00017040799999999999,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12523,Q#1612 - >seq4935,non-specific,274009,305,453,0.00093257,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12524,Q#1612 - >seq4935,superfamily,274009,305,453,0.00093257,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12525,Q#1612 - >seq4935,non-specific,226098,138,239,0.00165679,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12526,Q#1612 - >seq4935,non-specific,197314,7,192,0.00193556,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12527,Q#1612 - >seq4935,non-specific,235175,295,464,0.00371069,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12528,Q#1612 - >seq4935,superfamily,235175,295,464,0.00371069,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
12529,Q#1612 - >seq4935,non-specific,274008,263,500,0.00590101,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12530,Q#1612 - >seq4935,superfamily,274008,263,500,0.00590101,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
12531,Q#1612 - >seq4935,non-specific,239569,525,748,0.00859876,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs2_gorilla,marg,CompleteHit
12532,Q#1612 - >seq4935,non-specific,293702,337,451,0.00889232,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12533,Q#1612 - >seq4935,superfamily,293702,337,451,0.00889232,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs2_gorilla.marg.frame3,1909130924_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
12534,Q#1617 - >seq4940,specific,238827,510,772,1.5951899999999998e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12535,Q#1617 - >seq4940,superfamily,295487,510,772,1.5951899999999998e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12536,Q#1617 - >seq4940,specific,197310,9,236,1.1808499999999997e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12537,Q#1617 - >seq4940,superfamily,351117,9,236,1.1808499999999997e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12538,Q#1617 - >seq4940,non-specific,197306,9,236,2.5005399999999997e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12539,Q#1617 - >seq4940,specific,333820,516,772,3.17409e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12540,Q#1617 - >seq4940,superfamily,333820,516,772,3.17409e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12541,Q#1617 - >seq4940,non-specific,197307,9,236,3.3691100000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12542,Q#1617 - >seq4940,non-specific,223780,9,238,2.2457500000000002e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12543,Q#1617 - >seq4940,non-specific,197320,8,236,2.01255e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12544,Q#1617 - >seq4940,non-specific,197321,7,236,2.6023000000000003e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12545,Q#1617 - >seq4940,non-specific,273186,9,237,1.0629000000000001e-19,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12546,Q#1617 - >seq4940,specific,335306,10,229,1.28773e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12547,Q#1617 - >seq4940,non-specific,272954,9,236,2.2088099999999997e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12548,Q#1617 - >seq4940,non-specific,197319,8,236,4.24512e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12549,Q#1617 - >seq4940,non-specific,197336,7,235,6.42762e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12550,Q#1617 - >seq4940,non-specific,197322,9,236,2.72457e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12551,Q#1617 - >seq4940,non-specific,238828,516,737,1.34403e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12552,Q#1617 - >seq4940,non-specific,275209,467,800,9.79668e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12553,Q#1617 - >seq4940,superfamily,275209,467,800,9.79668e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12554,Q#1617 - >seq4940,non-specific,236970,9,238,1.14976e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12555,Q#1617 - >seq4940,non-specific,339261,108,232,2.12236e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12556,Q#1617 - >seq4940,non-specific,197311,7,236,1.6437400000000002e-08,55.7609,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12557,Q#1617 - >seq4940,non-specific,197317,139,229,2.3682e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,marg,N-TerminusTruncated
12558,Q#1617 - >seq4940,non-specific,238185,656,772,0.00017710099999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs1_chimp,marg,CompleteHit
12559,Q#1617 - >seq4940,non-specific,226098,138,239,0.000478507,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,marg,N-TerminusTruncated
12560,Q#1617 - >seq4940,non-specific,274009,305,453,0.0009109130000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,C-TerminusTruncated
12561,Q#1617 - >seq4940,superfamily,274009,305,453,0.0009109130000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,C-TerminusTruncated
12562,Q#1617 - >seq4940,non-specific,197314,7,192,0.00192016,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs1_chimp,marg,C-TerminusTruncated
12563,Q#1617 - >seq4940,non-specific,274008,157,500,0.00338321,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,N-TerminusTruncated
12564,Q#1617 - >seq4940,superfamily,274008,157,500,0.00338321,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,N-TerminusTruncated
12565,Q#1617 - >seq4940,non-specific,235175,295,464,0.00341499,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,BothTerminiTruncated
12566,Q#1617 - >seq4940,superfamily,235175,295,464,0.00341499,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,marg,BothTerminiTruncated
12567,Q#1617 - >seq4940,non-specific,293702,337,451,0.0080953,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs1_chimp,marg,C-TerminusTruncated
12568,Q#1617 - >seq4940,superfamily,293702,337,451,0.0080953,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs1_chimp.marg.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs1_chimp,marg,C-TerminusTruncated
12569,Q#1619 - >seq4942,specific,238827,510,772,1.7239999999999994e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12570,Q#1619 - >seq4942,superfamily,295487,510,772,1.7239999999999994e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12571,Q#1619 - >seq4942,specific,197310,9,236,1.3899899999999997e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12572,Q#1619 - >seq4942,superfamily,351117,9,236,1.3899899999999997e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12573,Q#1619 - >seq4942,non-specific,197306,9,236,2.1920299999999995e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12574,Q#1619 - >seq4942,specific,333820,516,772,3.10576e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12575,Q#1619 - >seq4942,superfamily,333820,516,772,3.10576e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12576,Q#1619 - >seq4942,non-specific,197307,9,236,3.0214e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12577,Q#1619 - >seq4942,non-specific,223780,9,238,1.93899e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12578,Q#1619 - >seq4942,non-specific,197320,8,236,1.94821e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12579,Q#1619 - >seq4942,non-specific,197321,7,236,2.3571e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12580,Q#1619 - >seq4942,non-specific,273186,9,237,9.35947e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12581,Q#1619 - >seq4942,specific,335306,10,229,1.25924e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12582,Q#1619 - >seq4942,non-specific,272954,9,236,1.85674e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12583,Q#1619 - >seq4942,non-specific,197319,8,236,3.8127099999999996e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12584,Q#1619 - >seq4942,non-specific,197336,7,235,5.163109999999999e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12585,Q#1619 - >seq4942,non-specific,197322,9,236,2.66159e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12586,Q#1619 - >seq4942,non-specific,238828,516,737,1.35197e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12587,Q#1619 - >seq4942,non-specific,275209,467,800,9.233080000000001e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12588,Q#1619 - >seq4942,superfamily,275209,467,800,9.233080000000001e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12589,Q#1619 - >seq4942,non-specific,236970,9,238,1.0347000000000002e-09,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12590,Q#1619 - >seq4942,non-specific,339261,108,232,2.1822199999999995e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12591,Q#1619 - >seq4942,non-specific,197311,7,236,1.5343799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12592,Q#1619 - >seq4942,non-specific,197317,139,229,2.25365e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,pars,N-TerminusTruncated
12593,Q#1619 - >seq4942,non-specific,238185,656,772,0.000166894,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs1_chimp,pars,CompleteHit
12594,Q#1619 - >seq4942,non-specific,226098,138,239,0.000468098,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs1_chimp,pars,N-TerminusTruncated
12595,Q#1619 - >seq4942,non-specific,274009,305,453,0.00103692,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,C-TerminusTruncated
12596,Q#1619 - >seq4942,superfamily,274009,305,453,0.00103692,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,C-TerminusTruncated
12597,Q#1619 - >seq4942,non-specific,197314,7,192,0.00186191,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs1_chimp,pars,C-TerminusTruncated
12598,Q#1619 - >seq4942,non-specific,235175,295,464,0.00441741,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,BothTerminiTruncated
12599,Q#1619 - >seq4942,superfamily,235175,295,464,0.00441741,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,BothTerminiTruncated
12600,Q#1619 - >seq4942,non-specific,274008,157,500,0.00563553,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,N-TerminusTruncated
12601,Q#1619 - >seq4942,superfamily,274008,157,500,0.00563553,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs1_chimp,pars,N-TerminusTruncated
12602,Q#1619 - >seq4942,non-specific,293702,337,451,0.00878617,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs1_chimp,pars,C-TerminusTruncated
12603,Q#1619 - >seq4942,superfamily,293702,337,451,0.00878617,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs1_chimp.pars.frame3,1909130924_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs1_chimp,pars,C-TerminusTruncated
12604,Q#1622 - >seq4945,specific,238827,510,772,5.420249999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12605,Q#1622 - >seq4945,superfamily,295487,510,772,5.420249999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12606,Q#1622 - >seq4945,specific,197310,9,236,4.522359999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12607,Q#1622 - >seq4945,superfamily,351117,9,236,4.522359999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12608,Q#1622 - >seq4945,non-specific,197306,9,236,1.4257699999999997e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12609,Q#1622 - >seq4945,specific,333820,516,772,3.053e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12610,Q#1622 - >seq4945,superfamily,333820,516,772,3.053e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12611,Q#1622 - >seq4945,non-specific,197307,9,236,2.14879e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12612,Q#1622 - >seq4945,non-specific,223780,9,238,1.32867e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12613,Q#1622 - >seq4945,non-specific,197320,8,236,2.04915e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12614,Q#1622 - >seq4945,non-specific,197321,7,236,6.91411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12615,Q#1622 - >seq4945,specific,335306,10,229,1.32427e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12616,Q#1622 - >seq4945,non-specific,273186,9,237,7.905749999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12617,Q#1622 - >seq4945,non-specific,272954,9,236,1.54873e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12618,Q#1622 - >seq4945,non-specific,197319,8,236,4.39545e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12619,Q#1622 - >seq4945,non-specific,197336,7,235,2.75635e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12620,Q#1622 - >seq4945,non-specific,238828,516,737,2.25636e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12621,Q#1622 - >seq4945,non-specific,197322,9,236,2.74523e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12622,Q#1622 - >seq4945,non-specific,275209,467,800,4.19516e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12623,Q#1622 - >seq4945,superfamily,275209,467,800,4.19516e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12624,Q#1622 - >seq4945,non-specific,236970,9,238,3.78675e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12625,Q#1622 - >seq4945,non-specific,339261,108,232,1.74117e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12626,Q#1622 - >seq4945,non-specific,197311,7,236,2.16559e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,marg,CompleteHit
12627,Q#1622 - >seq4945,non-specific,197317,139,229,1.32026e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,marg,N-TerminusTruncated
12628,Q#1622 - >seq4945,non-specific,238185,656,772,0.00017040799999999999,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12629,Q#1622 - >seq4945,non-specific,274009,305,453,0.000886425,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,C-TerminusTruncated
12630,Q#1622 - >seq4945,superfamily,274009,305,453,0.000886425,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,C-TerminusTruncated
12631,Q#1622 - >seq4945,non-specific,226098,138,239,0.00165679,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,marg,N-TerminusTruncated
12632,Q#1622 - >seq4945,non-specific,197314,7,192,0.00191828,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P1,ORF2,hs0_human,marg,C-TerminusTruncated
12633,Q#1622 - >seq4945,non-specific,235175,295,464,0.00332338,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,BothTerminiTruncated
12634,Q#1622 - >seq4945,superfamily,235175,295,464,0.00332338,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,BothTerminiTruncated
12635,Q#1622 - >seq4945,non-specific,274008,263,500,0.0056091,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,N-TerminusTruncated
12636,Q#1622 - >seq4945,superfamily,274008,263,500,0.0056091,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,marg,N-TerminusTruncated
12637,Q#1622 - >seq4945,non-specific,293702,337,451,0.0086642,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs0_human,marg,C-TerminusTruncated
12638,Q#1622 - >seq4945,superfamily,293702,337,451,0.0086642,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs0_human,marg,C-TerminusTruncated
12639,Q#1622 - >seq4945,non-specific,239569,525,748,0.00883647,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs0_human.marg.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs0_human,marg,CompleteHit
12640,Q#1625 - >seq4948,specific,197310,9,236,1.5067299999999998e-63,215.678,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12641,Q#1625 - >seq4948,superfamily,351117,9,236,1.5067299999999998e-63,215.678,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12642,Q#1625 - >seq4948,specific,238827,510,768,4.6925999999999996e-63,213.692,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12643,Q#1625 - >seq4948,superfamily,295487,510,768,4.6925999999999996e-63,213.692,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12644,Q#1625 - >seq4948,non-specific,197306,9,236,2.7159e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12645,Q#1625 - >seq4948,specific,333820,516,740,5.48346e-36,134.727,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12646,Q#1625 - >seq4948,superfamily,333820,516,740,5.48346e-36,134.727,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12647,Q#1625 - >seq4948,non-specific,197307,9,236,5.222719999999999e-28,113.92200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12648,Q#1625 - >seq4948,non-specific,223780,9,238,8.023650000000001e-25,104.988,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12649,Q#1625 - >seq4948,non-specific,197321,7,236,3.27442e-22,97.2376,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12650,Q#1625 - >seq4948,non-specific,197320,8,236,7.137639999999999e-22,96.0449,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12651,Q#1625 - >seq4948,specific,335306,10,229,1.27617e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12652,Q#1625 - >seq4948,non-specific,273186,9,237,1.42428e-19,89.2604,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12653,Q#1625 - >seq4948,non-specific,272954,9,236,9.09683e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12654,Q#1625 - >seq4948,non-specific,197319,8,236,1.0242900000000001e-15,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12655,Q#1625 - >seq4948,non-specific,197336,7,235,1.98783e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12656,Q#1625 - >seq4948,non-specific,238828,516,737,2.25128e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12657,Q#1625 - >seq4948,non-specific,197322,9,236,2.6410000000000002e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12658,Q#1625 - >seq4948,non-specific,236970,9,238,1.2236500000000002e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12659,Q#1625 - >seq4948,non-specific,275209,467,737,1.6470499999999998e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,C-TerminusTruncated
12660,Q#1625 - >seq4948,superfamily,275209,467,737,1.6470499999999998e-09,60.9344,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,C-TerminusTruncated
12661,Q#1625 - >seq4948,non-specific,339261,108,232,3.0994200000000004e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12662,Q#1625 - >seq4948,non-specific,197311,7,236,1.16895e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs0_human,pars,CompleteHit
12663,Q#1625 - >seq4948,non-specific,197317,139,229,1.15102e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,pars,N-TerminusTruncated
12664,Q#1625 - >seq4948,non-specific,238185,656,740,0.00037361800000000004,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12665,Q#1625 - >seq4948,non-specific,274009,305,453,0.000861023,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,pars,C-TerminusTruncated
12666,Q#1625 - >seq4948,superfamily,274009,305,453,0.000861023,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,pars,C-TerminusTruncated
12667,Q#1625 - >seq4948,non-specific,235175,295,464,0.00128116,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,pars,BothTerminiTruncated
12668,Q#1625 - >seq4948,superfamily,235175,295,464,0.00128116,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs0_human,pars,BothTerminiTruncated
12669,Q#1625 - >seq4948,non-specific,226098,138,239,0.00159788,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs0_human,pars,N-TerminusTruncated
12670,Q#1625 - >seq4948,non-specific,197314,7,192,0.00181738,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P1,ORF2,hs0_human,pars,C-TerminusTruncated
12671,Q#1625 - >seq4948,non-specific,239569,525,748,0.00321974,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs0_human.pars.frame3,1909130924_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs0_human,pars,CompleteHit
12672,Q#1630 - >seq4953,specific,238827,510,772,5.834949999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12673,Q#1630 - >seq4953,superfamily,295487,510,772,5.834949999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12674,Q#1630 - >seq4953,specific,197310,9,236,4.652439999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12675,Q#1630 - >seq4953,superfamily,351117,9,236,4.652439999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12676,Q#1630 - >seq4953,non-specific,197306,9,236,1.48471e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12677,Q#1630 - >seq4953,specific,333820,516,772,1.71042e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12678,Q#1630 - >seq4953,superfamily,333820,516,772,1.71042e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12679,Q#1630 - >seq4953,non-specific,197307,9,236,2.1507700000000002e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12680,Q#1630 - >seq4953,non-specific,223780,9,238,1.35558e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12681,Q#1630 - >seq4953,non-specific,197320,8,236,2.01255e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12682,Q#1630 - >seq4953,non-specific,197321,7,236,6.9868e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12683,Q#1630 - >seq4953,specific,335306,10,229,1.33784e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12684,Q#1630 - >seq4953,non-specific,273186,9,237,7.83901e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12685,Q#1630 - >seq4953,non-specific,272954,9,236,1.56493e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12686,Q#1630 - >seq4953,non-specific,197319,8,236,4.44127e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12687,Q#1630 - >seq4953,non-specific,197336,7,235,2.785e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12688,Q#1630 - >seq4953,non-specific,197322,9,236,2.77462e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12689,Q#1630 - >seq4953,non-specific,238828,516,737,2.82931e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12690,Q#1630 - >seq4953,non-specific,275209,467,800,2.0773300000000002e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12691,Q#1630 - >seq4953,superfamily,275209,467,800,2.0773300000000002e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12692,Q#1630 - >seq4953,non-specific,236970,9,238,4.1172299999999994e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12693,Q#1630 - >seq4953,non-specific,339261,108,232,1.7406999999999998e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12694,Q#1630 - >seq4953,non-specific,197311,7,236,2.24949e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,marg,CompleteHit
12695,Q#1630 - >seq4953,non-specific,197317,139,229,1.32162e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,marg,N-TerminusTruncated
12696,Q#1630 - >seq4953,non-specific,238185,656,772,0.000165421,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12697,Q#1630 - >seq4953,non-specific,274009,305,453,0.000895635,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,C-TerminusTruncated
12698,Q#1630 - >seq4953,superfamily,274009,305,453,0.000895635,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,C-TerminusTruncated
12699,Q#1630 - >seq4953,non-specific,226098,138,239,0.00167341,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,marg,N-TerminusTruncated
12700,Q#1630 - >seq4953,non-specific,197314,7,192,0.00195491,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P1,ORF2,hs3_orang,marg,C-TerminusTruncated
12701,Q#1630 - >seq4953,non-specific,235175,295,464,0.00335757,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,BothTerminiTruncated
12702,Q#1630 - >seq4953,superfamily,235175,295,464,0.00335757,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,BothTerminiTruncated
12703,Q#1630 - >seq4953,non-specific,239569,525,748,0.00419326,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs3_orang,marg,CompleteHit
12704,Q#1630 - >seq4953,non-specific,274008,263,500,0.0056667,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,N-TerminusTruncated
12705,Q#1630 - >seq4953,superfamily,274008,263,500,0.0056667,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,marg,N-TerminusTruncated
12706,Q#1630 - >seq4953,non-specific,293702,337,451,0.00867624,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs3_orang,marg,C-TerminusTruncated
12707,Q#1630 - >seq4953,superfamily,293702,337,451,0.00867624,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs3_orang.marg.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs3_orang,marg,C-TerminusTruncated
12708,Q#1633 - >seq4956,specific,238827,510,772,9.810769999999998e-67,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12709,Q#1633 - >seq4956,superfamily,295487,510,772,9.810769999999998e-67,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12710,Q#1633 - >seq4956,specific,197310,9,236,3.9218999999999994e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12711,Q#1633 - >seq4956,superfamily,351117,9,236,3.9218999999999994e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12712,Q#1633 - >seq4956,non-specific,197306,9,236,1.07746e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12713,Q#1633 - >seq4956,specific,333820,516,772,2.01817e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12714,Q#1633 - >seq4956,superfamily,333820,516,772,2.01817e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12715,Q#1633 - >seq4956,non-specific,197307,9,236,1.66187e-26,109.685,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12716,Q#1633 - >seq4956,non-specific,223780,9,238,1.0994500000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12717,Q#1633 - >seq4956,non-specific,197320,8,236,1.72858e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12718,Q#1633 - >seq4956,non-specific,197321,7,236,5.5624999999999996e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12719,Q#1633 - >seq4956,specific,335306,10,229,1.31317e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12720,Q#1633 - >seq4956,non-specific,273186,9,237,6.736480000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12721,Q#1633 - >seq4956,non-specific,272954,9,236,1.24846e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12722,Q#1633 - >seq4956,non-specific,197319,8,236,3.82164e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12723,Q#1633 - >seq4956,non-specific,197336,7,235,2.28889e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12724,Q#1633 - >seq4956,non-specific,197322,9,236,2.72117e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12725,Q#1633 - >seq4956,non-specific,238828,516,737,5.61764e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12726,Q#1633 - >seq4956,non-specific,275209,467,800,3.541369999999999e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12727,Q#1633 - >seq4956,superfamily,275209,467,800,3.541369999999999e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12728,Q#1633 - >seq4956,non-specific,236970,9,238,3.72029e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12729,Q#1633 - >seq4956,non-specific,339261,108,232,1.67816e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12730,Q#1633 - >seq4956,non-specific,197311,7,236,2.0305999999999997e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12731,Q#1633 - >seq4956,non-specific,197317,139,229,1.26234e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12732,Q#1633 - >seq4956,non-specific,238185,656,772,0.000280714,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,pars,CompleteHit
12733,Q#1633 - >seq4956,non-specific,274009,305,453,0.000981045,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12734,Q#1633 - >seq4956,superfamily,274009,305,453,0.000981045,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12735,Q#1633 - >seq4956,non-specific,226098,138,239,0.0016432000000000003,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12736,Q#1633 - >seq4956,non-specific,197314,7,192,0.0018855999999999999,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12737,Q#1633 - >seq4956,non-specific,235175,295,464,0.00329541,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12738,Q#1633 - >seq4956,superfamily,235175,295,464,0.00329541,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
12739,Q#1633 - >seq4956,non-specific,274008,263,500,0.00681346,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12740,Q#1633 - >seq4956,superfamily,274008,263,500,0.00681346,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
12741,Q#1633 - >seq4956,non-specific,293702,337,451,0.00866734,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12742,Q#1633 - >seq4956,superfamily,293702,337,451,0.00866734,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs4_gibbon.pars.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
12743,Q#1636 - >seq4959,specific,238827,510,772,1.1375799999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12744,Q#1636 - >seq4959,superfamily,295487,510,772,1.1375799999999998e-66,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12745,Q#1636 - >seq4959,specific,197310,9,236,5.032129999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12746,Q#1636 - >seq4959,superfamily,351117,9,236,5.032129999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12747,Q#1636 - >seq4959,non-specific,197306,9,236,1.2216799999999999e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12748,Q#1636 - >seq4959,specific,333820,516,772,2.3294399999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12749,Q#1636 - >seq4959,superfamily,333820,516,772,2.3294399999999997e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12750,Q#1636 - >seq4959,non-specific,197307,9,236,2.06825e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12751,Q#1636 - >seq4959,non-specific,223780,9,238,1.32867e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12752,Q#1636 - >seq4959,non-specific,197320,8,236,2.04915e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12753,Q#1636 - >seq4959,non-specific,197321,7,236,6.59356e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12754,Q#1636 - >seq4959,specific,335306,10,229,1.32427e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12755,Q#1636 - >seq4959,non-specific,273186,9,237,7.757530000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12756,Q#1636 - >seq4959,non-specific,272954,9,236,1.5342299999999999e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12757,Q#1636 - >seq4959,non-specific,197319,8,236,4.1161199999999997e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12758,Q#1636 - >seq4959,non-specific,197336,7,235,2.91505e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12759,Q#1636 - >seq4959,non-specific,197322,9,236,2.74523e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12760,Q#1636 - >seq4959,non-specific,238828,516,737,6.70766e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12761,Q#1636 - >seq4959,non-specific,275209,467,800,4.15792e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12762,Q#1636 - >seq4959,superfamily,275209,467,800,4.15792e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12763,Q#1636 - >seq4959,non-specific,236970,9,238,4.265979999999999e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12764,Q#1636 - >seq4959,non-specific,339261,108,232,1.81003e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12765,Q#1636 - >seq4959,non-specific,197311,7,236,2.2065e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12766,Q#1636 - >seq4959,non-specific,197317,139,229,1.39451e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12767,Q#1636 - >seq4959,non-specific,238185,656,772,0.000282873,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P1,ORF2,hs4_gibbon,marg,CompleteHit
12768,Q#1636 - >seq4959,non-specific,274009,305,453,0.000886425,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
12769,Q#1636 - >seq4959,superfamily,274009,305,453,0.000886425,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
12770,Q#1636 - >seq4959,non-specific,226098,138,239,0.00165679,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12771,Q#1636 - >seq4959,non-specific,197314,7,192,0.00202433,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
12772,Q#1636 - >seq4959,non-specific,235175,295,464,0.00310541,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
12773,Q#1636 - >seq4959,superfamily,235175,295,464,0.00310541,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
12774,Q#1636 - >seq4959,non-specific,274008,263,500,0.00595112,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12775,Q#1636 - >seq4959,superfamily,274008,263,500,0.00595112,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
12776,Q#1636 - >seq4959,non-specific,293702,337,451,0.00881562,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
12777,Q#1636 - >seq4959,superfamily,293702,337,451,0.00881562,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs4_gibbon.marg.frame3,1909130924_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
12778,Q#1638 - >seq4961,specific,238827,510,772,6.303619999999999e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12779,Q#1638 - >seq4961,superfamily,295487,510,772,6.303619999999999e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12780,Q#1638 - >seq4961,specific,197310,9,236,5.67353e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12781,Q#1638 - >seq4961,superfamily,351117,9,236,5.67353e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12782,Q#1638 - >seq4961,non-specific,197306,9,236,1.4566599999999996e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12783,Q#1638 - >seq4961,specific,333820,516,772,1.94232e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12784,Q#1638 - >seq4961,superfamily,333820,516,772,1.94232e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12785,Q#1638 - >seq4961,non-specific,197307,9,236,2.1324400000000003e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12786,Q#1638 - >seq4961,non-specific,223780,9,238,1.35679e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12787,Q#1638 - >seq4961,non-specific,197320,8,236,2.03366e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12788,Q#1638 - >seq4961,non-specific,197321,7,236,7.06011e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12789,Q#1638 - >seq4961,specific,335306,10,229,1.32674e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12790,Q#1638 - >seq4961,non-specific,273186,9,237,7.77234e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12791,Q#1638 - >seq4961,non-specific,272954,9,236,1.55167e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12792,Q#1638 - >seq4961,non-specific,197319,8,236,4.4452800000000003e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12793,Q#1638 - >seq4961,non-specific,197336,7,235,2.7615599999999998e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12794,Q#1638 - >seq4961,non-specific,197322,9,236,2.75057e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12795,Q#1638 - >seq4961,non-specific,238828,516,737,2.85917e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12796,Q#1638 - >seq4961,non-specific,275209,467,800,2.0774999999999998e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12797,Q#1638 - >seq4961,superfamily,275209,467,800,2.0774999999999998e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12798,Q#1638 - >seq4961,non-specific,236970,9,238,4.196399999999999e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12799,Q#1638 - >seq4961,non-specific,339261,108,232,1.88484e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12800,Q#1638 - >seq4961,non-specific,197311,7,236,2.3164e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs3_orang,pars,CompleteHit
12801,Q#1638 - >seq4961,non-specific,197317,139,229,1.3971000000000001e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,pars,N-TerminusTruncated
12802,Q#1638 - >seq4961,non-specific,238185,656,772,0.000167402,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12803,Q#1638 - >seq4961,non-specific,274009,305,453,0.000895642,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,C-TerminusTruncated
12804,Q#1638 - >seq4961,superfamily,274009,305,453,0.000895642,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,C-TerminusTruncated
12805,Q#1638 - >seq4961,non-specific,226098,138,239,0.00165981,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs3_orang,pars,N-TerminusTruncated
12806,Q#1638 - >seq4961,non-specific,197314,7,192,0.00202801,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P1,ORF2,hs3_orang,pars,C-TerminusTruncated
12807,Q#1638 - >seq4961,non-specific,235175,295,464,0.0033296,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,BothTerminiTruncated
12808,Q#1638 - >seq4961,superfamily,235175,295,464,0.0033296,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,BothTerminiTruncated
12809,Q#1638 - >seq4961,non-specific,239569,525,748,0.00423618,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs3_orang,pars,CompleteHit
12810,Q#1638 - >seq4961,non-specific,274008,263,500,0.00561957,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,N-TerminusTruncated
12811,Q#1638 - >seq4961,superfamily,274008,263,500,0.00561957,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF2,hs3_orang,pars,N-TerminusTruncated
12812,Q#1638 - >seq4961,non-specific,293702,337,451,0.00890866,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs3_orang,pars,C-TerminusTruncated
12813,Q#1638 - >seq4961,superfamily,293702,337,451,0.00890866,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P1.ORF2.hs3_orang.pars.frame3,1909130924_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P1,ORF2,hs3_orang,pars,C-TerminusTruncated
12814,Q#1679 - >seq5002,non-specific,271190,134,235,0.0063531,38.0976,cd01190,INT_StrepXerD_C_like,N,cl00213,"Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.",L1ME3Cz.ORF2.hs7_bushaby.marg.frame2,1909130925_L1ME3Cz.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3Cz,ORF2,hs7_bushaby,marg,N-TerminusTruncated
12815,Q#1679 - >seq5002,superfamily,350955,134,235,0.0063531,38.0976,cl00213,DNA_BRE_C superfamily,N, - ,"DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.",L1ME3Cz.ORF2.hs7_bushaby.marg.frame2,1909130925_L1ME3Cz.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3Cz,ORF2,hs7_bushaby,marg,N-TerminusTruncated
12816,Q#1703 - >seq5026,non-specific,114219,39,328,0.00108609,42.7865,pfam05483,SCP-1,N,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1ME3D.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3D.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3D,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
12817,Q#1703 - >seq5026,superfamily,114219,39,328,0.00108609,42.7865,cl30946,SCP-1 superfamily,N, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1ME3D.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3D.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3D,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
12818,Q#1710 - >seq5033,non-specific,335182,153,249,2.9307399999999997e-33,118.17399999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12819,Q#1710 - >seq5033,superfamily,335182,153,249,2.9307399999999997e-33,118.17399999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12820,Q#1710 - >seq5033,non-specific,340205,252,315,2.95222e-22,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12821,Q#1710 - >seq5033,superfamily,340205,252,315,2.95222e-22,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12822,Q#1710 - >seq5033,non-specific,340204,109,151,1.5341899999999998e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12823,Q#1710 - >seq5033,superfamily,340204,109,151,1.5341899999999998e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3Cz,ORF1,hs0_human,pars,CompleteHit
12824,Q#1710 - >seq5033,non-specific,226400,80,147,0.00927349,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3Cz,ORF1,hs0_human,pars,C-TerminusTruncated
12825,Q#1710 - >seq5033,superfamily,226400,80,147,0.00927349,37.0054,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3Cz.ORF1.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3Cz,ORF1,hs0_human,pars,C-TerminusTruncated
12826,Q#1711 - >seq5034,non-specific,335182,173,269,1.5786299999999998e-33,119.715,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12827,Q#1711 - >seq5034,superfamily,335182,173,269,1.5786299999999998e-33,119.715,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12828,Q#1711 - >seq5034,non-specific,340205,272,336,5.92417e-21,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12829,Q#1711 - >seq5034,superfamily,340205,272,336,5.92417e-21,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12830,Q#1711 - >seq5034,non-specific,340204,129,171,1.13634e-06,44.706,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12831,Q#1711 - >seq5034,superfamily,340204,129,171,1.13634e-06,44.706,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs0_human,marg,CompleteHit
12832,Q#1711 - >seq5034,non-specific,224117,32,219,0.00037797300000000004,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3Cz,ORF1,hs0_human,marg,N-TerminusTruncated
12833,Q#1711 - >seq5034,superfamily,224117,32,219,0.00037797300000000004,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF1.hs0_human.marg.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME3Cz,ORF1,hs0_human,marg,N-TerminusTruncated
12834,Q#1715 - >seq5038,non-specific,274009,280,430,0.000443719,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.pars.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12835,Q#1715 - >seq5038,superfamily,274009,280,430,0.000443719,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.pars.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12836,Q#1715 - >seq5038,non-specific,235175,292,452,0.000653708,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.pars.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12837,Q#1715 - >seq5038,superfamily,235175,292,452,0.000653708,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.pars.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12838,Q#1715 - >seq5038,non-specific,235175,269,418,0.00359797,41.2028,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.pars.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,pars,C-TerminusTruncated
12839,Q#1716 - >seq5039,specific,197310,9,236,6.41221e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12840,Q#1716 - >seq5039,superfamily,351117,9,236,6.41221e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12841,Q#1716 - >seq5039,non-specific,197306,9,236,6.77601e-33,127.598,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12842,Q#1716 - >seq5039,non-specific,197320,9,229,9.872629999999999e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12843,Q#1716 - >seq5039,non-specific,223780,9,237,1.4634100000000002e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12844,Q#1716 - >seq5039,non-specific,197307,9,236,2.07764e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12845,Q#1716 - >seq5039,specific,335306,10,229,2.03803e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12846,Q#1716 - >seq5039,non-specific,197319,13,236,2.71843e-17,82.7097,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12847,Q#1716 - >seq5039,non-specific,273186,9,237,3.0329999999999997e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12848,Q#1716 - >seq5039,non-specific,272954,9,236,6.523690000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12849,Q#1716 - >seq5039,non-specific,197321,7,236,1.6106100000000002e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12850,Q#1716 - >seq5039,non-specific,197336,9,194,2.35506e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12851,Q#1716 - >seq5039,non-specific,197322,8,236,4.32644e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12852,Q#1716 - >seq5039,non-specific,236970,9,189,2.9142e-06,49.8926,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,pars,C-TerminusTruncated
12853,Q#1716 - >seq5039,non-specific,197311,30,236,1.83642e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12854,Q#1716 - >seq5039,non-specific,339261,108,232,0.00327259,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs0_human.pars.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12855,Q#1718 - >seq5041,non-specific,235175,292,472,1.7234e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,BothTerminiTruncated
12856,Q#1718 - >seq5041,superfamily,235175,292,472,1.7234e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,BothTerminiTruncated
12857,Q#1718 - >seq5041,non-specific,274009,297,463,8.5639e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,BothTerminiTruncated
12858,Q#1718 - >seq5041,superfamily,274009,297,463,8.5639e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,BothTerminiTruncated
12859,Q#1718 - >seq5041,non-specific,274009,293,460,0.00019297,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,C-TerminusTruncated
12860,Q#1718 - >seq5041,non-specific,274009,280,432,0.000453581,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,BothTerminiTruncated
12861,Q#1718 - >seq5041,non-specific,226883,307,449,0.00555001,40.4361,COG4477,EzrA,N,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3Cz,ORF2,hs0_human,marg,N-TerminusTruncated
12862,Q#1718 - >seq5041,superfamily,226883,307,449,0.00555001,40.4361,cl34766,EzrA superfamily,N, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3Cz,ORF2,hs0_human,marg,N-TerminusTruncated
12863,Q#1718 - >seq5041,non-specific,235175,291,464,0.00660017,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,C-TerminusTruncated
12864,Q#1718 - >seq5041,non-specific,224117,245,471,0.00948706,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,N-TerminusTruncated
12865,Q#1718 - >seq5041,superfamily,224117,245,471,0.00948706,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs0_human.marg.frame2,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1ME3Cz,ORF2,hs0_human,marg,N-TerminusTruncated
12866,Q#1719 - >seq5042,specific,238827,488,749,1.3928099999999998e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12867,Q#1719 - >seq5042,superfamily,295487,488,749,1.3928099999999998e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12868,Q#1719 - >seq5042,specific,197310,9,236,3.0515099999999996e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12869,Q#1719 - >seq5042,superfamily,351117,9,236,3.0515099999999996e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12870,Q#1719 - >seq5042,non-specific,197306,9,236,2.77413e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12871,Q#1719 - >seq5042,specific,333820,494,749,1.5233899999999998e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12872,Q#1719 - >seq5042,superfamily,333820,494,749,1.5233899999999998e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12873,Q#1719 - >seq5042,non-specific,197320,9,229,1.14866e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12874,Q#1719 - >seq5042,non-specific,223780,9,237,7.331729999999999e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12875,Q#1719 - >seq5042,non-specific,197307,9,236,9.840979999999998e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12876,Q#1719 - >seq5042,specific,335306,10,229,2.13293e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12877,Q#1719 - >seq5042,non-specific,273186,9,237,7.920660000000001e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12878,Q#1719 - >seq5042,non-specific,197319,13,236,2.15592e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12879,Q#1719 - >seq5042,non-specific,272954,9,236,6.90526e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12880,Q#1719 - >seq5042,non-specific,197321,7,236,2.88035e-14,73.7404,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12881,Q#1719 - >seq5042,non-specific,238828,494,714,1.74631e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12882,Q#1719 - >seq5042,non-specific,197336,9,194,2.46571e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12883,Q#1719 - >seq5042,non-specific,197322,8,236,4.53406e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12884,Q#1719 - >seq5042,non-specific,275209,446,701,1.9731000000000002e-06,51.3044,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,C-TerminusTruncated
12885,Q#1719 - >seq5042,superfamily,275209,446,701,1.9731000000000002e-06,51.3044,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,C-TerminusTruncated
12886,Q#1719 - >seq5042,non-specific,236970,9,189,4.57969e-06,49.5074,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs0_human,marg,C-TerminusTruncated
12887,Q#1719 - >seq5042,non-specific,197311,30,236,2.53514e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12888,Q#1719 - >seq5042,non-specific,339261,108,232,0.00116928,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12889,Q#1719 - >seq5042,non-specific,238185,633,747,0.00242149,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12890,Q#1719 - >seq5042,non-specific,239569,518,724,0.00288669,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3Cz.ORF2.hs0_human.marg.frame3,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs0_human,marg,CompleteHit
12891,Q#1723 - >seq5046,specific,238827,460,720,4.06118e-62,210.99599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12892,Q#1723 - >seq5046,superfamily,295487,460,720,4.06118e-62,210.99599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12893,Q#1723 - >seq5046,specific,333820,466,689,4.5340799999999996e-30,117.779,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12894,Q#1723 - >seq5046,superfamily,333820,466,689,4.5340799999999996e-30,117.779,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12895,Q#1723 - >seq5046,non-specific,238828,466,686,1.28882e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12896,Q#1723 - >seq5046,non-specific,275209,536,673,7.995169999999999e-06,49.3784,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12897,Q#1723 - >seq5046,superfamily,275209,536,673,7.995169999999999e-06,49.3784,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,BothTerminiTruncated
12898,Q#1723 - >seq5046,non-specific,239569,490,696,0.00277943,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3Cz.ORF2.hs0_human.pars.frame1,1909130925_L1ME3Cz.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs0_human,pars,CompleteHit
12899,Q#1725 - >seq5048,non-specific,340205,95,157,5.48652e-22,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,CompleteHit
12900,Q#1725 - >seq5048,superfamily,340205,95,157,5.48652e-22,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,CompleteHit
12901,Q#1725 - >seq5048,non-specific,335182,44,92,3.2194899999999998e-15,66.9427,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,N-TerminusTruncated
12902,Q#1725 - >seq5048,superfamily,335182,44,92,3.2194899999999998e-15,66.9427,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,N-TerminusTruncated
12903,Q#1727 - >seq5050,non-specific,237177,45,124,0.0009803519999999999,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3Cz.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3Cz,ORF1,hs1_chimp,pars,C-TerminusTruncated
12904,Q#1727 - >seq5050,superfamily,237177,45,124,0.0009803519999999999,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3Cz.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3Cz,ORF1,hs1_chimp,pars,C-TerminusTruncated
12905,Q#1727 - >seq5050,non-specific,274008,34,122,0.00296176,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,pars,BothTerminiTruncated
12906,Q#1727 - >seq5050,superfamily,274008,34,122,0.00296176,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,pars,BothTerminiTruncated
12907,Q#1728 - >seq5051,non-specific,335182,123,219,6.18765e-35,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,pars,CompleteHit
12908,Q#1728 - >seq5051,superfamily,335182,123,219,6.18765e-35,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,pars,CompleteHit
12909,Q#1728 - >seq5051,non-specific,340205,222,285,8.79403e-27,99.3327,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,pars,CompleteHit
12910,Q#1728 - >seq5051,superfamily,340205,222,285,8.79403e-27,99.3327,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,pars,CompleteHit
12911,Q#1731 - >seq5054,non-specific,335182,146,242,2.63437e-32,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,marg,CompleteHit
12912,Q#1731 - >seq5054,superfamily,335182,146,242,2.63437e-32,115.478,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,marg,CompleteHit
12913,Q#1731 - >seq5054,non-specific,340205,245,308,1.07683e-26,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,marg,CompleteHit
12914,Q#1731 - >seq5054,superfamily,340205,245,308,1.07683e-26,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs1_chimp,marg,CompleteHit
12915,Q#1732 - >seq5055,non-specific,224117,21,200,0.000800704,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,BothTerminiTruncated
12916,Q#1732 - >seq5055,superfamily,224117,21,200,0.000800704,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,BothTerminiTruncated
12917,Q#1732 - >seq5055,non-specific,237177,43,146,0.00146129,39.7614,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3Cz,ORF1,hs1_chimp,marg,C-TerminusTruncated
12918,Q#1732 - >seq5055,superfamily,237177,43,146,0.00146129,39.7614,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3Cz,ORF1,hs1_chimp,marg,C-TerminusTruncated
12919,Q#1732 - >seq5055,non-specific,274009,25,179,0.00431831,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,BothTerminiTruncated
12920,Q#1732 - >seq5055,superfamily,274009,25,179,0.00431831,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,BothTerminiTruncated
12921,Q#1732 - >seq5055,non-specific,235175,50,239,0.00522259,38.1212,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,C-TerminusTruncated
12922,Q#1732 - >seq5055,superfamily,235175,50,239,0.00522259,38.1212,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF1.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs1_chimp,marg,C-TerminusTruncated
12923,Q#1733 - >seq5056,specific,238827,606,723,8.52603e-30,118.163,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,N-TerminusTruncated
12924,Q#1733 - >seq5056,superfamily,295487,606,723,8.52603e-30,118.163,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,N-TerminusTruncated
12925,Q#1733 - >seq5056,non-specific,333820,588,691,1.3417700000000002e-14,73.0954,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,N-TerminusTruncated
12926,Q#1733 - >seq5056,superfamily,333820,588,691,1.3417700000000002e-14,73.0954,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,N-TerminusTruncated
12927,Q#1733 - >seq5056,non-specific,238828,546,688,6.64033e-08,54.5144,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,N-TerminusTruncated
12928,Q#1733 - >seq5056,non-specific,238185,607,721,0.00015638700000000002,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12929,Q#1734 - >seq5057,specific,238827,474,587,2.55884e-36,136.65200000000002,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,pars,C-TerminusTruncated
12930,Q#1734 - >seq5057,superfamily,295487,474,587,2.55884e-36,136.65200000000002,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,pars,C-TerminusTruncated
12931,Q#1734 - >seq5057,non-specific,333820,480,585,1.46863e-14,73.0954,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,pars,C-TerminusTruncated
12932,Q#1734 - >seq5057,superfamily,333820,480,585,1.46863e-14,73.0954,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,pars,C-TerminusTruncated
12933,Q#1734 - >seq5057,non-specific,338310,971,1033,0.00145021,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3Cz,ORF2,hs1_chimp,pars,BothTerminiTruncated
12934,Q#1734 - >seq5057,superfamily,338310,971,1033,0.00145021,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3Cz.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3Cz,ORF2,hs1_chimp,pars,BothTerminiTruncated
12935,Q#1736 - >seq5059,specific,197310,9,237,1.24384e-50,178.699,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12936,Q#1736 - >seq5059,superfamily,351117,9,237,1.24384e-50,178.699,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12937,Q#1736 - >seq5059,non-specific,197306,9,237,3.1186199999999997e-24,102.56,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12938,Q#1736 - >seq5059,non-specific,197320,9,230,1.23571e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12939,Q#1736 - >seq5059,non-specific,197307,9,237,1.90971e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12940,Q#1736 - >seq5059,non-specific,223780,9,238,6.1607599999999996e-15,76.0979,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12941,Q#1736 - >seq5059,specific,335306,10,230,9.34265e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12942,Q#1736 - >seq5059,non-specific,197319,13,237,2.28014e-10,62.2941,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12943,Q#1736 - >seq5059,non-specific,273186,9,238,6.714830000000001e-10,60.7556,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12944,Q#1736 - >seq5059,non-specific,197321,7,237,3.2021e-09,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12945,Q#1736 - >seq5059,non-specific,272954,9,237,1.13359e-07,54.3113,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12946,Q#1736 - >seq5059,non-specific,197311,36,237,4.6286400000000005e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12947,Q#1736 - >seq5059,non-specific,224212,141,374,0.00040805699999999997,44.3053,COG1293,YloA,NC,cl34220,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3Cz,ORF2,hs1_chimp,pars,BothTerminiTruncated
12948,Q#1736 - >seq5059,superfamily,224212,141,374,0.00040805699999999997,44.3053,cl34220,YloA superfamily,NC, - ,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3Cz,ORF2,hs1_chimp,pars,BothTerminiTruncated
12949,Q#1736 - >seq5059,non-specific,339261,105,233,0.00366205,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs1_chimp,pars,CompleteHit
12950,Q#1737 - >seq5060,specific,238827,474,732,4.340729999999999e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12951,Q#1737 - >seq5060,superfamily,295487,474,732,4.340729999999999e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12952,Q#1737 - >seq5060,specific,333820,480,700,1.6411799999999999e-28,113.156,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12953,Q#1737 - >seq5060,superfamily,333820,480,700,1.6411799999999999e-28,113.156,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12954,Q#1737 - >seq5060,non-specific,238828,480,697,8.963850000000001e-08,54.1292,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12955,Q#1737 - >seq5060,non-specific,238185,620,730,0.00772928,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12956,Q#1738 - >seq5061,specific,197310,9,237,1.5061899999999998e-51,181.396,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12957,Q#1738 - >seq5061,superfamily,351117,9,237,1.5061899999999998e-51,181.396,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12958,Q#1738 - >seq5061,non-specific,197306,9,237,1.26489e-24,103.715,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12959,Q#1738 - >seq5061,non-specific,197320,9,230,1.2182500000000001e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12960,Q#1738 - >seq5061,non-specific,197307,9,237,1.6659800000000001e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12961,Q#1738 - >seq5061,non-specific,223780,9,238,6.07347e-15,76.0979,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12962,Q#1738 - >seq5061,specific,335306,10,230,9.21459e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12963,Q#1738 - >seq5061,non-specific,197319,13,237,3.77843e-10,61.5237,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12964,Q#1738 - >seq5061,non-specific,273186,9,238,6.62129e-10,60.7556,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12965,Q#1738 - >seq5061,non-specific,197321,7,237,6.6650600000000006e-09,57.9472,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12966,Q#1738 - >seq5061,non-specific,272954,9,237,6.69204e-08,54.6965,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12967,Q#1738 - >seq5061,non-specific,197311,36,237,4.56691e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12968,Q#1738 - >seq5061,non-specific,224212,141,374,0.000552077,43.9201,COG1293,YloA,NC,cl34220,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3Cz,ORF2,hs1_chimp,marg,BothTerminiTruncated
12969,Q#1738 - >seq5061,superfamily,224212,141,374,0.000552077,43.9201,cl34220,YloA superfamily,NC, - ,"Predicted component of the ribosome quality control (RQC) complex, YloA/Tae2 family, contains fibronectin-binding (FbpA) and DUF814 domains [Translation, ribosomal structure and biogenesis]; Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription].",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3Cz,ORF2,hs1_chimp,marg,BothTerminiTruncated
12970,Q#1738 - >seq5061,non-specific,339261,105,233,0.00173686,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3Cz.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs1_chimp,marg,CompleteHit
12971,Q#1739 - >seq5062,non-specific,335182,142,238,1.7222e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12972,Q#1739 - >seq5062,superfamily,335182,142,238,1.7222e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12973,Q#1739 - >seq5062,non-specific,340205,241,304,5.98014e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12974,Q#1739 - >seq5062,superfamily,340205,241,304,5.98014e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12975,Q#1739 - >seq5062,non-specific,340204,98,140,6.69165e-07,45.0912,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12976,Q#1739 - >seq5062,superfamily,340204,98,140,6.69165e-07,45.0912,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs2_gorilla,pars,CompleteHit
12977,Q#1739 - >seq5062,non-specific,235600,49,137,0.00700123,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1ME3Cz,ORF1,hs2_gorilla,pars,C-TerminusTruncated
12978,Q#1739 - >seq5062,superfamily,235600,49,137,0.00700123,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1ME3Cz.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1ME3Cz,ORF1,hs2_gorilla,pars,C-TerminusTruncated
12979,Q#1744 - >seq5067,non-specific,335182,157,253,7.164099999999999e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12980,Q#1744 - >seq5067,superfamily,335182,157,253,7.164099999999999e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12981,Q#1744 - >seq5067,non-specific,340205,256,319,5.94028e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12982,Q#1744 - >seq5067,superfamily,340205,256,319,5.94028e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12983,Q#1744 - >seq5067,non-specific,340204,113,155,1.7167500000000001e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12984,Q#1744 - >seq5067,superfamily,340204,113,155,1.7167500000000001e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3Cz,ORF1,hs2_gorilla,marg,CompleteHit
12985,Q#1744 - >seq5067,non-specific,274008,42,151,0.00887407,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs2_gorilla,marg,BothTerminiTruncated
12986,Q#1744 - >seq5067,superfamily,274008,42,151,0.00887407,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs2_gorilla,marg,BothTerminiTruncated
12987,Q#1748 - >seq5071,specific,238827,459,721,6.481489999999998e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12988,Q#1748 - >seq5071,superfamily,295487,459,721,6.481489999999998e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12989,Q#1748 - >seq5071,specific,333820,465,721,4.28102e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12990,Q#1748 - >seq5071,superfamily,333820,465,721,4.28102e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12991,Q#1748 - >seq5071,non-specific,238828,465,686,2.79986e-10,61.448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12992,Q#1748 - >seq5071,non-specific,238185,605,719,0.000327983,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
12993,Q#1748 - >seq5071,non-specific,275209,536,745,0.000927101,42.83,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,N-TerminusTruncated
12994,Q#1748 - >seq5071,superfamily,275209,536,745,0.000927101,42.83,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3C.ORF2.hs0_human.pars.frame3,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3C,ORF2,hs0_human,pars,N-TerminusTruncated
12995,Q#1751 - >seq5074,non-specific,335182,131,227,2.19692e-28,104.69200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
12996,Q#1751 - >seq5074,superfamily,335182,131,227,2.19692e-28,104.69200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
12997,Q#1751 - >seq5074,non-specific,340205,230,292,2.6063000000000002e-19,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
12998,Q#1751 - >seq5074,superfamily,340205,230,292,2.6063000000000002e-19,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
12999,Q#1751 - >seq5074,non-specific,340204,88,129,0.000711739,36.6168,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
13000,Q#1751 - >seq5074,superfamily,340204,88,129,0.000711739,36.6168,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1ME3C,ORF1,hs1_chimp,marg,CompleteHit
13001,Q#1755 - >seq5078,specific,197310,9,231,2.15958e-45,153.661,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13002,Q#1755 - >seq5078,superfamily,351117,9,231,2.15958e-45,153.661,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13003,Q#1755 - >seq5078,non-specific,197306,9,195,3.55721e-24,97.9372,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13004,Q#1755 - >seq5078,non-specific,197320,9,204,3.11573e-14,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13005,Q#1755 - >seq5078,non-specific,223780,9,203,1.5886700000000002e-13,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13006,Q#1755 - >seq5078,non-specific,272954,9,205,5.0474e-11,61.6301,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13007,Q#1755 - >seq5078,specific,335306,10,186,9.26094e-11,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13008,Q#1755 - >seq5078,non-specific,197307,9,206,1.4565799999999997e-10,60.3793,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13009,Q#1755 - >seq5078,non-specific,197319,13,192,1.8526599999999996e-08,54.2049,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13010,Q#1755 - >seq5078,non-specific,273186,9,206,1.19369e-07,51.5108,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13011,Q#1755 - >seq5078,non-specific,197321,7,192,5.78475e-07,49.4728,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13012,Q#1755 - >seq5078,non-specific,197336,9,192,0.000132323,42.5995,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,CompleteHit
13013,Q#1755 - >seq5078,non-specific,197311,30,144,0.000369878,40.7381,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs1_chimp.pars.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,pars,C-TerminusTruncated
13014,Q#1756 - >seq5079,non-specific,240271,328,631,0.00392961,40.4148,PTZ00108,PTZ00108,N,cl36510,DNA topoisomerase 2-like protein; Provisional,L1ME3C.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13015,Q#1756 - >seq5079,superfamily,240271,328,631,0.00392961,40.4148,cl36510,PTZ00108 superfamily,N, - ,DNA topoisomerase 2-like protein; Provisional,L1ME3C.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13016,Q#1757 - >seq5080,specific,238827,537,801,6.869079999999999e-61,207.52900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13017,Q#1757 - >seq5080,superfamily,295487,537,801,6.869079999999999e-61,207.52900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13018,Q#1757 - >seq5080,specific,197310,10,237,1.2592699999999998e-53,187.174,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13019,Q#1757 - >seq5080,superfamily,351117,10,237,1.2592699999999998e-53,187.174,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13020,Q#1757 - >seq5080,non-specific,197306,10,237,1.0919700000000001e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13021,Q#1757 - >seq5080,specific,333820,543,801,1.5073499999999998e-29,116.238,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13022,Q#1757 - >seq5080,superfamily,333820,543,801,1.5073499999999998e-29,116.238,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13023,Q#1757 - >seq5080,non-specific,223780,10,238,7.08475e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13024,Q#1757 - >seq5080,non-specific,197307,10,237,4.47339e-18,85.0321,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13025,Q#1757 - >seq5080,non-specific,197321,8,237,1.72773e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13026,Q#1757 - >seq5080,non-specific,197320,10,230,7.727930000000001e-17,81.4073,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13027,Q#1757 - >seq5080,non-specific,273186,10,238,8.990309999999999e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13028,Q#1757 - >seq5080,specific,335306,11,230,6.9349500000000004e-15,74.9741,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13029,Q#1757 - >seq5080,non-specific,272954,10,237,2.7443799999999998e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13030,Q#1757 - >seq5080,non-specific,197319,14,237,3.89403e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13031,Q#1757 - >seq5080,non-specific,238828,543,765,1.1024199999999999e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13032,Q#1757 - >seq5080,non-specific,197336,10,195,8.034029999999999e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13033,Q#1757 - >seq5080,non-specific,197322,9,237,1.4426700000000001e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13034,Q#1757 - >seq5080,non-specific,339261,109,233,0.00013057,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13035,Q#1757 - >seq5080,non-specific,197311,8,205,0.000853358,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3C,ORF2,hs0_human,marg,CompleteHit
13036,Q#1758 - >seq5081,non-specific,238827,598,712,4.85875e-18,83.4946,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3C.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13037,Q#1758 - >seq5081,superfamily,295487,598,712,4.85875e-18,83.4946,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3C.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13038,Q#1758 - >seq5081,non-specific,333820,604,689,1.01815e-07,52.2946,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13039,Q#1758 - >seq5081,superfamily,333820,604,689,1.01815e-07,52.2946,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3C,ORF2,hs1_chimp,marg,N-TerminusTruncated
13040,Q#1762 - >seq5085,non-specific,340205,152,210,1.58417e-18,76.2208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13041,Q#1762 - >seq5085,superfamily,340205,152,210,1.58417e-18,76.2208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13042,Q#1762 - >seq5085,non-specific,335182,49,139,5.9222e-16,70.4095,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13043,Q#1762 - >seq5085,superfamily,335182,49,139,5.9222e-16,70.4095,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13044,Q#1762 - >seq5085,non-specific,340204,5,47,5.77674e-07,44.706,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13045,Q#1762 - >seq5085,superfamily,340204,5,47,5.77674e-07,44.706,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs0_human.marg.frame1,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3C,ORF1,hs0_human,marg,CompleteHit
13046,Q#1766 - >seq5089,specific,197310,22,224,2.4649299999999997e-40,149.039,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13047,Q#1766 - >seq5089,superfamily,351117,22,224,2.4649299999999997e-40,149.039,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13048,Q#1766 - >seq5089,non-specific,197306,26,224,2.8471599999999995e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13049,Q#1766 - >seq5089,non-specific,197307,23,224,2.46511e-13,71.1649,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13050,Q#1766 - >seq5089,non-specific,273186,23,225,4.34604e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13051,Q#1766 - >seq5089,non-specific,223780,22,225,2.36496e-10,62.2307,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13052,Q#1766 - >seq5089,non-specific,197320,22,217,2.48987e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13053,Q#1766 - >seq5089,non-specific,197319,22,224,3.9280300000000005e-10,61.5237,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13054,Q#1766 - >seq5089,non-specific,197321,94,224,9.47614e-09,57.1768,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,N-TerminusTruncated
13055,Q#1766 - >seq5089,non-specific,272954,24,224,3.90196e-08,55.4669,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13056,Q#1766 - >seq5089,specific,335306,22,217,1.6477900000000003e-06,50.3214,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13057,Q#1766 - >seq5089,non-specific,339261,96,220,0.00050007,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13058,Q#1766 - >seq5089,non-specific,197311,21,192,0.00420662,39.5825,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs0_human.pars.frame2,1909130925_L1ME3C.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3C,ORF2,hs0_human,pars,CompleteHit
13059,Q#1767 - >seq5090,specific,197310,9,231,1.45619e-42,154.046,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13060,Q#1767 - >seq5090,superfamily,351117,9,231,1.45619e-42,154.046,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13061,Q#1767 - >seq5090,non-specific,197306,9,195,8.133129999999999e-23,97.9372,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13062,Q#1767 - >seq5090,non-specific,238827,478,567,2.15423e-17,81.5686,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3C,ORF2,hs1_chimp,marg,C-TerminusTruncated
13063,Q#1767 - >seq5090,superfamily,295487,478,567,2.15423e-17,81.5686,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3C,ORF2,hs1_chimp,marg,C-TerminusTruncated
13064,Q#1767 - >seq5090,non-specific,197320,9,204,1.5690199999999999e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13065,Q#1767 - >seq5090,non-specific,223780,9,203,7.65928e-13,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13066,Q#1767 - >seq5090,non-specific,272954,9,205,2.2083999999999998e-10,61.6301,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13067,Q#1767 - >seq5090,specific,335306,10,186,3.3302699999999996e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13068,Q#1767 - >seq5090,non-specific,197307,9,206,9.46997e-10,59.6089,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13069,Q#1767 - >seq5090,non-specific,197319,13,192,6.76592e-08,53.8197,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13070,Q#1767 - >seq5090,non-specific,273186,9,206,4.1453200000000005e-07,51.5108,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13071,Q#1767 - >seq5090,non-specific,333820,480,570,4.50165e-07,50.3686,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3C,ORF2,hs1_chimp,marg,C-TerminusTruncated
13072,Q#1767 - >seq5090,superfamily,333820,480,570,4.50165e-07,50.3686,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3C,ORF2,hs1_chimp,marg,C-TerminusTruncated
13073,Q#1767 - >seq5090,non-specific,197321,7,192,2.53665e-06,49.0876,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13074,Q#1767 - >seq5090,non-specific,197336,9,192,0.000419828,42.5995,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,CompleteHit
13075,Q#1767 - >seq5090,non-specific,197311,30,144,0.00042318300000000004,41.8937,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3C.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3C,ORF2,hs1_chimp,marg,C-TerminusTruncated
13076,Q#1768 - >seq5091,specific,238827,545,710,6.4093399999999995e-31,121.244,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13077,Q#1768 - >seq5091,superfamily,295487,545,710,6.4093399999999995e-31,121.244,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13078,Q#1768 - >seq5091,non-specific,333820,544,699,9.574749999999999e-21,90.8145,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13079,Q#1768 - >seq5091,superfamily,333820,544,699,9.574749999999999e-21,90.8145,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13080,Q#1768 - >seq5091,non-specific,238828,523,696,5.8599e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13081,Q#1768 - >seq5091,non-specific,275209,522,725,5.03278e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13082,Q#1768 - >seq5091,superfamily,275209,522,725,5.03278e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13083,Q#1768 - >seq5091,non-specific,238185,615,700,0.000572033,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame2,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13084,Q#1769 - >seq5092,specific,197310,9,236,1.3119800000000002e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13085,Q#1769 - >seq5092,superfamily,351117,9,236,1.3119800000000002e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13086,Q#1769 - >seq5092,non-specific,197306,9,236,1.7684599999999999e-29,117.96799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13087,Q#1769 - >seq5092,non-specific,197307,9,236,8.389880000000001e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13088,Q#1769 - >seq5092,non-specific,238827,507,586,8.43139e-21,91.969,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13089,Q#1769 - >seq5092,superfamily,295487,507,586,8.43139e-21,91.969,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13090,Q#1769 - >seq5092,non-specific,197320,9,229,3.85846e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13091,Q#1769 - >seq5092,non-specific,223780,9,237,1.94324e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13092,Q#1769 - >seq5092,specific,335306,10,229,2.7385e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13093,Q#1769 - >seq5092,non-specific,197321,7,236,3.00139e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13094,Q#1769 - >seq5092,non-specific,272954,9,236,1.25013e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13095,Q#1769 - >seq5092,non-specific,273186,9,237,1.47583e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13096,Q#1769 - >seq5092,non-specific,197319,13,236,5.07332e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13097,Q#1769 - >seq5092,non-specific,197336,9,194,1.49072e-08,56.8519,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13098,Q#1769 - >seq5092,non-specific,236970,9,237,1.08896e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13099,Q#1769 - >seq5092,non-specific,333820,513,566,1.43795e-06,49.5982,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13100,Q#1769 - >seq5092,superfamily,333820,513,566,1.43795e-06,49.5982,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13101,Q#1769 - >seq5092,non-specific,223496,316,443,0.00031424400000000004,44.7511,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13102,Q#1769 - >seq5092,superfamily,223496,316,443,0.00031424400000000004,44.7511,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13103,Q#1769 - >seq5092,non-specific,235175,294,457,0.000359285,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13104,Q#1769 - >seq5092,superfamily,235175,294,457,0.000359285,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13105,Q#1769 - >seq5092,non-specific,274009,307,455,0.00102958,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13106,Q#1769 - >seq5092,superfamily,274009,307,455,0.00102958,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13107,Q#1769 - >seq5092,non-specific,334125,212,409,0.00272533,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13108,Q#1769 - >seq5092,superfamily,334125,212,409,0.00272533,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs2_gorilla,pars,N-TerminusTruncated
13109,Q#1769 - >seq5092,non-specific,223496,249,443,0.0033770000000000002,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13110,Q#1769 - >seq5092,non-specific,339261,108,232,0.00567203,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs2_gorilla,pars,CompleteHit
13111,Q#1769 - >seq5092,non-specific,224117,218,430,0.0062089,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13112,Q#1769 - >seq5092,superfamily,224117,218,430,0.0062089,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13113,Q#1769 - >seq5092,non-specific,274009,253,444,0.00667812,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,pars,BothTerminiTruncated
13114,Q#1773 - >seq5096,specific,238827,511,768,2.676059999999999e-56,194.43200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13115,Q#1773 - >seq5096,superfamily,295487,511,768,2.676059999999999e-56,194.43200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13116,Q#1773 - >seq5096,specific,197310,3,231,1.5293699999999997e-47,169.84,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13117,Q#1773 - >seq5096,superfamily,351117,3,231,1.5293699999999997e-47,169.84,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13118,Q#1773 - >seq5096,specific,333820,517,738,1.0402e-29,116.62299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13119,Q#1773 - >seq5096,superfamily,333820,517,738,1.0402e-29,116.62299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13120,Q#1773 - >seq5096,non-specific,197306,3,231,2.48902e-25,106.02600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13121,Q#1773 - >seq5096,non-specific,197320,1,216,7.24451e-11,63.6882,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13122,Q#1773 - >seq5096,non-specific,238828,517,738,2.2563200000000002e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13123,Q#1773 - >seq5096,non-specific,197307,3,231,3.8784899999999995e-10,61.5349,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13124,Q#1773 - >seq5096,non-specific,223780,1,220,1.1453900000000001e-09,60.3047,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13125,Q#1773 - >seq5096,non-specific,197336,1,189,1.57754e-08,56.8519,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13126,Q#1773 - >seq5096,non-specific,272954,1,189,4.15766e-08,55.4669,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13127,Q#1773 - >seq5096,non-specific,197321,1,231,1.4494e-06,51.0136,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13128,Q#1773 - >seq5096,non-specific,197319,1,231,4.508630000000001e-06,49.1973,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13129,Q#1773 - >seq5096,specific,335306,4,224,1.90656e-05,47.2398,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13130,Q#1773 - >seq5096,non-specific,273186,1,232,6.50206e-05,45.7328,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,marg,CompleteHit
13131,Q#1773 - >seq5096,non-specific,274009,306,459,0.000139841,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13132,Q#1773 - >seq5096,superfamily,274009,306,459,0.000139841,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13133,Q#1773 - >seq5096,non-specific,235175,306,487,0.000144943,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,marg,BothTerminiTruncated
13134,Q#1773 - >seq5096,superfamily,235175,306,487,0.000144943,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,marg,BothTerminiTruncated
13135,Q#1773 - >seq5096,non-specific,275209,589,772,0.00056294,43.6004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13136,Q#1773 - >seq5096,superfamily,275209,589,772,0.00056294,43.6004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13137,Q#1775 - >seq5098,non-specific,340205,73,119,1.5994000000000001e-07,45.0196,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13138,Q#1775 - >seq5098,superfamily,340205,73,119,1.5994000000000001e-07,45.0196,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13139,Q#1777 - >seq5100,non-specific,340205,87,133,2.0944000000000003e-07,45.0196,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13140,Q#1777 - >seq5100,superfamily,340205,87,133,2.0944000000000003e-07,45.0196,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13141,Q#1779 - >seq5102,specific,197310,3,230,8.00262e-48,170.61,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13142,Q#1779 - >seq5102,superfamily,351117,3,230,8.00262e-48,170.61,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13143,Q#1779 - >seq5102,non-specific,197306,3,230,2.05439e-25,106.02600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13144,Q#1779 - >seq5102,non-specific,197320,1,215,1.8793599999999998e-12,68.3106,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13145,Q#1779 - >seq5102,non-specific,197307,3,230,6.65092e-12,66.9277,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13146,Q#1779 - >seq5102,non-specific,223780,1,219,3.59976e-11,64.5419,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13147,Q#1779 - >seq5102,non-specific,272954,1,188,4.36587e-10,61.2449,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13148,Q#1779 - >seq5102,non-specific,197319,1,230,2.42586e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13149,Q#1779 - >seq5102,non-specific,197336,1,188,2.65439e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13150,Q#1779 - >seq5102,non-specific,197321,1,230,7.493479999999999e-07,51.784,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13151,Q#1779 - >seq5102,non-specific,273186,1,231,8.400299999999999e-07,51.5108,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13152,Q#1779 - >seq5102,non-specific,235175,301,464,1.5231300000000001e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13153,Q#1779 - >seq5102,superfamily,235175,301,464,1.5231300000000001e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13154,Q#1779 - >seq5102,non-specific,334125,206,406,2.9987e-05,47.5292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13155,Q#1779 - >seq5102,superfamily,334125,206,406,2.9987e-05,47.5292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13156,Q#1779 - >seq5102,non-specific,274009,301,452,0.000106237,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13157,Q#1779 - >seq5102,superfamily,274009,301,452,0.000106237,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13158,Q#1779 - >seq5102,non-specific,223496,299,472,0.000482768,44.3659,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3Cz,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13159,Q#1779 - >seq5102,superfamily,223496,299,472,0.000482768,44.3659,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1ME3Cz,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13160,Q#1779 - >seq5102,non-specific,274009,305,457,0.00114566,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13161,Q#1779 - >seq5102,non-specific,224117,300,479,0.00309337,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13162,Q#1779 - >seq5102,superfamily,224117,300,479,0.00309337,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13163,Q#1779 - >seq5102,non-specific,274009,294,457,0.0047872,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13164,Q#1780 - >seq5103,non-specific,335182,1,69,9.48221e-08,46.5271,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13165,Q#1780 - >seq5103,superfamily,335182,1,69,9.48221e-08,46.5271,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13166,Q#1783 - >seq5106,specific,197310,2,195,1.24698e-30,120.149,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13167,Q#1783 - >seq5106,superfamily,351117,2,195,1.24698e-30,120.149,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13168,Q#1783 - >seq5106,non-specific,197306,2,195,2.55509e-14,72.8993,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13169,Q#1783 - >seq5106,non-specific,238827,553,744,3.01695e-14,72.3238,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13170,Q#1783 - >seq5106,superfamily,295487,553,744,3.01695e-14,72.3238,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13171,Q#1783 - >seq5106,non-specific,333820,550,721,5.88687e-06,47.287,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13172,Q#1783 - >seq5106,superfamily,333820,550,721,5.88687e-06,47.287,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,marg,CompleteHit
13173,Q#1783 - >seq5106,non-specific,197307,47,195,0.00184288,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3Cz,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13174,Q#1789 - >seq5112,non-specific,238827,143,348,8.20193e-21,89.2726,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,pars,CompleteHit
13175,Q#1789 - >seq5112,superfamily,295487,143,348,8.20193e-21,89.2726,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,pars,CompleteHit
13176,Q#1789 - >seq5112,non-specific,333820,186,334,4.47201e-09,54.99100000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13177,Q#1789 - >seq5112,superfamily,333820,186,334,4.47201e-09,54.99100000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME3Cz.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13178,Q#1791 - >seq5114,specific,238827,454,698,1.48936e-50,177.483,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13179,Q#1791 - >seq5114,superfamily,295487,454,698,1.48936e-50,177.483,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13180,Q#1791 - >seq5114,specific,333820,454,668,7.17756e-29,114.31200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13181,Q#1791 - >seq5114,superfamily,333820,454,668,7.17756e-29,114.31200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,CompleteHit
13182,Q#1791 - >seq5114,non-specific,238828,514,668,6.903279999999999e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13183,Q#1791 - >seq5114,non-specific,275209,519,702,0.000438048,43.6004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13184,Q#1791 - >seq5114,superfamily,275209,519,702,0.000438048,43.6004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3Cz,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13185,Q#1792 - >seq5115,non-specific,335182,1,54,1.98237e-09,51.9199,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13186,Q#1792 - >seq5115,superfamily,335182,1,54,1.98237e-09,51.9199,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.marg.frame3,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13187,Q#1794 - >seq5117,specific,197310,9,236,1.94396e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13188,Q#1794 - >seq5117,superfamily,351117,9,236,1.94396e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13189,Q#1794 - >seq5117,specific,238827,508,748,4.47885e-58,199.44,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13190,Q#1794 - >seq5117,superfamily,295487,508,748,4.47885e-58,199.44,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13191,Q#1794 - >seq5117,specific,333820,514,737,4.48303e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13192,Q#1794 - >seq5117,superfamily,333820,514,737,4.48303e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13193,Q#1794 - >seq5117,non-specific,197306,9,236,6.5892e-30,119.12299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13194,Q#1794 - >seq5117,non-specific,197307,9,236,9.319710000000001e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13195,Q#1794 - >seq5117,non-specific,197320,9,229,4.0103e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13196,Q#1794 - >seq5117,non-specific,223780,9,237,2.5830699999999996e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13197,Q#1794 - >seq5117,specific,335306,10,229,2.84308e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13198,Q#1794 - >seq5117,non-specific,197321,7,236,4.943419999999999e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13199,Q#1794 - >seq5117,non-specific,272954,9,236,9.7104e-15,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13200,Q#1794 - >seq5117,non-specific,273186,9,237,1.7819099999999998e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13201,Q#1794 - >seq5117,non-specific,197319,13,236,1.19142e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13202,Q#1794 - >seq5117,non-specific,238828,514,734,4.04948e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13203,Q#1794 - >seq5117,non-specific,275209,469,772,2.72416e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13204,Q#1794 - >seq5117,superfamily,275209,469,772,2.72416e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13205,Q#1794 - >seq5117,non-specific,197336,9,194,1.54805e-08,56.8519,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13206,Q#1794 - >seq5117,non-specific,236970,9,237,4.4040700000000003e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13207,Q#1794 - >seq5117,non-specific,235175,291,448,2.01604e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13208,Q#1794 - >seq5117,superfamily,235175,291,448,2.01604e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13209,Q#1794 - >seq5117,non-specific,334125,212,410,0.000216475,44.8328,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs2_gorilla,marg,N-TerminusTruncated
13210,Q#1794 - >seq5117,superfamily,334125,212,410,0.000216475,44.8328,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3Cz,ORF2,hs2_gorilla,marg,N-TerminusTruncated
13211,Q#1794 - >seq5117,specific,225881,481,677,0.00106693,42.5185,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13212,Q#1794 - >seq5117,superfamily,225881,481,677,0.00106693,42.5185,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13213,Q#1794 - >seq5117,non-specific,274009,307,456,0.00142592,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,marg,C-TerminusTruncated
13214,Q#1794 - >seq5117,superfamily,274009,307,456,0.00142592,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,marg,C-TerminusTruncated
13215,Q#1794 - >seq5117,non-specific,223496,249,444,0.00258443,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13216,Q#1794 - >seq5117,superfamily,223496,249,444,0.00258443,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13217,Q#1794 - >seq5117,non-specific,238185,653,738,0.00297896,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13218,Q#1794 - >seq5117,non-specific,223496,316,444,0.00301049,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13219,Q#1794 - >seq5117,non-specific,339261,108,232,0.0032604,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3Cz,ORF2,hs2_gorilla,marg,CompleteHit
13220,Q#1794 - >seq5117,non-specific,274009,253,445,0.00773984,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF2.hs2_gorilla.marg.frame3,1909130925_L1ME3Cz.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3Cz,ORF2,hs2_gorilla,marg,BothTerminiTruncated
13221,Q#1796 - >seq5119,non-specific,340205,231,275,9.859550000000001e-14,64.6648,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,N-TerminusTruncated
13222,Q#1796 - >seq5119,superfamily,340205,231,275,9.859550000000001e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,N-TerminusTruncated
13223,Q#1796 - >seq5119,non-specific,335182,121,153,4.7297200000000005e-05,41.1343,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,C-TerminusTruncated
13224,Q#1796 - >seq5119,superfamily,335182,121,153,4.7297200000000005e-05,41.1343,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,C-TerminusTruncated
13225,Q#1797 - >seq5120,non-specific,335182,165,215,2.3770700000000004e-09,53.4607,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,N-TerminusTruncated
13226,Q#1797 - >seq5120,superfamily,335182,165,215,2.3770700000000004e-09,53.4607,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3Cz,ORF1,hs3_orang,pars,N-TerminusTruncated
13227,Q#1797 - >seq5120,non-specific,274009,14,148,0.00927136,37.3547,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs3_orang,pars,BothTerminiTruncated
13228,Q#1797 - >seq5120,superfamily,274009,14,148,0.00927136,37.3547,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3Cz.ORF1.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3Cz,ORF1,hs3_orang,pars,BothTerminiTruncated
13229,Q#1798 - >seq5121,non-specific,335182,159,255,1.1575499999999999e-27,103.537,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13230,Q#1798 - >seq5121,superfamily,335182,159,255,1.1575499999999999e-27,103.537,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13231,Q#1798 - >seq5121,non-specific,340205,259,321,8.74485e-21,84.31,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13232,Q#1798 - >seq5121,superfamily,340205,259,321,8.74485e-21,84.31,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13233,Q#1798 - >seq5121,non-specific,340204,114,157,0.00427273,34.3056,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13234,Q#1798 - >seq5121,superfamily,340204,114,157,0.00427273,34.3056,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3Cz.ORF1.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3Cz,ORF1,hs3_orang,marg,CompleteHit
13235,Q#1802 - >seq5125,specific,238827,444,636,2.1970500000000003e-39,143.971,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13236,Q#1802 - >seq5125,superfamily,295487,444,636,2.1970500000000003e-39,143.971,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13237,Q#1802 - >seq5125,non-specific,333820,450,636,1.14076e-18,83.8809,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13238,Q#1802 - >seq5125,superfamily,333820,450,636,1.14076e-18,83.8809,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13239,Q#1802 - >seq5125,non-specific,197310,155,220,9.12748e-13,68.1469,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13240,Q#1802 - >seq5125,superfamily,351117,155,220,9.12748e-13,68.1469,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13241,Q#1802 - >seq5125,non-specific,238828,512,636,2.0144099999999997e-08,54.8996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13242,Q#1802 - >seq5125,non-specific,275209,513,597,7.4242e-05,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,BothTerminiTruncated
13243,Q#1802 - >seq5125,superfamily,275209,513,597,7.4242e-05,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3Cz,ORF2,hs3_orang,pars,BothTerminiTruncated
13244,Q#1802 - >seq5125,non-specific,273186,160,221,0.00128693,40.7252,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13245,Q#1802 - >seq5125,non-specific,197320,154,213,0.00614367,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13246,Q#1802 - >seq5125,non-specific,223780,160,221,0.00909695,38.3483,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs3_orang.pars.frame2,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,N-TerminusTruncated
13247,Q#1803 - >seq5126,specific,197310,3,147,6.73828e-29,114.756,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13248,Q#1803 - >seq5126,superfamily,351117,3,147,6.73828e-29,114.756,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13249,Q#1803 - >seq5126,non-specific,197306,3,151,3.750690000000001e-18,84.07,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13250,Q#1803 - >seq5126,non-specific,223780,1,145,8.83943e-09,56.4527,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13251,Q#1803 - >seq5126,non-specific,197320,1,145,1.0481599999999999e-08,56.3694,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13252,Q#1803 - >seq5126,non-specific,272954,1,145,3.27739e-08,54.6965,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13253,Q#1803 - >seq5126,specific,335306,4,170,1.1814299999999999e-07,52.6326,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,CompleteHit
13254,Q#1803 - >seq5126,non-specific,197307,3,154,2.85853e-07,51.9049,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13255,Q#1803 - >seq5126,non-specific,273186,1,145,0.000149079,43.4216,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13256,Q#1803 - >seq5126,non-specific,197319,1,156,0.000332104,42.6489,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13257,Q#1803 - >seq5126,non-specific,197321,1,138,0.00033842800000000005,42.5392,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13258,Q#1803 - >seq5126,non-specific,236970,3,145,0.0028468000000000005,39.8774,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3Cz.ORF2.hs3_orang.pars.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,pars,C-TerminusTruncated
13259,Q#1804 - >seq5127,specific,238827,492,738,1.6543499999999998e-54,189.03900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13260,Q#1804 - >seq5127,superfamily,295487,492,738,1.6543499999999998e-54,189.03900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13261,Q#1804 - >seq5127,non-specific,333820,498,720,1.4294999999999997e-26,107.76299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13262,Q#1804 - >seq5127,superfamily,333820,498,720,1.4294999999999997e-26,107.76299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13263,Q#1804 - >seq5127,non-specific,238828,567,717,2.38353e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,N-TerminusTruncated
13264,Q#1804 - >seq5127,non-specific,275209,568,719,0.000150533,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,BothTerminiTruncated
13265,Q#1804 - >seq5127,superfamily,275209,568,719,0.000150533,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3Cz.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3Cz,ORF2,hs3_orang,marg,BothTerminiTruncated
13266,Q#1806 - >seq5129,specific,197310,9,247,8.56025e-44,159.054,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13267,Q#1806 - >seq5129,superfamily,351117,9,247,8.56025e-44,159.054,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13268,Q#1806 - >seq5129,non-specific,197306,9,247,2.98766e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13269,Q#1806 - >seq5129,non-specific,197320,7,216,3.0574400000000002e-15,76.7849,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13270,Q#1806 - >seq5129,non-specific,223780,7,248,7.63224e-15,75.7127,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13271,Q#1806 - >seq5129,non-specific,197307,9,247,2.2686599999999998e-13,71.1649,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13272,Q#1806 - >seq5129,non-specific,272954,7,247,7.80573e-12,66.6377,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13273,Q#1806 - >seq5129,specific,335306,10,240,8.40277e-11,63.033,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13274,Q#1806 - >seq5129,non-specific,273186,7,248,4.144e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13275,Q#1806 - >seq5129,non-specific,197319,7,247,4.51728e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13276,Q#1806 - >seq5129,non-specific,197321,7,247,1.2625500000000001e-08,57.1768,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13277,Q#1806 - >seq5129,non-specific,197336,7,204,8.104979999999999e-05,45.2959,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3Cz.ORF2.hs3_orang.marg.frame3,1909130925_L1ME3Cz.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3Cz,ORF2,hs3_orang,marg,CompleteHit
13278,Q#1807 - >seq5130,non-specific,335182,13,66,2.2519e-09,51.9199,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13279,Q#1807 - >seq5130,superfamily,335182,13,66,2.2519e-09,51.9199,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame1,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13280,Q#1808 - >seq5131,non-specific,340205,108,170,1.24624e-22,85.4656,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame2,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,CompleteHit
13281,Q#1808 - >seq5131,superfamily,340205,108,170,1.24624e-22,85.4656,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame2,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,CompleteHit
13282,Q#1808 - >seq5131,non-specific,335182,57,105,1.3372e-15,68.4835,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame2,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,N-TerminusTruncated
13283,Q#1808 - >seq5131,superfamily,335182,57,105,1.3372e-15,68.4835,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3Cz.ORF1.hs4_gibbon.pars.frame2,1909130925_L1ME3Cz.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3Cz,ORF1,hs4_gibbon,pars,N-TerminusTruncated
13284,Q#1815 - >seq5138,non-specific,235638,52,272,0.000539654,43.6805,PRK05896,PRK05896,NC,cl35403,DNA polymerase III subunits gamma and tau; Validated,L1ME3D.ORF2.hs7_bushaby.marg.frame2,1909130925_L1ME3D.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3D,ORF2,hs7_bushaby,marg,BothTerminiTruncated
13285,Q#1815 - >seq5138,superfamily,235638,52,272,0.000539654,43.6805,cl35403,PRK05896 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1ME3D.ORF2.hs7_bushaby.marg.frame2,1909130925_L1ME3D.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3D,ORF2,hs7_bushaby,marg,BothTerminiTruncated
13286,Q#1831 - >seq5154,specific,311990,1182,1200,8.04861e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs3_orang.pars.frame1,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13287,Q#1831 - >seq5154,superfamily,311990,1182,1200,8.04861e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs3_orang.pars.frame1,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13288,Q#1832 - >seq5155,specific,238827,482,744,4.1244899999999993e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13289,Q#1832 - >seq5155,superfamily,295487,482,744,4.1244899999999993e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13290,Q#1832 - >seq5155,specific,333820,488,744,1.18456e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13291,Q#1832 - >seq5155,superfamily,333820,488,744,1.18456e-35,133.572,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13292,Q#1832 - >seq5155,non-specific,238828,488,709,1.76063e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13293,Q#1832 - >seq5155,non-specific,275209,439,772,6.71336e-08,55.9268,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13294,Q#1832 - >seq5155,superfamily,275209,439,772,6.71336e-08,55.9268,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13295,Q#1832 - >seq5155,non-specific,238185,628,744,3.19461e-06,46.5752,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13296,Q#1832 - >seq5155,specific,225881,378,711,0.00306276,40.9777,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13297,Q#1832 - >seq5155,superfamily,225881,378,711,0.00306276,40.9777,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs3_orang.pars.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13298,Q#1833 - >seq5156,specific,197310,9,236,7.764799999999999e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13299,Q#1833 - >seq5156,superfamily,351117,9,236,7.764799999999999e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13300,Q#1833 - >seq5156,non-specific,197306,9,236,2.4868000000000002e-48,172.28099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13301,Q#1833 - >seq5156,non-specific,197307,9,236,1.05772e-26,110.07,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13302,Q#1833 - >seq5156,non-specific,223780,9,237,7.63772e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13303,Q#1833 - >seq5156,non-specific,197320,8,229,6.54802e-23,99.1265,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13304,Q#1833 - >seq5156,non-specific,197321,7,236,5.94592e-20,90.6892,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13305,Q#1833 - >seq5156,specific,335306,10,229,1.0378e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13306,Q#1833 - >seq5156,non-specific,272954,9,236,1.38768e-16,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13307,Q#1833 - >seq5156,non-specific,273186,9,237,3.11024e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13308,Q#1833 - >seq5156,non-specific,197319,8,236,2.5695299999999998e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13309,Q#1833 - >seq5156,non-specific,197336,7,229,2.08557e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13310,Q#1833 - >seq5156,non-specific,197322,9,236,1.17364e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13311,Q#1833 - >seq5156,non-specific,339261,108,232,1.4254e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13312,Q#1833 - >seq5156,non-specific,236970,9,237,6.14059e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13313,Q#1833 - >seq5156,non-specific,197311,37,236,1.8190999999999999e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,pars,CompleteHit
13314,Q#1833 - >seq5156,non-specific,197317,139,229,0.00100806,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,pars,N-TerminusTruncated
13315,Q#1833 - >seq5156,non-specific,197314,7,192,0.00110727,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.pars.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA12,ORF2,hs3_orang,pars,C-TerminusTruncated
13316,Q#1839 - >seq5162,non-specific,238827,437,684,4.90019e-26,106.992,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3F.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13317,Q#1839 - >seq5162,superfamily,295487,437,684,4.90019e-26,106.992,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3F.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13318,Q#1839 - >seq5162,non-specific,333820,438,652,1.64405e-11,63.8506,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3F.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13319,Q#1839 - >seq5162,superfamily,333820,438,652,1.64405e-11,63.8506,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3F.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13320,Q#1839 - >seq5162,non-specific,238828,502,640,5.37563e-05,45.2697,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3F.ORF2.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,pars,N-TerminusTruncated
13321,Q#1840 - >seq5163,non-specific,197310,21,221,4.50209e-09,57.7465,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3F.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13322,Q#1840 - >seq5163,superfamily,351117,21,221,4.50209e-09,57.7465,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3F.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3F,ORF2,hs1_chimp,pars,CompleteHit
13323,Q#1842 - >seq5165,specific,238827,525,803,4.21974e-36,136.267,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13324,Q#1842 - >seq5165,superfamily,295487,525,803,4.21974e-36,136.267,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13325,Q#1842 - >seq5165,non-specific,197310,10,246,6.351440000000001e-20,90.1033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13326,Q#1842 - >seq5165,superfamily,351117,10,246,6.351440000000001e-20,90.1033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13327,Q#1842 - >seq5165,non-specific,333820,529,766,2.5129800000000003e-17,81.1846,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13328,Q#1842 - >seq5165,superfamily,333820,529,766,2.5129800000000003e-17,81.1846,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13329,Q#1842 - >seq5165,non-specific,238828,529,744,3.74093e-07,52.2032,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13330,Q#1842 - >seq5165,non-specific,197306,10,246,0.000177858,44.3945,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13331,Q#1842 - >seq5165,non-specific,238185,669,771,0.00695163,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3F.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3F,ORF2,hs1_chimp,marg,CompleteHit
13332,Q#1856 - >seq5179,non-specific,238827,341,377,0.00468037,38.4262,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3F.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3F.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3F,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13333,Q#1856 - >seq5179,superfamily,295487,341,377,0.00468037,38.4262,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3F.ORF2.hs2_gorilla.pars.frame3,1909130925_L1ME3F.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3F,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13334,Q#1857 - >seq5180,specific,238827,483,745,4.75036e-66,222.166,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13335,Q#1857 - >seq5180,superfamily,295487,483,745,4.75036e-66,222.166,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13336,Q#1857 - >seq5180,specific,333820,489,745,1.19247e-34,130.875,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13337,Q#1857 - >seq5180,superfamily,333820,489,745,1.19247e-34,130.875,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13338,Q#1857 - >seq5180,non-specific,238828,489,710,7.95551e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13339,Q#1857 - >seq5180,non-specific,275209,440,773,3.38314e-07,53.6156,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13340,Q#1857 - >seq5180,superfamily,275209,440,773,3.38314e-07,53.6156,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13341,Q#1857 - >seq5180,non-specific,238185,629,745,1.3770199999999999e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13342,Q#1857 - >seq5180,specific,311990,1213,1231,0.00023516900000000002,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13343,Q#1857 - >seq5180,superfamily,311990,1213,1231,0.00023516900000000002,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs3_orang.marg.frame2,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13344,Q#1858 - >seq5181,specific,197310,9,236,2.00489e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13345,Q#1858 - >seq5181,superfamily,351117,9,236,2.00489e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13346,Q#1858 - >seq5181,non-specific,197306,9,236,6.273479999999998e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13347,Q#1858 - >seq5181,non-specific,197307,9,236,4.5699399999999995e-27,111.226,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13348,Q#1858 - >seq5181,non-specific,223780,9,237,7.503669999999999e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13349,Q#1858 - >seq5181,non-specific,197320,8,229,6.433809999999999e-23,99.1265,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13350,Q#1858 - >seq5181,non-specific,197321,7,236,5.0679e-20,90.6892,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13351,Q#1858 - >seq5181,specific,335306,10,229,1.02022e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13352,Q#1858 - >seq5181,non-specific,272954,9,236,1.0085200000000001e-16,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13353,Q#1858 - >seq5181,non-specific,273186,9,237,3.05633e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13354,Q#1858 - >seq5181,non-specific,197319,8,236,1.95988e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13355,Q#1858 - >seq5181,non-specific,197336,7,229,2.0496e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13356,Q#1858 - >seq5181,non-specific,197322,9,236,1.1527999999999999e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13357,Q#1858 - >seq5181,non-specific,339261,108,232,1.4305599999999999e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13358,Q#1858 - >seq5181,non-specific,236970,9,237,1.56745e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13359,Q#1858 - >seq5181,non-specific,197311,37,236,1.7891099999999998e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs3_orang,marg,CompleteHit
13360,Q#1858 - >seq5181,non-specific,197317,139,229,0.000991331,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs3_orang,marg,N-TerminusTruncated
13361,Q#1858 - >seq5181,non-specific,197314,7,192,0.00108893,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA12,ORF2,hs3_orang,marg,C-TerminusTruncated
13362,Q#1858 - >seq5181,non-specific,235175,263,381,0.006988500000000001,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs3_orang,marg,BothTerminiTruncated
13363,Q#1858 - >seq5181,superfamily,235175,263,381,0.006988500000000001,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs3_orang.marg.frame3,1909130925_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs3_orang,marg,BothTerminiTruncated
13364,Q#1859 - >seq5182,specific,238827,468,730,8.983339999999998e-66,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13365,Q#1859 - >seq5182,superfamily,295487,468,730,8.983339999999998e-66,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13366,Q#1859 - >seq5182,specific,333820,474,730,1.9888699999999997e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13367,Q#1859 - >seq5182,superfamily,333820,474,730,1.9888699999999997e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13368,Q#1859 - >seq5182,non-specific,238828,540,695,2.80075e-11,64.5296,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13369,Q#1859 - >seq5182,non-specific,275209,425,758,3.22653e-07,53.6156,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13370,Q#1859 - >seq5182,superfamily,275209,425,758,3.22653e-07,53.6156,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13371,Q#1859 - >seq5182,non-specific,238185,614,730,1.44725e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs4_gibbon.pars.frame1,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13372,Q#1860 - >seq5183,non-specific,335182,152,247,1.06172e-36,127.419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs2_gorilla,pars,CompleteHit
13373,Q#1860 - >seq5183,superfamily,335182,152,247,1.06172e-36,127.419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs2_gorilla,pars,CompleteHit
13374,Q#1860 - >seq5183,non-specific,340205,250,313,1.4637e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs2_gorilla,pars,CompleteHit
13375,Q#1860 - >seq5183,superfamily,340205,250,313,1.4637e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs2_gorilla,pars,CompleteHit
13376,Q#1860 - >seq5183,non-specific,222878,50,122,0.000489023,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs2_gorilla,pars,BothTerminiTruncated
13377,Q#1860 - >seq5183,superfamily,222878,50,122,0.000489023,41.5385,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs2_gorilla.pars.frame1,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs2_gorilla,pars,BothTerminiTruncated
13378,Q#1864 - >seq5187,non-specific,335182,147,235,1.8582299999999996e-32,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs2_gorilla.marg.frame2,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13379,Q#1864 - >seq5187,superfamily,335182,147,235,1.8582299999999996e-32,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs2_gorilla.marg.frame2,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13380,Q#1864 - >seq5187,non-specific,340205,238,301,1.3488499999999998e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs2_gorilla.marg.frame2,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13381,Q#1864 - >seq5187,superfamily,340205,238,301,1.3488499999999998e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs2_gorilla.marg.frame2,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13382,Q#1865 - >seq5188,non-specific,222878,51,141,4.87119e-06,47.7017,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs2_gorilla,marg,BothTerminiTruncated
13383,Q#1865 - >seq5188,superfamily,222878,51,141,4.87119e-06,47.7017,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs2_gorilla,marg,BothTerminiTruncated
13384,Q#1865 - >seq5188,non-specific,340204,110,151,0.000226918,38.1576,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13385,Q#1865 - >seq5188,superfamily,340204,110,151,0.000226918,38.1576,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs2_gorilla,marg,CompleteHit
13386,Q#1865 - >seq5188,non-specific,224117,51,147,0.0011588,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs2_gorilla,marg,BothTerminiTruncated
13387,Q#1865 - >seq5188,superfamily,224117,51,147,0.0011588,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs2_gorilla.marg.frame3,1909130925_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs2_gorilla,marg,BothTerminiTruncated
13388,Q#1866 - >seq5189,non-specific,222878,50,140,3.0796299999999997e-06,48.4721,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13389,Q#1866 - >seq5189,superfamily,222878,50,140,3.0796299999999997e-06,48.4721,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13390,Q#1866 - >seq5189,non-specific,224117,50,143,0.00036555800000000004,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13391,Q#1866 - >seq5189,superfamily,224117,50,143,0.00036555800000000004,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13392,Q#1866 - >seq5189,non-specific,224117,35,148,0.00146635,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13393,Q#1866 - >seq5189,non-specific,340204,109,148,0.00192232,35.4612,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13394,Q#1866 - >seq5189,superfamily,340204,109,148,0.00192232,35.4612,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13395,Q#1866 - >seq5189,non-specific,235175,50,143,0.00289737,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13396,Q#1866 - >seq5189,superfamily,235175,50,143,0.00289737,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15,ORF1,hs3_orang,pars,BothTerminiTruncated
13397,Q#1866 - >seq5189,non-specific,310273,47,146,0.00327232,38.9582,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA15,ORF1,hs3_orang,pars,C-TerminusTruncated
13398,Q#1866 - >seq5189,superfamily,310273,47,146,0.00327232,38.9582,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA15,ORF1,hs3_orang,pars,C-TerminusTruncated
13399,Q#1866 - >seq5189,non-specific,224117,50,149,0.00533006,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.pars.frame1,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15,ORF1,hs3_orang,pars,N-TerminusTruncated
13400,Q#1867 - >seq5190,non-specific,335182,139,235,7.64015e-39,132.42700000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs3_orang.pars.frame2,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13401,Q#1867 - >seq5190,superfamily,335182,139,235,7.64015e-39,132.42700000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs3_orang.pars.frame2,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13402,Q#1867 - >seq5190,non-specific,340205,238,301,1.37417e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs3_orang.pars.frame2,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13403,Q#1867 - >seq5190,superfamily,340205,238,301,1.37417e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs3_orang.pars.frame2,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15,ORF1,hs3_orang,pars,CompleteHit
13404,Q#1868 - >seq5191,non-specific,335182,64,120,8.968079999999999e-13,61.9351,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
13405,Q#1868 - >seq5191,superfamily,335182,64,120,8.968079999999999e-13,61.9351,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
13406,Q#1871 - >seq5194,non-specific,335182,154,250,3.47401e-38,131.27100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13407,Q#1871 - >seq5194,superfamily,335182,154,250,3.47401e-38,131.27100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13408,Q#1871 - >seq5194,non-specific,340205,253,316,2.76603e-29,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13409,Q#1871 - >seq5194,superfamily,340205,253,316,2.76603e-29,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13410,Q#1871 - >seq5194,non-specific,222878,51,141,1.17421e-05,46.5461,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs3_orang,marg,BothTerminiTruncated
13411,Q#1871 - >seq5194,superfamily,222878,51,141,1.17421e-05,46.5461,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs3_orang,marg,BothTerminiTruncated
13412,Q#1871 - >seq5194,non-specific,340204,110,151,4.70818e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13413,Q#1871 - >seq5194,superfamily,340204,110,151,4.70818e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs3_orang,marg,CompleteHit
13414,Q#1871 - >seq5194,non-specific,224117,51,179,0.000298138,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs3_orang,marg,BothTerminiTruncated
13415,Q#1871 - >seq5194,superfamily,224117,51,179,0.000298138,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs3_orang,marg,BothTerminiTruncated
13416,Q#1871 - >seq5194,non-specific,224117,33,200,0.00115311,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs3_orang.marg.frame3,1909130925_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs3_orang,marg,N-TerminusTruncated
13417,Q#1872 - >seq5195,non-specific,335182,139,234,4.1699e-37,127.804,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs4_gibbon.pars.frame1,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13418,Q#1872 - >seq5195,superfamily,335182,139,234,4.1699e-37,127.804,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs4_gibbon.pars.frame1,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13419,Q#1872 - >seq5195,non-specific,340205,237,300,1.04591e-28,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs4_gibbon.pars.frame1,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13420,Q#1872 - >seq5195,superfamily,340205,237,300,1.04591e-28,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs4_gibbon.pars.frame1,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13421,Q#1874 - >seq5197,non-specific,222878,49,139,1.61697e-06,49.2425,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13422,Q#1874 - >seq5197,superfamily,222878,49,139,1.61697e-06,49.2425,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13423,Q#1874 - >seq5197,non-specific,224117,49,142,0.00044561300000000003,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13424,Q#1874 - >seq5197,superfamily,224117,49,142,0.00044561300000000003,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13425,Q#1874 - >seq5197,non-specific,340204,108,147,0.0005102619999999999,37.001999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13426,Q#1874 - >seq5197,superfamily,340204,108,147,0.0005102619999999999,37.001999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs4_gibbon,pars,CompleteHit
13427,Q#1874 - >seq5197,non-specific,235175,38,142,0.0008721960000000001,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13428,Q#1874 - >seq5197,superfamily,235175,38,142,0.0008721960000000001,40.8176,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13429,Q#1874 - >seq5197,non-specific,224117,34,147,0.00110598,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13430,Q#1874 - >seq5197,non-specific,310273,46,145,0.00175259,39.7286,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA15,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13431,Q#1874 - >seq5197,superfamily,310273,46,145,0.00175259,39.7286,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA15,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13432,Q#1874 - >seq5197,non-specific,224117,49,120,0.00205573,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13433,Q#1874 - >seq5197,non-specific,274009,49,144,0.00418634,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13434,Q#1874 - >seq5197,superfamily,274009,49,144,0.00418634,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13435,Q#1874 - >seq5197,non-specific,275316,52,144,0.00607007,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13436,Q#1874 - >seq5197,superfamily,275316,52,144,0.00607007,38.0776,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13437,Q#1874 - >seq5197,non-specific,224117,31,139,0.00815184,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13438,Q#1874 - >seq5197,non-specific,224117,48,147,0.00961899,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.pars.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,pars,BothTerminiTruncated
13439,Q#1877 - >seq5200,non-specific,335182,152,247,1.0730999999999999e-36,127.419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13440,Q#1877 - >seq5200,superfamily,335182,152,247,1.0730999999999999e-36,127.419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13441,Q#1877 - >seq5200,non-specific,340205,250,313,1.6438e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13442,Q#1877 - >seq5200,superfamily,340205,250,313,1.6438e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13443,Q#1877 - >seq5200,non-specific,222878,49,139,6.5989e-06,47.3165,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13444,Q#1877 - >seq5200,superfamily,222878,49,139,6.5989e-06,47.3165,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13445,Q#1877 - >seq5200,non-specific,340204,108,149,8.69057e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13446,Q#1877 - >seq5200,superfamily,340204,108,149,8.69057e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs4_gibbon,marg,CompleteHit
13447,Q#1877 - >seq5200,non-specific,224117,31,198,0.000960928,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13448,Q#1877 - >seq5200,superfamily,224117,31,198,0.000960928,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13449,Q#1877 - >seq5200,non-specific,274009,49,145,0.00179333,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13450,Q#1877 - >seq5200,superfamily,274009,49,145,0.00179333,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13451,Q#1877 - >seq5200,non-specific,310273,46,145,0.0092206,37.4174,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA15,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13452,Q#1877 - >seq5200,superfamily,310273,46,145,0.0092206,37.4174,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA15.ORF1.hs4_gibbon.marg.frame3,1909130925_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA15,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13453,Q#1879 - >seq5202,non-specific,340205,153,216,6.22273e-25,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,CompleteHit
13454,Q#1879 - >seq5202,superfamily,340205,153,216,6.22273e-25,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,CompleteHit
13455,Q#1879 - >seq5202,non-specific,335182,99,150,1.48955e-12,61.5499,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13456,Q#1879 - >seq5202,superfamily,335182,99,150,1.48955e-12,61.5499,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13457,Q#1882 - >seq5205,specific,311990,1158,1176,8.28793e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs4_gibbon.pars.frame2,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13458,Q#1882 - >seq5205,superfamily,311990,1158,1176,8.28793e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs4_gibbon.pars.frame2,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13459,Q#1883 - >seq5206,specific,197310,9,222,3.91157e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13460,Q#1883 - >seq5206,superfamily,351117,9,222,3.91157e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13461,Q#1883 - >seq5206,non-specific,197306,9,223,1.64675e-45,164.192,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13462,Q#1883 - >seq5206,non-specific,197307,9,221,6.564210000000001e-24,101.98100000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13463,Q#1883 - >seq5206,non-specific,197320,8,221,1.2986099999999998e-22,98.3561,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13464,Q#1883 - >seq5206,non-specific,223780,9,221,3.31972e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13465,Q#1883 - >seq5206,non-specific,197321,7,221,1.05395e-17,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13466,Q#1883 - >seq5206,specific,335306,10,212,9.56381e-17,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13467,Q#1883 - >seq5206,non-specific,272954,9,221,1.4741400000000001e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13468,Q#1883 - >seq5206,non-specific,273186,9,221,7.79224e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13469,Q#1883 - >seq5206,non-specific,197336,7,221,5.9445e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13470,Q#1883 - >seq5206,non-specific,197319,8,221,8.36085e-11,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13471,Q#1883 - >seq5206,non-specific,197322,9,221,9.240830000000001e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13472,Q#1883 - >seq5206,non-specific,236970,9,221,3.12525e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13473,Q#1883 - >seq5206,non-specific,339261,108,217,2.1535300000000004e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13474,Q#1883 - >seq5206,non-specific,197311,37,204,5.76649e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,pars,CompleteHit
13475,Q#1883 - >seq5206,non-specific,197314,7,192,0.00109708,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.pars.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA12,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13476,Q#1886 - >seq5209,specific,238827,508,770,1.6079999999999998e-64,217.929,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13477,Q#1886 - >seq5209,superfamily,295487,508,770,1.6079999999999998e-64,217.929,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13478,Q#1886 - >seq5209,specific,197310,9,236,1.1549299999999999e-61,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13479,Q#1886 - >seq5209,superfamily,351117,9,236,1.1549299999999999e-61,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13480,Q#1886 - >seq5209,non-specific,197306,9,236,1.8088e-47,169.97,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13481,Q#1886 - >seq5209,specific,333820,514,770,1.1035599999999998e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13482,Q#1886 - >seq5209,superfamily,333820,514,770,1.1035599999999998e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13483,Q#1886 - >seq5209,non-specific,197307,9,236,6.91449e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13484,Q#1886 - >seq5209,non-specific,223780,9,237,1.48134e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13485,Q#1886 - >seq5209,non-specific,197320,8,229,1.7268099999999998e-22,97.9709,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13486,Q#1886 - >seq5209,specific,335306,10,229,1.09642e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13487,Q#1886 - >seq5209,non-specific,197321,7,236,1.15269e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13488,Q#1886 - >seq5209,non-specific,273186,9,237,1.96689e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13489,Q#1886 - >seq5209,non-specific,272954,9,236,2.44929e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13490,Q#1886 - >seq5209,non-specific,197336,7,229,2.39929e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13491,Q#1886 - >seq5209,non-specific,197319,8,236,2.4292299999999997e-12,68.0721,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13492,Q#1886 - >seq5209,non-specific,197322,9,236,1.24311e-11,66.957,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13493,Q#1886 - >seq5209,non-specific,238828,580,735,5.75249e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13494,Q#1886 - >seq5209,non-specific,339261,108,232,8.797059999999999e-10,57.3471,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13495,Q#1886 - >seq5209,non-specific,236970,9,237,1.85911e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13496,Q#1886 - >seq5209,non-specific,275209,465,798,4.31948e-07,53.2304,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13497,Q#1886 - >seq5209,superfamily,275209,465,798,4.31948e-07,53.2304,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13498,Q#1886 - >seq5209,non-specific,197311,37,236,3.11552e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13499,Q#1886 - >seq5209,non-specific,238185,654,770,5.45302e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13500,Q#1886 - >seq5209,specific,311990,1239,1257,0.00038777699999999996,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13501,Q#1886 - >seq5209,superfamily,311990,1239,1257,0.00038777699999999996,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs4_gibbon,marg,CompleteHit
13502,Q#1886 - >seq5209,non-specific,197314,7,192,0.00116842,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA12,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13503,Q#1886 - >seq5209,non-specific,197317,139,229,0.00134312,41.8188,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA12.ORF2.hs4_gibbon.marg.frame3,1909130925_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13504,Q#1888 - >seq5211,specific,238827,496,758,2.50454e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13505,Q#1888 - >seq5211,superfamily,295487,496,758,2.50454e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13506,Q#1888 - >seq5211,specific,333820,502,758,3.5678699999999997e-34,129.72,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13507,Q#1888 - >seq5211,superfamily,333820,502,758,3.5678699999999997e-34,129.72,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13508,Q#1888 - >seq5211,non-specific,238828,568,755,1.13191e-11,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13509,Q#1888 - >seq5211,non-specific,275209,453,786,2.97845e-07,54.0008,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13510,Q#1888 - >seq5211,superfamily,275209,453,786,2.97845e-07,54.0008,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13511,Q#1888 - >seq5211,non-specific,238185,642,758,1.32988e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13512,Q#1888 - >seq5211,non-specific,224117,199,453,0.00361916,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA12,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13513,Q#1888 - >seq5211,superfamily,224117,199,453,0.00361916,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA12,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13514,Q#1889 - >seq5212,specific,197310,9,222,2.4757099999999995e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13515,Q#1889 - >seq5212,superfamily,351117,9,222,2.4757099999999995e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13516,Q#1889 - >seq5212,non-specific,197306,9,223,2.0500999999999998e-46,166.888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13517,Q#1889 - >seq5212,non-specific,197307,9,223,6.0686599999999995e-24,101.98100000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13518,Q#1889 - >seq5212,non-specific,197320,8,221,1.0711799999999998e-22,98.7413,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13519,Q#1889 - >seq5212,non-specific,223780,9,221,9.6781e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13520,Q#1889 - >seq5212,non-specific,197321,7,223,6.4939e-18,84.52600000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13521,Q#1889 - >seq5212,specific,335306,10,212,6.649939999999999e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13522,Q#1889 - >seq5212,non-specific,272954,9,221,1.75613e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13523,Q#1889 - >seq5212,non-specific,273186,9,221,1.33824e-13,71.9264,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13524,Q#1889 - >seq5212,non-specific,197336,7,221,6.46969e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13525,Q#1889 - >seq5212,non-specific,197319,8,223,6.92722e-11,63.8349,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13526,Q#1889 - >seq5212,non-specific,197322,9,222,2.48852e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13527,Q#1889 - >seq5212,non-specific,236970,9,221,3.31349e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13528,Q#1889 - >seq5212,non-specific,339261,108,217,3.99627e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13529,Q#1889 - >seq5212,specific,311990,1159,1177,7.08075e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13530,Q#1889 - >seq5212,superfamily,311990,1159,1177,7.08075e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13531,Q#1889 - >seq5212,non-specific,197311,37,204,0.000309221,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,pars,CompleteHit
13532,Q#1890 - >seq5213,specific,311990,1135,1153,0.00011659,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13533,Q#1890 - >seq5213,superfamily,311990,1135,1153,0.00011659,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13534,Q#1892 - >seq5215,specific,238827,491,753,1.8561599999999994e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13535,Q#1892 - >seq5215,superfamily,295487,491,753,1.8561599999999994e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13536,Q#1892 - >seq5215,specific,197310,9,222,1.0418000000000002e-56,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13537,Q#1892 - >seq5215,superfamily,351117,9,222,1.0418000000000002e-56,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13538,Q#1892 - >seq5215,non-specific,197306,9,223,1.1023899999999998e-44,161.88,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13539,Q#1892 - >seq5215,specific,333820,497,753,1.27111e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13540,Q#1892 - >seq5215,superfamily,333820,497,753,1.27111e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13541,Q#1892 - >seq5215,non-specific,197320,8,221,1.19696e-22,98.3561,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13542,Q#1892 - >seq5215,non-specific,197307,9,223,1.41463e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13543,Q#1892 - >seq5215,non-specific,223780,9,221,3.12869e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13544,Q#1892 - >seq5215,non-specific,197321,7,223,4.840640000000001e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13545,Q#1892 - >seq5215,specific,335306,10,212,7.00744e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13546,Q#1892 - >seq5215,non-specific,272954,9,221,8.781169999999999e-14,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13547,Q#1892 - >seq5215,non-specific,273186,9,221,2.49828e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13548,Q#1892 - >seq5215,non-specific,197336,7,221,6.82317e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13549,Q#1892 - >seq5215,non-specific,238828,563,750,1.85476e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13550,Q#1892 - >seq5215,non-specific,197319,8,223,9.70417e-10,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13551,Q#1892 - >seq5215,non-specific,197322,9,222,2.6274000000000003e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13552,Q#1892 - >seq5215,non-specific,236970,9,221,2.4769099999999997e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13553,Q#1892 - >seq5215,non-specific,275209,448,781,2.91269e-07,54.0008,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13554,Q#1892 - >seq5215,superfamily,275209,448,781,2.91269e-07,54.0008,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13555,Q#1892 - >seq5215,non-specific,238185,637,753,2.24179e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13556,Q#1892 - >seq5215,non-specific,339261,108,217,0.000136465,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13557,Q#1892 - >seq5215,non-specific,197311,37,204,0.000685823,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs5_gmonkey,marg,CompleteHit
13558,Q#1895 - >seq5218,non-specific,335182,154,250,7.61356e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13559,Q#1895 - >seq5218,superfamily,335182,154,250,7.61356e-43,143.21200000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13560,Q#1895 - >seq5218,non-specific,335182,154,250,7.61356e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13561,Q#1895 - >seq5218,non-specific,340205,253,317,8.91388e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13562,Q#1895 - >seq5218,superfamily,340205,253,317,8.91388e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13563,Q#1895 - >seq5218,non-specific,340205,253,317,8.91388e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13564,Q#1895 - >seq5218,non-specific,340204,110,151,2.93712e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13565,Q#1895 - >seq5218,superfamily,340204,110,151,2.93712e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13566,Q#1895 - >seq5218,non-specific,340204,110,151,2.93712e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,pars,CompleteHit
13567,Q#1895 - >seq5218,non-specific,224117,48,200,0.0012499,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13568,Q#1895 - >seq5218,superfamily,224117,48,200,0.0012499,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13569,Q#1895 - >seq5218,non-specific,224117,48,200,0.0012499,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13570,Q#1895 - >seq5218,non-specific,224117,54,147,0.00840902,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13571,Q#1895 - >seq5218,superfamily,224117,54,147,0.00840902,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13572,Q#1895 - >seq5218,non-specific,224117,54,147,0.00840902,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13573,Q#1895 - >seq5218,non-specific,235175,51,141,0.00919503,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13574,Q#1895 - >seq5218,superfamily,235175,51,141,0.00919503,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13575,Q#1895 - >seq5218,non-specific,235175,51,141,0.00919503,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.pars.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
13576,Q#1898 - >seq5221,non-specific,335182,154,250,7.61356e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13577,Q#1898 - >seq5221,superfamily,335182,154,250,7.61356e-43,143.21200000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13578,Q#1898 - >seq5221,non-specific,335182,154,250,7.61356e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13579,Q#1898 - >seq5221,non-specific,340205,253,317,8.91388e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13580,Q#1898 - >seq5221,superfamily,340205,253,317,8.91388e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13581,Q#1898 - >seq5221,non-specific,340205,253,317,8.91388e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13582,Q#1898 - >seq5221,non-specific,340204,110,151,2.93712e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13583,Q#1898 - >seq5221,superfamily,340204,110,151,2.93712e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13584,Q#1898 - >seq5221,non-specific,340204,110,151,2.93712e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs5_gmonkey,marg,CompleteHit
13585,Q#1898 - >seq5221,non-specific,224117,48,200,0.0012499,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13586,Q#1898 - >seq5221,superfamily,224117,48,200,0.0012499,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13587,Q#1898 - >seq5221,non-specific,224117,48,200,0.0012499,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
13588,Q#1898 - >seq5221,non-specific,224117,54,147,0.00840902,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13589,Q#1898 - >seq5221,superfamily,224117,54,147,0.00840902,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13590,Q#1898 - >seq5221,non-specific,224117,54,147,0.00840902,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13591,Q#1898 - >seq5221,non-specific,235175,51,141,0.00919503,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13592,Q#1898 - >seq5221,superfamily,235175,51,141,0.00919503,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13593,Q#1898 - >seq5221,non-specific,235175,51,141,0.00919503,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs5_gmonkey.marg.frame3,1909130925_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13594,Q#1899 - >seq5222,non-specific,335182,62,142,2.63039e-19,79.2691,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame1,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,CompleteHit
13595,Q#1899 - >seq5222,superfamily,335182,62,142,2.63039e-19,79.2691,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame1,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,CompleteHit
13596,Q#1900 - >seq5223,non-specific,340205,155,218,3.48965e-24,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,CompleteHit
13597,Q#1900 - >seq5223,superfamily,340205,155,218,3.48965e-24,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,CompleteHit
13598,Q#1900 - >seq5223,non-specific,335182,123,152,6.89672e-06,43.0603,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13599,Q#1900 - >seq5223,superfamily,335182,123,152,6.89672e-06,43.0603,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs5_gmonkey.pars.frame2,1909130925_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
13600,Q#1903 - >seq5226,non-specific,335182,154,238,9.23645e-29,106.618,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,marg,C-TerminusTruncated
13601,Q#1903 - >seq5226,superfamily,335182,154,238,9.23645e-29,106.618,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,marg,C-TerminusTruncated
13602,Q#1903 - >seq5226,non-specific,340205,250,314,2.4667599999999997e-18,77.7616,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,marg,CompleteHit
13603,Q#1903 - >seq5226,superfamily,340205,250,314,2.4667599999999997e-18,77.7616,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,marg,CompleteHit
13604,Q#1903 - >seq5226,non-specific,340204,112,151,4.1867e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3F,ORF1,hs1_chimp,marg,CompleteHit
13605,Q#1903 - >seq5226,superfamily,340204,112,151,4.1867e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3F.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3F,ORF1,hs1_chimp,marg,CompleteHit
13606,Q#1906 - >seq5229,non-specific,335182,70,166,5.52204e-30,107.389,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13607,Q#1906 - >seq5229,superfamily,335182,70,166,5.52204e-30,107.389,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13608,Q#1906 - >seq5229,non-specific,340205,169,231,2.31147e-19,78.9172,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13609,Q#1906 - >seq5229,superfamily,340205,169,231,2.31147e-19,78.9172,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13610,Q#1906 - >seq5229,non-specific,340204,27,68,0.000612911,36.6168,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13611,Q#1906 - >seq5229,superfamily,340204,27,68,0.000612911,36.6168,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3C.ORF1.hs1_chimp.pars.frame2,1909130925_L1ME3C.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1ME3C,ORF1,hs1_chimp,pars,CompleteHit
13612,Q#1910 - >seq5233,non-specific,335182,1,59,0.00334095,34.2007,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3D.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3D,ORF1,hs10_snmole,marg,BothTerminiTruncated
13613,Q#1910 - >seq5233,superfamily,335182,1,59,0.00334095,34.2007,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3D.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3D,ORF1,hs10_snmole,marg,BothTerminiTruncated
13614,Q#1916 - >seq5239,non-specific,238827,511,627,4.95758e-05,45.3598,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3D.ORF2.hs10_snmole.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3D,ORF2,hs10_snmole,marg,C-TerminusTruncated
13615,Q#1916 - >seq5239,superfamily,295487,511,627,4.95758e-05,45.3598,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3D.ORF2.hs10_snmole.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3D,ORF2,hs10_snmole,marg,C-TerminusTruncated
13616,Q#1931 - >seq5254,non-specific,335182,3,86,0.00357637,35.7415,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3D.ORF1.hs8_ctshrew.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3D,ORF1,hs8_ctshrew,marg,CompleteHit
13617,Q#1931 - >seq5254,superfamily,335182,3,86,0.00357637,35.7415,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3D.ORF1.hs8_ctshrew.marg.frame1,1909130925_L1ME3D.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3D,ORF1,hs8_ctshrew,marg,CompleteHit
13618,Q#1945 - >seq5268,non-specific,310000,270,347,0.0021703000000000004,40.8561,pfam05110,AF-4,NC,cl25851,"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.",L1ME3D.ORF2.hs8_ctshrew.pars.frame3,1909130925_L1ME3D.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3D,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
13619,Q#1945 - >seq5268,superfamily,310000,270,347,0.0021703000000000004,40.8561,cl25851,AF-4 superfamily,NC, - ,"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.",L1ME3D.ORF2.hs8_ctshrew.pars.frame3,1909130925_L1ME3D.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3D,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
13620,Q#1966 - >seq5289,non-specific,340205,70,120,8.28857e-09,48.1012,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,pars,CompleteHit
13621,Q#1966 - >seq5289,superfamily,340205,70,120,8.28857e-09,48.1012,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs1_chimp.pars.frame1,1909130925_L1ME3F.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3F,ORF1,hs1_chimp,pars,CompleteHit
13622,Q#1994 - >seq5317,specific,238827,504,740,4.34255e-29,116.23700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13623,Q#1994 - >seq5317,superfamily,295487,504,740,4.34255e-29,116.23700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13624,Q#1994 - >seq5317,non-specific,333820,519,733,1.01233e-11,65.0062,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13625,Q#1994 - >seq5317,superfamily,333820,519,733,1.01233e-11,65.0062,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13626,Q#1994 - >seq5317,non-specific,197310,11,248,1.3977e-09,59.6725,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13627,Q#1994 - >seq5317,superfamily,351117,11,248,1.3977e-09,59.6725,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3A,ORF2,hs2_gorilla,marg,CompleteHit
13628,Q#1998 - >seq5321,non-specific,340205,29,80,4.264430000000001e-06,40.3972,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3A,ORF1,hs3_orang,pars,CompleteHit
13629,Q#1998 - >seq5321,superfamily,340205,29,80,4.264430000000001e-06,40.3972,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs3_orang.pars.frame2,1909130925_L1ME3A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3A,ORF1,hs3_orang,pars,CompleteHit
13630,Q#2006 - >seq5329,non-specific,238827,534,742,8.30017e-08,54.2194,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs3_orang,marg,N-TerminusTruncated
13631,Q#2006 - >seq5329,superfamily,295487,534,742,8.30017e-08,54.2194,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs3_orang.marg.frame1,1909130925_L1ME3A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs3_orang,marg,N-TerminusTruncated
13632,Q#2011 - >seq5334,non-specific,340205,29,70,1.8816200000000002e-12,55.8052,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs4_gibbon.pars.frame3,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13633,Q#2011 - >seq5334,superfamily,340205,29,70,1.8816200000000002e-12,55.8052,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs4_gibbon.pars.frame3,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
13634,Q#2019 - >seq5342,non-specific,340205,32,88,1.08498e-10,52.3384,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs1_chimp.pars.frame3,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3A,ORF1,hs1_chimp,pars,CompleteHit
13635,Q#2019 - >seq5342,superfamily,340205,32,88,1.08498e-10,52.3384,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs1_chimp.pars.frame3,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3A,ORF1,hs1_chimp,pars,CompleteHit
13636,Q#2020 - >seq5343,non-specific,335182,139,230,2.22253e-11,59.2387,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs1_chimp,marg,CompleteHit
13637,Q#2020 - >seq5343,superfamily,335182,139,230,2.22253e-11,59.2387,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs1_chimp,marg,CompleteHit
13638,Q#2020 - >seq5343,non-specific,340205,233,305,1.4426e-10,56.1904,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs1_chimp,marg,CompleteHit
13639,Q#2020 - >seq5343,superfamily,340205,233,305,1.4426e-10,56.1904,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs1_chimp,marg,CompleteHit
13640,Q#2024 - >seq5347,non-specific,238827,451,557,3.8172099999999994e-25,104.681,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13641,Q#2024 - >seq5347,superfamily,295487,451,557,3.8172099999999994e-25,104.681,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13642,Q#2024 - >seq5347,non-specific,333820,466,557,3.79334e-10,59.9986,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13643,Q#2024 - >seq5347,superfamily,333820,466,557,3.79334e-10,59.9986,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
13644,Q#2025 - >seq5348,non-specific,238827,392,661,2.51931e-21,93.1246,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,pars,CompleteHit
13645,Q#2025 - >seq5348,superfamily,295487,392,661,2.51931e-21,93.1246,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,pars,CompleteHit
13646,Q#2025 - >seq5348,non-specific,333820,406,490,0.000272911,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,pars,C-TerminusTruncated
13647,Q#2025 - >seq5348,superfamily,333820,406,490,0.000272911,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs1_chimp.pars.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,pars,C-TerminusTruncated
13648,Q#2026 - >seq5349,non-specific,238827,489,686,2.0695299999999997e-08,55.7602,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs1_chimp,marg,N-TerminusTruncated
13649,Q#2026 - >seq5349,superfamily,295487,489,686,2.0695299999999997e-08,55.7602,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs1_chimp.marg.frame1,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3A,ORF2,hs1_chimp,marg,N-TerminusTruncated
13650,Q#2027 - >seq5350,non-specific,238827,470,553,2.2672199999999999e-13,70.3978,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,marg,C-TerminusTruncated
13651,Q#2027 - >seq5350,superfamily,295487,470,553,2.2672199999999999e-13,70.3978,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,marg,C-TerminusTruncated
13652,Q#2027 - >seq5350,non-specific,333820,484,530,0.00043158300000000003,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,marg,C-TerminusTruncated
13653,Q#2027 - >seq5350,superfamily,333820,484,530,0.00043158300000000003,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs1_chimp.marg.frame2,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs1_chimp,marg,C-TerminusTruncated
13654,Q#2028 - >seq5351,non-specific,197310,3,222,5.2795900000000006e-20,90.1033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs1_chimp,marg,CompleteHit
13655,Q#2028 - >seq5351,superfamily,351117,3,222,5.2795900000000006e-20,90.1033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3A,ORF2,hs1_chimp,marg,CompleteHit
13656,Q#2028 - >seq5351,non-specific,197306,3,223,4.3353699999999996e-10,61.3433,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs1_chimp.marg.frame3,1909130925_L1ME3A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3A,ORF2,hs1_chimp,marg,CompleteHit
13657,Q#2029 - >seq5352,non-specific,340205,133,197,4.52886e-08,48.1012,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,pars,CompleteHit
13658,Q#2029 - >seq5352,superfamily,340205,133,197,4.52886e-08,48.1012,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs2_gorilla.pars.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,pars,CompleteHit
13659,Q#2032 - >seq5355,non-specific,335182,153,224,1.4228199999999998e-09,54.2311,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,marg,N-TerminusTruncated
13660,Q#2032 - >seq5355,superfamily,335182,153,224,1.4228199999999998e-09,54.2311,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,marg,N-TerminusTruncated
13661,Q#2032 - >seq5355,non-specific,340205,227,291,1.21163e-07,47.716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,marg,CompleteHit
13662,Q#2032 - >seq5355,superfamily,340205,227,291,1.21163e-07,47.716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs2_gorilla.marg.frame1,1909130925_L1ME3A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs2_gorilla,marg,CompleteHit
13663,Q#2035 - >seq5358,non-specific,340205,282,343,3.7767800000000007e-16,71.9836,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3A,ORF1,hs4_gibbon,marg,CompleteHit
13664,Q#2035 - >seq5358,superfamily,340205,282,343,3.7767800000000007e-16,71.9836,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME3A,ORF1,hs4_gibbon,marg,CompleteHit
13665,Q#2037 - >seq5360,non-specific,238827,433,521,3.39182e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13666,Q#2037 - >seq5360,superfamily,295487,433,521,3.39182e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs4_gibbon.pars.frame1,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13667,Q#2043 - >seq5366,non-specific,214368,48,254,0.00194773,41.8483,CHL00117,rpoC2,NC,cl33332,RNA polymerase beta'' subunit; Reviewed,L1ME3A.ORF2.hs6_sqmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
13668,Q#2043 - >seq5366,superfamily,214368,48,254,0.00194773,41.8483,cl33332,rpoC2 superfamily,NC, - ,RNA polymerase beta'' subunit; Reviewed,L1ME3A.ORF2.hs6_sqmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
13669,Q#2046 - >seq5369,non-specific,107374,32,71,0.00869303,35.126,cd06379,PBP1_iGluR_NMDA_NR1,C,cl10011,"N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits.  The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor.  When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site",L1ME3A.ORF1.hs6_sqmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3A,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
13670,Q#2046 - >seq5369,superfamily,353040,32,71,0.00869303,35.126,cl10011,Periplasmic_Binding_Protein_Type_1 superfamily,C, - ,"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.",L1ME3A.ORF1.hs6_sqmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3A,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
13671,Q#2063 - >seq5386,specific,238827,484,757,6.64922e-34,130.10399999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs4_gibbon,marg,CompleteHit
13672,Q#2063 - >seq5386,superfamily,295487,484,757,6.64922e-34,130.10399999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs4_gibbon,marg,CompleteHit
13673,Q#2063 - >seq5386,non-specific,333820,510,757,7.683910000000001e-18,82.3401,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs4_gibbon,marg,CompleteHit
13674,Q#2063 - >seq5386,superfamily,333820,510,757,7.683910000000001e-18,82.3401,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs4_gibbon,marg,CompleteHit
13675,Q#2063 - >seq5386,non-specific,238828,586,721,3.18635e-05,46.4253,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3A.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME3A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13676,Q#2065 - >seq5388,non-specific,340205,56,94,5.70731e-07,42.7084,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs5_gmonkey.pars.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
13677,Q#2065 - >seq5388,superfamily,340205,56,94,5.70731e-07,42.7084,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs5_gmonkey.pars.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
13678,Q#2068 - >seq5391,non-specific,340205,317,377,1.72011e-13,64.6648,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,marg,CompleteHit
13679,Q#2068 - >seq5391,superfamily,340205,317,377,1.72011e-13,64.6648,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,marg,CompleteHit
13680,Q#2068 - >seq5391,non-specific,335182,246,313,2.50582e-05,42.6751,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,marg,CompleteHit
13681,Q#2068 - >seq5391,superfamily,335182,246,313,2.50582e-05,42.6751,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs5_gmonkey,marg,CompleteHit
13682,Q#2069 - >seq5392,non-specific,227278,100,214,0.00347277,38.9349,COG4942,EnvC,NC,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1ME3A.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13683,Q#2069 - >seq5392,superfamily,227278,100,214,0.00347277,38.9349,cl34844,EnvC superfamily,NC, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1ME3A.ORF1.hs5_gmonkey.marg.frame2,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13684,Q#2076 - >seq5399,non-specific,238827,641,739,5.56395e-05,45.3598,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13685,Q#2076 - >seq5399,superfamily,295487,641,739,5.56395e-05,45.3598,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13686,Q#2086 - >seq5409,specific,238827,295,555,4.24132e-40,147.438,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,CompleteHit
13687,Q#2086 - >seq5409,superfamily,295487,295,555,4.24132e-40,147.438,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,CompleteHit
13688,Q#2086 - >seq5409,non-specific,333820,301,555,1.74435e-19,86.9625,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,CompleteHit
13689,Q#2086 - >seq5409,superfamily,333820,301,555,1.74435e-19,86.9625,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,CompleteHit
13690,Q#2086 - >seq5409,non-specific,238828,369,523,0.00160261,41.0325,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13691,Q#2086 - >seq5409,non-specific,275209,370,579,0.00968503,38.978,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13692,Q#2086 - >seq5409,superfamily,275209,370,579,0.00968503,38.978,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME2z.ORF2.hs5_gmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
13693,Q#2089 - >seq5412,non-specific,238827,430,486,5.797810000000001e-13,69.2422,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13694,Q#2089 - >seq5412,superfamily,295487,430,486,5.797810000000001e-13,69.2422,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13695,Q#2089 - >seq5412,non-specific,333820,436,486,0.00120549,41.1238,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13696,Q#2089 - >seq5412,superfamily,333820,436,486,0.00120549,41.1238,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13697,Q#2092 - >seq5415,non-specific,238827,451,647,4.0069399999999997e-20,90.04299999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME2z,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13698,Q#2092 - >seq5415,superfamily,295487,451,647,4.0069399999999997e-20,90.04299999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME2z,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13699,Q#2092 - >seq5415,non-specific,333820,463,647,1.04537e-10,61.5394,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME2z,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13700,Q#2092 - >seq5415,superfamily,333820,463,647,1.04537e-10,61.5394,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME2z,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13701,Q#2092 - >seq5415,non-specific,238828,458,615,0.00171632,41.0325,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME2z.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME2z.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME2z,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
13702,Q#2098 - >seq5421,non-specific,235510,101,147,0.00858875,36.2339,PRK05573,rplU,N,cl00382,50S ribosomal protein L21; Validated,L1ME2z.ORF2.hs6_sqmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME2z,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
13703,Q#2098 - >seq5421,superfamily,351065,101,147,0.00858875,36.2339,cl00382,Ribosomal_L21p superfamily,N, - ,Ribosomal prokaryotic L21 protein; Ribosomal prokaryotic L21 protein.  ,L1ME2z.ORF2.hs6_sqmonkey.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME2z,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
13704,Q#2115 - >seq5438,non-specific,335182,157,253,8.756879999999998e-39,132.812,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13705,Q#2115 - >seq5438,superfamily,335182,157,253,8.756879999999998e-39,132.812,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13706,Q#2115 - >seq5438,non-specific,340205,257,320,7.76353e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13707,Q#2115 - >seq5438,superfamily,340205,257,320,7.76353e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13708,Q#2115 - >seq5438,non-specific,340204,112,154,2.87776e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13709,Q#2115 - >seq5438,superfamily,340204,112,154,2.87776e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME2z,ORF1,hs4_gibbon,marg,CompleteHit
13710,Q#2115 - >seq5438,non-specific,224117,66,195,0.00013265,43.5496,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13711,Q#2115 - >seq5438,superfamily,224117,66,195,0.00013265,43.5496,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13712,Q#2115 - >seq5438,non-specific,337766,52,142,0.000314807,41.8295,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13713,Q#2115 - >seq5438,superfamily,337766,52,142,0.000314807,41.8295,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13714,Q#2115 - >seq5438,non-specific,224117,55,151,0.00085821,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13715,Q#2115 - >seq5438,superfamily,224117,55,151,0.00085821,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13716,Q#2115 - >seq5438,non-specific,274009,56,204,0.00124317,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13717,Q#2115 - >seq5438,superfamily,274009,56,204,0.00124317,40.4363,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13718,Q#2115 - >seq5438,non-specific,335555,69,142,0.00166521,39.9364,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13719,Q#2115 - >seq5438,superfamily,354396,69,142,0.00166521,39.9364,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13720,Q#2115 - >seq5438,non-specific,336322,73,203,0.00444425,38.6522,pfam06160,EzrA,N,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13721,Q#2115 - >seq5438,superfamily,336322,73,203,0.00444425,38.6522,cl38199,EzrA superfamily,N, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13722,Q#2115 - >seq5438,non-specific,222878,67,151,0.00486556,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13723,Q#2115 - >seq5438,superfamily,222878,67,151,0.00486556,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13724,Q#2115 - >seq5438,non-specific,274008,56,207,0.00532087,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13725,Q#2115 - >seq5438,superfamily,274008,56,207,0.00532087,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13726,Q#2115 - >seq5438,non-specific,337715,71,135,0.00608272,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13727,Q#2115 - >seq5438,superfamily,337715,71,135,0.00608272,37.9785,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13728,Q#2115 - >seq5438,non-specific,224117,55,151,0.00652032,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13729,Q#2115 - >seq5438,non-specific,334565,53,126,0.00927652,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME2z,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13730,Q#2115 - >seq5438,superfamily,334565,53,126,0.00927652,37.4692,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME2z,ORF1,hs4_gibbon,marg,C-TerminusTruncated
13731,Q#2115 - >seq5438,non-specific,274009,48,203,0.00960236,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME2z,ORF1,hs4_gibbon,marg,BothTerminiTruncated
13732,Q#2115 - >seq5438,non-specific,275056,55,144,0.00988272,36.5245,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13733,Q#2115 - >seq5438,superfamily,275056,55,144,0.00988272,36.5245,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME2z.ORF1.hs4_gibbon.marg.frame1,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1ME2z,ORF1,hs4_gibbon,marg,N-TerminusTruncated
13734,Q#2120 - >seq5443,non-specific,238827,243,474,1.52873e-08,55.7602,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs4_gibbon,pars,CompleteHit
13735,Q#2120 - >seq5443,superfamily,295487,243,474,1.52873e-08,55.7602,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs4_gibbon,pars,CompleteHit
13736,Q#2120 - >seq5443,non-specific,333820,317,392,0.00567844,38.4274,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13737,Q#2120 - >seq5443,superfamily,333820,317,392,0.00567844,38.4274,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs4_gibbon.pars.frame3,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs4_gibbon,pars,BothTerminiTruncated
13738,Q#2122 - >seq5445,non-specific,238827,310,578,3.5388199999999994e-20,90.04299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME2z,ORF2,hs4_gibbon,marg,CompleteHit
13739,Q#2122 - >seq5445,superfamily,295487,310,578,3.5388199999999994e-20,90.04299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME2z,ORF2,hs4_gibbon,marg,CompleteHit
13740,Q#2122 - >seq5445,non-specific,333820,316,495,3.43773e-10,59.9986,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME2z,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13741,Q#2122 - >seq5445,superfamily,333820,316,495,3.43773e-10,59.9986,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME2z,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13742,Q#2122 - >seq5445,non-specific,238828,390,512,0.0044819,39.8769,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME2z.ORF2.hs4_gibbon.marg.frame2,1909130925_L1ME2z.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME2z,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13743,Q#2127 - >seq5450,non-specific,238827,286,324,3.0803600000000003e-09,57.6862,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs9_pika.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,pars,C-TerminusTruncated
13744,Q#2127 - >seq5450,superfamily,295487,286,324,3.0803600000000003e-09,57.6862,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs9_pika.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,pars,C-TerminusTruncated
13745,Q#2127 - >seq5450,non-specific,333820,286,324,0.00585207,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs9_pika.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,pars,C-TerminusTruncated
13746,Q#2127 - >seq5450,superfamily,333820,286,324,0.00585207,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs9_pika.pars.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,pars,C-TerminusTruncated
13747,Q#2130 - >seq5453,non-specific,238827,395,494,5.86231e-15,75.0202,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs9_pika.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,marg,C-TerminusTruncated
13748,Q#2130 - >seq5453,superfamily,295487,395,494,5.86231e-15,75.0202,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs9_pika.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,marg,C-TerminusTruncated
13749,Q#2130 - >seq5453,non-specific,333820,418,467,0.00137211,40.7386,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs9_pika.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,marg,C-TerminusTruncated
13750,Q#2130 - >seq5453,superfamily,333820,418,467,0.00137211,40.7386,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME2z.ORF2.hs9_pika.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs9_pika,marg,C-TerminusTruncated
13751,Q#2140 - >seq5463,non-specific,335182,82,154,7.34005e-06,43.0603,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.pars.frame2,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs0_human,pars,CompleteHit
13752,Q#2140 - >seq5463,superfamily,335182,82,154,7.34005e-06,43.0603,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.pars.frame2,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs0_human,pars,CompleteHit
13753,Q#2140 - >seq5463,non-specific,340205,174,204,7.62636e-05,39.2416,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs0_human.pars.frame2,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs0_human,pars,C-TerminusTruncated
13754,Q#2140 - >seq5463,superfamily,340205,174,204,7.62636e-05,39.2416,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs0_human.pars.frame2,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME2z,ORF1,hs0_human,pars,C-TerminusTruncated
13755,Q#2142 - >seq5465,non-specific,335182,86,150,3.87061e-06,43.8307,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.marg.frame1,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs0_human,marg,CompleteHit
13756,Q#2142 - >seq5465,superfamily,335182,86,150,3.87061e-06,43.8307,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.marg.frame1,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs0_human,marg,CompleteHit
13757,Q#2144 - >seq5467,non-specific,340205,179,207,0.0010881999999999999,36.16,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs0_human,marg,C-TerminusTruncated
13758,Q#2144 - >seq5467,superfamily,340205,179,207,0.0010881999999999999,36.16,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs0_human,marg,C-TerminusTruncated
13759,Q#2144 - >seq5467,non-specific,340204,31,73,0.00203213,35.076,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME2z,ORF1,hs0_human,marg,CompleteHit
13760,Q#2144 - >seq5467,superfamily,340204,31,73,0.00203213,35.076,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME2z,ORF1,hs0_human,marg,CompleteHit
13761,Q#2144 - >seq5467,non-specific,225177,1,149,0.00568697,37.1194,COG2268,YqiK,NC,cl34451,"Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].",L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME2z,ORF1,hs0_human,marg,BothTerminiTruncated
13762,Q#2144 - >seq5467,superfamily,225177,1,149,0.00568697,37.1194,cl34451,YqiK superfamily,NC, - ,"Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].",L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME2z,ORF1,hs0_human,marg,BothTerminiTruncated
13763,Q#2144 - >seq5467,non-specific,335182,115,165,0.00980936,34.2007,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs0_human,marg,N-TerminusTruncated
13764,Q#2144 - >seq5467,superfamily,335182,115,165,0.00980936,34.2007,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME2z.ORF1.hs0_human.marg.frame3,1909130925_L1ME2z.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME2z,ORF1,hs0_human,marg,N-TerminusTruncated
13765,Q#2150 - >seq5473,non-specific,238827,274,313,0.00963352,38.4262,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs7_bushaby.pars.frame3,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs7_bushaby,pars,C-TerminusTruncated
13766,Q#2150 - >seq5473,superfamily,295487,274,313,0.00963352,38.4262,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs7_bushaby.pars.frame3,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME2z,ORF2,hs7_bushaby,pars,C-TerminusTruncated
13767,Q#2151 - >seq5474,non-specific,238827,446,486,0.00118849,41.5078,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME2z.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs7_bushaby,marg,C-TerminusTruncated
13768,Q#2151 - >seq5474,superfamily,295487,446,486,0.00118849,41.5078,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME2z.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME2z,ORF2,hs7_bushaby,marg,C-TerminusTruncated
13769,Q#2151 - >seq5474,non-specific,197310,11,125,0.00787993,39.2569,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2z.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2z,ORF2,hs7_bushaby,marg,BothTerminiTruncated
13770,Q#2151 - >seq5474,superfamily,351117,11,125,0.00787993,39.2569,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2z.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME2z,ORF2,hs7_bushaby,marg,BothTerminiTruncated
13771,Q#2157 - >seq5480,non-specific,340205,135,164,0.00277801,34.6192,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs8_ctshrew.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
13772,Q#2157 - >seq5480,superfamily,340205,135,164,0.00277801,34.6192,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME2z.ORF1.hs8_ctshrew.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME2z,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
13773,Q#2163 - >seq5486,non-specific,197310,3,92,0.000953008,41.9533,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME2z.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME2z,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
13774,Q#2163 - >seq5486,superfamily,351117,3,92,0.000953008,41.9533,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME2z.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME2z.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME2z,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
13775,Q#2174 - >seq5497,non-specific,197310,6,174,3.11617e-11,64.6801,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3B,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
13776,Q#2174 - >seq5497,superfamily,351117,6,174,3.11617e-11,64.6801,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
13777,Q#2174 - >seq5497,non-specific,238827,461,555,1.43012e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
13778,Q#2174 - >seq5497,superfamily,295487,461,555,1.43012e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
13779,Q#2174 - >seq5497,non-specific,197306,1,141,0.00280289,40.9277,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
13780,Q#2174 - >seq5497,non-specific,234767,144,361,0.00740852,40.5916,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1ME3B,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
13781,Q#2174 - >seq5497,superfamily,234767,144,361,0.00740852,40.5916,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1ME3B.ORF2.hs6_sqmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1ME3B,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
13782,Q#2179 - >seq5502,non-specific,197310,23,81,0.00011391,44.2645,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs7_bushaby.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3B,ORF2,hs7_bushaby,pars,N-TerminusTruncated
13783,Q#2179 - >seq5502,superfamily,351117,23,81,0.00011391,44.2645,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs7_bushaby.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3B,ORF2,hs7_bushaby,pars,N-TerminusTruncated
13784,Q#2181 - >seq5504,non-specific,197310,4,212,3.7619999999999995e-12,67.3765,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3B,ORF2,hs7_bushaby,marg,CompleteHit
13785,Q#2181 - >seq5504,superfamily,351117,4,212,3.7619999999999995e-12,67.3765,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs7_bushaby,marg,CompleteHit
13786,Q#2181 - >seq5504,non-specific,197306,4,213,0.000147074,44.7797,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs7_bushaby.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs7_bushaby,marg,CompleteHit
13787,Q#2188 - >seq5511,non-specific,340205,78,139,7.96657e-09,48.8716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs8_ctshrew.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs8_ctshrew,marg,CompleteHit
13788,Q#2188 - >seq5511,superfamily,340205,78,139,7.96657e-09,48.8716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs8_ctshrew.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs8_ctshrew,marg,CompleteHit
13789,Q#2189 - >seq5512,non-specific,238828,381,460,4.6186e-05,44.8845,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3B.ORF2.hs8_ctshrew.pars.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3B,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
13790,Q#2189 - >seq5512,superfamily,295487,381,460,4.6186e-05,44.8845,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs8_ctshrew.pars.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3B,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
13791,Q#2189 - >seq5512,non-specific,238827,373,450,0.000317193,42.2782,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs8_ctshrew.pars.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3B,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
13792,Q#2192 - >seq5515,non-specific,340205,1,31,0.000222041,33.4636,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs6_sqmonkey.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
13793,Q#2192 - >seq5515,superfamily,340205,1,31,0.000222041,33.4636,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs6_sqmonkey.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
13794,Q#2200 - >seq5523,non-specific,335182,158,253,9.03444e-12,60.7795,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3B,ORF1,hs5_gmonkey,marg,CompleteHit
13795,Q#2200 - >seq5523,superfamily,335182,158,253,9.03444e-12,60.7795,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3B,ORF1,hs5_gmonkey,marg,CompleteHit
13796,Q#2200 - >seq5523,non-specific,340204,115,150,0.00019953900000000002,38.1576,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3B,ORF1,hs5_gmonkey,marg,CompleteHit
13797,Q#2200 - >seq5523,superfamily,340204,115,150,0.00019953900000000002,38.1576,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3B,ORF1,hs5_gmonkey,marg,CompleteHit
13798,Q#2200 - >seq5523,non-specific,308892,57,236,0.00547853,38.2019,pfam03528,Rabaptin,NC,cl25724,Rabaptin; Rabaptin.  ,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3B,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13799,Q#2200 - >seq5523,superfamily,308892,57,236,0.00547853,38.2019,cl25724,Rabaptin superfamily,NC, - ,Rabaptin; Rabaptin.  ,L1ME3B.ORF1.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3B,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
13800,Q#2204 - >seq5527,non-specific,197310,20,108,3.03636e-08,55.0501,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3B,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
13801,Q#2204 - >seq5527,superfamily,351117,20,108,3.03636e-08,55.0501,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3B,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
13802,Q#2204 - >seq5527,non-specific,197306,20,122,0.00272506,40.1573,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs5_gmonkey.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3B,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
13803,Q#2205 - >seq5528,non-specific,238827,464,702,4.1213900000000005e-12,66.1606,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3B,ORF2,hs5_gmonkey,pars,CompleteHit
13804,Q#2205 - >seq5528,superfamily,295487,464,702,4.1213900000000005e-12,66.1606,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs5_gmonkey.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3B,ORF2,hs5_gmonkey,pars,CompleteHit
13805,Q#2206 - >seq5529,non-specific,197310,77,221,1.17096e-06,50.8129,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3B,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13806,Q#2206 - >seq5529,superfamily,351117,77,221,1.17096e-06,50.8129,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13807,Q#2206 - >seq5529,non-specific,197306,77,225,0.00021624,44.0093,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs5_gmonkey.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13808,Q#2208 - >seq5531,non-specific,238827,648,876,1.2715799999999999e-10,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3B,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13809,Q#2208 - >seq5531,superfamily,295487,648,876,1.2715799999999999e-10,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs5_gmonkey.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3B,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
13810,Q#2210 - >seq5533,non-specific,335182,23,64,3.81278e-07,45.3715,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs6_sqmonkey.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13811,Q#2210 - >seq5533,superfamily,335182,23,64,3.81278e-07,45.3715,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs6_sqmonkey.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13812,Q#2211 - >seq5534,non-specific,340205,113,149,1.2105899999999999e-05,40.7824,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs6_sqmonkey.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13813,Q#2211 - >seq5534,superfamily,340205,113,149,1.2105899999999999e-05,40.7824,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs6_sqmonkey.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3B,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13814,Q#2213 - >seq5536,non-specific,238827,609,645,0.0009077919999999999,41.893,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
13815,Q#2213 - >seq5536,superfamily,295487,609,645,0.0009077919999999999,41.893,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
13816,Q#2213 - >seq5536,non-specific,197310,4,236,0.00335988,40.0273,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3B.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3B,ORF2,hs8_ctshrew,marg,CompleteHit
13817,Q#2213 - >seq5536,superfamily,351117,4,236,0.00335988,40.0273,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3B.ORF2.hs8_ctshrew.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3B,ORF2,hs8_ctshrew,marg,CompleteHit
13818,Q#2218 - >seq5541,non-specific,238827,444,504,0.0023436999999999998,39.5818,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs11_armadillo.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3B,ORF2,hs11_armadillo,pars,BothTerminiTruncated
13819,Q#2218 - >seq5541,superfamily,295487,444,504,0.0023436999999999998,39.5818,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs11_armadillo.pars.frame2,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3B,ORF2,hs11_armadillo,pars,BothTerminiTruncated
13820,Q#2220 - >seq5543,non-specific,238827,545,629,5.93583e-05,44.9746,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs11_armadillo.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs11_armadillo,marg,N-TerminusTruncated
13821,Q#2220 - >seq5543,superfamily,295487,545,629,5.93583e-05,44.9746,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs11_armadillo.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME3B,ORF2,hs11_armadillo,marg,N-TerminusTruncated
13822,Q#2243 - >seq5566,non-specific,340205,109,160,1.29709e-06,43.4788,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs9_pika.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs9_pika,marg,CompleteHit
13823,Q#2243 - >seq5566,superfamily,340205,109,160,1.29709e-06,43.4788,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs9_pika.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3B,ORF1,hs9_pika,marg,CompleteHit
13824,Q#2246 - >seq5569,non-specific,238827,264,391,0.000284633,42.2782,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs9_pika.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3B,ORF2,hs9_pika,pars,C-TerminusTruncated
13825,Q#2246 - >seq5569,superfamily,295487,264,391,0.000284633,42.2782,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs9_pika.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3B,ORF2,hs9_pika,pars,C-TerminusTruncated
13826,Q#2249 - >seq5572,non-specific,238827,515,551,0.00243762,39.967,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3B.ORF2.hs9_pika.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3B,ORF2,hs9_pika,marg,BothTerminiTruncated
13827,Q#2249 - >seq5572,superfamily,295487,515,551,0.00243762,39.967,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3B.ORF2.hs9_pika.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3B,ORF2,hs9_pika,marg,BothTerminiTruncated
13828,Q#2249 - >seq5572,non-specific,238828,462,555,0.00266162,39.8769,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3B.ORF2.hs9_pika.marg.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3B,ORF2,hs9_pika,marg,BothTerminiTruncated
13829,Q#2250 - >seq5573,non-specific,340205,42,79,7.83469e-10,49.641999999999996,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs10_snmole.pars.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3B,ORF1,hs10_snmole,pars,C-TerminusTruncated
13830,Q#2250 - >seq5573,superfamily,340205,42,79,7.83469e-10,49.641999999999996,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs10_snmole.pars.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3B,ORF1,hs10_snmole,pars,C-TerminusTruncated
13831,Q#2252 - >seq5575,non-specific,335182,1,36,0.00194337,33.8155,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs10_snmole.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3B,ORF1,hs10_snmole,pars,N-TerminusTruncated
13832,Q#2252 - >seq5575,superfamily,335182,1,36,0.00194337,33.8155,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3B.ORF1.hs10_snmole.pars.frame3,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3B,ORF1,hs10_snmole,pars,N-TerminusTruncated
13833,Q#2253 - >seq5576,non-specific,340205,106,149,7.32469e-12,56.9608,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3B,ORF1,hs10_snmole,marg,C-TerminusTruncated
13834,Q#2253 - >seq5576,superfamily,340205,106,149,7.32469e-12,56.9608,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3B.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3B.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3B,ORF1,hs10_snmole,marg,C-TerminusTruncated
13835,Q#2265 - >seq5588,non-specific,335460,173,220,0.00860004,37.1023,pfam03755,YicC_N,C,cl26779,"YicC-like family, N-terminal region; Family of bacterial proteins. Although poorly characterized, the members of this protein family have been demonstrated to play a role in stationary phase survival. These proteins are not essential during stationary phase.",L1ME3A.ORF2.hs10_snmole.pars.frame2,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3A,ORF2,hs10_snmole,pars,C-TerminusTruncated
13836,Q#2265 - >seq5588,superfamily,355573,173,220,0.00860004,37.1023,cl26779,YicC_N superfamily,C, - ,"YicC-like family, N-terminal region; Family of bacterial proteins. Although poorly characterized, the members of this protein family have been demonstrated to play a role in stationary phase survival. These proteins are not essential during stationary phase.",L1ME3A.ORF2.hs10_snmole.pars.frame2,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3A,ORF2,hs10_snmole,pars,C-TerminusTruncated
13837,Q#2267 - >seq5590,non-specific,335460,207,255,0.00542741,38.2579,pfam03755,YicC_N,C,cl26779,"YicC-like family, N-terminal region; Family of bacterial proteins. Although poorly characterized, the members of this protein family have been demonstrated to play a role in stationary phase survival. These proteins are not essential during stationary phase.",L1ME3A.ORF2.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3A,ORF2,hs10_snmole,marg,C-TerminusTruncated
13838,Q#2267 - >seq5590,superfamily,355573,207,255,0.00542741,38.2579,cl26779,YicC_N superfamily,C, - ,"YicC-like family, N-terminal region; Family of bacterial proteins. Although poorly characterized, the members of this protein family have been demonstrated to play a role in stationary phase survival. These proteins are not essential during stationary phase.",L1ME3A.ORF2.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3A,ORF2,hs10_snmole,marg,C-TerminusTruncated
13839,Q#2271 - >seq5594,non-specific,340205,139,172,5.258240000000001e-06,42.3232,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3A,ORF1,hs0_human,pars,BothTerminiTruncated
13840,Q#2271 - >seq5594,superfamily,340205,139,172,5.258240000000001e-06,42.3232,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3A,ORF1,hs0_human,pars,BothTerminiTruncated
13841,Q#2275 - >seq5598,non-specific,340205,186,226,5.189640000000001e-10,53.8792,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3A,ORF1,hs0_human,marg,N-TerminusTruncated
13842,Q#2275 - >seq5598,superfamily,340205,186,226,5.189640000000001e-10,53.8792,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3A,ORF1,hs0_human,marg,N-TerminusTruncated
13843,Q#2275 - >seq5598,non-specific,335182,60,129,6.8847000000000004e-09,51.9199,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3A,ORF1,hs0_human,marg,CompleteHit
13844,Q#2275 - >seq5598,superfamily,335182,60,129,6.8847000000000004e-09,51.9199,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3A,ORF1,hs0_human,marg,CompleteHit
13845,Q#2276 - >seq5599,specific,197310,17,221,4.57834e-50,176.773,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13846,Q#2276 - >seq5599,superfamily,351117,17,221,4.57834e-50,176.773,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13847,Q#2276 - >seq5599,non-specific,197306,4,221,6.6778e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13848,Q#2276 - >seq5599,non-specific,223780,11,218,1.23545e-17,83.8019,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13849,Q#2276 - >seq5599,non-specific,197320,11,218,1.77354e-16,80.2517,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13850,Q#2276 - >seq5599,non-specific,197307,17,218,7.335539999999999e-16,78.0985,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13851,Q#2276 - >seq5599,specific,335306,17,218,3.99048e-13,69.5814,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13852,Q#2276 - >seq5599,non-specific,272954,13,196,1.68149e-11,65.4821,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13853,Q#2276 - >seq5599,non-specific,197319,17,218,9.29625e-11,63.0645,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13854,Q#2276 - >seq5599,non-specific,197321,11,218,1.77389e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13855,Q#2276 - >seq5599,non-specific,273186,11,218,3.7928699999999996e-10,61.526,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13856,Q#2276 - >seq5599,non-specific,197311,10,135,6.54641e-08,53.8349,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,C-TerminusTruncated
13857,Q#2276 - >seq5599,non-specific,339261,97,221,1.0152e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13858,Q#2276 - >seq5599,non-specific,197336,15,183,0.000386661,42.9847,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3A.ORF2.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13859,Q#2277 - >seq5600,specific,238827,440,690,4.95888e-37,138.578,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13860,Q#2277 - >seq5600,superfamily,295487,440,690,4.95888e-37,138.578,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13861,Q#2277 - >seq5600,non-specific,333820,446,669,3.6919199999999993e-22,94.6665,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13862,Q#2277 - >seq5600,superfamily,333820,446,669,3.6919199999999993e-22,94.6665,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,CompleteHit
13863,Q#2277 - >seq5600,non-specific,238828,524,666,1.5237e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,N-TerminusTruncated
13864,Q#2277 - >seq5600,non-specific,275209,518,713,4.69269e-06,49.7636,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,N-TerminusTruncated
13865,Q#2277 - >seq5600,superfamily,275209,518,713,4.69269e-06,49.7636,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3A.ORF2.hs0_human.pars.frame2,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3A,ORF2,hs0_human,pars,N-TerminusTruncated
13866,Q#2279 - >seq5602,non-specific,335182,44,112,1.68972e-09,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs0_human,pars,CompleteHit
13867,Q#2279 - >seq5602,superfamily,335182,44,112,1.68972e-09,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs0_human.pars.frame1,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs0_human,pars,CompleteHit
13868,Q#2280 - >seq5603,non-specific,340205,70,105,1.1050800000000001e-07,45.4048,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs10_snmole.pars.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,pars,C-TerminusTruncated
13869,Q#2280 - >seq5603,superfamily,340205,70,105,1.1050800000000001e-07,45.4048,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs10_snmole.pars.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,pars,C-TerminusTruncated
13870,Q#2295 - >seq5618,non-specific,340205,166,207,0.000196598,38.4712,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs9_pika.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs9_pika,marg,C-TerminusTruncated
13871,Q#2295 - >seq5618,superfamily,340205,166,207,0.000196598,38.4712,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs9_pika.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs9_pika,marg,C-TerminusTruncated
13872,Q#2304 - >seq5627,non-specific,335182,19,119,1.1135399999999999e-09,53.0755,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,marg,CompleteHit
13873,Q#2304 - >seq5627,superfamily,335182,19,119,1.1135399999999999e-09,53.0755,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3A.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,marg,CompleteHit
13874,Q#2304 - >seq5627,non-specific,340205,123,158,3.4046599999999997e-07,45.4048,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,marg,C-TerminusTruncated
13875,Q#2304 - >seq5627,superfamily,340205,123,158,3.4046599999999997e-07,45.4048,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3A.ORF1.hs10_snmole.marg.frame1,1909130925_L1ME3A.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3A,ORF1,hs10_snmole,marg,C-TerminusTruncated
13876,Q#2322 - >seq5645,specific,197310,3,226,9.620939999999999e-59,201.81099999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13877,Q#2322 - >seq5645,superfamily,351117,3,226,9.620939999999999e-59,201.81099999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13878,Q#2322 - >seq5645,specific,238827,468,729,9.21011e-40,146.667,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13879,Q#2322 - >seq5645,superfamily,295487,468,729,9.21011e-40,146.667,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13880,Q#2322 - >seq5645,non-specific,197306,3,226,1.4424100000000001e-30,121.04899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13881,Q#2322 - >seq5645,non-specific,333820,474,729,6.8188e-22,94.2813,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13882,Q#2322 - >seq5645,superfamily,333820,474,729,6.8188e-22,94.2813,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13883,Q#2322 - >seq5645,non-specific,223780,3,223,8.83297e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13884,Q#2322 - >seq5645,non-specific,197307,3,223,4.68785e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13885,Q#2322 - >seq5645,non-specific,197320,3,223,2.94806e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13886,Q#2322 - >seq5645,specific,335306,4,223,4.55448e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13887,Q#2322 - >seq5645,non-specific,272954,3,201,6.63906e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13888,Q#2322 - >seq5645,non-specific,197321,1,223,1.1569e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13889,Q#2322 - >seq5645,non-specific,273186,3,223,4.08654e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13890,Q#2322 - >seq5645,non-specific,197319,3,223,1.57076e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13891,Q#2322 - >seq5645,non-specific,238828,552,729,5.06023e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,N-TerminusTruncated
13892,Q#2322 - >seq5645,non-specific,197336,3,188,5.14911e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13893,Q#2322 - >seq5645,non-specific,197322,2,223,8.855930000000001e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13894,Q#2322 - >seq5645,non-specific,197311,1,140,1.93638e-07,52.6793,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3A,ORF2,hs0_human,marg,C-TerminusTruncated
13895,Q#2322 - >seq5645,non-specific,275209,546,748,8.76387e-07,52.46,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,N-TerminusTruncated
13896,Q#2322 - >seq5645,superfamily,275209,546,748,8.76387e-07,52.46,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3A,ORF2,hs0_human,marg,N-TerminusTruncated
13897,Q#2322 - >seq5645,non-specific,339261,102,226,7.3099399999999995e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13898,Q#2322 - >seq5645,non-specific,236970,3,223,0.000131932,44.885,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME3A.ORF2.hs0_human.marg.frame3,1909130925_L1ME3A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3A,ORF2,hs0_human,marg,CompleteHit
13899,Q#2348 - >seq5671,non-specific,335182,34,100,1.41402e-13,60.7795,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13900,Q#2348 - >seq5671,superfamily,335182,34,100,1.41402e-13,60.7795,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
13901,Q#2350 - >seq5673,non-specific,197310,9,76,3.5381099999999998e-12,65.8357,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13902,Q#2350 - >seq5673,superfamily,351117,9,76,3.5381099999999998e-12,65.8357,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13903,Q#2350 - >seq5673,non-specific,197306,9,73,1.50403e-10,60.9581,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13904,Q#2350 - >seq5673,non-specific,223780,9,46,0.000535804,41.4299,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13905,Q#2350 - >seq5673,non-specific,197321,7,52,0.00179142,39.8428,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13906,Q#2350 - >seq5673,non-specific,197307,9,52,0.00383233,38.8081,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13907,Q#2350 - >seq5673,non-specific,197336,7,46,0.00903888,37.5919,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4c.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13908,Q#2353 - >seq5676,specific,197310,62,232,5.75258e-42,149.424,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13909,Q#2353 - >seq5676,superfamily,351117,62,232,5.75258e-42,149.424,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13910,Q#2353 - >seq5676,non-specific,197306,64,232,1.1167100000000001e-36,135.30200000000002,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13911,Q#2353 - >seq5676,non-specific,197307,64,232,7.44813e-16,76.9429,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13912,Q#2353 - >seq5676,non-specific,223780,68,234,1.14023e-14,73.7867,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13913,Q#2353 - >seq5676,non-specific,197320,68,232,1.77013e-13,70.2366,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13914,Q#2353 - >seq5676,non-specific,197321,62,232,2.15091e-11,63.7252,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13915,Q#2353 - >seq5676,non-specific,273186,67,233,8.05501e-11,62.2964,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13916,Q#2353 - >seq5676,non-specific,339261,104,228,2.88433e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME4c,ORF2,hs4_gibbon,marg,CompleteHit
13917,Q#2353 - >seq5676,non-specific,335306,36,225,5.6074599999999996e-09,56.0994,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,CompleteHit
13918,Q#2353 - >seq5676,non-specific,197319,62,232,1.1455600000000001e-07,52.6641,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13919,Q#2353 - >seq5676,non-specific,272954,64,232,1.41353e-07,52.3853,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13920,Q#2353 - >seq5676,non-specific,197322,87,232,1.6199500000000002e-07,52.7046,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13921,Q#2353 - >seq5676,non-specific,236970,64,234,3.40365e-07,51.4334,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13922,Q#2353 - >seq5676,non-specific,197317,135,225,3.93322e-07,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13923,Q#2353 - >seq5676,non-specific,197311,68,232,6.71471e-06,46.9013,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13924,Q#2353 - >seq5676,non-specific,226098,134,235,0.0005645709999999999,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13925,Q#2353 - >seq5676,non-specific,339176,222,346,0.00143957,39.929,pfam14335,DUF4391,N,cl20517,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13926,Q#2353 - >seq5676,superfamily,339176,222,346,0.00143957,39.929,cl20517,DUF4391 superfamily,N, - ,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4c,ORF2,hs4_gibbon,marg,N-TerminusTruncated
13927,Q#2353 - >seq5676,non-specific,274009,301,449,0.00604254,39.2807,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13928,Q#2353 - >seq5676,superfamily,274009,301,449,0.00604254,39.2807,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
13929,Q#2354 - >seq5677,specific,197310,9,236,5.491269999999999e-66,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13930,Q#2354 - >seq5677,superfamily,351117,9,236,5.491269999999999e-66,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13931,Q#2354 - >seq5677,non-specific,197306,9,236,1.1467200000000002e-56,188.84400000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13932,Q#2354 - >seq5677,non-specific,197307,9,236,7.790939999999999e-28,111.226,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13933,Q#2354 - >seq5677,non-specific,223780,9,238,5.427189999999999e-25,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13934,Q#2354 - >seq5677,non-specific,197320,8,236,3.0747399999999997e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13935,Q#2354 - >seq5677,non-specific,197321,7,236,1.01152e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13936,Q#2354 - >seq5677,specific,335306,10,229,5.0035499999999995e-20,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13937,Q#2354 - >seq5677,non-specific,273186,9,237,6.86882e-20,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13938,Q#2354 - >seq5677,non-specific,272954,9,236,8.22423e-16,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13939,Q#2354 - >seq5677,non-specific,197319,8,236,2.2026900000000003e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13940,Q#2354 - >seq5677,non-specific,197336,7,235,1.4619e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13941,Q#2354 - >seq5677,non-specific,197322,9,236,1.46466e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13942,Q#2354 - >seq5677,non-specific,236970,9,238,4.1348800000000007e-10,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13943,Q#2354 - >seq5677,non-specific,339261,108,232,1.22262e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13944,Q#2354 - >seq5677,non-specific,197311,7,236,2.05864e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs4_gibbon,pars,CompleteHit
13945,Q#2354 - >seq5677,non-specific,197317,139,229,3.97753e-07,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13946,Q#2354 - >seq5677,non-specific,226098,138,239,0.000570614,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13947,Q#2354 - >seq5677,non-specific,197314,7,192,0.00124935,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1ME4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13948,Q#2354 - >seq5677,non-specific,339176,226,350,0.00169869,39.5438,pfam14335,DUF4391,N,cl20517,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13949,Q#2354 - >seq5677,superfamily,339176,226,350,0.00169869,39.5438,cl20517,DUF4391 superfamily,N, - ,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF2,hs4_gibbon,pars,N-TerminusTruncated
13950,Q#2354 - >seq5677,non-specific,274009,305,453,0.00305357,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13951,Q#2354 - >seq5677,superfamily,274009,305,453,0.00305357,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
13952,Q#2359 - >seq5682,non-specific,340204,108,150,2.0202400000000003e-12,60.4992,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4c,ORF1,hs3_orang,pars,CompleteHit
13953,Q#2359 - >seq5682,superfamily,340204,108,150,2.0202400000000003e-12,60.4992,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4c,ORF1,hs3_orang,pars,CompleteHit
13954,Q#2359 - >seq5682,non-specific,235175,51,139,2.33328e-05,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13955,Q#2359 - >seq5682,superfamily,235175,51,139,2.33328e-05,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13956,Q#2359 - >seq5682,non-specific,235175,50,153,3.2036500000000004e-05,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13957,Q#2359 - >seq5682,non-specific,274008,37,160,6.96719e-05,44.2771,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13958,Q#2359 - >seq5682,superfamily,274008,37,160,6.96719e-05,44.2771,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13959,Q#2359 - >seq5682,non-specific,224117,33,159,0.00015529200000000002,43.1644,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13960,Q#2359 - >seq5682,superfamily,224117,33,159,0.00015529200000000002,43.1644,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13961,Q#2359 - >seq5682,non-specific,224117,38,224,0.00102839,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13962,Q#2359 - >seq5682,superfamily,224117,38,224,0.00102839,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13963,Q#2359 - >seq5682,non-specific,275056,34,133,0.00115511,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13964,Q#2359 - >seq5682,superfamily,275056,34,133,0.00115511,39.2209,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13965,Q#2359 - >seq5682,non-specific,274009,29,159,0.00121973,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13966,Q#2359 - >seq5682,superfamily,274009,29,159,0.00121973,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13967,Q#2359 - >seq5682,non-specific,335336,55,119,0.0012259,38.9066,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13968,Q#2359 - >seq5682,superfamily,355101,55,119,0.0012259,38.9066,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13969,Q#2359 - >seq5682,non-specific,224117,38,147,0.00126834,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13970,Q#2359 - >seq5682,non-specific,224117,39,174,0.00134832,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13971,Q#2359 - >seq5682,non-specific,335623,51,145,0.00170879,39.465,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13972,Q#2359 - >seq5682,superfamily,335623,51,145,0.00170879,39.465,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13973,Q#2359 - >seq5682,non-specific,274009,48,147,0.00192096,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13974,Q#2359 - >seq5682,non-specific,273690,52,153,0.00198136,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13975,Q#2359 - >seq5682,superfamily,355611,52,153,0.00198136,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13976,Q#2359 - >seq5682,non-specific,335556,60,149,0.00214498,38.2829,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13977,Q#2359 - >seq5682,superfamily,335556,60,149,0.00214498,38.2829,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13978,Q#2359 - >seq5682,non-specific,337663,47,144,0.00228366,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13979,Q#2359 - >seq5682,superfamily,337663,47,144,0.00228366,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13980,Q#2359 - >seq5682,non-specific,335182,153,175,0.0028743,36.5119,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13981,Q#2359 - >seq5682,superfamily,335182,153,175,0.0028743,36.5119,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13982,Q#2359 - >seq5682,non-specific,225288,51,146,0.00311633,38.9172,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13983,Q#2359 - >seq5682,superfamily,331991,51,146,0.00311633,38.9172,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13984,Q#2359 - >seq5682,non-specific,336322,47,164,0.0040541,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13985,Q#2359 - >seq5682,superfamily,336322,47,164,0.0040541,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13986,Q#2359 - >seq5682,non-specific,224117,41,177,0.00438081,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13987,Q#2359 - >seq5682,non-specific,274008,1,159,0.00557303,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13988,Q#2359 - >seq5682,non-specific,237178,21,159,0.00573552,38.1518,PRK12705,PRK12705,C,cl36167,hypothetical protein; Provisional,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13989,Q#2359 - >seq5682,superfamily,237178,21,159,0.00573552,38.1518,cl36167,PRK12705 superfamily,C, - ,hypothetical protein; Provisional,L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,C-TerminusTruncated
13990,Q#2359 - >seq5682,non-specific,313461,78,145,0.00599262,37.5454,pfam10234,Cluap1,NC,cl25650,"Clusterin-associated protein-1; This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13991,Q#2359 - >seq5682,superfamily,313461,78,145,0.00599262,37.5454,cl25650,Cluap1 superfamily,NC, - ,"Clusterin-associated protein-1; This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell.",L1ME4c.ORF1.hs3_orang.pars.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,pars,BothTerminiTruncated
13992,Q#2361 - >seq5684,non-specific,335182,165,238,2.05308e-34,121.256,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame2,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13993,Q#2361 - >seq5684,superfamily,335182,165,238,2.05308e-34,121.256,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame2,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs3_orang,pars,N-TerminusTruncated
13994,Q#2361 - >seq5684,non-specific,340205,241,305,2.3555999999999997e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame2,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs3_orang,pars,CompleteHit
13995,Q#2361 - >seq5684,superfamily,340205,241,305,2.3555999999999997e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs3_orang.pars.frame2,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs3_orang,pars,CompleteHit
13996,Q#2363 - >seq5686,non-specific,335182,158,256,1.16865e-27,103.92200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,marg,CompleteHit
13997,Q#2363 - >seq5686,superfamily,335182,158,256,1.16865e-27,103.92200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,marg,CompleteHit
13998,Q#2363 - >seq5686,non-specific,340205,259,310,3.1054e-12,60.8128,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
13999,Q#2363 - >seq5686,superfamily,340205,259,310,3.1054e-12,60.8128,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
14000,Q#2364 - >seq5687,specific,197310,9,236,3.0254199999999997e-63,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14001,Q#2364 - >seq5687,superfamily,351117,9,236,3.0254199999999997e-63,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14002,Q#2364 - >seq5687,non-specific,197306,9,236,8.327949999999999e-55,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14003,Q#2364 - >seq5687,non-specific,197307,9,236,3.441599999999999e-27,111.226,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14004,Q#2364 - >seq5687,non-specific,223780,9,238,3.30569e-25,105.758,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14005,Q#2364 - >seq5687,non-specific,238827,510,589,9.89033e-24,100.05799999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14006,Q#2364 - >seq5687,superfamily,295487,510,589,9.89033e-24,100.05799999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14007,Q#2364 - >seq5687,non-specific,197321,7,236,3.6399599999999996e-22,96.4672,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14008,Q#2364 - >seq5687,non-specific,197320,8,236,8.557310000000001e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14009,Q#2364 - >seq5687,non-specific,273186,9,237,2.2232e-20,91.5716,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14010,Q#2364 - >seq5687,specific,335306,10,229,8.983760000000001e-20,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14011,Q#2364 - >seq5687,non-specific,272954,9,236,5.7321e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14012,Q#2364 - >seq5687,non-specific,197319,8,236,1.63245e-16,80.0133,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14013,Q#2364 - >seq5687,non-specific,197336,7,235,2.8995599999999997e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14014,Q#2364 - >seq5687,non-specific,236970,9,238,1.42347e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14015,Q#2364 - >seq5687,non-specific,197322,9,236,1.68225e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14016,Q#2364 - >seq5687,non-specific,333820,516,570,1.66068e-08,54.99100000000001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14017,Q#2364 - >seq5687,superfamily,333820,516,570,1.66068e-08,54.99100000000001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14018,Q#2364 - >seq5687,non-specific,339261,108,232,2.5117099999999998e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14019,Q#2364 - >seq5687,non-specific,197311,7,236,4.11685e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14020,Q#2364 - >seq5687,non-specific,197317,139,229,9.07949e-07,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14021,Q#2364 - >seq5687,non-specific,226098,138,239,2.38958e-05,46.6248,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14022,Q#2364 - >seq5687,non-specific,197314,7,192,7.23468e-05,45.0271,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14023,Q#2364 - >seq5687,non-specific,225565,2,238,0.000811505,42.4284,COG3021,YafD,N,cl00490,"Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only]; Uncharacterized protein conserved in bacteria [Function unknown].",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14024,Q#2364 - >seq5687,non-specific,235175,295,464,0.00174228,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14025,Q#2364 - >seq5687,superfamily,235175,295,464,0.00174228,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14026,Q#2364 - >seq5687,non-specific,274009,305,453,0.00427121,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14027,Q#2364 - >seq5687,superfamily,274009,305,453,0.00427121,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14028,Q#2364 - >seq5687,non-specific,223496,305,464,0.00483522,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14029,Q#2364 - >seq5687,superfamily,223496,305,464,0.00483522,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14030,Q#2364 - >seq5687,non-specific,312723,270,464,0.00591778,39.1363,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14031,Q#2364 - >seq5687,superfamily,312723,270,464,0.00591778,39.1363,cl25728,DUF1978 superfamily, - , - ,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1ME4c.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14032,Q#2365 - >seq5688,non-specific,282383,192,370,0.00135442,41.6495,pfam04514,BTV_NS2,NC,cl04557,"Bluetongue virus non-structural protein NS2; This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs.",L1ME4c.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14033,Q#2365 - >seq5688,superfamily,282383,192,370,0.00135442,41.6495,cl04557,BTV_NS2 superfamily,NC, - ,"Bluetongue virus non-structural protein NS2; This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs.",L1ME4c.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4c,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14034,Q#2366 - >seq5689,non-specific,335182,154,251,1.0253099999999998e-45,150.916,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14035,Q#2366 - >seq5689,superfamily,335182,154,251,1.0253099999999998e-45,150.916,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14036,Q#2366 - >seq5689,non-specific,340205,254,318,4.124629999999999e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14037,Q#2366 - >seq5689,superfamily,340205,254,318,4.124629999999999e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14038,Q#2366 - >seq5689,non-specific,340204,109,151,3.15545e-11,57.4176,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14039,Q#2366 - >seq5689,superfamily,340204,109,151,3.15545e-11,57.4176,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4c,ORF1,hs3_orang,marg,CompleteHit
14040,Q#2366 - >seq5689,non-specific,235175,52,183,5.24035e-05,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14041,Q#2366 - >seq5689,superfamily,235175,52,183,5.24035e-05,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14042,Q#2366 - >seq5689,non-specific,235175,51,154,9.02316e-05,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14043,Q#2366 - >seq5689,superfamily,235175,51,154,9.02316e-05,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14044,Q#2366 - >seq5689,non-specific,337663,48,145,0.00267813,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14045,Q#2366 - >seq5689,superfamily,337663,48,145,0.00267813,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14046,Q#2366 - >seq5689,non-specific,224117,34,183,0.0026808000000000005,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,N-TerminusTruncated
14047,Q#2366 - >seq5689,superfamily,224117,34,183,0.0026808000000000005,39.3124,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4c,ORF1,hs3_orang,marg,N-TerminusTruncated
14048,Q#2366 - >seq5689,non-specific,335336,56,120,0.00324762,37.751,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14049,Q#2366 - >seq5689,superfamily,355101,56,120,0.00324762,37.751,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14050,Q#2366 - >seq5689,non-specific,335623,52,146,0.00525169,37.9242,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14051,Q#2366 - >seq5689,superfamily,335623,52,146,0.00525169,37.9242,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,C-TerminusTruncated
14052,Q#2366 - >seq5689,non-specific,275056,35,134,0.00629872,36.9097,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,N-TerminusTruncated
14053,Q#2366 - >seq5689,superfamily,275056,35,134,0.00629872,36.9097,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME4c,ORF1,hs3_orang,marg,N-TerminusTruncated
14054,Q#2366 - >seq5689,non-specific,335556,61,150,0.00662378,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14055,Q#2366 - >seq5689,superfamily,335556,61,150,0.00662378,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14056,Q#2366 - >seq5689,non-specific,224117,39,195,0.00837837,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14057,Q#2366 - >seq5689,non-specific,274009,30,202,0.00975821,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14058,Q#2366 - >seq5689,superfamily,274009,30,202,0.00975821,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs3_orang.marg.frame3,1909130926_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4c,ORF1,hs3_orang,marg,BothTerminiTruncated
14059,Q#2369 - >seq5692,non-specific,238827,434,503,1.09855e-12,68.0866,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
14060,Q#2369 - >seq5692,superfamily,295487,434,503,1.09855e-12,68.0866,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
14061,Q#2369 - >seq5692,non-specific,197310,106,161,2.48529e-05,46.5757,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
14062,Q#2369 - >seq5692,superfamily,351117,106,161,2.48529e-05,46.5757,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
14063,Q#2370 - >seq5693,specific,238827,535,718,2.5419899999999995e-37,139.349,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14064,Q#2370 - >seq5693,superfamily,295487,535,718,2.5419899999999995e-37,139.349,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14065,Q#2370 - >seq5693,non-specific,333820,536,718,6.353980000000001e-23,96.5925,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14066,Q#2370 - >seq5693,superfamily,333820,536,718,6.353980000000001e-23,96.5925,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14067,Q#2370 - >seq5693,non-specific,238828,535,683,6.62687e-12,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14068,Q#2370 - >seq5693,non-specific,275209,537,746,4.65677e-09,59.0084,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14069,Q#2370 - >seq5693,superfamily,275209,537,746,4.65677e-09,59.0084,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14070,Q#2370 - >seq5693,non-specific,238185,602,718,2.77934e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs2_gorilla,marg,CompleteHit
14071,Q#2373 - >seq5696,non-specific,197310,37,189,0.00649481,39.2569,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
14072,Q#2373 - >seq5696,superfamily,351117,37,189,0.00649481,39.2569,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
14073,Q#2384 - >seq5707,non-specific,318019,270,388,0.00182313,42.1137,pfam15718,MNR,NC,cl24325,Protein moonraker; Protein moonraker is a centriolar satellite component involved in centriole duplication. It promotes centriole duplication by localizing WDR62 to the centrosome.,L1ME4c.ORF2.hs6_sqmonkey.marg.frame2,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4c,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
14074,Q#2384 - >seq5707,superfamily,318019,270,388,0.00182313,42.1137,cl24325,MNR superfamily,NC, - ,Protein moonraker; Protein moonraker is a centriolar satellite component involved in centriole duplication. It promotes centriole duplication by localizing WDR62 to the centrosome.,L1ME4c.ORF2.hs6_sqmonkey.marg.frame2,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4c,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
14075,Q#2385 - >seq5708,specific,238827,540,795,1.3242299999999999e-45,163.616,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14076,Q#2385 - >seq5708,superfamily,295487,540,795,1.3242299999999999e-45,163.616,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14077,Q#2385 - >seq5708,specific,197310,10,237,5.068749999999999e-28,113.6,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14078,Q#2385 - >seq5708,superfamily,351117,10,237,5.068749999999999e-28,113.6,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14079,Q#2385 - >seq5708,non-specific,333820,546,771,4.98264e-20,88.8885,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14080,Q#2385 - >seq5708,superfamily,333820,546,771,4.98264e-20,88.8885,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14081,Q#2385 - >seq5708,non-specific,197306,10,237,7.33712e-18,84.07,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14082,Q#2385 - >seq5708,non-specific,238828,546,768,7.39203e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14083,Q#2385 - >seq5708,non-specific,197320,109,208,2.5235400000000003e-06,50.2062,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
14084,Q#2385 - >seq5708,non-specific,223780,10,238,6.09332e-06,49.1339,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14085,Q#2385 - >seq5708,non-specific,197307,10,237,1.09109e-05,48.0529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14086,Q#2385 - >seq5708,non-specific,197321,8,237,6.61218e-05,45.6208,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14087,Q#2385 - >seq5708,specific,335306,11,230,8.275760000000001e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,CompleteHit
14088,Q#2385 - >seq5708,non-specific,272954,10,196,0.000124532,45.0665,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
14089,Q#2385 - >seq5708,non-specific,197319,76,237,0.00437979,40.3377,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
14090,Q#2386 - >seq5709,non-specific,238827,494,606,1.49225e-10,61.9234,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14091,Q#2386 - >seq5709,superfamily,295487,494,606,1.49225e-10,61.9234,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14092,Q#2386 - >seq5709,non-specific,238828,494,605,3.1853e-06,49.1216,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs6_sqmonkey.pars.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
14093,Q#2386 - >seq5709,non-specific,333820,494,605,4.56319e-06,48.0574,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14094,Q#2386 - >seq5709,superfamily,333820,494,605,4.56319e-06,48.0574,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14095,Q#2387 - >seq5710,non-specific,197310,14,99,0.000324232,43.1089,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame2,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14096,Q#2387 - >seq5710,superfamily,351117,14,99,0.000324232,43.1089,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs6_sqmonkey.pars.frame2,1909130926_L1ME4c.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4c,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
14097,Q#2388 - >seq5711,non-specific,340205,109,162,1.36689e-08,48.8716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs8_ctshrew,marg,CompleteHit
14098,Q#2388 - >seq5711,superfamily,340205,109,162,1.36689e-08,48.8716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs8_ctshrew,marg,CompleteHit
14099,Q#2388 - >seq5711,non-specific,335182,20,105,5.36233e-05,39.9787,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs8_ctshrew,marg,CompleteHit
14100,Q#2388 - >seq5711,superfamily,335182,20,105,5.36233e-05,39.9787,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME4c.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs8_ctshrew,marg,CompleteHit
14101,Q#2389 - >seq5712,specific,238827,510,772,9.809069999999999e-68,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14102,Q#2389 - >seq5712,superfamily,295487,510,772,9.809069999999999e-68,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14103,Q#2389 - >seq5712,specific,197310,9,236,2.4825299999999994e-63,213.752,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14104,Q#2389 - >seq5712,superfamily,351117,9,236,2.4825299999999994e-63,213.752,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14105,Q#2389 - >seq5712,non-specific,197306,9,236,1.0760999999999998e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14106,Q#2389 - >seq5712,specific,333820,516,772,5.72065e-36,134.342,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14107,Q#2389 - >seq5712,superfamily,333820,516,772,5.72065e-36,134.342,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14108,Q#2389 - >seq5712,non-specific,197307,9,236,8.457700000000001e-27,110.07,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14109,Q#2389 - >seq5712,non-specific,223780,9,238,4.79811e-25,105.37299999999999,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14110,Q#2389 - >seq5712,non-specific,197321,7,236,6.632519999999999e-22,95.6968,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14111,Q#2389 - >seq5712,non-specific,197320,8,236,8.64861e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14112,Q#2389 - >seq5712,non-specific,273186,9,237,2.24689e-20,91.5716,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14113,Q#2389 - >seq5712,specific,335306,10,229,9.07605e-20,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14114,Q#2389 - >seq5712,non-specific,272954,9,236,6.86466e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14115,Q#2389 - >seq5712,non-specific,197319,8,236,6.592169999999999e-16,78.4725,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14116,Q#2389 - >seq5712,non-specific,197336,7,235,2.93004e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14117,Q#2389 - >seq5712,non-specific,238828,516,737,8.2566e-12,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14118,Q#2389 - >seq5712,non-specific,275209,467,800,5.21364e-11,65.1716,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14119,Q#2389 - >seq5712,superfamily,275209,467,800,5.21364e-11,65.1716,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14120,Q#2389 - >seq5712,non-specific,236970,9,238,8.211900000000001e-10,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14121,Q#2389 - >seq5712,non-specific,197322,9,236,1.7003800000000003e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14122,Q#2389 - >seq5712,non-specific,339261,108,232,1.22506e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14123,Q#2389 - >seq5712,non-specific,197311,7,236,4.04267e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14124,Q#2389 - >seq5712,non-specific,197317,139,229,9.172239999999999e-07,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14125,Q#2389 - >seq5712,non-specific,226098,138,239,2.4138200000000002e-05,46.6248,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14126,Q#2389 - >seq5712,non-specific,197314,7,192,7.30739e-05,45.0271,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1ME4c,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14127,Q#2389 - >seq5712,non-specific,238185,656,772,7.84289e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14128,Q#2389 - >seq5712,non-specific,225565,2,238,0.0008197289999999999,42.4284,COG3021,YafD,N,cl00490,"Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only]; Uncharacterized protein conserved in bacteria [Function unknown].",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14129,Q#2389 - >seq5712,non-specific,312723,270,464,0.00641996,39.1363,pfam09321,DUF1978, - ,cl25728,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14130,Q#2389 - >seq5712,superfamily,312723,270,464,0.00641996,39.1363,cl25728,DUF1978 superfamily, - , - ,"Domain of unknown function (DUF1978); Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.",L1ME4c.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4c,ORF2,hs2_gorilla,pars,CompleteHit
14131,Q#2393 - >seq5716,non-specific,341202,215,308,0.00770147,37.0763,cd17521,RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like,N,cl38903,"Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD2-CR2, Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) TRD1-CR1 and Pseudoalteromonas species P1-1; Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'...  TCTANNNNNNRTTC ... 3', and the recognition sequences of Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) and Pseudoalteromonas species P1-13-1a S subunit (S.Psp1bORF2093P) are undetermined. The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD1 recognizes TCTA/TAGA, and -TRD2 recognizes GAAY/RTTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. In addition, this family includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P.",L1ME4a.ORF2.hs6_sqmonkey.marg.frame2,1909130926_L1ME4a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
14132,Q#2393 - >seq5716,superfamily,365779,215,308,0.00770147,37.0763,cl38903,RMtype1_S_TRD-CR_like superfamily,N, - ,"Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains; The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P.",L1ME4a.ORF2.hs6_sqmonkey.marg.frame2,1909130926_L1ME4a.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME4a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
14133,Q#2410 - >seq5733,non-specific,214368,118,364,0.00443717,40.3075,CHL00117,rpoC2,NC,cl33332,RNA polymerase beta'' subunit; Reviewed,L1ME3.ORF2.hs5_gmonkey.pars.frame1,1909130926_L1ME3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
14134,Q#2410 - >seq5733,superfamily,214368,118,364,0.00443717,40.3075,cl33332,rpoC2 superfamily,NC, - ,RNA polymerase beta'' subunit; Reviewed,L1ME3.ORF2.hs5_gmonkey.pars.frame1,1909130926_L1ME3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
14135,Q#2413 - >seq5736,specific,238827,509,773,2.4859499999999995e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14136,Q#2413 - >seq5736,superfamily,295487,509,773,2.4859499999999995e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14137,Q#2413 - >seq5736,specific,197310,9,236,2.7969e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14138,Q#2413 - >seq5736,superfamily,351117,9,236,2.7969e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14139,Q#2413 - >seq5736,specific,333820,515,739,3.97905e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14140,Q#2413 - >seq5736,superfamily,333820,515,739,3.97905e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14141,Q#2413 - >seq5736,non-specific,197306,9,236,6.77205e-32,124.90100000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14142,Q#2413 - >seq5736,non-specific,197320,9,206,3.9861399999999996e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14143,Q#2413 - >seq5736,non-specific,223780,9,237,7.83454e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14144,Q#2413 - >seq5736,non-specific,197307,9,236,2.53929e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14145,Q#2413 - >seq5736,specific,335306,10,229,2.0135099999999998e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14146,Q#2413 - >seq5736,non-specific,273186,9,237,1.39295e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14147,Q#2413 - >seq5736,non-specific,197319,13,236,7.1162e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14148,Q#2413 - >seq5736,non-specific,238828,515,736,1.04243e-14,74.5448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14149,Q#2413 - >seq5736,non-specific,272954,9,236,1.15727e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14150,Q#2413 - >seq5736,non-specific,197321,7,236,1.80168e-14,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14151,Q#2413 - >seq5736,non-specific,197336,9,194,1.56384e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14152,Q#2413 - >seq5736,non-specific,275209,466,797,1.8115e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14153,Q#2413 - >seq5736,superfamily,275209,466,797,1.8115e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14154,Q#2413 - >seq5736,non-specific,197322,8,236,1.65872e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14155,Q#2413 - >seq5736,non-specific,236970,9,189,7.70654e-07,51.8186,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,pars,C-TerminusTruncated
14156,Q#2413 - >seq5736,non-specific,197311,30,236,1.00198e-05,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14157,Q#2413 - >seq5736,non-specific,239569,524,786,0.00014457899999999999,44.1007,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14158,Q#2413 - >seq5736,non-specific,235175,294,468,0.00067403,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,BothTerminiTruncated
14159,Q#2413 - >seq5736,superfamily,235175,294,468,0.00067403,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,BothTerminiTruncated
14160,Q#2413 - >seq5736,non-specific,238185,655,732,0.000950213,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,C-TerminusTruncated
14161,Q#2413 - >seq5736,non-specific,274009,307,455,0.000971705,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,C-TerminusTruncated
14162,Q#2413 - >seq5736,superfamily,274009,307,455,0.000971705,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,C-TerminusTruncated
14163,Q#2413 - >seq5736,non-specific,274009,305,462,0.00226405,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,BothTerminiTruncated
14164,Q#2413 - >seq5736,non-specific,334125,212,409,0.00270233,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME4a,ORF2,hs0_human,pars,N-TerminusTruncated
14165,Q#2413 - >seq5736,superfamily,334125,212,409,0.00270233,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME4a,ORF2,hs0_human,pars,N-TerminusTruncated
14166,Q#2413 - >seq5736,non-specific,339261,108,232,0.00278681,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs0_human,pars,CompleteHit
14167,Q#2413 - >seq5736,non-specific,274009,294,433,0.00379278,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,pars,BothTerminiTruncated
14168,Q#2413 - >seq5736,specific,225881,514,734,0.00820699,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,N-TerminusTruncated
14169,Q#2413 - >seq5736,superfamily,225881,514,734,0.00820699,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs0_human.pars.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs0_human,pars,N-TerminusTruncated
14170,Q#2414 - >seq5737,specific,238827,580,707,2.8426699999999997e-28,113.54,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14171,Q#2414 - >seq5737,superfamily,295487,580,707,2.8426699999999997e-28,113.54,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14172,Q#2414 - >seq5737,non-specific,333820,542,673,9.688519999999999e-15,73.4806,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14173,Q#2414 - >seq5737,superfamily,333820,542,673,9.688519999999999e-15,73.4806,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14174,Q#2414 - >seq5737,non-specific,238828,576,670,4.23763e-07,51.818000000000005,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14175,Q#2414 - >seq5737,non-specific,238185,589,666,0.000752176,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14176,Q#2414 - >seq5737,non-specific,275209,587,731,0.0011827,42.4448,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14177,Q#2414 - >seq5737,superfamily,275209,587,731,0.0011827,42.4448,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14178,Q#2414 - >seq5737,non-specific,239569,591,720,0.0035388000000000004,39.8635,cd03487,RT_Bac_retron_II,N,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs0_human.marg.frame1,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14179,Q#2417 - >seq5740,non-specific,335182,154,253,5.25487e-33,117.789,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14180,Q#2417 - >seq5740,superfamily,335182,154,253,5.25487e-33,117.789,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14181,Q#2417 - >seq5740,non-specific,340205,256,320,1.8432000000000002e-26,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14182,Q#2417 - >seq5740,superfamily,340205,256,320,1.8432000000000002e-26,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14183,Q#2417 - >seq5740,non-specific,340204,109,151,1.3533899999999999e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14184,Q#2417 - >seq5740,superfamily,340204,109,151,1.3533899999999999e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4c,ORF1,hs2_gorilla,marg,CompleteHit
14185,Q#2417 - >seq5740,non-specific,274008,35,147,0.000933291,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14186,Q#2417 - >seq5740,superfamily,274008,35,147,0.000933291,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14187,Q#2417 - >seq5740,non-specific,224117,44,201,0.00099523,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14188,Q#2417 - >seq5740,superfamily,224117,44,201,0.00099523,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14189,Q#2417 - >seq5740,non-specific,223250,47,167,0.00169839,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_tRNAsynthetase,L1ME4c,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14190,Q#2417 - >seq5740,superfamily,223250,47,167,0.00169839,39.8889,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_tRNAsynthetase,L1ME4c,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14191,Q#2417 - >seq5740,non-specific,235175,43,140,0.00201358,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14192,Q#2417 - >seq5740,superfamily,235175,43,140,0.00201358,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14193,Q#2417 - >seq5740,non-specific,224117,47,148,0.00386982,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14194,Q#2417 - >seq5740,non-specific,222878,36,154,0.00684627,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14195,Q#2417 - >seq5740,superfamily,222878,36,154,0.00684627,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4c.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14196,Q#2419 - >seq5742,non-specific,335182,55,149,1.85358e-19,79.6543,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,CompleteHit
14197,Q#2419 - >seq5742,superfamily,335182,55,149,1.85358e-19,79.6543,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,CompleteHit
14198,Q#2419 - >seq5742,non-specific,340205,152,176,3.26045e-08,48.8716,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,C-TerminusTruncated
14199,Q#2419 - >seq5742,superfamily,340205,152,176,3.26045e-08,48.8716,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,C-TerminusTruncated
14200,Q#2420 - >seq5743,non-specific,335182,102,135,0.00173328,36.5119,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
14201,Q#2420 - >seq5743,superfamily,335182,102,135,0.00173328,36.5119,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs2_gorilla.pars.frame1,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4c,ORF1,hs2_gorilla,pars,N-TerminusTruncated
14202,Q#2421 - >seq5744,non-specific,238827,558,596,0.00019727299999999998,43.818999999999996,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs0_human.marg.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4b,ORF2,hs0_human,marg,BothTerminiTruncated
14203,Q#2421 - >seq5744,superfamily,295487,558,596,0.00019727299999999998,43.818999999999996,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs0_human.marg.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4b,ORF2,hs0_human,marg,BothTerminiTruncated
14204,Q#2422 - >seq5745,non-specific,197310,151,189,0.00188909,40.7977,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.marg.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME4b,ORF2,hs0_human,marg,N-TerminusTruncated
14205,Q#2422 - >seq5745,superfamily,351117,151,189,0.00188909,40.7977,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.marg.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,marg,N-TerminusTruncated
14206,Q#2423 - >seq5746,specific,238827,521,780,6.868789999999998e-38,141.275,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14207,Q#2423 - >seq5746,superfamily,295487,521,780,6.868789999999998e-38,141.275,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14208,Q#2423 - >seq5746,non-specific,197310,34,240,9.26369e-26,106.667,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14209,Q#2423 - >seq5746,superfamily,351117,34,240,9.26369e-26,106.667,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14210,Q#2423 - >seq5746,non-specific,197306,34,240,1.02916e-17,83.6848,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14211,Q#2423 - >seq5746,non-specific,333820,535,743,3.09256e-12,66.1618,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14212,Q#2423 - >seq5746,superfamily,333820,535,743,3.09256e-12,66.1618,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14213,Q#2423 - >seq5746,non-specific,197307,34,240,1.04637e-05,48.0529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14214,Q#2423 - >seq5746,non-specific,197319,34,240,4.3684700000000005e-05,46.1157,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14215,Q#2423 - >seq5746,specific,335306,35,233,0.000152534,44.1582,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,marg,CompleteHit
14216,Q#2423 - >seq5746,non-specific,197311,38,147,0.0006686610000000001,41.8937,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs0_human,marg,C-TerminusTruncated
14217,Q#2423 - >seq5746,non-specific,197320,34,147,0.00105587,41.7318,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs0_human.marg.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs0_human,marg,C-TerminusTruncated
14218,Q#2424 - >seq5747,non-specific,282383,192,370,0.00139506,41.6495,pfam04514,BTV_NS2,NC,cl04557,"Bluetongue virus non-structural protein NS2; This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs.",L1ME4c.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME4c,ORF2,hs2_gorilla,pars,BothTerminiTruncated
14219,Q#2424 - >seq5747,superfamily,282383,192,370,0.00139506,41.6495,cl04557,BTV_NS2 superfamily,NC, - ,"Bluetongue virus non-structural protein NS2; This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs.",L1ME4c.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME4c,ORF2,hs2_gorilla,pars,BothTerminiTruncated
14220,Q#2425 - >seq5748,non-specific,238827,459,626,1.22418e-20,91.1986,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs0_human,pars,C-TerminusTruncated
14221,Q#2425 - >seq5748,superfamily,295487,459,626,1.22418e-20,91.1986,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs0_human,pars,C-TerminusTruncated
14222,Q#2425 - >seq5748,non-specific,197310,139,212,9.37146e-13,68.5321,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs0_human,pars,N-TerminusTruncated
14223,Q#2425 - >seq5748,superfamily,351117,139,212,9.37146e-13,68.5321,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,pars,N-TerminusTruncated
14224,Q#2425 - >seq5748,non-specific,333820,473,631,3.7582199999999997e-10,59.9986,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs0_human,pars,C-TerminusTruncated
14225,Q#2425 - >seq5748,superfamily,333820,473,631,3.7582199999999997e-10,59.9986,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs0_human,pars,C-TerminusTruncated
14226,Q#2425 - >seq5748,non-specific,197306,150,212,0.000103862,44.7797,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,pars,N-TerminusTruncated
14227,Q#2425 - >seq5748,non-specific,238828,547,650,0.0008818360000000001,41.8029,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs0_human.pars.frame3,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs0_human,pars,BothTerminiTruncated
14228,Q#2426 - >seq5749,non-specific,238827,514,692,8.50517e-08,53.8342,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs0_human.pars.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs0_human,pars,N-TerminusTruncated
14229,Q#2426 - >seq5749,superfamily,295487,514,692,8.50517e-08,53.8342,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs0_human.pars.frame1,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs0_human,pars,N-TerminusTruncated
14230,Q#2427 - >seq5750,non-specific,340205,260,324,6.502130000000001e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,CompleteHit
14231,Q#2427 - >seq5750,superfamily,340205,260,324,6.502130000000001e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,CompleteHit
14232,Q#2427 - >seq5750,non-specific,335182,199,257,8.44445e-21,86.2026,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,N-TerminusTruncated
14233,Q#2427 - >seq5750,superfamily,335182,199,257,8.44445e-21,86.2026,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,N-TerminusTruncated
14234,Q#2428 - >seq5751,non-specific,335182,149,188,8.745560000000001e-10,55.3867,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,C-TerminusTruncated
14235,Q#2428 - >seq5751,superfamily,335182,149,188,8.745560000000001e-10,55.3867,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.marg.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME4b,ORF1,hs1_chimp,marg,C-TerminusTruncated
14236,Q#2430 - >seq5753,non-specific,340205,238,302,6.62548e-31,110.889,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,CompleteHit
14237,Q#2430 - >seq5753,superfamily,340205,238,302,6.62548e-31,110.889,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,CompleteHit
14238,Q#2430 - >seq5753,non-specific,335182,179,235,5.99255e-19,80.0395,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,N-TerminusTruncated
14239,Q#2430 - >seq5753,superfamily,335182,179,235,5.99255e-19,80.0395,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,N-TerminusTruncated
14240,Q#2431 - >seq5754,non-specific,335182,137,176,1.28139e-09,54.2311,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,C-TerminusTruncated
14241,Q#2431 - >seq5754,superfamily,335182,137,176,1.28139e-09,54.2311,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs1_chimp,pars,C-TerminusTruncated
14242,Q#2431 - >seq5754,non-specific,340204,96,134,1.30701e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4b.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1ME4b,ORF1,hs1_chimp,pars,CompleteHit
14243,Q#2431 - >seq5754,superfamily,340204,96,134,1.30701e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4b.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1ME4b,ORF1,hs1_chimp,pars,CompleteHit
14244,Q#2433 - >seq5756,specific,197310,9,236,2.0121900000000002e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14245,Q#2433 - >seq5756,superfamily,351117,9,236,2.0121900000000002e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14246,Q#2433 - >seq5756,specific,238827,515,628,9.89385e-35,132.415,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14247,Q#2433 - >seq5756,superfamily,295487,515,628,9.89385e-35,132.415,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14248,Q#2433 - >seq5756,non-specific,197306,9,236,4.4950499999999995e-32,125.286,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14249,Q#2433 - >seq5756,non-specific,197320,9,206,3.9589499999999995e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14250,Q#2433 - >seq5756,non-specific,223780,9,237,7.780819999999999e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14251,Q#2433 - >seq5756,non-specific,197307,9,236,1.64629e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14252,Q#2433 - >seq5756,specific,335306,10,229,2.0001799999999998e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14253,Q#2433 - >seq5756,non-specific,273186,9,237,1.3835e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14254,Q#2433 - >seq5756,non-specific,197319,13,236,3.52522e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14255,Q#2433 - >seq5756,non-specific,197321,7,236,1.22926e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14256,Q#2433 - >seq5756,non-specific,272954,9,236,1.31084e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14257,Q#2433 - >seq5756,non-specific,333820,521,626,2.59896e-13,69.2434,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14258,Q#2433 - >seq5756,superfamily,333820,521,626,2.59896e-13,69.2434,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14259,Q#2433 - >seq5756,non-specific,197336,9,194,1.55335e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14260,Q#2433 - >seq5756,non-specific,197322,8,236,1.64737e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14261,Q#2433 - >seq5756,non-specific,236970,9,189,1.25999e-06,51.0482,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14262,Q#2433 - >seq5756,non-specific,197311,30,236,8.98796e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14263,Q#2433 - >seq5756,non-specific,235175,310,464,0.000296528,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,marg,BothTerminiTruncated
14264,Q#2433 - >seq5756,superfamily,235175,310,464,0.000296528,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,marg,BothTerminiTruncated
14265,Q#2433 - >seq5756,non-specific,274009,307,456,0.00048642199999999997,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14266,Q#2433 - >seq5756,superfamily,274009,307,456,0.00048642199999999997,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,marg,C-TerminusTruncated
14267,Q#2433 - >seq5756,non-specific,334125,212,410,0.000789132,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14268,Q#2433 - >seq5756,superfamily,334125,212,410,0.000789132,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME4a,ORF2,hs0_human,marg,N-TerminusTruncated
14269,Q#2433 - >seq5756,non-specific,274009,294,434,0.00131987,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF2,hs0_human,marg,BothTerminiTruncated
14270,Q#2433 - >seq5756,non-specific,339261,108,232,0.00342458,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs0_human.marg.frame3,1909130926_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs0_human,marg,CompleteHit
14271,Q#2435 - >seq5758,non-specific,197310,53,148,2.4271900000000003e-13,70.4581,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.pars.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4b,ORF2,hs0_human,pars,BothTerminiTruncated
14272,Q#2435 - >seq5758,superfamily,351117,53,148,2.4271900000000003e-13,70.4581,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.pars.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,pars,BothTerminiTruncated
14273,Q#2435 - >seq5758,non-specific,197306,41,172,1.31178e-10,62.4989,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs0_human.pars.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4b,ORF2,hs0_human,pars,C-TerminusTruncated
14274,Q#2435 - >seq5758,non-specific,197311,66,138,0.00014678100000000002,43.8197,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs0_human.pars.frame2,1909130926_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4b,ORF2,hs0_human,pars,BothTerminiTruncated
14275,Q#2442 - >seq5765,non-specific,238827,254,343,5.54852e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14276,Q#2442 - >seq5765,superfamily,295487,254,343,5.54852e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs4_gibbon.marg.frame1,1909130926_L1ME5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14277,Q#2444 - >seq5767,non-specific,238827,156,188,0.00113535,40.7374,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14278,Q#2444 - >seq5767,superfamily,295487,156,188,0.00113535,40.7374,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14279,Q#2448 - >seq5771,specific,197310,10,235,2.90537e-29,117.06700000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME5,ORF2,hs3_orang,marg,CompleteHit
14280,Q#2448 - >seq5771,superfamily,351117,10,235,2.90537e-29,117.06700000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME5,ORF2,hs3_orang,marg,CompleteHit
14281,Q#2448 - >seq5771,non-specific,197306,10,235,2.3374900000000004e-14,73.6696,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME5,ORF2,hs3_orang,marg,CompleteHit
14282,Q#2448 - >seq5771,non-specific,223780,10,193,1.5475700000000003e-08,56.8379,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME5,ORF2,hs3_orang,marg,C-TerminusTruncated
14283,Q#2448 - >seq5771,non-specific,197336,10,192,7.295780000000001e-07,51.4591,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME5,ORF2,hs3_orang,marg,C-TerminusTruncated
14284,Q#2448 - >seq5771,non-specific,197320,10,209,1.39929e-06,50.5914,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME5,ORF2,hs3_orang,marg,CompleteHit
14285,Q#2448 - >seq5771,non-specific,238827,531,644,5.3030200000000004e-06,48.4414,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME5,ORF2,hs3_orang,marg,C-TerminusTruncated
14286,Q#2448 - >seq5771,superfamily,295487,531,644,5.3030200000000004e-06,48.4414,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME5,ORF2,hs3_orang,marg,C-TerminusTruncated
14287,Q#2448 - >seq5771,specific,335306,11,134,0.0009615839999999999,41.847,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME5,ORF2,hs3_orang,marg,C-TerminusTruncated
14288,Q#2448 - >seq5771,non-specific,197307,10,195,0.00702167,39.1933,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME5.ORF2.hs3_orang.marg.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME5,ORF2,hs3_orang,marg,CompleteHit
14289,Q#2451 - >seq5774,non-specific,238827,329,366,0.00245131,39.1966,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs3_orang.pars.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME5,ORF2,hs3_orang,pars,C-TerminusTruncated
14290,Q#2451 - >seq5774,superfamily,295487,329,366,0.00245131,39.1966,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs3_orang.pars.frame1,1909130926_L1ME5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME5,ORF2,hs3_orang,pars,C-TerminusTruncated
14291,Q#2453 - >seq5776,non-specific,238827,518,587,3.11902e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14292,Q#2453 - >seq5776,superfamily,295487,518,587,3.11902e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14293,Q#2454 - >seq5777,non-specific,197310,42,221,9.351560000000001e-16,77.7769,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME5.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME5,ORF2,hs2_gorilla,marg,CompleteHit
14294,Q#2454 - >seq5777,superfamily,351117,42,221,9.351560000000001e-16,77.7769,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME5,ORF2,hs2_gorilla,marg,CompleteHit
14295,Q#2454 - >seq5777,non-specific,197306,40,213,2.6512699999999996e-07,52.4837,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME5,ORF2,hs2_gorilla,marg,CompleteHit
14296,Q#2455 - >seq5778,non-specific,197310,16,190,2.19344e-15,75.0805,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME5.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME5,ORF2,hs2_gorilla,pars,CompleteHit
14297,Q#2455 - >seq5778,superfamily,351117,16,190,2.19344e-15,75.0805,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs2_gorilla,pars,CompleteHit
14298,Q#2455 - >seq5778,non-specific,197306,14,183,1.6832999999999997e-07,51.7133,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs2_gorilla,pars,CompleteHit
14299,Q#2468 - >seq5791,non-specific,197310,211,304,1.1169600000000001e-12,68.5321,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14300,Q#2468 - >seq5791,superfamily,351117,211,304,1.1169600000000001e-12,68.5321,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14301,Q#2468 - >seq5791,non-specific,197306,211,304,2.1978999999999997e-06,50.1725,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14302,Q#2468 - >seq5791,specific,335306,137,297,3.63607e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14303,Q#2468 - >seq5791,non-specific,238827,716,775,0.00041837900000000003,42.6634,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14304,Q#2468 - >seq5791,superfamily,295487,716,775,0.00041837900000000003,42.6634,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14305,Q#2468 - >seq5791,non-specific,197320,208,280,0.00111852,41.7318,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14306,Q#2468 - >seq5791,non-specific,223780,205,279,0.00117991,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs1_chimp,marg,N-TerminusTruncated
14307,Q#2472 - >seq5795,non-specific,197310,89,213,2.4165200000000003e-16,78.9325,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14308,Q#2472 - >seq5795,superfamily,351117,89,213,2.4165200000000003e-16,78.9325,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14309,Q#2472 - >seq5795,non-specific,197306,107,213,1.0981000000000001e-08,56.3357,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14310,Q#2472 - >seq5795,non-specific,223780,103,206,9.09439e-06,47.9783,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14311,Q#2472 - >seq5795,specific,335306,104,206,3.02952e-05,46.0842,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14312,Q#2472 - >seq5795,non-specific,197322,105,213,4.6279499999999996e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14313,Q#2472 - >seq5795,non-specific,197320,106,206,0.000117125,44.4282,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14314,Q#2472 - >seq5795,non-specific,197307,110,213,0.000295491,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14315,Q#2472 - >seq5795,non-specific,238827,609,668,0.000459084,42.2782,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14316,Q#2472 - >seq5795,superfamily,295487,609,668,0.000459084,42.2782,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14317,Q#2472 - >seq5795,non-specific,197317,94,206,0.00876811,38.7372,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MEc.ORF2.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs1_chimp,pars,N-TerminusTruncated
14318,Q#2474 - >seq5797,non-specific,340205,172,207,3.33869e-07,46.1752,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs1_chimp,marg,C-TerminusTruncated
14319,Q#2474 - >seq5797,superfamily,340205,172,207,3.33869e-07,46.1752,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs1_chimp.marg.frame3,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs1_chimp,marg,C-TerminusTruncated
14320,Q#2478 - >seq5801,non-specific,340205,149,173,4.4109799999999996e-05,39.6268,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs1_chimp,pars,C-TerminusTruncated
14321,Q#2478 - >seq5801,superfamily,340205,149,173,4.4109799999999996e-05,39.6268,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs1_chimp.pars.frame2,1909130926_L1MEc.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs1_chimp,pars,C-TerminusTruncated
14322,Q#2483 - >seq5806,non-specific,335182,150,246,1.1273500000000002e-19,82.3507,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME5,ORF1,hs2_gorilla,marg,CompleteHit
14323,Q#2483 - >seq5806,superfamily,335182,150,246,1.1273500000000002e-19,82.3507,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME5,ORF1,hs2_gorilla,marg,CompleteHit
14324,Q#2483 - >seq5806,non-specific,340205,249,307,1.41609e-06,45.0196,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME5,ORF1,hs2_gorilla,marg,CompleteHit
14325,Q#2483 - >seq5806,superfamily,340205,249,307,1.41609e-06,45.0196,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME5,ORF1,hs2_gorilla,marg,CompleteHit
14326,Q#2483 - >seq5806,non-specific,235461,43,153,0.000985322,40.4366,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_tRNAsynthetase,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14327,Q#2483 - >seq5806,superfamily,235461,43,153,0.000985322,40.4366,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_tRNAsynthetase,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14328,Q#2483 - >seq5806,non-specific,237177,46,143,0.00141396,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14329,Q#2483 - >seq5806,superfamily,237177,46,143,0.00141396,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14330,Q#2483 - >seq5806,non-specific,224117,21,196,0.00145251,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14331,Q#2483 - >seq5806,superfamily,224117,21,196,0.00145251,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14332,Q#2483 - >seq5806,non-specific,336159,56,139,0.00181492,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_HOOK,L1ME5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14333,Q#2483 - >seq5806,superfamily,336159,56,139,0.00181492,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_HOOK,L1ME5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
14334,Q#2483 - >seq5806,non-specific,235600,66,182,0.00338579,39.1404,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14335,Q#2483 - >seq5806,superfamily,235600,66,182,0.00338579,39.1404,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14336,Q#2483 - >seq5806,non-specific,236995,111,178,0.00341152,38.8771,PRK11824,PRK11824,NC,cl36064,polynucleotide phosphorylase/polyadenylase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14337,Q#2483 - >seq5806,superfamily,236995,111,178,0.00341152,38.8771,cl36064,PRK11824 superfamily,NC, - ,polynucleotide phosphorylase/polyadenylase; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14338,Q#2483 - >seq5806,non-specific,188306,39,178,0.00438081,38.7534,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14339,Q#2483 - >seq5806,superfamily,188306,39,178,0.00438081,38.7534,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14340,Q#2483 - >seq5806,non-specific,237178,50,175,0.00782718,37.7666,PRK12705,PRK12705,C,cl36167,hypothetical protein; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14341,Q#2483 - >seq5806,superfamily,237178,50,175,0.00782718,37.7666,cl36167,PRK12705 superfamily,C, - ,hypothetical protein; Provisional,L1ME5.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME5,ORF1,hs2_gorilla,marg,C-TerminusTruncated
14342,Q#2484 - >seq5807,non-specific,335182,12,44,0.000142495,38.8231,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME5,ORF1,hs2_gorilla,pars,C-TerminusTruncated
14343,Q#2484 - >seq5807,superfamily,335182,12,44,0.000142495,38.8231,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME5,ORF1,hs2_gorilla,pars,C-TerminusTruncated
14344,Q#2499 - >seq5822,non-specific,238827,448,706,0.000157605,44.2042,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs9_pika.marg.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs9_pika,marg,CompleteHit
14345,Q#2499 - >seq5822,superfamily,295487,448,706,0.000157605,44.2042,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs9_pika.marg.frame3,1909130926_L1ME4c.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME4c,ORF2,hs9_pika,marg,CompleteHit
14346,Q#2504 - >seq5827,non-specific,340205,4,43,1.18088e-12,56.1904,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4c,ORF1,hs0_human,pars,C-TerminusTruncated
14347,Q#2504 - >seq5827,superfamily,340205,4,43,1.18088e-12,56.1904,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4c,ORF1,hs0_human,pars,C-TerminusTruncated
14348,Q#2505 - >seq5828,non-specific,340205,79,143,1.06798e-22,85.0804,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs0_human,marg,CompleteHit
14349,Q#2505 - >seq5828,superfamily,340205,79,143,1.06798e-22,85.0804,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4c.ORF1.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs0_human,marg,CompleteHit
14350,Q#2505 - >seq5828,non-specific,335182,28,76,0.0023982,35.3563,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs0_human,marg,N-TerminusTruncated
14351,Q#2505 - >seq5828,superfamily,335182,28,76,0.0023982,35.3563,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4c,ORF1,hs0_human,marg,N-TerminusTruncated
14352,Q#2506 - >seq5829,non-specific,335182,8,68,5.12452e-13,60.7795,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME4c,ORF1,hs0_human,marg,N-TerminusTruncated
14353,Q#2506 - >seq5829,superfamily,335182,8,68,5.12452e-13,60.7795,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4c.ORF1.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1ME4c,ORF1,hs0_human,marg,N-TerminusTruncated
14354,Q#2510 - >seq5833,specific,197310,9,233,8.132489999999999e-43,155.972,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14355,Q#2510 - >seq5833,superfamily,351117,9,233,8.132489999999999e-43,155.972,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14356,Q#2510 - >seq5833,non-specific,197306,9,233,6.3488299999999995e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14357,Q#2510 - >seq5833,non-specific,223780,9,227,5.43251e-13,69.9347,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14358,Q#2510 - >seq5833,non-specific,238827,511,629,7.61184e-11,63.07899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME5,ORF2,hs1_chimp,marg,C-TerminusTruncated
14359,Q#2510 - >seq5833,superfamily,295487,511,629,7.61184e-11,63.07899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME5,ORF2,hs1_chimp,marg,C-TerminusTruncated
14360,Q#2510 - >seq5833,specific,335306,10,227,3.49354e-09,58.0254,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14361,Q#2510 - >seq5833,non-specific,197320,9,193,2.2202599999999995e-08,55.9842,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME5,ORF2,hs1_chimp,marg,C-TerminusTruncated
14362,Q#2510 - >seq5833,non-specific,197307,9,227,5.69543e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14363,Q#2510 - >seq5833,non-specific,273186,9,227,6.0464e-06,48.8144,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14364,Q#2510 - >seq5833,non-specific,197321,7,227,7.98526e-06,48.3172,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14365,Q#2510 - >seq5833,non-specific,235175,323,464,5.31563e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF2,hs1_chimp,marg,BothTerminiTruncated
14366,Q#2510 - >seq5833,superfamily,235175,323,464,5.31563e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF2,hs1_chimp,marg,BothTerminiTruncated
14367,Q#2510 - >seq5833,non-specific,272954,9,193,0.00016392799999999998,44.2961,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,marg,C-TerminusTruncated
14368,Q#2510 - >seq5833,non-specific,197336,9,193,0.00046230800000000003,42.9847,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,marg,CompleteHit
14369,Q#2510 - >seq5833,non-specific,334125,212,412,0.00462255,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME5,ORF2,hs1_chimp,marg,N-TerminusTruncated
14370,Q#2510 - >seq5833,superfamily,334125,212,412,0.00462255,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME5.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME5,ORF2,hs1_chimp,marg,N-TerminusTruncated
14371,Q#2513 - >seq5836,non-specific,197310,1,104,7.03546e-10,60.0577,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME5,ORF2,hs1_chimp,pars,N-TerminusTruncated
14372,Q#2513 - >seq5836,superfamily,351117,1,104,7.03546e-10,60.0577,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs1_chimp,pars,N-TerminusTruncated
14373,Q#2513 - >seq5836,non-specific,197306,1,97,7.3165e-06,47.8613,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME5,ORF2,hs1_chimp,pars,N-TerminusTruncated
14374,Q#2513 - >seq5836,non-specific,235175,220,354,2.24399e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME5,ORF2,hs1_chimp,pars,BothTerminiTruncated
14375,Q#2513 - >seq5836,superfamily,235175,220,354,2.24399e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME5,ORF2,hs1_chimp,pars,BothTerminiTruncated
14376,Q#2513 - >seq5836,non-specific,224117,103,357,0.00744186,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME5,ORF2,hs1_chimp,pars,N-TerminusTruncated
14377,Q#2513 - >seq5836,superfamily,224117,103,357,0.00744186,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME5,ORF2,hs1_chimp,pars,N-TerminusTruncated
14378,Q#2514 - >seq5837,non-specific,238827,375,484,1.5624200000000001e-12,67.3162,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME5.ORF2.hs1_chimp.pars.frame2,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME5,ORF2,hs1_chimp,pars,C-TerminusTruncated
14379,Q#2514 - >seq5837,superfamily,295487,375,484,1.5624200000000001e-12,67.3162,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME5.ORF2.hs1_chimp.pars.frame2,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME5,ORF2,hs1_chimp,pars,C-TerminusTruncated
14380,Q#2516 - >seq5839,non-specific,335182,159,256,8.33929e-33,117.404,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14381,Q#2516 - >seq5839,superfamily,335182,159,256,8.33929e-33,117.404,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14382,Q#2516 - >seq5839,non-specific,340205,259,324,6.3714600000000005e-24,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14383,Q#2516 - >seq5839,superfamily,340205,259,324,6.3714600000000005e-24,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14384,Q#2516 - >seq5839,non-specific,340204,114,156,1.40591e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14385,Q#2516 - >seq5839,superfamily,340204,114,156,1.40591e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME5,ORF1,hs1_chimp,marg,CompleteHit
14386,Q#2516 - >seq5839,non-specific,313406,77,185,4.8170799999999996e-05,45.0282,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14387,Q#2516 - >seq5839,superfamily,313406,77,185,4.8170799999999996e-05,45.0282,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14388,Q#2516 - >seq5839,non-specific,237177,35,135,6.42839e-05,44.3838,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14389,Q#2516 - >seq5839,superfamily,237177,35,135,6.42839e-05,44.3838,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14390,Q#2516 - >seq5839,non-specific,237177,73,152,0.00013472200000000002,43.2282,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14391,Q#2516 - >seq5839,non-specific,224117,90,249,0.00027905299999999997,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,BothTerminiTruncated
14392,Q#2516 - >seq5839,superfamily,224117,90,249,0.00027905299999999997,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME5,ORF1,hs1_chimp,marg,BothTerminiTruncated
14393,Q#2516 - >seq5839,non-specific,130141,76,180,0.00036606,42.1141,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14394,Q#2516 - >seq5839,superfamily,130141,76,180,0.00036606,42.1141,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14395,Q#2516 - >seq5839,non-specific,235461,96,179,0.00111061,40.4366,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14396,Q#2516 - >seq5839,superfamily,235461,96,179,0.00111061,40.4366,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14397,Q#2516 - >seq5839,non-specific,224117,43,189,0.00221663,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14398,Q#2516 - >seq5839,superfamily,224117,43,189,0.00221663,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14399,Q#2516 - >seq5839,non-specific,274009,72,188,0.00301922,39.2807,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14400,Q#2516 - >seq5839,superfamily,274009,72,188,0.00301922,39.2807,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,N-TerminusTruncated
14401,Q#2516 - >seq5839,non-specific,274009,77,152,0.00402222,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,BothTerminiTruncated
14402,Q#2516 - >seq5839,superfamily,274009,77,152,0.00402222,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME5,ORF1,hs1_chimp,marg,BothTerminiTruncated
14403,Q#2516 - >seq5839,non-specific,337663,77,155,0.00412657,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14404,Q#2516 - >seq5839,superfamily,337663,77,155,0.00412657,38.5599,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14405,Q#2516 - >seq5839,non-specific,188306,86,135,0.007254999999999999,37.983000000000004,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14406,Q#2516 - >seq5839,superfamily,188306,86,135,0.007254999999999999,37.983000000000004,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME5.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME5,ORF1,hs1_chimp,marg,C-TerminusTruncated
14407,Q#2520 - >seq5843,non-specific,340205,249,271,0.00119034,36.5452,pfam17490,Tnp_22_dsRBD,NC,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME5,ORF1,hs1_chimp,pars,BothTerminiTruncated
14408,Q#2520 - >seq5843,superfamily,340205,249,271,0.00119034,36.5452,cl38762,Tnp_22_dsRBD superfamily,NC, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME5,ORF1,hs1_chimp,pars,BothTerminiTruncated
14409,Q#2521 - >seq5844,non-specific,335182,141,237,4.57978e-30,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14410,Q#2521 - >seq5844,superfamily,335182,141,237,4.57978e-30,109.315,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14411,Q#2521 - >seq5844,non-specific,340205,240,302,5.44121e-09,51.568000000000005,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14412,Q#2521 - >seq5844,superfamily,340205,240,302,5.44121e-09,51.568000000000005,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14413,Q#2521 - >seq5844,non-specific,340204,96,138,1.0561300000000002e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14414,Q#2521 - >seq5844,superfamily,340204,96,138,1.0561300000000002e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME5,ORF1,hs1_chimp,pars,CompleteHit
14415,Q#2521 - >seq5844,non-specific,237177,98,169,0.000342609,41.6874,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME5,ORF1,hs1_chimp,pars,C-TerminusTruncated
14416,Q#2521 - >seq5844,superfamily,237177,98,169,0.000342609,41.6874,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME5.ORF1.hs1_chimp.pars.frame1,1909130926_L1ME5.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME5,ORF1,hs1_chimp,pars,C-TerminusTruncated
14417,Q#2523 - >seq5846,non-specific,238827,481,650,1.69546e-07,53.0638,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs0_human,marg,C-TerminusTruncated
14418,Q#2523 - >seq5846,superfamily,295487,481,650,1.69546e-07,53.0638,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs0_human,marg,C-TerminusTruncated
14419,Q#2523 - >seq5846,non-specific,333820,496,642,0.00478203,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs0_human,marg,C-TerminusTruncated
14420,Q#2523 - >seq5846,superfamily,333820,496,642,0.00478203,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.marg.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs0_human,marg,C-TerminusTruncated
14421,Q#2524 - >seq5847,specific,197310,10,246,2.69132e-38,143.261,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14422,Q#2524 - >seq5847,superfamily,351117,10,246,2.69132e-38,143.261,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14423,Q#2524 - >seq5847,non-specific,197306,10,246,1.61441e-23,100.634,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14424,Q#2524 - >seq5847,non-specific,238827,586,791,7.38923e-18,83.4946,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs0_human,marg,N-TerminusTruncated
14425,Q#2524 - >seq5847,superfamily,295487,586,791,7.38923e-18,83.4946,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs0_human,marg,N-TerminusTruncated
14426,Q#2524 - >seq5847,non-specific,223780,10,247,6.591939999999999e-08,54.9119,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14427,Q#2524 - >seq5847,non-specific,197307,10,246,4.43591e-07,52.2901,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14428,Q#2524 - >seq5847,non-specific,333820,617,774,9.95374e-07,49.9834,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs0_human,marg,N-TerminusTruncated
14429,Q#2524 - >seq5847,superfamily,333820,617,774,9.95374e-07,49.9834,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs0_human,marg,N-TerminusTruncated
14430,Q#2524 - >seq5847,non-specific,197320,117,239,7.611289999999999e-06,48.6654,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,marg,N-TerminusTruncated
14431,Q#2524 - >seq5847,specific,335306,11,239,3.79272e-05,46.0842,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14432,Q#2524 - >seq5847,non-specific,339261,117,242,0.000184527,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14433,Q#2524 - >seq5847,non-specific,197321,10,246,0.000863719,42.153999999999996,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs0_human.marg.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs0_human,marg,CompleteHit
14434,Q#2525 - >seq5848,non-specific,238827,607,724,2.0271e-23,99.2878,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14435,Q#2525 - >seq5848,superfamily,295487,607,724,2.0271e-23,99.2878,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14436,Q#2525 - >seq5848,non-specific,333820,591,698,1.26089e-11,64.2358,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14437,Q#2525 - >seq5848,superfamily,333820,591,698,1.26089e-11,64.2358,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14438,Q#2525 - >seq5848,non-specific,238828,597,689,0.0008342689999999999,41.8029,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs0_human.pars.frame3,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14439,Q#2526 - >seq5849,non-specific,238827,472,568,1.08362e-20,91.5838,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs0_human.pars.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4c,ORF2,hs0_human,pars,C-TerminusTruncated
14440,Q#2526 - >seq5849,superfamily,295487,472,568,1.08362e-20,91.5838,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs0_human.pars.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4c,ORF2,hs0_human,pars,C-TerminusTruncated
14441,Q#2526 - >seq5849,non-specific,333820,478,574,4.70487e-09,56.917,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.pars.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4c,ORF2,hs0_human,pars,C-TerminusTruncated
14442,Q#2526 - >seq5849,superfamily,333820,478,574,4.70487e-09,56.917,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs0_human.pars.frame2,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4c,ORF2,hs0_human,pars,C-TerminusTruncated
14443,Q#2527 - >seq5850,specific,197310,21,213,4.2813599999999996e-33,127.853,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14444,Q#2527 - >seq5850,superfamily,351117,21,213,4.2813599999999996e-33,127.853,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14445,Q#2527 - >seq5850,non-specific,197306,14,226,1.09939e-20,92.1592,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14446,Q#2527 - >seq5850,non-specific,223780,17,205,5.20284e-06,48.7487,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14447,Q#2527 - >seq5850,non-specific,197307,17,208,2.03655e-05,46.8973,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14448,Q#2527 - >seq5850,non-specific,197320,100,205,3.3095e-05,46.3542,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4c,ORF2,hs0_human,pars,N-TerminusTruncated
14449,Q#2527 - >seq5850,specific,335306,27,202,8.789059999999999e-05,44.9286,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14450,Q#2527 - >seq5850,non-specific,272954,14,199,0.00104495,41.9849,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs0_human.pars.frame1,1909130926_L1ME4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4c,ORF2,hs0_human,pars,CompleteHit
14451,Q#2530 - >seq5853,non-specific,197310,9,83,2.03266e-17,82.7845,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14452,Q#2530 - >seq5853,superfamily,351117,9,83,2.03266e-17,82.7845,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14453,Q#2530 - >seq5853,non-specific,197306,9,81,4.95958e-10,60.9581,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14454,Q#2530 - >seq5853,specific,335306,10,77,1.15231e-06,50.7066,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14455,Q#2530 - >seq5853,non-specific,197321,7,80,1.70659e-05,47.5468,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14456,Q#2530 - >seq5853,non-specific,223780,9,80,8.50173e-05,45.2819,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14457,Q#2530 - >seq5853,non-specific,197336,9,76,0.000216669,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14458,Q#2530 - >seq5853,non-specific,197307,9,80,0.00041364099999999997,43.0453,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14459,Q#2530 - >seq5853,non-specific,197320,9,76,0.0006441730000000001,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14460,Q#2530 - >seq5853,non-specific,273186,9,43,0.00387607,40.34,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14461,Q#2532 - >seq5855,specific,238827,511,778,1.1770899999999998e-62,212.53599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14462,Q#2532 - >seq5855,superfamily,295487,511,778,1.1770899999999998e-62,212.53599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14463,Q#2532 - >seq5855,specific,197310,9,236,4.22191e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14464,Q#2532 - >seq5855,superfamily,351117,9,236,4.22191e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14465,Q#2532 - >seq5855,specific,333820,517,741,5.30589e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14466,Q#2532 - >seq5855,superfamily,333820,517,741,5.30589e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14467,Q#2532 - >seq5855,non-specific,197306,9,236,4.88206e-32,125.286,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14468,Q#2532 - >seq5855,non-specific,197320,9,229,1.54104e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14469,Q#2532 - >seq5855,non-specific,223780,9,237,1.7190099999999998e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14470,Q#2532 - >seq5855,non-specific,197307,9,236,1.4368499999999998e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14471,Q#2532 - >seq5855,specific,335306,10,229,6.80199e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14472,Q#2532 - >seq5855,non-specific,273186,9,237,1.2089399999999999e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14473,Q#2532 - >seq5855,non-specific,197321,7,236,6.05765e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14474,Q#2532 - >seq5855,non-specific,197319,13,236,6.11903e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14475,Q#2532 - >seq5855,non-specific,272954,9,236,7.23314e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14476,Q#2532 - >seq5855,non-specific,238828,517,738,1.0413e-14,74.5448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14477,Q#2532 - >seq5855,non-specific,197336,9,194,2.67617e-11,64.9411,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14478,Q#2532 - >seq5855,non-specific,197322,8,236,6.16807e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14479,Q#2532 - >seq5855,non-specific,275209,468,738,1.1962600000000001e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14480,Q#2532 - >seq5855,superfamily,275209,468,738,1.1962600000000001e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14481,Q#2532 - >seq5855,non-specific,236970,9,189,1.2299000000000002e-07,54.1298,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14482,Q#2532 - >seq5855,non-specific,235175,306,470,1.37423e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14483,Q#2532 - >seq5855,superfamily,235175,306,470,1.37423e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14484,Q#2532 - >seq5855,non-specific,197311,7,236,3.53505e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14485,Q#2532 - >seq5855,non-specific,223496,231,429,7.90983e-05,46.6771,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14486,Q#2532 - >seq5855,superfamily,223496,231,429,7.90983e-05,46.6771,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14487,Q#2532 - >seq5855,non-specific,238185,657,734,0.00028844,41.1824,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14488,Q#2532 - >seq5855,non-specific,339261,108,232,0.0009071169999999999,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14489,Q#2532 - >seq5855,non-specific,239569,526,739,0.00123372,41.4043,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,CompleteHit
14490,Q#2532 - >seq5855,non-specific,274009,307,460,0.00143553,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14491,Q#2532 - >seq5855,superfamily,274009,307,460,0.00143553,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,marg,C-TerminusTruncated
14492,Q#2532 - >seq5855,non-specific,274009,294,435,0.00204777,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14493,Q#2532 - >seq5855,specific,225881,516,681,0.0046971,40.5925,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14494,Q#2532 - >seq5855,superfamily,225881,516,681,0.0046971,40.5925,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14495,Q#2534 - >seq5857,non-specific,338310,943,1006,5.73534e-05,45.2568,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs3_orang.marg.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14496,Q#2534 - >seq5857,superfamily,338310,943,1006,5.73534e-05,45.2568,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs3_orang.marg.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3G,ORF2,hs3_orang,marg,BothTerminiTruncated
14497,Q#2535 - >seq5858,specific,238827,505,754,1.3032599999999999e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14498,Q#2535 - >seq5858,superfamily,295487,505,754,1.3032599999999999e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14499,Q#2535 - >seq5858,specific,197310,3,230,1.6016899999999998e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14500,Q#2535 - >seq5858,superfamily,351117,3,230,1.6016899999999998e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14501,Q#2535 - >seq5858,specific,333820,511,735,6.14678e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14502,Q#2535 - >seq5858,superfamily,333820,511,735,6.14678e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14503,Q#2535 - >seq5858,non-specific,197306,3,230,1.3846e-32,126.82700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14504,Q#2535 - >seq5858,non-specific,197320,3,223,1.19985e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14505,Q#2535 - >seq5858,non-specific,223780,3,231,2.6738499999999998e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14506,Q#2535 - >seq5858,non-specific,197307,3,230,2.80198e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14507,Q#2535 - >seq5858,specific,335306,4,223,6.656539999999999e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14508,Q#2535 - >seq5858,non-specific,273186,3,231,4.12066e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14509,Q#2535 - >seq5858,non-specific,197319,7,230,7.00594e-16,78.4725,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14510,Q#2535 - >seq5858,non-specific,197321,1,230,1.16452e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14511,Q#2535 - >seq5858,non-specific,238828,511,732,2.324e-15,76.4708,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14512,Q#2535 - >seq5858,non-specific,272954,3,230,2.89811e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14513,Q#2535 - >seq5858,non-specific,197336,3,188,2.61813e-11,64.9411,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14514,Q#2535 - >seq5858,non-specific,275209,462,732,3.31833e-09,59.7788,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14515,Q#2535 - >seq5858,superfamily,275209,462,732,3.31833e-09,59.7788,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14516,Q#2535 - >seq5858,non-specific,197322,2,230,6.03163e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14517,Q#2535 - >seq5858,non-specific,236970,3,183,1.19244e-07,54.1298,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14518,Q#2535 - >seq5858,non-specific,235175,300,464,1.11477e-05,49.6772,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14519,Q#2535 - >seq5858,superfamily,235175,300,464,1.11477e-05,49.6772,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14520,Q#2535 - >seq5858,non-specific,197311,1,230,1.84258e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14521,Q#2535 - >seq5858,non-specific,238185,651,728,9.68042e-05,42.338,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14522,Q#2535 - >seq5858,non-specific,223496,225,423,0.0001499,45.9067,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14523,Q#2535 - >seq5858,superfamily,223496,225,423,0.0001499,45.9067,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14524,Q#2535 - >seq5858,non-specific,239569,520,733,0.000347792,42.9451,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14525,Q#2535 - >seq5858,specific,225881,510,675,0.000531029,43.2889,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14526,Q#2535 - >seq5858,superfamily,225881,510,675,0.000531029,43.2889,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14527,Q#2535 - >seq5858,non-specific,339261,102,226,0.000979331,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs3_orang,pars,CompleteHit
14528,Q#2535 - >seq5858,non-specific,274009,301,454,0.00174992,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14529,Q#2535 - >seq5858,superfamily,274009,301,454,0.00174992,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,pars,C-TerminusTruncated
14530,Q#2535 - >seq5858,non-specific,274009,288,429,0.00253893,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14531,Q#2535 - >seq5858,non-specific,334125,206,405,0.00861339,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs3_orang,pars,N-TerminusTruncated
14532,Q#2535 - >seq5858,superfamily,334125,206,405,0.00861339,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs3_orang.pars.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs3_orang,pars,N-TerminusTruncated
14533,Q#2536 - >seq5859,non-specific,338310,970,1033,7.497600000000001e-05,44.8716,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs3_orang.pars.frame2,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14534,Q#2536 - >seq5859,superfamily,338310,970,1033,7.497600000000001e-05,44.8716,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs3_orang.pars.frame2,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3G,ORF2,hs3_orang,pars,BothTerminiTruncated
14535,Q#2538 - >seq5861,non-specific,335182,136,232,7.949379999999999e-30,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14536,Q#2538 - >seq5861,superfamily,335182,136,232,7.949379999999999e-30,108.544,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14537,Q#2538 - >seq5861,non-specific,335182,136,232,7.949379999999999e-30,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14538,Q#2538 - >seq5861,non-specific,340205,235,298,5.47299e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14539,Q#2538 - >seq5861,superfamily,340205,235,298,5.47299e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14540,Q#2538 - >seq5861,non-specific,340205,235,298,5.47299e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14541,Q#2538 - >seq5861,non-specific,340204,91,133,1.13106e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14542,Q#2538 - >seq5861,superfamily,340204,91,133,1.13106e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14543,Q#2538 - >seq5861,non-specific,340204,91,133,1.13106e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs3_orang,marg,CompleteHit
14544,Q#2538 - >seq5861,non-specific,235175,29,136,0.00010993299999999999,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14545,Q#2538 - >seq5861,superfamily,235175,29,136,0.00010993299999999999,43.513999999999996,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14546,Q#2538 - >seq5861,non-specific,235175,29,136,0.00010993299999999999,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14547,Q#2538 - >seq5861,non-specific,237177,22,129,0.000111915,43.2282,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14548,Q#2538 - >seq5861,superfamily,237177,22,129,0.000111915,43.2282,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14549,Q#2538 - >seq5861,non-specific,237177,22,129,0.000111915,43.2282,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14550,Q#2538 - >seq5861,non-specific,274009,13,130,0.000289359,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14551,Q#2538 - >seq5861,superfamily,274009,13,130,0.000289359,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14552,Q#2538 - >seq5861,non-specific,274009,13,130,0.000289359,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14553,Q#2538 - >seq5861,non-specific,223250,27,130,0.00131997,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14554,Q#2538 - >seq5861,superfamily,223250,27,130,0.00131997,39.8889,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14555,Q#2538 - >seq5861,non-specific,223250,27,130,0.00131997,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14556,Q#2538 - >seq5861,non-specific,337663,44,127,0.00246496,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14557,Q#2538 - >seq5861,superfamily,337663,44,127,0.00246496,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14558,Q#2538 - >seq5861,non-specific,337663,44,127,0.00246496,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14559,Q#2538 - >seq5861,non-specific,336159,40,125,0.0031155,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14560,Q#2538 - >seq5861,superfamily,336159,40,125,0.0031155,38.8897,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14561,Q#2538 - >seq5861,non-specific,336159,40,125,0.0031155,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14562,Q#2538 - >seq5861,non-specific,274008,21,182,0.00352981,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14563,Q#2538 - >seq5861,superfamily,274008,21,182,0.00352981,38.8843,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14564,Q#2538 - >seq5861,non-specific,274008,21,182,0.00352981,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,N-TerminusTruncated
14565,Q#2538 - >seq5861,non-specific,224117,8,141,0.00548759,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14566,Q#2538 - >seq5861,superfamily,224117,8,141,0.00548759,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14567,Q#2538 - >seq5861,non-specific,224117,8,141,0.00548759,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14568,Q#2538 - >seq5861,non-specific,226400,59,129,0.008289399999999999,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14569,Q#2538 - >seq5861,superfamily,226400,59,129,0.008289399999999999,37.0054,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14570,Q#2538 - >seq5861,non-specific,226400,59,129,0.008289399999999999,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs3_orang,marg,C-TerminusTruncated
14571,Q#2538 - >seq5861,non-specific,227512,30,123,0.00908462,37.269,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14572,Q#2538 - >seq5861,superfamily,227512,30,123,0.00908462,37.269,cl34933,HEC1 superfamily,NC, - ,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14573,Q#2538 - >seq5861,non-specific,227512,30,123,0.00908462,37.269,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.marg.frame3,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs3_orang,marg,BothTerminiTruncated
14574,Q#2543 - >seq5866,non-specific,335182,136,232,7.949379999999999e-30,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14575,Q#2543 - >seq5866,superfamily,335182,136,232,7.949379999999999e-30,108.544,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14576,Q#2543 - >seq5866,non-specific,335182,136,232,7.949379999999999e-30,108.544,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14577,Q#2543 - >seq5866,non-specific,340205,235,298,5.47299e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14578,Q#2543 - >seq5866,superfamily,340205,235,298,5.47299e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14579,Q#2543 - >seq5866,non-specific,340205,235,298,5.47299e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14580,Q#2543 - >seq5866,non-specific,340204,91,133,1.13106e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14581,Q#2543 - >seq5866,superfamily,340204,91,133,1.13106e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14582,Q#2543 - >seq5866,non-specific,340204,91,133,1.13106e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3G,ORF1,hs3_orang,pars,CompleteHit
14583,Q#2543 - >seq5866,non-specific,235175,29,136,0.00010993299999999999,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14584,Q#2543 - >seq5866,superfamily,235175,29,136,0.00010993299999999999,43.513999999999996,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14585,Q#2543 - >seq5866,non-specific,235175,29,136,0.00010993299999999999,43.513999999999996,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14586,Q#2543 - >seq5866,non-specific,237177,22,129,0.000111915,43.2282,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14587,Q#2543 - >seq5866,superfamily,237177,22,129,0.000111915,43.2282,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14588,Q#2543 - >seq5866,non-specific,237177,22,129,0.000111915,43.2282,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14589,Q#2543 - >seq5866,non-specific,274009,13,130,0.000289359,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14590,Q#2543 - >seq5866,superfamily,274009,13,130,0.000289359,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14591,Q#2543 - >seq5866,non-specific,274009,13,130,0.000289359,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14592,Q#2543 - >seq5866,non-specific,223250,27,130,0.00131997,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14593,Q#2543 - >seq5866,superfamily,223250,27,130,0.00131997,39.8889,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14594,Q#2543 - >seq5866,non-specific,223250,27,130,0.00131997,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_tRNAsynthetase,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14595,Q#2543 - >seq5866,non-specific,337663,44,127,0.00246496,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14596,Q#2543 - >seq5866,superfamily,337663,44,127,0.00246496,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14597,Q#2543 - >seq5866,non-specific,337663,44,127,0.00246496,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14598,Q#2543 - >seq5866,non-specific,336159,40,125,0.0031155,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_HOOK,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14599,Q#2543 - >seq5866,superfamily,336159,40,125,0.0031155,38.8897,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_HOOK,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14600,Q#2543 - >seq5866,non-specific,336159,40,125,0.0031155,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_HOOK,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14601,Q#2543 - >seq5866,non-specific,274008,21,182,0.00352981,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14602,Q#2543 - >seq5866,superfamily,274008,21,182,0.00352981,38.8843,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14603,Q#2543 - >seq5866,non-specific,274008,21,182,0.00352981,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,N-TerminusTruncated
14604,Q#2543 - >seq5866,non-specific,224117,8,141,0.00548759,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14605,Q#2543 - >seq5866,superfamily,224117,8,141,0.00548759,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14606,Q#2543 - >seq5866,non-specific,224117,8,141,0.00548759,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14607,Q#2543 - >seq5866,non-specific,226400,59,129,0.008289399999999999,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14608,Q#2543 - >seq5866,superfamily,226400,59,129,0.008289399999999999,37.0054,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14609,Q#2543 - >seq5866,non-specific,226400,59,129,0.008289399999999999,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs3_orang,pars,C-TerminusTruncated
14610,Q#2543 - >seq5866,non-specific,227512,30,123,0.00908462,37.269,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14611,Q#2543 - >seq5866,superfamily,227512,30,123,0.00908462,37.269,cl34933,HEC1 superfamily,NC, - ,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14612,Q#2543 - >seq5866,non-specific,227512,30,123,0.00908462,37.269,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1ME3G.ORF1.hs3_orang.pars.frame1,1909130926_L1ME3G.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs3_orang,pars,BothTerminiTruncated
14613,Q#2544 - >seq5867,specific,238827,510,767,1.3340799999999997e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14614,Q#2544 - >seq5867,superfamily,295487,510,767,1.3340799999999997e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14615,Q#2544 - >seq5867,specific,197310,9,236,6.941149999999999e-57,196.418,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14616,Q#2544 - >seq5867,superfamily,351117,9,236,6.941149999999999e-57,196.418,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14617,Q#2544 - >seq5867,specific,333820,516,739,1.51825e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14618,Q#2544 - >seq5867,superfamily,333820,516,739,1.51825e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14619,Q#2544 - >seq5867,non-specific,197306,9,236,2.3941599999999997e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14620,Q#2544 - >seq5867,non-specific,197320,9,206,2.5477799999999998e-18,85.6445,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14621,Q#2544 - >seq5867,non-specific,223780,9,237,3.25313e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14622,Q#2544 - >seq5867,non-specific,197307,9,236,4.738060000000001e-17,81.9505,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14623,Q#2544 - >seq5867,specific,335306,10,229,1.40754e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14624,Q#2544 - >seq5867,non-specific,238828,516,736,1.25618e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14625,Q#2544 - >seq5867,non-specific,197321,7,236,5.64344e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14626,Q#2544 - >seq5867,non-specific,197319,13,236,1.9104e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14627,Q#2544 - >seq5867,non-specific,272954,9,236,7.17508e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14628,Q#2544 - >seq5867,non-specific,273186,9,237,1.85482e-12,68.4596,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14629,Q#2544 - >seq5867,non-specific,275209,467,796,1.11417e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14630,Q#2544 - >seq5867,superfamily,275209,467,796,1.11417e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14631,Q#2544 - >seq5867,non-specific,197336,9,194,7.43907e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14632,Q#2544 - >seq5867,non-specific,239569,540,768,6.12685e-05,45.2563,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14633,Q#2544 - >seq5867,non-specific,236970,9,189,0.000213815,44.1146,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14634,Q#2544 - >seq5867,non-specific,274009,311,472,0.00179859,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14635,Q#2544 - >seq5867,superfamily,274009,311,472,0.00179859,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14636,Q#2544 - >seq5867,specific,225881,515,734,0.00189009,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14637,Q#2544 - >seq5867,superfamily,225881,515,734,0.00189009,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14638,Q#2544 - >seq5867,non-specific,197311,7,236,0.00193133,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs2_gorilla,marg,CompleteHit
14639,Q#2544 - >seq5867,non-specific,238185,655,732,0.00234297,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs2_gorilla,marg,C-TerminusTruncated
14640,Q#2544 - >seq5867,non-specific,334125,212,411,0.0023495,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14641,Q#2544 - >seq5867,superfamily,334125,212,411,0.0023495,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs2_gorilla,marg,N-TerminusTruncated
14642,Q#2544 - >seq5867,non-specific,235175,306,463,0.00423803,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14643,Q#2544 - >seq5867,superfamily,235175,306,463,0.00423803,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs2_gorilla.marg.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14644,Q#2545 - >seq5868,non-specific,338310,988,1050,0.00370004,39.864000000000004,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14645,Q#2545 - >seq5868,superfamily,338310,988,1050,0.00370004,39.864000000000004,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs2_gorilla.marg.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1ME3G,ORF2,hs2_gorilla,marg,BothTerminiTruncated
14646,Q#2547 - >seq5870,specific,197310,76,230,4.056119999999999e-30,119.37799999999999,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14647,Q#2547 - >seq5870,superfamily,351117,76,230,4.056119999999999e-30,119.37799999999999,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14648,Q#2547 - >seq5870,non-specific,197306,86,230,2.4446799999999998e-14,73.6696,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14649,Q#2547 - >seq5870,non-specific,197320,100,200,1.08877e-08,57.1398,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14650,Q#2547 - >seq5870,non-specific,197307,61,230,3.14893e-08,55.7569,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14651,Q#2547 - >seq5870,non-specific,197319,100,230,5.063470000000001e-07,52.2789,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14652,Q#2547 - >seq5870,non-specific,223780,87,231,2.48424e-06,49.9043,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14653,Q#2547 - >seq5870,non-specific,272954,84,230,3.71895e-05,46.6073,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14654,Q#2547 - >seq5870,non-specific,273186,100,231,0.000102185,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14655,Q#2547 - >seq5870,non-specific,197321,100,230,0.00194458,40.9984,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs2_gorilla.pars.frame2,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14656,Q#2548 - >seq5871,specific,238827,483,744,4.739319999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14657,Q#2548 - >seq5871,superfamily,295487,483,744,4.739319999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14658,Q#2548 - >seq5871,specific,333820,489,712,6.008919999999999e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14659,Q#2548 - >seq5871,superfamily,333820,489,712,6.008919999999999e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14660,Q#2548 - >seq5871,non-specific,238828,489,709,6.34428e-15,75.3152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14661,Q#2548 - >seq5871,non-specific,275209,440,709,5.5391099999999995e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14662,Q#2548 - >seq5871,superfamily,275209,440,709,5.5391099999999995e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,C-TerminusTruncated
14663,Q#2548 - >seq5871,non-specific,239569,513,757,2.76931e-05,46.4119,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14664,Q#2548 - >seq5871,non-specific,238185,628,742,0.000297544,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,CompleteHit
14665,Q#2548 - >seq5871,specific,225881,488,707,0.00111525,42.5185,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14666,Q#2548 - >seq5871,superfamily,225881,488,707,0.00111525,42.5185,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs2_gorilla.pars.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs2_gorilla,pars,N-TerminusTruncated
14667,Q#2551 - >seq5874,non-specific,335182,154,250,4.1805e-34,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14668,Q#2551 - >seq5874,superfamily,335182,154,250,4.1805e-34,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14669,Q#2551 - >seq5874,non-specific,340205,253,316,1.8271e-23,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14670,Q#2551 - >seq5874,superfamily,340205,253,316,1.8271e-23,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14671,Q#2551 - >seq5874,non-specific,237177,42,147,3.0733600000000003e-06,48.2358,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs4_gibbon,pars,C-TerminusTruncated
14672,Q#2551 - >seq5874,superfamily,237177,42,147,3.0733600000000003e-06,48.2358,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME3G,ORF1,hs4_gibbon,pars,C-TerminusTruncated
14673,Q#2551 - >seq5874,non-specific,340204,109,151,1.22753e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14674,Q#2551 - >seq5874,superfamily,340204,109,151,1.22753e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME3G,ORF1,hs4_gibbon,pars,CompleteHit
14675,Q#2551 - >seq5874,non-specific,274008,41,200,0.00035044,41.9659,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,N-TerminusTruncated
14676,Q#2551 - >seq5874,superfamily,274008,41,200,0.00035044,41.9659,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,N-TerminusTruncated
14677,Q#2551 - >seq5874,non-specific,235175,41,142,0.00068253,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14678,Q#2551 - >seq5874,superfamily,235175,41,142,0.00068253,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14679,Q#2551 - >seq5874,non-specific,226513,37,146,0.00254131,38.7384,COG4026,COG4026,NC,cl26606,"Uncharacterized protein, contains TOPRIM domain, potential nuclease  [General function prediction only]; Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only].",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14680,Q#2551 - >seq5874,superfamily,226513,37,146,0.00254131,38.7384,cl26606,COG4026 superfamily,NC, - ,"Uncharacterized protein, contains TOPRIM domain, potential nuclease  [General function prediction only]; Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only].",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14681,Q#2551 - >seq5874,non-specific,235175,49,154,0.00344623,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,C-TerminusTruncated
14682,Q#2551 - >seq5874,non-specific,274008,45,148,0.00677322,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14683,Q#2551 - >seq5874,non-specific,130673,52,147,0.0082925,37.7236,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14684,Q#2551 - >seq5874,superfamily,130673,52,147,0.0082925,37.7236,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF1.hs4_gibbon.pars.frame1,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME3G,ORF1,hs4_gibbon,pars,BothTerminiTruncated
14685,Q#2556 - >seq5879,non-specific,197310,18,161,1.29844e-14,74.3101,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
14686,Q#2556 - >seq5879,superfamily,351117,18,161,1.29844e-14,74.3101,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
14687,Q#2556 - >seq5879,non-specific,197306,18,203,4.00055e-12,67.1213,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14688,Q#2556 - >seq5879,specific,335306,18,196,4.4076300000000004e-05,45.699,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14689,Q#2556 - >seq5879,non-specific,339261,114,155,0.00244415,38.8575,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME3G,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
14690,Q#2557 - >seq5880,non-specific,130673,587,981,0.000206535,45.4275,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF2.hs5_gmonkey.pars.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3G,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
14691,Q#2557 - >seq5880,superfamily,130673,587,981,0.000206535,45.4275,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF2.hs5_gmonkey.pars.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME3G,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
14692,Q#2558 - >seq5881,specific,238827,501,749,2.24509e-49,174.40200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14693,Q#2558 - >seq5881,superfamily,295487,501,749,2.24509e-49,174.40200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14694,Q#2558 - >seq5881,specific,197310,32,231,1.4328799999999999e-27,112.06,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14695,Q#2558 - >seq5881,superfamily,351117,32,231,1.4328799999999999e-27,112.06,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14696,Q#2558 - >seq5881,non-specific,333820,507,717,8.99062e-27,108.149,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14697,Q#2558 - >seq5881,superfamily,333820,507,717,8.99062e-27,108.149,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14698,Q#2558 - >seq5881,non-specific,197306,32,231,6.20229e-17,81.3736,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14699,Q#2558 - >seq5881,non-specific,197320,103,224,2.65937e-10,62.1474,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14700,Q#2558 - >seq5881,non-specific,197307,88,224,5.27724e-10,61.1497,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14701,Q#2558 - >seq5881,non-specific,238828,560,718,6.34756e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14702,Q#2558 - >seq5881,non-specific,223780,88,224,1.07525e-09,60.3047,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14703,Q#2558 - >seq5881,non-specific,275209,565,786,1.19705e-08,58.238,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14704,Q#2558 - >seq5881,superfamily,275209,565,786,1.19705e-08,58.238,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14705,Q#2558 - >seq5881,non-specific,197319,103,231,3.05457e-06,49.5825,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14706,Q#2558 - >seq5881,non-specific,273186,103,224,3.55716e-06,49.5848,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14707,Q#2558 - >seq5881,specific,335306,12,224,1.65252e-05,47.2398,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14708,Q#2558 - >seq5881,non-specific,272954,88,202,7.66174e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14709,Q#2558 - >seq5881,non-specific,238185,634,749,0.00179398,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs5_gmonkey,pars,CompleteHit
14710,Q#2558 - >seq5881,non-specific,197321,103,224,0.00357444,40.228,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs5_gmonkey.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
14711,Q#2562 - >seq5885,non-specific,335182,61,128,1.73814e-13,64.2463,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
14712,Q#2562 - >seq5885,superfamily,335182,61,128,1.73814e-13,64.2463,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs5_gmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
14713,Q#2565 - >seq5888,non-specific,335182,37,73,6.65601e-05,39.5935,pfam02994,Transposase_22,NC,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs5_gmonkey.pars.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
14714,Q#2565 - >seq5888,superfamily,335182,37,73,6.65601e-05,39.5935,cl25509,Transposase_22 superfamily,NC, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs5_gmonkey.pars.frame1,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME3G,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
14715,Q#2566 - >seq5889,specific,197310,9,235,2.4145599999999997e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14716,Q#2566 - >seq5889,superfamily,351117,9,235,2.4145599999999997e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14717,Q#2566 - >seq5889,non-specific,197306,9,235,3.8112699999999995e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14718,Q#2566 - >seq5889,non-specific,197320,9,205,1.33758e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14719,Q#2566 - >seq5889,non-specific,223780,9,236,1.6707499999999999e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14720,Q#2566 - >seq5889,non-specific,197307,9,235,8.84094e-18,84.2617,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14721,Q#2566 - >seq5889,specific,335306,10,228,2.1978800000000002e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14722,Q#2566 - >seq5889,non-specific,273186,9,236,4.64525e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14723,Q#2566 - >seq5889,non-specific,197319,13,235,1.99999e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14724,Q#2566 - >seq5889,non-specific,272954,9,235,3.3818399999999997e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14725,Q#2566 - >seq5889,non-specific,197321,7,235,4.47656e-14,73.3552,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14726,Q#2566 - >seq5889,non-specific,197336,9,193,1.3401300000000002e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14727,Q#2566 - >seq5889,non-specific,197322,8,235,5.66296e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14728,Q#2566 - >seq5889,non-specific,236970,9,188,2.47663e-07,53.3594,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14729,Q#2566 - >seq5889,non-specific,197311,30,235,2.3502900000000003e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14730,Q#2566 - >seq5889,non-specific,339261,107,231,0.000830025,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14731,Q#2567 - >seq5890,specific,238827,476,733,4.214779999999999e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14732,Q#2567 - >seq5890,superfamily,295487,476,733,4.214779999999999e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14733,Q#2567 - >seq5890,specific,333820,482,706,7.41189e-35,131.26,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14734,Q#2567 - >seq5890,superfamily,333820,482,706,7.41189e-35,131.26,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14735,Q#2567 - >seq5890,non-specific,238828,530,703,8.87245e-14,71.8484,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,N-TerminusTruncated
14736,Q#2567 - >seq5890,non-specific,275209,432,703,2.37704e-08,57.0824,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14737,Q#2567 - >seq5890,superfamily,275209,432,703,2.37704e-08,57.0824,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14738,Q#2567 - >seq5890,non-specific,239569,491,713,2.31921e-05,46.4119,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,CompleteHit
14739,Q#2567 - >seq5890,non-specific,238185,622,699,0.000222462,41.1824,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs4_gibbon.marg.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,marg,C-TerminusTruncated
14740,Q#2569 - >seq5892,specific,197310,9,235,2.4145599999999997e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14741,Q#2569 - >seq5892,superfamily,351117,9,235,2.4145599999999997e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14742,Q#2569 - >seq5892,non-specific,197306,9,235,3.8112699999999995e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14743,Q#2569 - >seq5892,non-specific,197320,9,205,1.33758e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14744,Q#2569 - >seq5892,non-specific,223780,9,236,1.6707499999999999e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14745,Q#2569 - >seq5892,non-specific,197307,9,235,8.84094e-18,84.2617,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14746,Q#2569 - >seq5892,specific,335306,10,228,2.1978800000000002e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14747,Q#2569 - >seq5892,non-specific,273186,9,236,4.64525e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14748,Q#2569 - >seq5892,non-specific,197319,13,235,1.99999e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14749,Q#2569 - >seq5892,non-specific,272954,9,235,3.3818399999999997e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14750,Q#2569 - >seq5892,non-specific,197321,7,235,4.47656e-14,73.3552,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14751,Q#2569 - >seq5892,non-specific,197336,9,193,1.3401300000000002e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14752,Q#2569 - >seq5892,non-specific,197322,8,235,5.66296e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14753,Q#2569 - >seq5892,non-specific,236970,9,188,2.47663e-07,53.3594,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14754,Q#2569 - >seq5892,non-specific,197311,30,235,2.3502900000000003e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14755,Q#2569 - >seq5892,non-specific,339261,107,231,0.000830025,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs4_gibbon.pars.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14756,Q#2570 - >seq5893,specific,238827,476,733,4.214779999999999e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14757,Q#2570 - >seq5893,superfamily,295487,476,733,4.214779999999999e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14758,Q#2570 - >seq5893,specific,333820,482,706,7.41189e-35,131.26,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14759,Q#2570 - >seq5893,superfamily,333820,482,706,7.41189e-35,131.26,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14760,Q#2570 - >seq5893,non-specific,238828,530,703,8.87245e-14,71.8484,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,N-TerminusTruncated
14761,Q#2570 - >seq5893,non-specific,275209,432,703,2.37704e-08,57.0824,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14762,Q#2570 - >seq5893,superfamily,275209,432,703,2.37704e-08,57.0824,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14763,Q#2570 - >seq5893,non-specific,239569,491,713,2.31921e-05,46.4119,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,CompleteHit
14764,Q#2570 - >seq5893,non-specific,238185,622,699,0.000222462,41.1824,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs4_gibbon.pars.frame2,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs4_gibbon,pars,C-TerminusTruncated
14765,Q#2572 - >seq5895,non-specific,335182,154,250,4.966119999999999e-34,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14766,Q#2572 - >seq5895,superfamily,335182,154,250,4.966119999999999e-34,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14767,Q#2572 - >seq5895,non-specific,340205,253,316,1.69848e-23,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14768,Q#2572 - >seq5895,superfamily,340205,253,316,1.69848e-23,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14769,Q#2572 - >seq5895,non-specific,237177,42,147,2.75175e-06,48.621,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs4_gibbon,marg,C-TerminusTruncated
14770,Q#2572 - >seq5895,superfamily,237177,42,147,2.75175e-06,48.621,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs4_gibbon,marg,C-TerminusTruncated
14771,Q#2572 - >seq5895,non-specific,340204,109,151,1.23529e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14772,Q#2572 - >seq5895,superfamily,340204,109,151,1.23529e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs4_gibbon,marg,CompleteHit
14773,Q#2572 - >seq5895,non-specific,274008,41,200,0.000325003,42.3511,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,N-TerminusTruncated
14774,Q#2572 - >seq5895,superfamily,274008,41,200,0.000325003,42.3511,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,N-TerminusTruncated
14775,Q#2572 - >seq5895,non-specific,235175,41,142,0.0006108859999999999,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14776,Q#2572 - >seq5895,superfamily,235175,41,142,0.0006108859999999999,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14777,Q#2572 - >seq5895,non-specific,226513,37,146,0.00232603,38.7384,COG4026,COG4026,NC,cl26606,"Uncharacterized protein, contains TOPRIM domain, potential nuclease  [General function prediction only]; Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only].",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14778,Q#2572 - >seq5895,superfamily,226513,37,146,0.00232603,38.7384,cl26606,COG4026 superfamily,NC, - ,"Uncharacterized protein, contains TOPRIM domain, potential nuclease  [General function prediction only]; Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only].",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14779,Q#2572 - >seq5895,non-specific,235175,49,154,0.00313763,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,C-TerminusTruncated
14780,Q#2572 - >seq5895,non-specific,274008,45,148,0.00672906,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14781,Q#2572 - >seq5895,non-specific,130673,52,147,0.00954882,37.7236,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14782,Q#2572 - >seq5895,superfamily,130673,52,147,0.00954882,37.7236,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME3G.ORF1.hs4_gibbon.marg.frame3,1909130926_L1ME3G.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1ME3G,ORF1,hs4_gibbon,marg,BothTerminiTruncated
14783,Q#2575 - >seq5898,specific,238827,509,773,1.94972e-51,180.18,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14784,Q#2575 - >seq5898,superfamily,295487,509,773,1.94972e-51,180.18,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14785,Q#2575 - >seq5898,non-specific,333820,515,740,3.63627e-27,109.304,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14786,Q#2575 - >seq5898,superfamily,333820,515,740,3.63627e-27,109.304,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14787,Q#2575 - >seq5898,non-specific,197310,145,233,5.708e-11,63.9097,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14788,Q#2575 - >seq5898,superfamily,351117,145,233,5.708e-11,63.9097,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14789,Q#2575 - >seq5898,non-specific,238828,582,726,1.38484e-09,59.522,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14790,Q#2575 - >seq5898,non-specific,275209,466,810,2.3058400000000002e-08,57.4676,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14791,Q#2575 - >seq5898,superfamily,275209,466,810,2.3058400000000002e-08,57.4676,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14792,Q#2575 - >seq5898,non-specific,238185,656,741,0.00133601,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,CompleteHit
14793,Q#2575 - >seq5898,specific,225881,482,738,0.00199922,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14794,Q#2575 - >seq5898,superfamily,225881,482,738,0.00199922,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14795,Q#2575 - >seq5898,non-specific,197320,168,226,0.00220667,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14796,Q#2575 - >seq5898,non-specific,197307,162,226,0.00350962,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs5_gmonkey.marg.frame3,1909130926_L1ME3G.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
14797,Q#2576 - >seq5899,non-specific,335182,147,243,2.06635e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14798,Q#2576 - >seq5899,superfamily,335182,147,243,2.06635e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14799,Q#2576 - >seq5899,non-specific,340205,246,309,2.2393200000000002e-24,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14800,Q#2576 - >seq5899,superfamily,340205,246,309,2.2393200000000002e-24,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14801,Q#2576 - >seq5899,non-specific,340204,102,144,3.2800999999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14802,Q#2576 - >seq5899,superfamily,340204,102,144,3.2800999999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs2_gorilla.pars.frame3,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3G,ORF1,hs2_gorilla,pars,CompleteHit
14803,Q#2593 - >seq5916,non-specific,340205,59,107,0.00993652,31.9228,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME3F.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
14804,Q#2593 - >seq5916,superfamily,340205,59,107,0.00993652,31.9228,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3F.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME3F.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3F,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
14805,Q#2601 - >seq5924,specific,238827,477,742,1.8700299999999997e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14806,Q#2601 - >seq5924,superfamily,295487,477,742,1.8700299999999997e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14807,Q#2601 - >seq5924,specific,333820,483,707,1.7450899999999997e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14808,Q#2601 - >seq5924,superfamily,333820,483,707,1.7450899999999997e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14809,Q#2601 - >seq5924,non-specific,238828,483,704,4.1346699999999996e-14,72.6188,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14810,Q#2601 - >seq5924,non-specific,197310,9,71,1.7427099999999997e-10,62.3689,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14811,Q#2601 - >seq5924,superfamily,351117,9,71,1.7427099999999997e-10,62.3689,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14812,Q#2601 - >seq5924,non-specific,275209,433,704,2.24197e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14813,Q#2601 - >seq5924,superfamily,275209,433,704,2.24197e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14814,Q#2601 - >seq5924,non-specific,197306,9,89,1.3323799999999998e-08,56.7209,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14815,Q#2601 - >seq5924,specific,335306,10,74,0.00025094099999999997,43.773,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14816,Q#2601 - >seq5924,non-specific,239569,492,705,0.000347762,42.9451,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14817,Q#2601 - >seq5924,non-specific,223780,9,43,0.000479676,42.9707,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14818,Q#2601 - >seq5924,non-specific,197321,7,62,0.000966993,42.153999999999996,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14819,Q#2601 - >seq5924,non-specific,238185,623,700,0.0013203,39.2564,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14820,Q#2601 - >seq5924,non-specific,273186,9,43,0.00776136,39.1844,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14821,Q#2603 - >seq5926,specific,197310,39,228,9.653539999999998e-38,141.335,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14822,Q#2603 - >seq5926,superfamily,351117,39,228,9.653539999999998e-38,141.335,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14823,Q#2603 - >seq5926,non-specific,197306,64,228,1.54439e-17,83.2996,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14824,Q#2603 - >seq5926,non-specific,197320,60,198,1.55379e-11,65.6142,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14825,Q#2603 - >seq5926,non-specific,197307,53,228,6.4795e-10,60.7645,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14826,Q#2603 - >seq5926,non-specific,223780,60,229,8.165160000000001e-10,60.6899,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14827,Q#2603 - >seq5926,non-specific,197319,64,228,1.07557e-08,57.2865,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14828,Q#2603 - >seq5926,non-specific,272954,60,228,2.0917200000000002e-07,53.1557,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14829,Q#2603 - >seq5926,non-specific,235175,298,461,2.73401e-07,54.6847,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14830,Q#2603 - >seq5926,superfamily,235175,298,461,2.73401e-07,54.6847,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14831,Q#2603 - >seq5926,non-specific,273186,98,229,5.978009999999999e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14832,Q#2603 - >seq5926,specific,335306,58,221,9.446089999999999e-06,48.0102,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14833,Q#2603 - >seq5926,non-specific,223496,223,421,4.82933e-05,47.4475,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14834,Q#2603 - >seq5926,superfamily,223496,223,421,4.82933e-05,47.4475,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14835,Q#2603 - >seq5926,non-specific,197321,83,228,5.63375e-05,46.006,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14836,Q#2603 - >seq5926,non-specific,334125,204,403,0.0008173789999999999,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14837,Q#2603 - >seq5926,superfamily,334125,204,403,0.0008173789999999999,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14838,Q#2603 - >seq5926,non-specific,274009,286,473,0.0013528,42.7475,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14839,Q#2603 - >seq5926,superfamily,274009,286,473,0.0013528,42.7475,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,N-TerminusTruncated
14840,Q#2603 - >seq5926,non-specific,235175,275,461,0.00167262,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14841,Q#2603 - >seq5926,non-specific,338310,990,1052,0.00221755,40.6344,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14842,Q#2603 - >seq5926,superfamily,338310,990,1052,0.00221755,40.6344,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14843,Q#2603 - >seq5926,non-specific,339261,100,224,0.00244698,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME3G,ORF2,hs1_chimp,marg,CompleteHit
14844,Q#2603 - >seq5926,non-specific,274009,299,470,0.00284852,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,C-TerminusTruncated
14845,Q#2603 - >seq5926,non-specific,274009,286,464,0.00523831,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME3G,ORF2,hs1_chimp,marg,BothTerminiTruncated
14846,Q#2604 - >seq5927,specific,197310,9,233,5.89386e-48,170.995,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14847,Q#2604 - >seq5927,superfamily,351117,9,233,5.89386e-48,170.995,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14848,Q#2604 - >seq5927,non-specific,197306,9,233,3.43678e-30,119.89399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14849,Q#2604 - >seq5927,non-specific,223780,9,234,1.2105600000000002e-16,81.1055,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14850,Q#2604 - >seq5927,non-specific,197307,9,233,1.6409900000000003e-16,80.4097,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14851,Q#2604 - >seq5927,non-specific,197319,13,233,3.3970500000000002e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14852,Q#2604 - >seq5927,non-specific,197321,7,233,3.6874000000000004e-14,73.3552,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14853,Q#2604 - >seq5927,non-specific,197320,9,203,6.32105e-14,72.933,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14854,Q#2604 - >seq5927,specific,335306,10,226,3.32138e-13,69.9666,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14855,Q#2604 - >seq5927,non-specific,273186,9,234,5.81802e-12,66.9188,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14856,Q#2604 - >seq5927,non-specific,272954,9,233,6.283280000000001e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14857,Q#2604 - >seq5927,non-specific,197336,9,191,1.6824000000000002e-06,50.6887,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14858,Q#2605 - >seq5928,non-specific,338310,976,1038,0.00148728,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3G,ORF2,hs1_chimp,pars,BothTerminiTruncated
14859,Q#2605 - >seq5928,superfamily,338310,976,1038,0.00148728,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1ME3G.ORF2.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3G,ORF2,hs1_chimp,pars,BothTerminiTruncated
14860,Q#2606 - >seq5929,specific,238827,457,722,4.4023999999999985e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14861,Q#2606 - >seq5929,superfamily,295487,457,722,4.4023999999999985e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14862,Q#2606 - >seq5929,specific,333820,463,687,2.0180499999999996e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14863,Q#2606 - >seq5929,superfamily,333820,463,687,2.0180499999999996e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14864,Q#2606 - >seq5929,non-specific,238828,463,684,3.58603e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14865,Q#2606 - >seq5929,non-specific,275209,413,684,1.7587700000000001e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,C-TerminusTruncated
14866,Q#2606 - >seq5929,superfamily,275209,413,684,1.7587700000000001e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,C-TerminusTruncated
14867,Q#2606 - >seq5929,non-specific,239569,472,685,0.000169874,44.1007,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,CompleteHit
14868,Q#2606 - >seq5929,non-specific,238185,603,680,0.00226069,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,C-TerminusTruncated
14869,Q#2606 - >seq5929,specific,225881,462,682,0.00754187,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,N-TerminusTruncated
14870,Q#2606 - >seq5929,superfamily,225881,462,682,0.00754187,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs1_chimp.pars.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME3G,ORF2,hs1_chimp,pars,N-TerminusTruncated
14871,Q#2607 - >seq5930,non-specific,223250,13,90,0.000849327,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME3G,ORF1,hs1_chimp,marg,C-TerminusTruncated
14872,Q#2607 - >seq5930,superfamily,223250,13,90,0.000849327,40.2741,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs1_chimp.marg.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME3G,ORF1,hs1_chimp,marg,C-TerminusTruncated
14873,Q#2609 - >seq5932,non-specific,340205,213,276,3.43838e-26,97.792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs1_chimp,marg,CompleteHit
14874,Q#2609 - >seq5932,superfamily,340205,213,276,3.43838e-26,97.792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs1_chimp,marg,CompleteHit
14875,Q#2609 - >seq5932,non-specific,335182,114,210,3.332489999999999e-24,93.5214,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs1_chimp,marg,CompleteHit
14876,Q#2609 - >seq5932,superfamily,335182,114,210,3.332489999999999e-24,93.5214,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs1_chimp,marg,CompleteHit
14877,Q#2610 - >seq5933,non-specific,340205,211,274,2.7528399999999997e-26,97.792,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs1_chimp,pars,CompleteHit
14878,Q#2610 - >seq5933,superfamily,340205,211,274,2.7528399999999997e-26,97.792,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs1_chimp,pars,CompleteHit
14879,Q#2610 - >seq5933,non-specific,335182,112,208,2.67575e-24,93.5214,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs1_chimp,pars,CompleteHit
14880,Q#2610 - >seq5933,superfamily,335182,112,208,2.67575e-24,93.5214,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs1_chimp.pars.frame3,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs1_chimp,pars,CompleteHit
14881,Q#2611 - >seq5934,non-specific,223250,13,89,0.00269763,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_tRNAsynthetase,L1ME3G,ORF1,hs1_chimp,pars,C-TerminusTruncated
14882,Q#2611 - >seq5934,superfamily,223250,13,89,0.00269763,38.3481,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME3G.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_tRNAsynthetase,L1ME3G,ORF1,hs1_chimp,pars,C-TerminusTruncated
14883,Q#2611 - >seq5934,non-specific,235505,30,111,0.00767612,37.1574,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1ME3G.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1ME3G,ORF1,hs1_chimp,pars,BothTerminiTruncated
14884,Q#2611 - >seq5934,superfamily,235505,30,111,0.00767612,37.1574,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1ME3G.ORF1.hs1_chimp.pars.frame2,1909130926_L1ME3G.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1ME3G,ORF1,hs1_chimp,pars,BothTerminiTruncated
14885,Q#2622 - >seq5945,non-specific,335182,147,243,1.0375999999999998e-31,113.93700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14886,Q#2622 - >seq5945,superfamily,335182,147,243,1.0375999999999998e-31,113.93700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14887,Q#2622 - >seq5945,non-specific,340205,246,309,3.44666e-24,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14888,Q#2622 - >seq5945,superfamily,340205,246,309,3.44666e-24,93.1696,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14889,Q#2622 - >seq5945,non-specific,340204,102,144,4.40488e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14890,Q#2622 - >seq5945,superfamily,340204,102,144,4.40488e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME3G,ORF1,hs2_gorilla,marg,CompleteHit
14891,Q#2622 - >seq5945,non-specific,310273,75,138,0.00488745,38.1878,pfam05557,MAD,NC,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME3G,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14892,Q#2622 - >seq5945,superfamily,310273,75,138,0.00488745,38.1878,cl37733,MAD superfamily,NC, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME3G.ORF1.hs2_gorilla.marg.frame1,1909130926_L1ME3G.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME3G,ORF1,hs2_gorilla,marg,BothTerminiTruncated
14893,Q#2628 - >seq5951,non-specific,335182,115,212,1.534e-40,136.279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3,ORF1,hs1_chimp,marg,CompleteHit
14894,Q#2628 - >seq5951,superfamily,335182,115,212,1.534e-40,136.279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3,ORF1,hs1_chimp,marg,CompleteHit
14895,Q#2628 - >seq5951,non-specific,340205,227,279,2.5912199999999997e-17,74.2948,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3,ORF1,hs1_chimp,marg,CompleteHit
14896,Q#2628 - >seq5951,superfamily,340205,227,279,2.5912199999999997e-17,74.2948,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3.ORF1.hs1_chimp.marg.frame1,1909130926_L1ME3.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3,ORF1,hs1_chimp,marg,CompleteHit
14897,Q#2632 - >seq5955,specific,238827,503,761,1.9356699999999997e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14898,Q#2632 - >seq5955,superfamily,295487,503,761,1.9356699999999997e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14899,Q#2632 - >seq5955,specific,197310,3,230,5.2235e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14900,Q#2632 - >seq5955,superfamily,351117,3,230,5.2235e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14901,Q#2632 - >seq5955,specific,333820,509,733,2.22452e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14902,Q#2632 - >seq5955,superfamily,333820,509,733,2.22452e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14903,Q#2632 - >seq5955,non-specific,197306,3,230,1.9494499999999998e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14904,Q#2632 - >seq5955,non-specific,197320,3,223,7.61537e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14905,Q#2632 - >seq5955,non-specific,197307,3,230,2.5388700000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14906,Q#2632 - >seq5955,non-specific,223780,3,231,3.12812e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14907,Q#2632 - >seq5955,specific,335306,4,223,1.29135e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14908,Q#2632 - >seq5955,non-specific,197321,1,230,2.7461900000000005e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14909,Q#2632 - >seq5955,non-specific,197319,7,230,2.7462400000000003e-16,79.6281,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14910,Q#2632 - >seq5955,non-specific,272954,3,230,7.313060000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14911,Q#2632 - >seq5955,non-specific,273186,3,231,2.6447399999999997e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14912,Q#2632 - >seq5955,non-specific,238828,509,730,6.8238200000000005e-15,74.93,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14913,Q#2632 - >seq5955,non-specific,197336,3,188,7.706979999999999e-10,60.7039,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14914,Q#2632 - >seq5955,non-specific,236970,3,243,8.7293e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14915,Q#2632 - >seq5955,non-specific,275209,460,730,5.32782e-08,55.9268,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,C-TerminusTruncated
14916,Q#2632 - >seq5955,superfamily,275209,460,730,5.32782e-08,55.9268,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,C-TerminusTruncated
14917,Q#2632 - >seq5955,non-specific,197322,2,230,3.4586999999999996e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14918,Q#2632 - >seq5955,non-specific,197311,1,230,4.3112100000000004e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14919,Q#2632 - >seq5955,non-specific,235175,300,453,6.475010000000001e-05,46.9808,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14920,Q#2632 - >seq5955,superfamily,235175,300,453,6.475010000000001e-05,46.9808,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14921,Q#2632 - >seq5955,non-specific,238185,649,726,0.00030260000000000004,40.7972,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,C-TerminusTruncated
14922,Q#2632 - >seq5955,non-specific,274009,305,467,0.000584353,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14923,Q#2632 - >seq5955,superfamily,274009,305,467,0.000584353,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14924,Q#2632 - >seq5955,non-specific,339261,102,226,0.0005978590000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14925,Q#2632 - >seq5955,non-specific,239569,518,731,0.00100316,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,CompleteHit
14926,Q#2632 - >seq5955,specific,225881,476,673,0.00377819,40.5925,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14927,Q#2632 - >seq5955,superfamily,225881,476,673,0.00377819,40.5925,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1ME3G,ORF2,hs0_human,marg,BothTerminiTruncated
14928,Q#2632 - >seq5955,non-specific,334125,206,404,0.00597066,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs0_human,marg,N-TerminusTruncated
14929,Q#2632 - >seq5955,superfamily,334125,206,404,0.00597066,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1ME3G.ORF2.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1ME3G,ORF2,hs0_human,marg,N-TerminusTruncated
14930,Q#2635 - >seq5958,specific,197310,3,230,4.034559999999999e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14931,Q#2635 - >seq5958,superfamily,351117,3,230,4.034559999999999e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14932,Q#2635 - >seq5958,non-specific,197306,3,230,2.15227e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14933,Q#2635 - >seq5958,non-specific,197320,3,223,7.348689999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14934,Q#2635 - >seq5958,non-specific,197307,3,230,1.5684e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14935,Q#2635 - >seq5958,non-specific,223780,3,231,3.01801e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14936,Q#2635 - >seq5958,non-specific,197319,7,230,7.92689e-17,81.1689,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14937,Q#2635 - >seq5958,specific,335306,4,223,1.24746e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14938,Q#2635 - >seq5958,non-specific,197321,1,230,4.0122099999999996e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14939,Q#2635 - >seq5958,non-specific,272954,3,230,7.260489999999999e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14940,Q#2635 - >seq5958,non-specific,273186,3,231,2.5527e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14941,Q#2635 - >seq5958,non-specific,197336,3,188,7.44219e-10,60.7039,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14942,Q#2635 - >seq5958,non-specific,236970,3,243,1.0315299999999998e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14943,Q#2635 - >seq5958,non-specific,197322,2,230,3.33835e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14944,Q#2635 - >seq5958,non-specific,197311,1,230,4.16921e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14945,Q#2635 - >seq5958,non-specific,339261,102,226,0.000459319,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME3G.ORF2.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14946,Q#2636 - >seq5959,specific,238827,480,738,1.01707e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14947,Q#2636 - >seq5959,superfamily,295487,480,738,1.01707e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14948,Q#2636 - >seq5959,specific,333820,486,710,9.42743e-35,131.26,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14949,Q#2636 - >seq5959,superfamily,333820,486,710,9.42743e-35,131.26,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14950,Q#2636 - >seq5959,non-specific,238828,486,707,2.2099799999999997e-15,76.4708,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14951,Q#2636 - >seq5959,non-specific,275209,437,707,4.82552e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,C-TerminusTruncated
14952,Q#2636 - >seq5959,superfamily,275209,437,707,4.82552e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,C-TerminusTruncated
14953,Q#2636 - >seq5959,non-specific,238185,626,703,0.00016418299999999998,41.5676,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,C-TerminusTruncated
14954,Q#2636 - >seq5959,non-specific,239569,495,739,0.000500443,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,CompleteHit
14955,Q#2636 - >seq5959,specific,225881,453,681,0.00128892,42.1333,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,N-TerminusTruncated
14956,Q#2636 - >seq5959,superfamily,225881,453,681,0.00128892,42.1333,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1ME3G.ORF2.hs0_human.pars.frame2,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME3G,ORF2,hs0_human,pars,N-TerminusTruncated
14957,Q#2638 - >seq5961,non-specific,335182,156,252,6.704069999999998e-30,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14958,Q#2638 - >seq5961,superfamily,335182,156,252,6.704069999999998e-30,109.315,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14959,Q#2638 - >seq5961,non-specific,335182,156,252,6.704069999999998e-30,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14960,Q#2638 - >seq5961,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14961,Q#2638 - >seq5961,superfamily,340205,255,318,7.4266099999999995e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14962,Q#2638 - >seq5961,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14963,Q#2638 - >seq5961,non-specific,340204,112,154,4.08308e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14964,Q#2638 - >seq5961,superfamily,340204,112,154,4.08308e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14965,Q#2638 - >seq5961,non-specific,340204,112,154,4.08308e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,marg,CompleteHit
14966,Q#2638 - >seq5961,non-specific,274008,28,150,0.0006228,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14967,Q#2638 - >seq5961,superfamily,274008,28,150,0.0006228,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14968,Q#2638 - >seq5961,non-specific,274008,28,150,0.0006228,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14969,Q#2638 - >seq5961,non-specific,274008,41,150,0.000914778,40.8103,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14970,Q#2638 - >seq5961,non-specific,274008,41,150,0.000914778,40.8103,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14971,Q#2638 - >seq5961,non-specific,237177,44,150,0.00138696,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14972,Q#2638 - >seq5961,superfamily,237177,44,150,0.00138696,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14973,Q#2638 - >seq5961,non-specific,237177,44,150,0.00138696,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14974,Q#2638 - >seq5961,non-specific,274009,33,151,0.00211343,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14975,Q#2638 - >seq5961,superfamily,274009,33,151,0.00211343,39.6659,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14976,Q#2638 - >seq5961,non-specific,274009,33,151,0.00211343,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,BothTerminiTruncated
14977,Q#2638 - >seq5961,non-specific,235175,48,156,0.00250557,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14978,Q#2638 - >seq5961,superfamily,235175,48,156,0.00250557,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14979,Q#2638 - >seq5961,non-specific,235175,48,156,0.00250557,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14980,Q#2638 - >seq5961,non-specific,112704,2,123,0.00613681,37.3003,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14981,Q#2638 - >seq5961,superfamily,112704,2,123,0.00613681,37.3003,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14982,Q#2638 - >seq5961,non-specific,112704,2,123,0.00613681,37.3003,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.marg.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1ME3G,ORF1,hs0_human,marg,C-TerminusTruncated
14983,Q#2641 - >seq5964,non-specific,335182,156,252,6.704069999999998e-30,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14984,Q#2641 - >seq5964,superfamily,335182,156,252,6.704069999999998e-30,109.315,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14985,Q#2641 - >seq5964,non-specific,335182,156,252,6.704069999999998e-30,109.315,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14986,Q#2641 - >seq5964,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14987,Q#2641 - >seq5964,superfamily,340205,255,318,7.4266099999999995e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14988,Q#2641 - >seq5964,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14989,Q#2641 - >seq5964,non-specific,340204,112,154,4.08308e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14990,Q#2641 - >seq5964,superfamily,340204,112,154,4.08308e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14991,Q#2641 - >seq5964,non-specific,340204,112,154,4.08308e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME3G,ORF1,hs0_human,pars,CompleteHit
14992,Q#2641 - >seq5964,non-specific,274008,28,150,0.0006228,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
14993,Q#2641 - >seq5964,superfamily,274008,28,150,0.0006228,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
14994,Q#2641 - >seq5964,non-specific,274008,28,150,0.0006228,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
14995,Q#2641 - >seq5964,non-specific,274008,41,150,0.000914778,40.8103,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
14996,Q#2641 - >seq5964,non-specific,274008,41,150,0.000914778,40.8103,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
14997,Q#2641 - >seq5964,non-specific,237177,44,150,0.00138696,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
14998,Q#2641 - >seq5964,superfamily,237177,44,150,0.00138696,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
14999,Q#2641 - >seq5964,non-specific,237177,44,150,0.00138696,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15000,Q#2641 - >seq5964,non-specific,274009,33,151,0.00211343,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
15001,Q#2641 - >seq5964,superfamily,274009,33,151,0.00211343,39.6659,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
15002,Q#2641 - >seq5964,non-specific,274009,33,151,0.00211343,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,BothTerminiTruncated
15003,Q#2641 - >seq5964,non-specific,235175,48,156,0.00250557,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15004,Q#2641 - >seq5964,superfamily,235175,48,156,0.00250557,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15005,Q#2641 - >seq5964,non-specific,235175,48,156,0.00250557,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15006,Q#2641 - >seq5964,non-specific,112704,2,123,0.00613681,37.3003,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15007,Q#2641 - >seq5964,superfamily,112704,2,123,0.00613681,37.3003,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15008,Q#2641 - >seq5964,non-specific,112704,2,123,0.00613681,37.3003,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME3G.ORF1.hs0_human.pars.frame3,1909130926_L1ME3G.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME3G,ORF1,hs0_human,pars,C-TerminusTruncated
15009,Q#2676 - >seq5999,non-specific,340205,189,229,0.00012821799999999998,38.8564,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
15010,Q#2676 - >seq5999,superfamily,340205,189,229,0.00012821799999999998,38.8564,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs8_ctshrew.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs8_ctshrew,marg,C-TerminusTruncated
15011,Q#2677 - >seq6000,non-specific,340205,77,113,0.00249847,33.8488,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs8_ctshrew.pars.frame3,1909130926_L1ME3G.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
15012,Q#2677 - >seq6000,superfamily,340205,77,113,0.00249847,33.8488,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs8_ctshrew.pars.frame3,1909130926_L1ME3G.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME3G,ORF1,hs8_ctshrew,pars,C-TerminusTruncated
15013,Q#2682 - >seq6005,non-specific,197310,16,233,3.61496e-08,55.4353,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3G.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3G,ORF2,hs6_sqmonkey,marg,CompleteHit
15014,Q#2682 - >seq6005,superfamily,351117,16,233,3.61496e-08,55.4353,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3G.ORF2.hs6_sqmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3G,ORF2,hs6_sqmonkey,marg,CompleteHit
15015,Q#2691 - >seq6014,non-specific,340205,139,173,0.000191917,38.086,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15016,Q#2691 - >seq6014,superfamily,340205,139,173,0.000191917,38.086,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME3G.ORF1.hs6_sqmonkey.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15017,Q#2692 - >seq6015,non-specific,335182,27,79,0.00183608,35.3563,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs9_pika.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3G,ORF1,hs9_pika,pars,N-TerminusTruncated
15018,Q#2692 - >seq6015,superfamily,335182,27,79,0.00183608,35.3563,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs9_pika.pars.frame2,1909130926_L1ME3G.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME3G,ORF1,hs9_pika,pars,N-TerminusTruncated
15019,Q#2710 - >seq6033,non-specific,335182,35,93,9.375059999999999e-05,39.2083,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs9_pika.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs9_pika,marg,N-TerminusTruncated
15020,Q#2710 - >seq6033,superfamily,335182,35,93,9.375059999999999e-05,39.2083,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME3G.ORF1.hs9_pika.marg.frame1,1909130926_L1ME3G.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME3G,ORF1,hs9_pika,marg,N-TerminusTruncated
15021,Q#2733 - >seq6056,non-specific,178652,16,67,0.00608379,36.3843,PLN03105,TCP24,C,cl23822,"transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional",L1MEc.ORF1.hs11_armadillo.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MEc,ORF1,hs11_armadillo,pars,C-TerminusTruncated
15022,Q#2733 - >seq6056,superfamily,355059,16,67,0.00608379,36.3843,cl23822,TCP superfamily,C, - ,"TCP family transcription factor; This is a family of TCP plant transcription factors. TCP proteins were named after the first characterized members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways. This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure.",L1MEc.ORF1.hs11_armadillo.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MEc,ORF1,hs11_armadillo,pars,C-TerminusTruncated
15023,Q#2736 - >seq6059,non-specific,340205,112,175,1.0387000000000001e-18,75.4504,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs10_snmole,pars,CompleteHit
15024,Q#2736 - >seq6059,superfamily,340205,112,175,1.0387000000000001e-18,75.4504,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs10_snmole,pars,CompleteHit
15025,Q#2736 - >seq6059,non-specific,335182,30,108,5.50642e-11,56.1571,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs10_snmole,pars,N-TerminusTruncated
15026,Q#2736 - >seq6059,superfamily,335182,30,108,5.50642e-11,56.1571,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs10_snmole,pars,N-TerminusTruncated
15027,Q#2738 - >seq6061,non-specific,340205,171,234,7.963130000000001e-19,77.3764,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs10_snmole.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs10_snmole,marg,CompleteHit
15028,Q#2738 - >seq6061,superfamily,340205,171,234,7.963130000000001e-19,77.3764,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs10_snmole.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs10_snmole,marg,CompleteHit
15029,Q#2738 - >seq6061,non-specific,335182,75,167,2.11146e-12,61.1647,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs10_snmole.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs10_snmole,marg,CompleteHit
15030,Q#2738 - >seq6061,superfamily,335182,75,167,2.11146e-12,61.1647,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs10_snmole.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs10_snmole,marg,CompleteHit
15031,Q#2742 - >seq6065,specific,197310,5,230,2.44077e-48,171.38,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15032,Q#2742 - >seq6065,superfamily,351117,5,230,2.44077e-48,171.38,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15033,Q#2742 - >seq6065,non-specific,197306,5,230,1.12607e-22,97.552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15034,Q#2742 - >seq6065,non-specific,223780,5,223,3.54914e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15035,Q#2742 - >seq6065,non-specific,197307,5,230,1.6477999999999999e-15,76.9429,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15036,Q#2742 - >seq6065,non-specific,197320,5,223,4.02984e-15,76.0145,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15037,Q#2742 - >seq6065,non-specific,273186,5,231,5.78552e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15038,Q#2742 - >seq6065,specific,335306,6,223,3.5499e-12,66.4998,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15039,Q#2742 - >seq6065,non-specific,197321,3,230,3.72404e-11,64.1104,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15040,Q#2742 - >seq6065,non-specific,272954,5,201,1.19934e-07,53.5409,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15041,Q#2742 - >seq6065,non-specific,197319,5,230,1.52016e-07,53.4345,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15042,Q#2742 - >seq6065,non-specific,197322,85,230,4.11985e-06,49.623000000000005,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,N-TerminusTruncated
15043,Q#2742 - >seq6065,non-specific,197336,5,188,5.13404e-05,45.6811,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15044,Q#2742 - >seq6065,non-specific,339261,102,226,0.000798082,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs10_snmole,pars,CompleteHit
15045,Q#2742 - >seq6065,non-specific,238827,628,679,0.00911531,38.4262,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MEc,ORF2,hs10_snmole,pars,BothTerminiTruncated
15046,Q#2742 - >seq6065,superfamily,295487,628,679,0.00911531,38.4262,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs10_snmole.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MEc,ORF2,hs10_snmole,pars,BothTerminiTruncated
15047,Q#2745 - >seq6068,specific,197310,9,237,1.33966e-48,172.53599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15048,Q#2745 - >seq6068,superfamily,351117,9,237,1.33966e-48,172.53599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15049,Q#2745 - >seq6068,non-specific,197306,9,237,2.18846e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15050,Q#2745 - >seq6068,non-specific,223780,9,230,3.3431300000000005e-16,79.5647,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15051,Q#2745 - >seq6068,non-specific,197307,9,237,1.7185300000000001e-15,76.9429,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15052,Q#2745 - >seq6068,non-specific,197320,9,230,2.00084e-15,76.7849,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15053,Q#2745 - >seq6068,non-specific,273186,9,238,1.61452e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15054,Q#2745 - >seq6068,specific,335306,10,230,7.06903e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15055,Q#2745 - >seq6068,non-specific,197321,7,237,2.96553e-11,64.4956,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15056,Q#2745 - >seq6068,non-specific,272954,9,208,2.75217e-08,55.8521,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15057,Q#2745 - >seq6068,non-specific,197319,9,237,6.566849999999999e-08,54.5901,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15058,Q#2745 - >seq6068,non-specific,197322,92,237,4.67045e-06,49.623000000000005,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,N-TerminusTruncated
15059,Q#2745 - >seq6068,non-specific,197336,9,195,2.5686199999999998e-05,46.8367,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15060,Q#2745 - >seq6068,non-specific,339261,109,233,0.0009266319999999999,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs10_snmole.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs10_snmole,marg,CompleteHit
15061,Q#2747 - >seq6070,non-specific,340205,125,190,5.1373e-16,68.902,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs11_armadillo,pars,CompleteHit
15062,Q#2747 - >seq6070,superfamily,340205,125,190,5.1373e-16,68.902,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs11_armadillo,pars,CompleteHit
15063,Q#2747 - >seq6070,non-specific,335182,53,106,3.7094700000000005e-07,46.5271,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs11_armadillo,pars,N-TerminusTruncated
15064,Q#2747 - >seq6070,superfamily,335182,53,106,3.7094700000000005e-07,46.5271,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs11_armadillo,pars,N-TerminusTruncated
15065,Q#2748 - >seq6071,non-specific,340205,151,216,2.68306e-16,70.4428,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs11_armadillo.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs11_armadillo,marg,CompleteHit
15066,Q#2748 - >seq6071,superfamily,340205,151,216,2.68306e-16,70.4428,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs11_armadillo.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs11_armadillo,marg,CompleteHit
15067,Q#2748 - >seq6071,non-specific,335182,51,132,2.25667e-12,60.7795,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs11_armadillo.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs11_armadillo,marg,CompleteHit
15068,Q#2748 - >seq6071,superfamily,335182,51,132,2.25667e-12,60.7795,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs11_armadillo.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs11_armadillo,marg,CompleteHit
15069,Q#2751 - >seq6074,non-specific,238827,454,491,2.79633e-05,44.9746,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs11_armadillo.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs11_armadillo,pars,C-TerminusTruncated
15070,Q#2751 - >seq6074,superfamily,295487,454,491,2.79633e-05,44.9746,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs11_armadillo.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs11_armadillo,pars,C-TerminusTruncated
15071,Q#2753 - >seq6076,non-specific,197310,139,201,9.87529e-09,55.8205,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs11_armadillo,pars,N-TerminusTruncated
15072,Q#2753 - >seq6076,superfamily,351117,139,201,9.87529e-09,55.8205,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs11_armadillo.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs11_armadillo,pars,N-TerminusTruncated
15073,Q#2754 - >seq6077,non-specific,197310,111,247,7.73301e-18,83.9401,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15074,Q#2754 - >seq6077,superfamily,351117,111,247,7.73301e-18,83.9401,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15075,Q#2754 - >seq6077,non-specific,238827,523,741,2.75512e-12,67.3162,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEc,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15076,Q#2754 - >seq6077,superfamily,295487,523,741,2.75512e-12,67.3162,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEc,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15077,Q#2754 - >seq6077,non-specific,197320,117,219,9.355800000000001e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15078,Q#2754 - >seq6077,non-specific,197306,111,247,9.951799999999999e-05,44.7797,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15079,Q#2754 - >seq6077,non-specific,223780,117,218,0.00017909799999999999,44.1263,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15080,Q#2754 - >seq6077,non-specific,197307,117,247,0.00107202,41.8897,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15081,Q#2754 - >seq6077,non-specific,197322,117,247,0.00686026,39.6078,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MEc,ORF2,hs11_armadillo,marg,N-TerminusTruncated
15082,Q#2754 - >seq6077,non-specific,333820,529,721,0.00844822,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEc,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15083,Q#2754 - >seq6077,superfamily,333820,529,721,0.00844822,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEc.ORF2.hs11_armadillo.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEc,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15084,Q#2762 - >seq6085,non-specific,197310,1,54,8.1103e-06,46.5757,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEd.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEd.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEd,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15085,Q#2762 - >seq6085,superfamily,351117,1,54,8.1103e-06,46.5757,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEd.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEd.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEd,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15086,Q#2774 - >seq6097,non-specific,234767,150,406,0.00110205,42.9028,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MEd.ORF2.hs8_ctshrew.marg.frame1,1909130927_L1MEd.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MEd,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
15087,Q#2774 - >seq6097,superfamily,234767,150,406,0.00110205,42.9028,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MEd.ORF2.hs8_ctshrew.marg.frame1,1909130927_L1MEd.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MEd,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
15088,Q#2803 - >seq6126,non-specific,337447,413,529,0.00027659900000000004,44.1681,pfam09586,YfhO,N,cl26628,Bacterial membrane protein YfhO; This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family.,L1MEc.ORF2.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MEc,ORF2,hs9_pika,marg,N-TerminusTruncated
15089,Q#2803 - >seq6126,superfamily,337447,413,529,0.00027659900000000004,44.1681,cl26628,YfhO superfamily,N, - ,Bacterial membrane protein YfhO; This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family.,L1MEc.ORF2.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MEc,ORF2,hs9_pika,marg,N-TerminusTruncated
15090,Q#2804 - >seq6127,non-specific,197310,21,217,3.29615e-16,77.7769,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs4_gibbon,pars,CompleteHit
15091,Q#2804 - >seq6127,superfamily,351117,21,217,3.29615e-16,77.7769,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs4_gibbon,pars,CompleteHit
15092,Q#2809 - >seq6132,non-specific,197310,11,224,2.9581299999999996e-19,87.4069,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs4_gibbon.marg.frame3,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs4_gibbon,marg,CompleteHit
15093,Q#2809 - >seq6132,superfamily,351117,11,224,2.9581299999999996e-19,87.4069,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs4_gibbon.marg.frame3,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs4_gibbon,marg,CompleteHit
15094,Q#2809 - >seq6132,non-specific,197306,9,224,8.40211e-06,47.8613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs4_gibbon.marg.frame3,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs4_gibbon,marg,CompleteHit
15095,Q#2811 - >seq6134,non-specific,340205,145,191,9.84966e-16,68.5168,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs5_gmonkey.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
15096,Q#2811 - >seq6134,superfamily,340205,145,191,9.84966e-16,68.5168,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs5_gmonkey.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
15097,Q#2811 - >seq6134,non-specific,335182,43,141,1.2667100000000001e-05,42.2899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs5_gmonkey.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs5_gmonkey,pars,CompleteHit
15098,Q#2811 - >seq6134,superfamily,335182,43,141,1.2667100000000001e-05,42.2899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs5_gmonkey.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEc,ORF1,hs5_gmonkey,pars,CompleteHit
15099,Q#2814 - >seq6137,specific,197310,9,229,8.34684e-40,147.113,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15100,Q#2814 - >seq6137,superfamily,351117,9,229,8.34684e-40,147.113,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15101,Q#2814 - >seq6137,non-specific,197306,9,229,1.8994699999999998e-18,85.6108,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15102,Q#2814 - >seq6137,non-specific,223780,9,222,1.1439599999999999e-10,63.0011,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15103,Q#2814 - >seq6137,non-specific,197307,9,229,1.50464e-10,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15104,Q#2814 - >seq6137,specific,335306,10,222,4.98485e-09,57.255,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15105,Q#2814 - >seq6137,non-specific,197320,9,222,7.42308e-07,51.3618,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15106,Q#2814 - >seq6137,non-specific,273186,9,230,4.40855e-06,48.8144,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15107,Q#2814 - >seq6137,non-specific,197321,7,229,5.1254499999999995e-05,45.6208,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15108,Q#2814 - >seq6137,non-specific,197322,85,222,0.00211642,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,marg,N-TerminusTruncated
15109,Q#2814 - >seq6137,non-specific,272954,9,200,0.00290136,40.4441,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,marg,CompleteHit
15110,Q#2814 - >seq6137,non-specific,235175,255,488,0.00954461,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MEc,ORF2,hs9_pika,marg,BothTerminiTruncated
15111,Q#2814 - >seq6137,superfamily,235175,255,488,0.00954461,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MEc.ORF2.hs9_pika.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MEc,ORF2,hs9_pika,marg,BothTerminiTruncated
15112,Q#2816 - >seq6139,non-specific,340205,177,223,2.61917e-15,68.1316,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
15113,Q#2816 - >seq6139,superfamily,340205,177,223,2.61917e-15,68.1316,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
15114,Q#2816 - >seq6139,non-specific,335182,74,173,3.25218e-05,41.5195,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs5_gmonkey,marg,CompleteHit
15115,Q#2816 - >seq6139,superfamily,335182,74,173,3.25218e-05,41.5195,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs5_gmonkey,marg,CompleteHit
15116,Q#2819 - >seq6142,specific,197310,9,226,7.10128e-28,112.83,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15117,Q#2819 - >seq6142,superfamily,351117,9,226,7.10128e-28,112.83,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15118,Q#2819 - >seq6142,non-specific,197306,9,226,3.31656e-14,72.8993,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15119,Q#2819 - >seq6142,non-specific,197320,110,201,1.39685e-07,53.2878,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
15120,Q#2819 - >seq6142,non-specific,197307,9,226,1.8519700000000001e-07,53.0605,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15121,Q#2819 - >seq6142,non-specific,197321,7,226,3.15323e-05,46.3912,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15122,Q#2819 - >seq6142,specific,335306,122,219,0.00017262400000000002,43.773,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
15123,Q#2819 - >seq6142,non-specific,223780,9,200,0.000362833,42.9707,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15124,Q#2819 - >seq6142,non-specific,272954,9,200,0.000628862,42.3701,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs5_gmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,pars,CompleteHit
15125,Q#2822 - >seq6145,specific,197310,9,227,1.8775999999999998e-30,120.149,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15126,Q#2822 - >seq6145,superfamily,351117,9,227,1.8775999999999998e-30,120.149,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15127,Q#2822 - >seq6145,non-specific,197306,9,227,2.32719e-15,76.366,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15128,Q#2822 - >seq6145,non-specific,197307,9,227,3.3326e-09,58.4533,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15129,Q#2822 - >seq6145,non-specific,197320,111,202,2.00187e-07,53.2878,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
15130,Q#2822 - >seq6145,specific,335306,10,220,8.04862e-06,48.0102,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15131,Q#2822 - >seq6145,non-specific,197321,7,227,3.8914899999999996e-05,46.006,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15132,Q#2822 - >seq6145,non-specific,223780,90,201,0.000265842,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
15133,Q#2822 - >seq6145,non-specific,272954,9,201,0.0022482,40.8293,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs5_gmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs5_gmonkey,marg,CompleteHit
15134,Q#2825 - >seq6148,non-specific,340205,134,193,5.36712e-08,47.716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame2,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15135,Q#2825 - >seq6148,superfamily,340205,134,193,5.36712e-08,47.716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame2,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15136,Q#2827 - >seq6150,non-specific,197310,132,196,1.15967e-11,65.0653,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs2_gorilla.pars.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15137,Q#2827 - >seq6150,superfamily,351117,132,196,1.15967e-11,65.0653,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs2_gorilla.pars.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15138,Q#2827 - >seq6150,non-specific,223780,104,190,0.000554449,42.2003,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs2_gorilla.pars.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15139,Q#2827 - >seq6150,non-specific,197320,101,190,0.00100336,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.pars.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15140,Q#2827 - >seq6150,non-specific,197307,134,190,0.00310415,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.pars.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15141,Q#2829 - >seq6152,non-specific,197310,28,132,1.98313e-11,64.2949,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs2_gorilla.pars.frame3,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs2_gorilla,pars,C-TerminusTruncated
15142,Q#2829 - >seq6152,superfamily,351117,28,132,1.98313e-11,64.2949,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs2_gorilla.pars.frame3,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,C-TerminusTruncated
15143,Q#2829 - >seq6152,non-specific,197306,40,125,0.000121581,44.0093,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs2_gorilla.pars.frame3,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,BothTerminiTruncated
15144,Q#2829 - >seq6152,specific,335306,35,161,0.00389626,39.5358,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs2_gorilla.pars.frame3,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15145,Q#2830 - >seq6153,specific,197310,45,220,1.1751899999999999e-27,112.06,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15146,Q#2830 - >seq6153,superfamily,351117,45,220,1.1751899999999999e-27,112.06,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15147,Q#2830 - >seq6153,non-specific,197306,53,220,1.81251e-13,70.9733,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15148,Q#2830 - >seq6153,non-specific,223780,45,213,1.92397e-09,59.1491,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15149,Q#2830 - >seq6153,non-specific,197320,46,213,8.93106e-09,57.1398,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15150,Q#2830 - >seq6153,specific,335306,48,213,1.39731e-07,53.0178,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15151,Q#2830 - >seq6153,non-specific,197307,45,220,4.73559e-07,51.9049,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15152,Q#2830 - >seq6153,non-specific,197322,94,213,7.54826e-06,48.4674,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15153,Q#2830 - >seq6153,non-specific,197319,90,220,4.5013500000000005e-05,45.7305,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15154,Q#2830 - >seq6153,non-specific,197321,48,220,0.000449326,42.5392,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15155,Q#2830 - >seq6153,non-specific,272954,56,191,0.00305733,40.0589,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs2_gorilla.marg.frame1,1909130927_L1MEc.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15156,Q#2839 - >seq6162,specific,197310,30,215,2.75728e-34,130.934,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,CompleteHit
15157,Q#2839 - >seq6162,superfamily,351117,30,215,2.75728e-34,130.934,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,pars,CompleteHit
15158,Q#2839 - >seq6162,non-specific,197306,33,215,4.9691e-16,78.292,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,pars,CompleteHit
15159,Q#2839 - >seq6162,non-specific,223780,54,208,2.70131e-09,58.7639,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15160,Q#2839 - >seq6162,non-specific,197320,54,208,4.5975699999999995e-09,57.9102,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15161,Q#2839 - >seq6162,specific,335306,43,208,1.4942e-07,53.0178,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15162,Q#2839 - >seq6162,non-specific,197322,88,215,1.22496e-06,51.1638,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15163,Q#2839 - >seq6162,non-specific,197307,72,215,2.0778599999999998e-06,49.5937,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15164,Q#2839 - >seq6162,non-specific,273186,87,216,4.77608e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15165,Q#2839 - >seq6162,non-specific,197319,87,215,1.0659e-05,47.6565,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15166,Q#2839 - >seq6162,non-specific,339261,89,211,3.44394e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MEc,ORF2,hs3_orang,pars,CompleteHit
15167,Q#2839 - >seq6162,non-specific,272954,72,186,0.000649446,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15168,Q#2839 - >seq6162,non-specific,238827,549,707,0.00191662,40.3522,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs3_orang,pars,BothTerminiTruncated
15169,Q#2839 - >seq6162,superfamily,295487,549,707,0.00191662,40.3522,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs3_orang,pars,BothTerminiTruncated
15170,Q#2839 - >seq6162,non-specific,197321,87,215,0.00238408,40.228,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.pars.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,pars,N-TerminusTruncated
15171,Q#2842 - >seq6165,specific,197310,30,217,1.14831e-34,132.475,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,marg,CompleteHit
15172,Q#2842 - >seq6165,superfamily,351117,30,217,1.14831e-34,132.475,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,marg,CompleteHit
15173,Q#2842 - >seq6165,non-specific,197306,33,217,4.32412e-16,78.6772,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,marg,CompleteHit
15174,Q#2842 - >seq6165,non-specific,223780,54,210,1.79587e-09,59.5343,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15175,Q#2842 - >seq6165,non-specific,197320,54,210,1.88763e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15176,Q#2842 - >seq6165,specific,335306,43,210,3.07978e-07,52.2474,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15177,Q#2842 - >seq6165,non-specific,197307,72,217,8.68861e-07,51.1345,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15178,Q#2842 - >seq6165,non-specific,197322,88,217,1.00884e-06,51.549,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15179,Q#2842 - >seq6165,non-specific,273186,87,218,3.89163e-06,49.1996,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15180,Q#2842 - >seq6165,non-specific,339261,89,213,7.77997e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MEc,ORF2,hs3_orang,marg,CompleteHit
15181,Q#2842 - >seq6165,non-specific,197319,87,217,1.16101e-05,47.6565,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15182,Q#2842 - >seq6165,non-specific,238827,575,721,0.000167408,43.818999999999996,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEc,ORF2,hs3_orang,marg,BothTerminiTruncated
15183,Q#2842 - >seq6165,superfamily,295487,575,721,0.000167408,43.818999999999996,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEc,ORF2,hs3_orang,marg,BothTerminiTruncated
15184,Q#2842 - >seq6165,non-specific,272954,72,188,0.000329272,43.1405,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs3_orang.marg.frame1,1909130927_L1MEc.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs3_orang,marg,N-TerminusTruncated
15185,Q#2844 - >seq6167,non-specific,340205,112,167,1.5973399999999998e-09,51.1828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,pars,CompleteHit
15186,Q#2844 - >seq6167,superfamily,340205,112,167,1.5973399999999998e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,pars,CompleteHit
15187,Q#2844 - >seq6167,non-specific,335182,5,89,3.62719e-09,51.1495,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,pars,CompleteHit
15188,Q#2844 - >seq6167,superfamily,335182,5,89,3.62719e-09,51.1495,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs4_gibbon.pars.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,pars,CompleteHit
15189,Q#2846 - >seq6169,non-specific,335182,39,106,2.50781e-09,52.6903,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15190,Q#2846 - >seq6169,superfamily,335182,39,106,2.50781e-09,52.6903,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15191,Q#2846 - >seq6169,non-specific,340205,155,208,2.14468e-06,43.4788,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15192,Q#2846 - >seq6169,superfamily,340205,155,208,2.14468e-06,43.4788,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs4_gibbon.marg.frame1,1909130927_L1MEc.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs4_gibbon,marg,CompleteHit
15193,Q#2849 - >seq6172,non-specific,340205,161,208,9.10568e-10,53.1088,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs6_sqmonkey.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15194,Q#2849 - >seq6172,superfamily,340205,161,208,9.10568e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs6_sqmonkey.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15195,Q#2849 - >seq6172,non-specific,335182,85,159,6.2990100000000006e-09,51.9199,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs6_sqmonkey.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
15196,Q#2849 - >seq6172,superfamily,335182,85,159,6.2990100000000006e-09,51.9199,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs6_sqmonkey.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
15197,Q#2852 - >seq6175,non-specific,340205,160,224,5.830449999999999e-10,53.494,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,marg,CompleteHit
15198,Q#2852 - >seq6175,superfamily,340205,160,224,5.830449999999999e-10,53.494,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,marg,CompleteHit
15199,Q#2852 - >seq6175,non-specific,335182,64,157,1.36167e-07,48.0679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,marg,CompleteHit
15200,Q#2852 - >seq6175,superfamily,335182,64,157,1.36167e-07,48.0679,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,marg,CompleteHit
15201,Q#2854 - >seq6177,non-specific,333820,550,646,8.899440000000001e-05,43.435,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEc.ORF2.hs8_ctshrew.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
15202,Q#2854 - >seq6177,superfamily,333820,550,646,8.899440000000001e-05,43.435,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEc.ORF2.hs8_ctshrew.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
15203,Q#2854 - >seq6177,non-specific,238827,598,647,0.000150852,43.4338,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs8_ctshrew.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
15204,Q#2854 - >seq6177,superfamily,295487,598,647,0.000150852,43.4338,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs8_ctshrew.pars.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEc,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
15205,Q#2855 - >seq6178,specific,197310,5,233,6.07492e-51,177.158,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15206,Q#2855 - >seq6178,superfamily,351117,5,233,6.07492e-51,177.158,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15207,Q#2855 - >seq6178,non-specific,197306,5,233,1.9936800000000001e-25,105.256,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15208,Q#2855 - >seq6178,non-specific,223780,5,226,1.77729e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15209,Q#2855 - >seq6178,non-specific,197307,5,233,4.5093199999999994e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15210,Q#2855 - >seq6178,non-specific,197320,5,226,1.06225e-14,74.4737,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15211,Q#2855 - >seq6178,specific,335306,6,226,2.45317e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15212,Q#2855 - >seq6178,non-specific,273186,5,234,3.53237e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15213,Q#2855 - >seq6178,non-specific,197321,3,233,1.23411e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15214,Q#2855 - >seq6178,non-specific,272954,5,204,2.10511e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15215,Q#2855 - >seq6178,non-specific,197319,5,233,7.15166e-09,56.9013,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15216,Q#2855 - >seq6178,non-specific,197336,5,191,6.991710000000001e-08,54.1555,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15217,Q#2855 - >seq6178,non-specific,197322,4,233,8.580840000000001e-07,51.1638,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15218,Q#2855 - >seq6178,non-specific,197311,34,233,6.248880000000001e-06,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15219,Q#2855 - >seq6178,non-specific,339261,105,229,7.8081e-05,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs8_ctshrew,pars,CompleteHit
15220,Q#2858 - >seq6181,specific,197310,5,233,7.0988e-51,177.929,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15221,Q#2858 - >seq6181,superfamily,351117,5,233,7.0988e-51,177.929,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15222,Q#2858 - >seq6181,non-specific,197306,5,233,1.4266199999999997e-25,106.02600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15223,Q#2858 - >seq6181,non-specific,223780,5,226,1.7128099999999997e-17,83.0315,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15224,Q#2858 - >seq6181,non-specific,197307,5,233,4.99361e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15225,Q#2858 - >seq6181,non-specific,197320,5,226,8.311299999999999e-15,74.8589,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15226,Q#2858 - >seq6181,specific,335306,6,226,2.85516e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15227,Q#2858 - >seq6181,non-specific,273186,5,234,3.39791e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15228,Q#2858 - >seq6181,non-specific,197321,3,233,1.33949e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15229,Q#2858 - >seq6181,non-specific,272954,5,204,1.8803499999999996e-09,58.9337,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15230,Q#2858 - >seq6181,non-specific,197319,5,233,1.1100099999999999e-08,56.5161,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15231,Q#2858 - >seq6181,non-specific,197336,5,191,8.148530000000001e-08,54.1555,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15232,Q#2858 - >seq6181,non-specific,197322,4,233,1.0042200000000002e-06,51.1638,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15233,Q#2858 - >seq6181,non-specific,197311,34,233,3.06938e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15234,Q#2858 - >seq6181,non-specific,339261,105,229,3.70013e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs8_ctshrew.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs8_ctshrew,marg,CompleteHit
15235,Q#2859 - >seq6182,non-specific,340205,140,202,1.6116e-12,60.0424,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs9_pika.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs9_pika,pars,CompleteHit
15236,Q#2859 - >seq6182,superfamily,340205,140,202,1.6116e-12,60.0424,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs9_pika.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs9_pika,pars,CompleteHit
15237,Q#2859 - >seq6182,non-specific,335182,44,136,3.67453e-09,51.9199,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs9_pika.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs9_pika,pars,CompleteHit
15238,Q#2859 - >seq6182,superfamily,335182,44,136,3.67453e-09,51.9199,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs9_pika.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEc,ORF1,hs9_pika,pars,CompleteHit
15239,Q#2862 - >seq6185,non-specific,340205,154,216,2.33709e-13,62.3536,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs9_pika,marg,CompleteHit
15240,Q#2862 - >seq6185,superfamily,340205,154,216,2.33709e-13,62.3536,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs9_pika,marg,CompleteHit
15241,Q#2862 - >seq6185,non-specific,335182,59,147,2.5184099999999998e-08,49.9939,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs9_pika,marg,CompleteHit
15242,Q#2862 - >seq6185,superfamily,335182,59,147,2.5184099999999998e-08,49.9939,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs9_pika.marg.frame2,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEc,ORF1,hs9_pika,marg,CompleteHit
15243,Q#2866 - >seq6189,specific,197310,9,234,2.62718e-39,145.572,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15244,Q#2866 - >seq6189,superfamily,351117,9,234,2.62718e-39,145.572,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15245,Q#2866 - >seq6189,non-specific,197306,9,234,3.0519e-17,81.7588,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15246,Q#2866 - >seq6189,non-specific,197307,9,234,3.90727e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15247,Q#2866 - >seq6189,non-specific,223780,9,227,1.89973e-10,62.2307,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15248,Q#2866 - >seq6189,specific,335306,10,227,3.6642700000000002e-09,57.6402,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15249,Q#2866 - >seq6189,non-specific,273186,9,235,4.81504e-07,51.896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15250,Q#2866 - >seq6189,non-specific,197320,9,227,1.00215e-06,50.9766,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15251,Q#2866 - >seq6189,non-specific,197321,7,234,0.00013951,44.08,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15252,Q#2866 - >seq6189,non-specific,272954,9,205,0.000964232,41.5997,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15253,Q#2866 - >seq6189,non-specific,197322,90,227,0.0019182000000000001,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,N-TerminusTruncated
15254,Q#2866 - >seq6189,non-specific,197319,9,234,0.00863306,38.7969,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs9_pika.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs9_pika,pars,CompleteHit
15255,Q#2868 - >seq6191,non-specific,340205,103,150,4.104269999999999e-10,53.1088,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
15256,Q#2868 - >seq6191,superfamily,340205,103,150,4.104269999999999e-10,53.1088,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
15257,Q#2868 - >seq6191,non-specific,335182,29,87,4.5238699999999995e-10,53.8459,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
15258,Q#2868 - >seq6191,superfamily,335182,29,87,4.5238699999999995e-10,53.8459,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
15259,Q#2869 - >seq6192,non-specific,335182,62,156,6.291750000000001e-10,54.2311,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,pars,CompleteHit
15260,Q#2869 - >seq6192,superfamily,335182,62,156,6.291750000000001e-10,54.2311,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,pars,CompleteHit
15261,Q#2869 - >seq6192,non-specific,340205,159,224,3.36146e-08,48.8716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,pars,CompleteHit
15262,Q#2869 - >seq6192,superfamily,340205,159,224,3.36146e-08,48.8716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs8_ctshrew.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs8_ctshrew,pars,CompleteHit
15263,Q#2872 - >seq6195,non-specific,225087,471,794,0.00288629,41.1505,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1MEc.ORF2.hs7_bushaby.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MEc,ORF2,hs7_bushaby,marg,C-TerminusTruncated
15264,Q#2872 - >seq6195,superfamily,225087,471,794,0.00288629,41.1505,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1MEc.ORF2.hs7_bushaby.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MEc,ORF2,hs7_bushaby,marg,C-TerminusTruncated
15265,Q#2876 - >seq6199,non-specific,238827,587,671,1.3415600000000002e-06,50.3674,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs6_sqmonkey.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15266,Q#2876 - >seq6199,superfamily,295487,587,671,1.3415600000000002e-06,50.3674,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs6_sqmonkey.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15267,Q#2878 - >seq6201,specific,197310,19,235,5.79345e-38,142.105,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15268,Q#2878 - >seq6201,superfamily,351117,19,235,5.79345e-38,142.105,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15269,Q#2878 - >seq6201,non-specific,197306,20,235,1.95579e-15,77.1364,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15270,Q#2878 - >seq6201,non-specific,223780,61,220,1.48478e-09,59.9195,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15271,Q#2878 - >seq6201,non-specific,197320,61,220,2.51716e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15272,Q#2878 - >seq6201,specific,335306,16,228,1.90838e-07,53.0178,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15273,Q#2878 - >seq6201,non-specific,197307,23,235,2.16587e-07,53.0605,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15274,Q#2878 - >seq6201,non-specific,197322,105,235,4.8382e-06,49.623000000000005,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15275,Q#2878 - >seq6201,non-specific,273186,106,236,0.000123599,44.9624,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15276,Q#2878 - >seq6201,non-specific,197319,105,235,0.00016291,44.5749,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15277,Q#2878 - >seq6201,non-specific,339261,107,231,0.00323815,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs6_sqmonkey,pars,CompleteHit
15278,Q#2878 - >seq6201,non-specific,272954,61,206,0.0061005,39.6737,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs6_sqmonkey.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15279,Q#2880 - >seq6203,specific,197310,19,235,3.12959e-38,142.876,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15280,Q#2880 - >seq6203,superfamily,351117,19,235,3.12959e-38,142.876,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15281,Q#2880 - >seq6203,non-specific,197306,20,235,2.33992e-15,76.7512,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15282,Q#2880 - >seq6203,non-specific,223780,61,220,2.6274200000000004e-09,59.1491,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15283,Q#2880 - >seq6203,non-specific,197320,61,220,4.02948e-09,58.2954,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15284,Q#2880 - >seq6203,specific,335306,16,228,1.90838e-07,53.0178,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15285,Q#2880 - >seq6203,non-specific,197307,23,235,5.07263e-07,51.9049,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15286,Q#2880 - >seq6203,non-specific,197322,105,235,4.8382e-06,49.623000000000005,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15287,Q#2880 - >seq6203,non-specific,238827,642,723,5.648e-06,48.4414,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15288,Q#2880 - >seq6203,superfamily,295487,642,723,5.648e-06,48.4414,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15289,Q#2880 - >seq6203,non-specific,273186,106,236,0.000193891,44.192,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15290,Q#2880 - >seq6203,non-specific,197319,105,235,0.000311543,43.4193,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15291,Q#2880 - >seq6203,non-specific,339261,107,231,0.00256894,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEc,ORF2,hs6_sqmonkey,marg,CompleteHit
15292,Q#2880 - >seq6203,non-specific,272954,61,206,0.0099602,38.9033,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs6_sqmonkey.marg.frame3,1909130927_L1MEc.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEc,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15293,Q#2884 - >seq6207,non-specific,340205,155,218,1.45526e-21,83.9248,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs7_bushaby,marg,CompleteHit
15294,Q#2884 - >seq6207,superfamily,340205,155,218,1.45526e-21,83.9248,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs7_bushaby,marg,CompleteHit
15295,Q#2884 - >seq6207,non-specific,335182,61,152,0.000481892,38.0527,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs7_bushaby,marg,CompleteHit
15296,Q#2884 - >seq6207,superfamily,335182,61,152,0.000481892,38.0527,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEc,ORF1,hs7_bushaby,marg,CompleteHit
15297,Q#2887 - >seq6210,specific,197310,29,228,3.4653800000000003e-40,147.498,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15298,Q#2887 - >seq6210,superfamily,351117,29,228,3.4653800000000003e-40,147.498,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15299,Q#2887 - >seq6210,non-specific,197306,13,228,2.71608e-20,90.6184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15300,Q#2887 - >seq6210,non-specific,197307,14,228,6.60401e-10,59.9941,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15301,Q#2887 - >seq6210,specific,335306,17,221,7.165629999999999e-10,59.5662,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15302,Q#2887 - >seq6210,non-specific,223780,17,221,2.00267e-09,58.7639,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15303,Q#2887 - >seq6210,non-specific,197320,29,221,2.6598e-08,55.2138,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15304,Q#2887 - >seq6210,non-specific,273186,21,229,2.3313000000000002e-07,52.2812,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15305,Q#2887 - >seq6210,non-specific,197311,29,228,1.0033300000000001e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15306,Q#2887 - >seq6210,non-specific,272954,23,199,1.79396e-05,46.6073,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15307,Q#2887 - >seq6210,non-specific,197322,83,228,0.000110277,44.6154,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15308,Q#2887 - >seq6210,non-specific,197319,23,228,0.000119378,44.1897,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15309,Q#2887 - >seq6210,non-specific,339261,100,224,0.000682317,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs7_bushaby.pars.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MEc,ORF2,hs7_bushaby,pars,CompleteHit
15310,Q#2890 - >seq6213,non-specific,340205,146,209,7.64087e-21,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs7_bushaby.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs7_bushaby,pars,CompleteHit
15311,Q#2890 - >seq6213,superfamily,340205,146,209,7.64087e-21,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEc.ORF1.hs7_bushaby.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs7_bushaby,pars,CompleteHit
15312,Q#2890 - >seq6213,non-specific,335182,74,143,0.00823249,34.5859,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs7_bushaby.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs7_bushaby,pars,N-TerminusTruncated
15313,Q#2890 - >seq6213,superfamily,335182,74,143,0.00823249,34.5859,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEc.ORF1.hs7_bushaby.pars.frame3,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEc,ORF1,hs7_bushaby,pars,N-TerminusTruncated
15314,Q#2891 - >seq6214,specific,197310,22,228,9.1855e-39,144.031,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15315,Q#2891 - >seq6214,superfamily,351117,22,228,9.1855e-39,144.031,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15316,Q#2891 - >seq6214,non-specific,197306,22,228,6.0164099999999995e-21,92.5444,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15317,Q#2891 - >seq6214,specific,335306,23,221,9.13809e-10,59.5662,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15318,Q#2891 - >seq6214,non-specific,223780,23,221,2.00401e-09,59.1491,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15319,Q#2891 - >seq6214,non-specific,197320,23,221,1.2495e-08,56.3694,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15320,Q#2891 - >seq6214,non-specific,197307,14,228,1.31447e-08,56.5273,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15321,Q#2891 - >seq6214,non-specific,273186,23,229,1.4725999999999998e-07,53.4368,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15322,Q#2891 - >seq6214,non-specific,272954,23,199,1.08668e-05,47.7629,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15323,Q#2891 - >seq6214,non-specific,197311,30,228,1.1480899999999999e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15324,Q#2891 - >seq6214,non-specific,197319,23,228,2.6516999999999997e-05,46.5009,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15325,Q#2891 - >seq6214,non-specific,197322,83,228,0.00013333100000000001,44.6154,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEc,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15326,Q#2891 - >seq6214,non-specific,339261,100,224,0.00106704,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEc.ORF2.hs7_bushaby.marg.frame1,1909130927_L1MEc.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MEc,ORF2,hs7_bushaby,marg,CompleteHit
15327,Q#2893 - >seq6216,non-specific,340205,122,183,3.15535e-13,61.5832,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs5_gmonkey.marg.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs5_gmonkey,marg,CompleteHit
15328,Q#2893 - >seq6216,superfamily,340205,122,183,3.15535e-13,61.5832,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs5_gmonkey.marg.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs5_gmonkey,marg,CompleteHit
15329,Q#2894 - >seq6217,non-specific,197310,8,132,2.4893499999999997e-16,78.5473,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs4_gibbon.pars.frame3,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs4_gibbon,pars,C-TerminusTruncated
15330,Q#2894 - >seq6217,superfamily,351117,8,132,2.4893499999999997e-16,78.5473,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.pars.frame3,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,C-TerminusTruncated
15331,Q#2894 - >seq6217,non-specific,223780,8,108,0.000371391,42.5855,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs4_gibbon.pars.frame3,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,C-TerminusTruncated
15332,Q#2894 - >seq6217,non-specific,197306,8,109,0.000458403,42.0833,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.pars.frame3,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,C-TerminusTruncated
15333,Q#2896 - >seq6219,specific,197310,50,230,5.7506e-31,120.919,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MEf,ORF2,hs4_gibbon,marg,CompleteHit
15334,Q#2896 - >seq6219,superfamily,351117,50,230,5.7506e-31,120.919,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,marg,CompleteHit
15335,Q#2896 - >seq6219,non-specific,197306,69,230,1.2643500000000001e-10,62.1137,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,marg,N-TerminusTruncated
15336,Q#2896 - >seq6219,non-specific,197320,57,223,1.4171200000000002e-07,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEf,ORF2,hs4_gibbon,marg,N-TerminusTruncated
15337,Q#2896 - >seq6219,non-specific,223780,63,223,6.56738e-05,44.8967,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEf,ORF2,hs4_gibbon,marg,CompleteHit
15338,Q#2896 - >seq6219,non-specific,197311,73,145,0.000163161,43.0493,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MEf,ORF2,hs4_gibbon,marg,BothTerminiTruncated
15339,Q#2896 - >seq6219,non-specific,197307,107,230,0.0031812,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs4_gibbon.marg.frame2,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MEf,ORF2,hs4_gibbon,marg,N-TerminusTruncated
15340,Q#2899 - >seq6222,non-specific,340205,102,160,2.08664e-15,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs5_gmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs5_gmonkey,pars,CompleteHit
15341,Q#2899 - >seq6222,superfamily,340205,102,160,2.08664e-15,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs5_gmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs5_gmonkey,pars,CompleteHit
15342,Q#2904 - >seq6227,non-specific,197310,115,209,2.05377e-12,66.9913,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs4_gibbon,pars,N-TerminusTruncated
15343,Q#2904 - >seq6227,superfamily,351117,115,209,2.05377e-12,66.9913,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,N-TerminusTruncated
15344,Q#2904 - >seq6227,non-specific,197320,117,202,0.00311963,39.8058,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,N-TerminusTruncated
15345,Q#2904 - >seq6227,non-specific,197306,115,209,0.00613397,38.6165,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs4_gibbon,pars,N-TerminusTruncated
15346,Q#2905 - >seq6228,specific,197310,34,220,3.8281599999999995e-28,113.215,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,pars,CompleteHit
15347,Q#2905 - >seq6228,superfamily,351117,34,220,3.8281599999999995e-28,113.215,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,pars,CompleteHit
15348,Q#2905 - >seq6228,non-specific,197306,53,220,5.49871e-10,60.1877,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15349,Q#2905 - >seq6228,non-specific,197320,41,192,8.03164e-08,54.0582,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15350,Q#2905 - >seq6228,non-specific,223780,47,191,1.26891e-07,53.3711,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,pars,CompleteHit
15351,Q#2905 - >seq6228,specific,335306,47,213,5.36381e-07,51.0918,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15352,Q#2905 - >seq6228,non-specific,339261,94,216,8.96593e-05,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MEf,ORF2,hs3_orang,pars,CompleteHit
15353,Q#2905 - >seq6228,non-specific,273186,93,221,0.000142473,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15354,Q#2905 - >seq6228,non-specific,197311,57,220,0.000158886,43.4345,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15355,Q#2905 - >seq6228,non-specific,197322,89,198,0.0006084430000000001,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15356,Q#2905 - >seq6228,non-specific,197307,94,220,0.00604173,38.8081,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.pars.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,pars,N-TerminusTruncated
15357,Q#2907 - >seq6230,non-specific,340205,143,204,1.60328e-11,57.346000000000004,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs4_gibbon.marg.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs4_gibbon,marg,CompleteHit
15358,Q#2907 - >seq6230,superfamily,340205,143,204,1.60328e-11,57.346000000000004,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs4_gibbon.marg.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs4_gibbon,marg,CompleteHit
15359,Q#2910 - >seq6233,non-specific,340205,135,196,1.13889e-11,57.7312,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs4_gibbon,pars,CompleteHit
15360,Q#2910 - >seq6233,superfamily,340205,135,196,1.13889e-11,57.7312,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs4_gibbon.pars.frame1,1909130928_L1MEf.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs4_gibbon,pars,CompleteHit
15361,Q#2911 - >seq6234,specific,197310,14,200,6.15652e-29,115.52600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,marg,CompleteHit
15362,Q#2911 - >seq6234,superfamily,351117,14,200,6.15652e-29,115.52600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,marg,CompleteHit
15363,Q#2911 - >seq6234,non-specific,197306,33,200,1.58225e-10,61.7285,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15364,Q#2911 - >seq6234,non-specific,223780,27,171,2.40271e-08,55.6823,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,marg,CompleteHit
15365,Q#2911 - >seq6234,non-specific,197320,21,172,6.880389999999999e-08,54.0582,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15366,Q#2911 - >seq6234,specific,335306,27,193,4.94883e-07,51.0918,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15367,Q#2911 - >seq6234,non-specific,339261,74,196,1.71218e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEf,ORF2,hs3_orang,marg,CompleteHit
15368,Q#2911 - >seq6234,non-specific,273186,73,201,4.33474e-05,45.3476,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15369,Q#2911 - >seq6234,non-specific,197311,37,200,5.02053e-05,44.5901,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15370,Q#2911 - >seq6234,non-specific,197322,69,178,0.000587626,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15371,Q#2911 - >seq6234,non-specific,197307,74,200,0.00245146,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs3_orang.marg.frame3,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs3_orang,marg,N-TerminusTruncated
15372,Q#2919 - >seq6242,non-specific,238827,421,456,0.00579103,38.041,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs5_gmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEf,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
15373,Q#2919 - >seq6242,superfamily,295487,421,456,0.00579103,38.041,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs5_gmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEf,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
15374,Q#2921 - >seq6244,specific,197310,26,215,8.78026e-32,123.23,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs5_gmonkey,marg,CompleteHit
15375,Q#2921 - >seq6244,superfamily,351117,26,215,8.78026e-32,123.23,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,CompleteHit
15376,Q#2921 - >seq6244,non-specific,197306,36,215,8.03718e-11,62.4989,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,CompleteHit
15377,Q#2921 - >seq6244,non-specific,223780,36,173,3.83035e-07,51.8303,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
15378,Q#2921 - >seq6244,non-specific,197320,40,173,1.03362e-06,50.2062,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
15379,Q#2921 - >seq6244,specific,335306,39,208,1.1924e-06,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
15380,Q#2921 - >seq6244,non-specific,197307,36,173,3.8332e-05,45.3565,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs5_gmonkey,marg,CompleteHit
15381,Q#2921 - >seq6244,non-specific,197321,35,173,5.20416e-05,45.2356,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs5_gmonkey,marg,CompleteHit
15382,Q#2921 - >seq6244,non-specific,197311,55,215,0.000205474,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
15383,Q#2921 - >seq6244,non-specific,273186,90,216,0.00383737,39.1844,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
15384,Q#2921 - >seq6244,non-specific,272954,38,173,0.00462772,38.9033,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
15385,Q#2921 - >seq6244,non-specific,238827,475,559,0.00674467,38.4262,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEf,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
15386,Q#2921 - >seq6244,superfamily,295487,475,559,0.00674467,38.4262,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs5_gmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEf,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
15387,Q#2925 - >seq6248,specific,197310,9,230,8.968999999999999e-36,134.786,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15388,Q#2925 - >seq6248,superfamily,351117,9,230,8.968999999999999e-36,134.786,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15389,Q#2925 - >seq6248,non-specific,197306,8,230,5.89934e-12,65.9657,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15390,Q#2925 - >seq6248,non-specific,197320,66,223,5.37908e-10,60.2214,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15391,Q#2925 - >seq6248,non-specific,223780,66,223,2.0767800000000003e-09,58.3787,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15392,Q#2925 - >seq6248,non-specific,197307,9,230,9.708839999999998e-08,53.4457,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15393,Q#2925 - >seq6248,specific,335306,34,223,1.43172e-07,52.6326,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15394,Q#2925 - >seq6248,non-specific,197322,85,230,3.20704e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15395,Q#2925 - >seq6248,non-specific,197319,9,230,3.46691e-07,51.8937,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15396,Q#2925 - >seq6248,non-specific,197321,23,230,4.1746400000000004e-07,51.3988,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15397,Q#2925 - >seq6248,non-specific,339261,102,226,0.000288632,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MEf,ORF2,hs7_bushaby,marg,CompleteHit
15398,Q#2925 - >seq6248,non-specific,272954,85,201,0.000397958,42.3701,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15399,Q#2926 - >seq6249,specific,197310,8,217,7.011539999999999e-31,120.53399999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,CompleteHit
15400,Q#2926 - >seq6249,superfamily,351117,8,217,7.011539999999999e-31,120.53399999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,pars,CompleteHit
15401,Q#2926 - >seq6249,non-specific,197320,65,197,6.84235e-09,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15402,Q#2926 - >seq6249,non-specific,197306,7,207,8.38792e-09,56.3357,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,pars,CompleteHit
15403,Q#2926 - >seq6249,non-specific,223780,65,196,1.8715e-08,55.6823,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15404,Q#2926 - >seq6249,non-specific,197322,72,207,2.57073e-05,46.1562,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15405,Q#2926 - >seq6249,non-specific,272954,82,196,0.000191363,43.1405,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15406,Q#2926 - >seq6249,specific,335306,33,199,0.000273875,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs7_bushaby,pars,CompleteHit
15407,Q#2926 - >seq6249,non-specific,273186,97,197,0.000430402,42.266000000000005,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15408,Q#2926 - >seq6249,non-specific,197319,8,183,0.000674415,41.4933,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,CompleteHit
15409,Q#2926 - >seq6249,non-specific,197311,65,175,0.00367192,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs7_bushaby,pars,BothTerminiTruncated
15410,Q#2930 - >seq6253,non-specific,335182,54,147,1.67377e-14,66.5575,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs7_bushaby,marg,CompleteHit
15411,Q#2930 - >seq6253,superfamily,335182,54,147,1.67377e-14,66.5575,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs7_bushaby.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs7_bushaby,marg,CompleteHit
15412,Q#2931 - >seq6254,non-specific,274328,14,74,0.00237723,35.0521,TIGR02865,spore_II_E,NC,cl37180,"stage II sporulation protein E; Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. [Cellular processes, Sporulation and germination]",L1MEf.ORF1.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MEf,ORF1,hs7_bushaby,pars,BothTerminiTruncated
15413,Q#2931 - >seq6254,superfamily,274328,14,74,0.00237723,35.0521,cl37180,spore_II_E superfamily,NC, - ,"stage II sporulation protein E; Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. [Cellular processes, Sporulation and germination]",L1MEf.ORF1.hs7_bushaby.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MEf,ORF1,hs7_bushaby,pars,BothTerminiTruncated
15414,Q#2933 - >seq6256,non-specific,335182,12,56,0.0010012999999999999,35.3563,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs7_bushaby.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs7_bushaby,pars,N-TerminusTruncated
15415,Q#2933 - >seq6256,superfamily,335182,12,56,0.0010012999999999999,35.3563,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs7_bushaby.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs7_bushaby,pars,N-TerminusTruncated
15416,Q#2936 - >seq6259,specific,197310,2,217,8.019839999999999e-28,110.51899999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,CompleteHit
15417,Q#2936 - >seq6259,superfamily,351117,2,217,8.019839999999999e-28,110.51899999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,CompleteHit
15418,Q#2936 - >seq6259,non-specific,197306,2,217,7.06914e-10,59.0321,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,CompleteHit
15419,Q#2936 - >seq6259,non-specific,197320,44,188,3.5128499999999996e-08,54.0582,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15420,Q#2936 - >seq6259,specific,335306,3,210,2.36993e-06,48.3954,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,CompleteHit
15421,Q#2936 - >seq6259,non-specific,223780,54,188,0.00023066900000000002,42.5855,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15422,Q#2936 - >seq6259,non-specific,197307,92,217,0.00171449,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15423,Q#2936 - >seq6259,non-specific,197322,92,188,0.00388779,38.8375,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
15424,Q#2938 - >seq6261,non-specific,197310,2,211,3.0107299999999997e-27,108.59299999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,CompleteHit
15425,Q#2938 - >seq6261,superfamily,351117,2,211,3.0107299999999997e-27,108.59299999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,CompleteHit
15426,Q#2938 - >seq6261,non-specific,197306,2,210,3.4310799999999997e-09,57.1061,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,CompleteHit
15427,Q#2938 - >seq6261,non-specific,197320,44,188,3.47795e-08,54.0582,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15428,Q#2938 - >seq6261,specific,335306,3,210,2.57574e-06,48.0102,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,CompleteHit
15429,Q#2938 - >seq6261,non-specific,223780,54,188,0.000365032,41.8151,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15430,Q#2938 - >seq6261,non-specific,197322,92,188,0.00385201,38.8375,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15431,Q#2938 - >seq6261,non-specific,197307,92,210,0.00469367,38.4229,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs6_sqmonkey.pars.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
15432,Q#2941 - >seq6264,non-specific,340205,61,109,1.2037e-12,58.8868,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15433,Q#2941 - >seq6264,superfamily,340205,61,109,1.2037e-12,58.8868,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs6_sqmonkey.marg.frame1,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
15434,Q#2943 - >seq6266,non-specific,340205,51,108,4.04692e-16,66.5908,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs6_sqmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs6_sqmonkey,pars,CompleteHit
15435,Q#2943 - >seq6266,superfamily,340205,51,108,4.04692e-16,66.5908,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs6_sqmonkey.pars.frame2,1909130928_L1MEf.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs6_sqmonkey,pars,CompleteHit
15436,Q#2947 - >seq6270,specific,197310,31,215,3.4589699999999997e-32,122.845,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs5_gmonkey,pars,CompleteHit
15437,Q#2947 - >seq6270,superfamily,351117,31,215,3.4589699999999997e-32,122.845,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,CompleteHit
15438,Q#2947 - >seq6270,non-specific,197306,36,215,5.0462e-11,62.4989,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,CompleteHit
15439,Q#2947 - >seq6270,non-specific,223780,36,173,2.37124e-07,51.8303,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
15440,Q#2947 - >seq6270,non-specific,197320,40,173,6.0347e-07,50.5914,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
15441,Q#2947 - >seq6270,specific,335306,39,208,9.165299999999999e-07,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
15442,Q#2947 - >seq6270,non-specific,197307,36,173,1.9755e-05,45.7417,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs5_gmonkey,pars,CompleteHit
15443,Q#2947 - >seq6270,non-specific,197311,55,215,2.08815e-05,45.3605,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
15444,Q#2947 - >seq6270,non-specific,197321,35,173,3.75306e-05,44.8504,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs5_gmonkey,pars,CompleteHit
15445,Q#2947 - >seq6270,non-specific,273186,90,216,0.00272837,39.1844,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
15446,Q#2947 - >seq6270,non-specific,272954,38,173,0.00326376,38.9033,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs5_gmonkey.pars.frame3,1909130928_L1MEf.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
15447,Q#2948 - >seq6271,non-specific,340205,231,283,2.3418599999999996e-10,55.42,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs3_orang.marg.frame1,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs3_orang,marg,CompleteHit
15448,Q#2948 - >seq6271,superfamily,340205,231,283,2.3418599999999996e-10,55.42,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs3_orang.marg.frame1,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs3_orang,marg,CompleteHit
15449,Q#2954 - >seq6277,non-specific,236326,233,370,0.00558191,39.2002,PRK08655,PRK08655,N,cl35733,prephenate dehydrogenase; Provisional,L1MEd.ORF2.hs10_snmole.marg.frame1,1909130928_L1MEd.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MEd,ORF2,hs10_snmole,marg,N-TerminusTruncated
15450,Q#2954 - >seq6277,superfamily,236326,233,370,0.00558191,39.2002,cl35733,PRK08655 superfamily,N, - ,prephenate dehydrogenase; Provisional,L1MEd.ORF2.hs10_snmole.marg.frame1,1909130928_L1MEd.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MEd,ORF2,hs10_snmole,marg,N-TerminusTruncated
15451,Q#2981 - >seq6304,non-specific,340205,105,157,7.52292e-11,54.6496,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs3_orang.pars.frame1,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs3_orang,pars,CompleteHit
15452,Q#2981 - >seq6304,superfamily,340205,105,157,7.52292e-11,54.6496,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs3_orang.pars.frame1,1909130928_L1MEf.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs3_orang,pars,CompleteHit
15453,Q#2982 - >seq6305,non-specific,197310,9,215,4.06277e-22,94.3405,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs2_gorilla,marg,CompleteHit
15454,Q#2982 - >seq6305,superfamily,351117,9,215,4.06277e-22,94.3405,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs2_gorilla,marg,CompleteHit
15455,Q#2982 - >seq6305,non-specific,197306,66,212,9.74902e-05,43.6241,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15456,Q#2982 - >seq6305,non-specific,197320,104,209,0.000306534,42.117,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15457,Q#2985 - >seq6308,non-specific,197310,36,208,1.71655e-20,89.7181,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEf,ORF2,hs2_gorilla,pars,CompleteHit
15458,Q#2985 - >seq6308,superfamily,351117,36,208,1.71655e-20,89.7181,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEf,ORF2,hs2_gorilla,pars,CompleteHit
15459,Q#2985 - >seq6308,non-specific,197306,59,205,0.00022489599999999998,42.4685,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEf,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15460,Q#2985 - >seq6308,non-specific,197320,97,202,0.0005760180000000001,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEf,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15461,Q#2987 - >seq6310,non-specific,340205,83,140,1.371e-10,53.494,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs2_gorilla,marg,CompleteHit
15462,Q#2987 - >seq6310,superfamily,340205,83,140,1.371e-10,53.494,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs2_gorilla.marg.frame3,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs2_gorilla,marg,CompleteHit
15463,Q#2991 - >seq6314,non-specific,340205,64,123,1.4677e-10,52.7236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs2_gorilla,pars,CompleteHit
15464,Q#2991 - >seq6314,superfamily,340205,64,123,1.4677e-10,52.7236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs2_gorilla.pars.frame2,1909130928_L1MEf.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEf,ORF1,hs2_gorilla,pars,CompleteHit
15465,Q#2995 - >seq6318,non-specific,197310,235,302,5.05325e-09,57.3613,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs1_chimp.marg.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs1_chimp,marg,N-TerminusTruncated
15466,Q#2995 - >seq6318,superfamily,351117,235,302,5.05325e-09,57.3613,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs1_chimp.marg.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs1_chimp,marg,N-TerminusTruncated
15467,Q#2995 - >seq6318,non-specific,197320,234,274,0.00788296,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs1_chimp.marg.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs1_chimp,marg,N-TerminusTruncated
15468,Q#2999 - >seq6322,non-specific,340205,66,128,8.08075e-09,48.8716,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs1_chimp.marg.frame2,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs1_chimp,marg,CompleteHit
15469,Q#2999 - >seq6322,superfamily,340205,66,128,8.08075e-09,48.8716,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs1_chimp.marg.frame2,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs1_chimp,marg,CompleteHit
15470,Q#3000 - >seq6323,non-specific,340205,97,159,3.2324999999999997e-09,50.4124,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs1_chimp.pars.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs1_chimp,pars,CompleteHit
15471,Q#3000 - >seq6323,superfamily,340205,97,159,3.2324999999999997e-09,50.4124,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs1_chimp.pars.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs1_chimp,pars,CompleteHit
15472,Q#3002 - >seq6325,non-specific,197310,171,238,5.029670000000001e-09,57.3613,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs1_chimp.pars.frame2,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEf,ORF2,hs1_chimp,pars,N-TerminusTruncated
15473,Q#3002 - >seq6325,superfamily,351117,171,238,5.029670000000001e-09,57.3613,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs1_chimp.pars.frame2,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEf,ORF2,hs1_chimp,pars,N-TerminusTruncated
15474,Q#3002 - >seq6325,non-specific,197320,170,210,0.00662328,38.6502,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs1_chimp.pars.frame2,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEf,ORF2,hs1_chimp,pars,N-TerminusTruncated
15475,Q#3003 - >seq6326,non-specific,197310,65,136,4.42173e-10,60.4429,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs1_chimp.pars.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs1_chimp,pars,C-TerminusTruncated
15476,Q#3003 - >seq6326,superfamily,351117,65,136,4.42173e-10,60.4429,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs1_chimp.pars.frame3,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs1_chimp,pars,C-TerminusTruncated
15477,Q#3004 - >seq6327,non-specific,197310,86,197,8.01566e-13,68.5321,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs1_chimp.marg.frame1,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEf,ORF2,hs1_chimp,marg,C-TerminusTruncated
15478,Q#3004 - >seq6327,superfamily,351117,86,197,8.01566e-13,68.5321,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs1_chimp.marg.frame1,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs1_chimp,marg,C-TerminusTruncated
15479,Q#3004 - >seq6327,non-specific,197306,86,196,0.00453019,39.3869,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs1_chimp.marg.frame1,1909130928_L1MEf.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs1_chimp,marg,C-TerminusTruncated
15480,Q#3009 - >seq6332,non-specific,340205,142,184,0.00525986,34.234,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs3_orang.marg.frame3,1909130929_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs3_orang,marg,CompleteHit
15481,Q#3009 - >seq6332,superfamily,340205,142,184,0.00525986,34.234,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs3_orang.marg.frame3,1909130929_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs3_orang,marg,CompleteHit
15482,Q#3013 - >seq6336,non-specific,335182,1,97,2.0941e-07,46.5271,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs4_gibbon.marg.frame1,1909130929_L1MEg.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEg,ORF1,hs4_gibbon,marg,CompleteHit
15483,Q#3013 - >seq6336,superfamily,335182,1,97,2.0941e-07,46.5271,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs4_gibbon.marg.frame1,1909130929_L1MEg.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEg,ORF1,hs4_gibbon,marg,CompleteHit
15484,Q#3018 - >seq6341,non-specific,335182,1,52,0.00152511,36.1267,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs3_orang.marg.frame1,1909130929_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEg,ORF1,hs3_orang,marg,C-TerminusTruncated
15485,Q#3018 - >seq6341,superfamily,335182,1,52,0.00152511,36.1267,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs3_orang.marg.frame1,1909130929_L1MEg.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEg,ORF1,hs3_orang,marg,C-TerminusTruncated
15486,Q#3023 - >seq6346,non-specific,238827,588,621,6.0918e-05,44.5894,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs0_human.marg.frame1,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEf,ORF2,hs0_human,marg,BothTerminiTruncated
15487,Q#3023 - >seq6346,superfamily,295487,588,621,6.0918e-05,44.5894,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs0_human.marg.frame1,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEf,ORF2,hs0_human,marg,BothTerminiTruncated
15488,Q#3027 - >seq6350,non-specific,340205,148,199,4.0618800000000006e-10,53.494,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs0_human.marg.frame3,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs0_human,marg,CompleteHit
15489,Q#3027 - >seq6350,superfamily,340205,148,199,4.0618800000000006e-10,53.494,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs0_human.marg.frame3,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs0_human,marg,CompleteHit
15490,Q#3060 - >seq6383,non-specific,197310,9,111,5.87231e-16,76.2361,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15491,Q#3060 - >seq6383,superfamily,351117,9,111,5.87231e-16,76.2361,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15492,Q#3060 - >seq6383,non-specific,197306,9,133,1.03567e-07,52.0985,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15493,Q#3060 - >seq6383,non-specific,223780,9,82,5.81586e-07,50.2895,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15494,Q#3060 - >seq6383,specific,335306,10,83,5.18021e-06,46.8546,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15495,Q#3060 - >seq6383,non-specific,197321,7,94,5.73386e-06,47.1616,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15496,Q#3060 - >seq6383,non-specific,273186,9,76,8.739389999999999e-06,46.5032,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15497,Q#3060 - >seq6383,non-specific,197307,9,43,3.34129e-05,44.5861,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15498,Q#3060 - >seq6383,non-specific,197336,9,43,3.62437e-05,44.5255,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15499,Q#3060 - >seq6383,non-specific,197320,9,76,0.000506964,40.9614,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15500,Q#3060 - >seq6383,non-specific,272954,9,76,0.0006928310000000001,40.8293,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15501,Q#3060 - >seq6383,non-specific,197319,9,43,0.00174132,39.5673,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,pars,C-TerminusTruncated
15502,Q#3062 - >seq6385,non-specific,197310,96,220,8.485889999999999e-21,90.4885,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15503,Q#3062 - >seq6385,superfamily,351117,96,220,8.485889999999999e-21,90.4885,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15504,Q#3062 - >seq6385,non-specific,197306,95,220,1.78204e-10,60.5729,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15505,Q#3062 - >seq6385,non-specific,223780,96,222,5.84542e-08,53.3711,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15506,Q#3062 - >seq6385,non-specific,197307,96,220,8.93717e-08,52.6753,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15507,Q#3062 - >seq6385,non-specific,197320,96,213,9.952919999999999e-08,52.5174,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15508,Q#3062 - >seq6385,non-specific,197322,96,220,1.17052e-06,49.623000000000005,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15509,Q#3062 - >seq6385,specific,335306,110,213,1.5836700000000002e-06,48.7806,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15510,Q#3062 - >seq6385,non-specific,273186,81,221,1.70095e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15511,Q#3062 - >seq6385,non-specific,339261,96,216,3.4556599999999995e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MEf,ORF2,hs9_pika,pars,CompleteHit
15512,Q#3062 - >seq6385,non-specific,197321,96,220,2.63751e-05,45.2356,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15513,Q#3062 - >seq6385,non-specific,197319,96,220,0.000492349,41.1081,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15514,Q#3062 - >seq6385,non-specific,197317,105,213,0.00793031,37.5816,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MEf.ORF2.hs9_pika.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,pars,N-TerminusTruncated
15515,Q#3063 - >seq6386,non-specific,340205,154,217,3.16322e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,marg,CompleteHit
15516,Q#3063 - >seq6386,superfamily,340205,154,217,3.16322e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,marg,CompleteHit
15517,Q#3063 - >seq6386,non-specific,335182,57,151,6.70951e-17,72.7207,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,marg,CompleteHit
15518,Q#3063 - >seq6386,superfamily,335182,57,151,6.70951e-17,72.7207,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,marg,CompleteHit
15519,Q#3066 - >seq6389,non-specific,340205,146,209,3.95283e-23,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,pars,CompleteHit
15520,Q#3066 - >seq6389,superfamily,340205,146,209,3.95283e-23,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,pars,CompleteHit
15521,Q#3066 - >seq6389,non-specific,335182,49,143,1.07257e-16,71.9503,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,pars,CompleteHit
15522,Q#3066 - >seq6389,superfamily,335182,49,143,1.07257e-16,71.9503,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs9_pika.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs9_pika,pars,CompleteHit
15523,Q#3070 - >seq6393,specific,197310,9,235,9.34159e-41,147.88299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15524,Q#3070 - >seq6393,superfamily,351117,9,235,9.34159e-41,147.88299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15525,Q#3070 - >seq6393,non-specific,197306,9,235,7.02747e-22,94.8556,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15526,Q#3070 - >seq6393,non-specific,197307,9,235,2.39717e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15527,Q#3070 - >seq6393,non-specific,223780,9,220,5.28937e-10,60.3047,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15528,Q#3070 - >seq6393,non-specific,197320,9,220,2.60865e-09,57.9102,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15529,Q#3070 - >seq6393,non-specific,197321,7,235,3.2892300000000004e-08,54.8656,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15530,Q#3070 - >seq6393,specific,335306,10,228,5.83325e-07,50.7066,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15531,Q#3070 - >seq6393,non-specific,272954,9,206,2.28868e-06,49.3037,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,marg,CompleteHit
15532,Q#3070 - >seq6393,non-specific,197311,74,203,0.000102723,43.4345,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
15533,Q#3070 - >seq6393,non-specific,197322,91,221,0.0006895260000000001,41.919,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
15534,Q#3072 - >seq6395,non-specific,238827,426,465,4.421040000000001e-06,47.67100000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs8_ctshrew.pars.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEf,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
15535,Q#3072 - >seq6395,superfamily,295487,426,465,4.421040000000001e-06,47.67100000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs8_ctshrew.pars.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MEf,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
15536,Q#3074 - >seq6397,non-specific,340205,155,218,9.8773e-19,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,marg,CompleteHit
15537,Q#3074 - >seq6397,superfamily,340205,155,218,9.8773e-19,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,marg,CompleteHit
15538,Q#3074 - >seq6397,non-specific,335182,76,152,3.37299e-16,71.1799,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
15539,Q#3074 - >seq6397,superfamily,335182,76,152,3.37299e-16,71.1799,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs8_ctshrew.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
15540,Q#3077 - >seq6400,non-specific,340205,67,130,1.59754e-19,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,pars,CompleteHit
15541,Q#3077 - >seq6400,superfamily,340205,67,130,1.59754e-19,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,pars,CompleteHit
15542,Q#3077 - >seq6400,non-specific,335182,1,64,8.36086e-11,55.0015,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
15543,Q#3077 - >seq6400,superfamily,335182,1,64,8.36086e-11,55.0015,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
15544,Q#3081 - >seq6404,non-specific,238827,458,553,5.975939999999999e-07,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs8_ctshrew.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
15545,Q#3081 - >seq6404,superfamily,295487,458,553,5.975939999999999e-07,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs8_ctshrew.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
15546,Q#3082 - >seq6405,specific,197310,9,234,3.9315300000000004e-46,159.82399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15547,Q#3082 - >seq6405,superfamily,351117,9,234,3.9315300000000004e-46,159.82399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15548,Q#3082 - >seq6405,non-specific,197306,9,234,8.789930000000001e-25,102.17399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15549,Q#3082 - >seq6405,non-specific,223780,9,227,4.2754000000000005e-22,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15550,Q#3082 - >seq6405,non-specific,197307,9,234,1.41429e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15551,Q#3082 - >seq6405,non-specific,197320,9,227,1.3920400000000001e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15552,Q#3082 - >seq6405,non-specific,273186,9,235,6.32457e-18,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15553,Q#3082 - >seq6405,specific,335306,10,227,7.87003e-18,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15554,Q#3082 - >seq6405,non-specific,197321,7,234,1.1580399999999999e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15555,Q#3082 - >seq6405,non-specific,197336,9,227,1.63192e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15556,Q#3082 - >seq6405,non-specific,197319,9,234,4.617279999999999e-13,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15557,Q#3082 - >seq6405,non-specific,272954,9,205,6.470960000000001e-13,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15558,Q#3082 - >seq6405,non-specific,197322,8,234,6.94573e-08,53.8602,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15559,Q#3082 - >seq6405,non-specific,339261,106,230,1.8466099999999997e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15560,Q#3082 - >seq6405,non-specific,197311,30,234,0.0006636680000000001,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs9_pika.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs9_pika,marg,CompleteHit
15561,Q#3083 - >seq6406,specific,197310,9,225,1.86592e-38,141.72,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15562,Q#3083 - >seq6406,superfamily,351117,9,225,1.86592e-38,141.72,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15563,Q#3083 - >seq6406,non-specific,197306,9,225,2.16029e-20,90.6184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15564,Q#3083 - >seq6406,non-specific,197307,9,225,1.73574e-11,64.6165,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15565,Q#3083 - >seq6406,non-specific,223780,9,210,1.87667e-11,64.5419,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15566,Q#3083 - >seq6406,non-specific,197320,9,210,5.3347e-10,60.2214,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15567,Q#3083 - >seq6406,non-specific,197321,7,225,5.4198800000000004e-08,54.0952,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15568,Q#3083 - >seq6406,specific,335306,10,218,9.65629e-07,49.9362,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15569,Q#3083 - >seq6406,non-specific,272954,9,196,2.1258899999999997e-05,46.2221,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,pars,CompleteHit
15570,Q#3083 - >seq6406,non-specific,197311,67,193,0.000318273,41.8937,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs8_ctshrew.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
15571,Q#3085 - >seq6408,non-specific,340205,94,145,1.78973e-09,50.7976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs0_human.pars.frame1,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs0_human,pars,CompleteHit
15572,Q#3085 - >seq6408,superfamily,340205,94,145,1.78973e-09,50.7976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs0_human.pars.frame1,1909130929_L1MEf.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs0_human,pars,CompleteHit
15573,Q#3087 - >seq6410,non-specific,197310,8,235,1.21103e-07,53.1241,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs11_armadillo.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs11_armadillo,marg,CompleteHit
15574,Q#3087 - >seq6410,superfamily,351117,8,235,1.21103e-07,53.1241,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs11_armadillo.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs11_armadillo,marg,CompleteHit
15575,Q#3088 - >seq6411,non-specific,238827,500,664,5.96832e-07,50.7526,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs11_armadillo.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15576,Q#3088 - >seq6411,superfamily,295487,500,664,5.96832e-07,50.7526,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs11_armadillo.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15577,Q#3088 - >seq6411,non-specific,333820,501,666,0.000209717,42.6646,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEf.ORF2.hs11_armadillo.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15578,Q#3088 - >seq6411,superfamily,333820,501,666,0.000209717,42.6646,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEf.ORF2.hs11_armadillo.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1MEf,ORF2,hs11_armadillo,marg,C-TerminusTruncated
15579,Q#3090 - >seq6413,non-specific,197310,5,204,1.1413799999999998e-08,55.4353,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs11_armadillo.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs11_armadillo,pars,CompleteHit
15580,Q#3090 - >seq6413,superfamily,351117,5,204,1.1413799999999998e-08,55.4353,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs11_armadillo.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs11_armadillo,pars,CompleteHit
15581,Q#3094 - >seq6417,non-specific,340205,147,199,3.59436e-14,64.6648,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs11_armadillo.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs11_armadillo,marg,CompleteHit
15582,Q#3094 - >seq6417,superfamily,340205,147,199,3.59436e-14,64.6648,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs11_armadillo.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs11_armadillo,marg,CompleteHit
15583,Q#3097 - >seq6420,non-specific,340205,71,123,8.52103e-15,63.8944,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs11_armadillo.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs11_armadillo,pars,CompleteHit
15584,Q#3097 - >seq6420,superfamily,340205,71,123,8.52103e-15,63.8944,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs11_armadillo.pars.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESCLETCEOD_1906201541.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEf,ORF1,hs11_armadillo,pars,CompleteHit
15585,Q#3098 - >seq6421,non-specific,335182,64,159,4.8977800000000005e-15,68.0983,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs10_snmole,marg,CompleteHit
15586,Q#3098 - >seq6421,superfamily,335182,64,159,4.8977800000000005e-15,68.0983,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs10_snmole,marg,CompleteHit
15587,Q#3098 - >seq6421,non-specific,340205,162,227,2.06927e-05,41.1676,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs10_snmole,marg,CompleteHit
15588,Q#3098 - >seq6421,superfamily,340205,162,227,2.06927e-05,41.1676,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame1,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1MEf,ORF1,hs10_snmole,marg,CompleteHit
15589,Q#3099 - >seq6422,non-specific,335182,63,143,7.51018e-13,61.9351,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs10_snmole,pars,CompleteHit
15590,Q#3099 - >seq6422,superfamily,335182,63,143,7.51018e-13,61.9351,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEf.ORF1.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs10_snmole,pars,CompleteHit
15591,Q#3099 - >seq6422,non-specific,340205,146,201,0.000568758,36.9304,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs10_snmole,pars,CompleteHit
15592,Q#3099 - >seq6422,superfamily,340205,146,201,0.000568758,36.9304,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEf,ORF1,hs10_snmole,pars,CompleteHit
15593,Q#3101 - >seq6424,non-specific,340205,165,214,0.00313603,35.0044,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs10_snmole,marg,N-TerminusTruncated
15594,Q#3101 - >seq6424,superfamily,340205,165,214,0.00313603,35.0044,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEf.ORF1.hs10_snmole.marg.frame2,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEf,ORF1,hs10_snmole,marg,N-TerminusTruncated
15595,Q#3105 - >seq6428,specific,197310,7,215,1.9382799999999998e-35,132.86,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15596,Q#3105 - >seq6428,superfamily,351117,7,215,1.9382799999999998e-35,132.86,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15597,Q#3105 - >seq6428,non-specific,197306,7,218,2.37683e-16,78.6772,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15598,Q#3105 - >seq6428,non-specific,197307,7,216,2.43961e-11,63.8461,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15599,Q#3105 - >seq6428,non-specific,197321,5,227,6.05627e-11,62.5696,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15600,Q#3105 - >seq6428,non-specific,223780,7,205,2.49547e-10,61.0751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15601,Q#3105 - >seq6428,non-specific,197320,70,206,1.52521e-09,58.6806,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,pars,N-TerminusTruncated
15602,Q#3105 - >seq6428,specific,335306,8,210,3.5548599999999994e-08,54.1734,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15603,Q#3105 - >seq6428,non-specific,273186,7,232,3.96932e-07,51.1256,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15604,Q#3105 - >seq6428,non-specific,197322,89,216,8.08152e-05,44.6154,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,N-TerminusTruncated
15605,Q#3105 - >seq6428,non-specific,272954,7,205,0.000129676,43.5257,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15606,Q#3105 - >seq6428,non-specific,197319,7,192,0.0009490789999999999,41.1081,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,CompleteHit
15607,Q#3105 - >seq6428,non-specific,197311,70,202,0.00366423,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs10_snmole.pars.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,pars,N-TerminusTruncated
15608,Q#3108 - >seq6431,specific,197310,7,234,3.90463e-41,149.424,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15609,Q#3108 - >seq6431,superfamily,351117,7,234,3.90463e-41,149.424,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15610,Q#3108 - >seq6431,non-specific,197306,7,234,5.63867e-19,86.3812,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15611,Q#3108 - >seq6431,non-specific,197307,7,234,1.46289e-13,70.7797,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15612,Q#3108 - >seq6431,non-specific,197321,5,234,2.70843e-12,67.192,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15613,Q#3108 - >seq6431,non-specific,223780,7,227,2.38897e-11,64.5419,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15614,Q#3108 - >seq6431,specific,335306,8,227,9.88408e-11,61.8774,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15615,Q#3108 - >seq6431,non-specific,197320,70,227,2.4012799999999996e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEf,ORF2,hs10_snmole,marg,N-TerminusTruncated
15616,Q#3108 - >seq6431,non-specific,238827,525,661,4.0847499999999996e-09,56.9158,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEf,ORF2,hs10_snmole,marg,C-TerminusTruncated
15617,Q#3108 - >seq6431,superfamily,295487,525,661,4.0847499999999996e-09,56.9158,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEf,ORF2,hs10_snmole,marg,C-TerminusTruncated
15618,Q#3108 - >seq6431,non-specific,273186,7,235,1.06834e-08,56.1332,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15619,Q#3108 - >seq6431,non-specific,197322,89,234,3.50315e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,N-TerminusTruncated
15620,Q#3108 - >seq6431,non-specific,197319,7,234,1.17913e-06,49.9677,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15621,Q#3108 - >seq6431,non-specific,339261,106,230,0.000180018,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15622,Q#3108 - >seq6431,non-specific,272954,7,205,0.000198918,43.5257,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,CompleteHit
15623,Q#3108 - >seq6431,non-specific,197311,70,234,0.004084900000000001,38.8121,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEf,ORF2,hs10_snmole,marg,N-TerminusTruncated
15624,Q#3108 - >seq6431,non-specific,333820,525,659,0.00994342,37.657,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEf,ORF2,hs10_snmole,marg,C-TerminusTruncated
15625,Q#3108 - >seq6431,superfamily,333820,525,659,0.00994342,37.657,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEf.ORF2.hs10_snmole.marg.frame3,1909130929_L1MEf.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1MEf,ORF2,hs10_snmole,marg,C-TerminusTruncated
15626,Q#3143 - >seq6466,non-specific,238827,669,777,0.00583033,39.1966,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEh.ORF2.hs0_human.marg.frame1,1909130930_L1MEh.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEh,ORF2,hs0_human,marg,N-TerminusTruncated
15627,Q#3143 - >seq6466,superfamily,295487,669,777,0.00583033,39.1966,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEh.ORF2.hs0_human.marg.frame1,1909130930_L1MEh.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEh,ORF2,hs0_human,marg,N-TerminusTruncated
15628,Q#3148 - >seq6471,non-specific,130673,62,238,0.00485209,38.1088,TIGR01612,235kDa-fam,N,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1MEj.ORF2.hs7_bushaby.pars.frame3,1909130930_L1MEj.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MEj,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15629,Q#3148 - >seq6471,superfamily,130673,62,238,0.00485209,38.1088,cl31124,235kDa-fam superfamily,N, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1MEj.ORF2.hs7_bushaby.pars.frame3,1909130930_L1MEj.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MEj,ORF2,hs7_bushaby,pars,N-TerminusTruncated
15630,Q#3163 - >seq6486,non-specific,240274,125,250,0.00609795,40.3585,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MEh.ORF2.hs0_human.marg.frame3,1909130930_L1MEh.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MEh,ORF2,hs0_human,marg,C-TerminusTruncated
15631,Q#3163 - >seq6486,superfamily,240274,125,250,0.00609795,40.3585,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MEh.ORF2.hs0_human.marg.frame3,1909130930_L1MEh.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MEh,ORF2,hs0_human,marg,C-TerminusTruncated
15632,Q#3180 - >seq6503,non-specific,238827,433,486,1.19147e-08,55.7602,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEg.ORF2.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEg,ORF2,hs9_pika,pars,C-TerminusTruncated
15633,Q#3180 - >seq6503,superfamily,295487,433,486,1.19147e-08,55.7602,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEg.ORF2.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MEg,ORF2,hs9_pika,pars,C-TerminusTruncated
15634,Q#3180 - >seq6503,non-specific,214368,376,639,0.0059011,39.9223,CHL00117,rpoC2,NC,cl33332,RNA polymerase beta'' subunit; Reviewed,L1MEg.ORF2.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MEg,ORF2,hs9_pika,pars,BothTerminiTruncated
15635,Q#3180 - >seq6503,superfamily,214368,376,639,0.0059011,39.9223,cl33332,rpoC2 superfamily,NC, - ,RNA polymerase beta'' subunit; Reviewed,L1MEg.ORF2.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MEg,ORF2,hs9_pika,pars,BothTerminiTruncated
15636,Q#3182 - >seq6505,non-specific,335182,77,153,1.8562200000000002e-07,47.6827,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs9_pika.marg.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEg,ORF1,hs9_pika,marg,N-TerminusTruncated
15637,Q#3182 - >seq6505,superfamily,335182,77,153,1.8562200000000002e-07,47.6827,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs9_pika.marg.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEg,ORF1,hs9_pika,marg,N-TerminusTruncated
15638,Q#3186 - >seq6509,non-specific,335182,21,98,1.18521e-05,41.5195,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEg,ORF1,hs9_pika,pars,N-TerminusTruncated
15639,Q#3186 - >seq6509,superfamily,335182,21,98,1.18521e-05,41.5195,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs9_pika.pars.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MEg,ORF1,hs9_pika,pars,N-TerminusTruncated
15640,Q#3187 - >seq6510,non-specific,197310,58,208,6.70821e-16,77.7769,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEg,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
15641,Q#3187 - >seq6510,superfamily,351117,58,208,6.70821e-16,77.7769,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
15642,Q#3187 - >seq6510,non-specific,197320,108,192,1.6458e-05,47.1246,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEg,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
15643,Q#3187 - >seq6510,non-specific,197306,93,209,1.79831e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
15644,Q#3187 - >seq6510,non-specific,339261,110,205,0.00037243800000000006,40.7835,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MEg,ORF2,hs8_ctshrew,marg,C-TerminusTruncated
15645,Q#3187 - >seq6510,non-specific,197307,93,190,0.00800647,38.8081,cd09073,ExoIII_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEg.ORF2.hs8_ctshrew.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MEg,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
15646,Q#3191 - >seq6514,non-specific,197310,6,111,1.0042899999999999e-08,55.8205,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEg,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
15647,Q#3191 - >seq6514,superfamily,351117,6,111,1.0042899999999999e-08,55.8205,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEg,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
15648,Q#3191 - >seq6514,non-specific,223780,51,107,0.00312363,39.5039,COG0708,XthA,NC,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEg.ORF2.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MEg,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
15649,Q#3191 - >seq6514,non-specific,197311,3,105,0.00458703,38.4269,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEg,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
15650,Q#3194 - >seq6517,non-specific,335182,96,168,5.936600000000002e-11,57.3127,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs8_ctshrew.marg.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEg,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
15651,Q#3194 - >seq6517,superfamily,335182,96,168,5.936600000000002e-11,57.3127,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs8_ctshrew.marg.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1MEg,ORF1,hs8_ctshrew,marg,N-TerminusTruncated
15652,Q#3196 - >seq6519,non-specific,335182,1,64,7.929979999999999e-09,48.8383,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs8_ctshrew.pars.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEg,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
15653,Q#3196 - >seq6519,superfamily,335182,1,64,7.929979999999999e-09,48.8383,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs8_ctshrew.pars.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MEg,ORF1,hs8_ctshrew,pars,N-TerminusTruncated
15654,Q#3203 - >seq6526,non-specific,197310,87,196,2.59913e-07,51.9685,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs9_pika.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MEg,ORF2,hs9_pika,pars,N-TerminusTruncated
15655,Q#3203 - >seq6526,superfamily,351117,87,196,2.59913e-07,51.9685,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs9_pika.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MEg,ORF2,hs9_pika,pars,N-TerminusTruncated
15656,Q#3206 - >seq6529,non-specific,197310,41,118,0.000737111,40.4125,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs7_bushaby.pars.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MEg,ORF2,hs7_bushaby,pars,BothTerminiTruncated
15657,Q#3206 - >seq6529,superfamily,351117,41,118,0.000737111,40.4125,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs7_bushaby.pars.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs7_bushaby,pars,BothTerminiTruncated
15658,Q#3207 - >seq6530,non-specific,197310,68,242,3.1853899999999996e-08,54.2797,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs7_bushaby.marg.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEg,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15659,Q#3207 - >seq6530,superfamily,351117,68,242,3.1853899999999996e-08,54.2797,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs7_bushaby.marg.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEg,ORF2,hs7_bushaby,marg,N-TerminusTruncated
15660,Q#3212 - >seq6535,non-specific,238827,488,535,1.7405e-08,55.7602,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEg.ORF2.hs9_pika.marg.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs9_pika,marg,C-TerminusTruncated
15661,Q#3212 - >seq6535,superfamily,295487,488,535,1.7405e-08,55.7602,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEg.ORF2.hs9_pika.marg.frame1,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs9_pika,marg,C-TerminusTruncated
15662,Q#3213 - >seq6536,non-specific,340205,66,114,8.37288e-09,48.1012,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEg,ORF1,hs8_ctshrew,pars,CompleteHit
15663,Q#3213 - >seq6536,superfamily,340205,66,114,8.37288e-09,48.1012,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs8_ctshrew.pars.frame2,1909130930_L1MEg.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MEg,ORF1,hs8_ctshrew,pars,CompleteHit
15664,Q#3214 - >seq6537,non-specific,197310,961,1184,1.46309e-13,71.6137,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs0_human.marg.frame3,1909130930_L1MEg.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEg,ORF2,hs0_human,marg,CompleteHit
15665,Q#3214 - >seq6537,superfamily,351117,961,1184,1.46309e-13,71.6137,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs0_human.marg.frame3,1909130930_L1MEg.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs0_human,marg,CompleteHit
15666,Q#3214 - >seq6537,non-specific,197306,961,1184,0.00227935,40.9277,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs0_human.marg.frame3,1909130930_L1MEg.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs0_human,marg,CompleteHit
15667,Q#3218 - >seq6541,specific,197310,2,179,3.7924399999999997e-31,122.075,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15668,Q#3218 - >seq6541,superfamily,351117,2,179,3.7924399999999997e-31,122.075,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15669,Q#3218 - >seq6541,non-specific,197306,8,180,1.6084300000000003e-25,106.02600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15670,Q#3218 - >seq6541,non-specific,197320,24,178,3.56456e-11,64.4586,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15671,Q#3218 - >seq6541,non-specific,197307,13,180,3.76168e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15672,Q#3218 - >seq6541,non-specific,223780,28,178,1.7241400000000002e-09,59.5343,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15673,Q#3218 - >seq6541,non-specific,197322,47,179,3.54232e-05,46.5414,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15674,Q#3218 - >seq6541,non-specific,273186,63,178,5.60972e-05,45.7328,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15675,Q#3218 - >seq6541,non-specific,197321,23,180,6.019399999999999e-05,45.6208,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15676,Q#3218 - >seq6541,non-specific,272954,47,178,7.22325e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15677,Q#3218 - >seq6541,non-specific,197319,28,180,0.00267184,40.3377,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,N-TerminusTruncated
15678,Q#3218 - >seq6541,non-specific,339261,65,174,0.00327262,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15679,Q#3218 - >seq6541,non-specific,238827,501,758,0.00649299,38.8114,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15680,Q#3218 - >seq6541,superfamily,295487,501,758,0.00649299,38.8114,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1MEh,ORF2,hs3_orang,marg,CompleteHit
15681,Q#3218 - >seq6541,non-specific,197311,28,103,0.00693036,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEh.ORF2.hs3_orang.marg.frame1,1909130930_L1MEh.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEh,ORF2,hs3_orang,marg,BothTerminiTruncated
15682,Q#3223 - >seq6546,non-specific,197310,30,203,1.63335e-07,53.5093,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs0_human.marg.frame1,1909130930_L1MEg.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MEg,ORF2,hs0_human,marg,CompleteHit
15683,Q#3223 - >seq6546,superfamily,351117,30,203,1.63335e-07,53.5093,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs0_human.marg.frame1,1909130930_L1MEg.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MEg,ORF2,hs0_human,marg,CompleteHit
15684,Q#3232 - >seq6555,non-specific,197310,87,205,8.45975e-12,65.8357,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MEg.ORF2.hs9_pika.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MEg,ORF2,hs9_pika,marg,N-TerminusTruncated
15685,Q#3232 - >seq6555,superfamily,351117,87,205,8.45975e-12,65.8357,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MEg.ORF2.hs9_pika.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MEg,ORF2,hs9_pika,marg,N-TerminusTruncated
15686,Q#3238 - >seq6561,non-specific,335182,73,164,3.5119100000000004e-07,46.9123,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs10_snmole.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs10_snmole,marg,CompleteHit
15687,Q#3238 - >seq6561,superfamily,335182,73,164,3.5119100000000004e-07,46.9123,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MEg.ORF1.hs10_snmole.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs10_snmole,marg,CompleteHit
15688,Q#3238 - >seq6561,non-specific,340205,169,211,0.00420817,34.6192,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs10_snmole.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs10_snmole,marg,C-TerminusTruncated
15689,Q#3238 - >seq6561,superfamily,340205,169,211,0.00420817,34.6192,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MEg.ORF1.hs10_snmole.marg.frame3,1909130930_L1MEg.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MEg,ORF1,hs10_snmole,marg,C-TerminusTruncated
15690,Q#3247 - >seq6570,non-specific,335182,143,240,9.73822e-49,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15691,Q#3247 - >seq6570,superfamily,335182,143,240,9.73822e-49,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15692,Q#3247 - >seq6570,non-specific,340205,243,307,6.1338199999999994e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15693,Q#3247 - >seq6570,superfamily,340205,243,307,6.1338199999999994e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15694,Q#3247 - >seq6570,non-specific,340204,98,140,1.7282299999999998e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15695,Q#3247 - >seq6570,superfamily,340204,98,140,1.7282299999999998e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1P3,ORF1,hs2_gorilla,pars,CompleteHit
15696,Q#3247 - >seq6570,non-specific,274009,82,191,0.00735215,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
15697,Q#3247 - >seq6570,superfamily,274009,82,191,0.00735215,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.pars.frame1,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
15698,Q#3248 - >seq6571,non-specific,335182,157,254,2.2593200000000002e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15699,Q#3248 - >seq6571,superfamily,335182,157,254,2.2593200000000002e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15700,Q#3248 - >seq6571,non-specific,340205,257,321,3.744639999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15701,Q#3248 - >seq6571,superfamily,340205,257,321,3.744639999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15702,Q#3248 - >seq6571,non-specific,340204,112,154,8.90141e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15703,Q#3248 - >seq6571,superfamily,340204,112,154,8.90141e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs1_chimp,marg,CompleteHit
15704,Q#3248 - >seq6571,non-specific,222878,67,151,1.81195e-05,46.1609,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15705,Q#3248 - >seq6571,superfamily,222878,67,151,1.81195e-05,46.1609,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15706,Q#3248 - >seq6571,non-specific,313022,71,154,7.48914e-05,44.068999999999996,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15707,Q#3248 - >seq6571,superfamily,313022,71,154,7.48914e-05,44.068999999999996,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15708,Q#3248 - >seq6571,non-specific,235175,55,146,0.00010379,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15709,Q#3248 - >seq6571,superfamily,235175,55,146,0.00010379,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15710,Q#3248 - >seq6571,non-specific,224117,66,151,0.000305742,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15711,Q#3248 - >seq6571,superfamily,224117,66,151,0.000305742,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15712,Q#3248 - >seq6571,non-specific,235175,69,157,0.00035008,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15713,Q#3248 - >seq6571,non-specific,274008,47,244,0.00042083400000000003,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15714,Q#3248 - >seq6571,superfamily,274008,47,244,0.00042083400000000003,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15715,Q#3248 - >seq6571,non-specific,224117,71,241,0.000558065,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15716,Q#3248 - >seq6571,superfamily,224117,71,241,0.000558065,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15717,Q#3248 - >seq6571,non-specific,336322,36,153,0.000599226,41.3486,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15718,Q#3248 - >seq6571,superfamily,336322,36,153,0.000599226,41.3486,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15719,Q#3248 - >seq6571,non-specific,335556,66,153,0.000741071,39.8237,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15720,Q#3248 - >seq6571,superfamily,335556,66,153,0.000741071,39.8237,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15721,Q#3248 - >seq6571,non-specific,337766,52,133,0.0008331310000000001,40.6739,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15722,Q#3248 - >seq6571,superfamily,337766,52,133,0.0008331310000000001,40.6739,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15723,Q#3248 - >seq6571,non-specific,224117,50,151,0.000917089,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15724,Q#3248 - >seq6571,non-specific,335555,66,137,0.00108692,40.3216,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15725,Q#3248 - >seq6571,superfamily,354396,66,137,0.00108692,40.3216,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15726,Q#3248 - >seq6571,non-specific,179385,61,140,0.00140183,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15727,Q#3248 - >seq6571,superfamily,179385,61,140,0.00140183,40.4086,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15728,Q#3248 - >seq6571,non-specific,224117,66,157,0.0017019000000000001,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15729,Q#3248 - >seq6571,non-specific,222878,53,198,0.00173869,39.9977,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15730,Q#3248 - >seq6571,non-specific,224117,55,151,0.00204322,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15731,Q#3248 - >seq6571,non-specific,274765,48,128,0.00226265,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15732,Q#3248 - >seq6571,superfamily,274765,48,128,0.00226265,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15733,Q#3248 - >seq6571,non-specific,274008,56,212,0.00248775,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15734,Q#3248 - >seq6571,superfamily,274008,56,212,0.00248775,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15735,Q#3248 - >seq6571,non-specific,336322,66,168,0.00257141,39.4226,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15736,Q#3248 - >seq6571,non-specific,224117,55,151,0.00258436,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15737,Q#3248 - >seq6571,non-specific,179877,36,153,0.00322728,39.0486,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15738,Q#3248 - >seq6571,superfamily,179877,36,153,0.00322728,39.0486,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15739,Q#3248 - >seq6571,non-specific,235175,66,145,0.00420925,38.8916,PRK03918,PRK03918,N,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15740,Q#3248 - >seq6571,non-specific,235175,69,156,0.00432072,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15741,Q#3248 - >seq6571,non-specific,274009,55,150,0.00433769,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15742,Q#3248 - >seq6571,superfamily,274009,55,150,0.00433769,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15743,Q#3248 - >seq6571,non-specific,224117,55,151,0.00500514,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15744,Q#3248 - >seq6571,non-specific,274009,50,211,0.00525207,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15745,Q#3248 - >seq6571,non-specific,235175,56,162,0.00561118,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,marg,BothTerminiTruncated
15746,Q#3248 - >seq6571,non-specific,273690,75,197,0.00623851,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15747,Q#3248 - >seq6571,superfamily,355611,75,197,0.00623851,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15748,Q#3248 - >seq6571,non-specific,316375,56,151,0.0075336,36.8095,pfam13851,GAS,C,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15749,Q#3248 - >seq6571,superfamily,316375,56,151,0.0075336,36.8095,cl25894,GAS superfamily,C, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15750,Q#3248 - >seq6571,non-specific,197874,57,163,0.00920959,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15751,Q#3248 - >seq6571,superfamily,197874,57,163,0.00920959,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,marg,N-TerminusTruncated
15752,Q#3248 - >seq6571,non-specific,235461,59,130,0.0095175,37.355,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15753,Q#3248 - >seq6571,superfamily,235461,59,130,0.0095175,37.355,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs1_chimp.marg.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs1_chimp,marg,C-TerminusTruncated
15754,Q#3253 - >seq6576,non-specific,335182,156,253,1.5420499999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15755,Q#3253 - >seq6576,superfamily,335182,156,253,1.5420499999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15756,Q#3253 - >seq6576,non-specific,340205,256,320,3.40654e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15757,Q#3253 - >seq6576,superfamily,340205,256,320,3.40654e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15758,Q#3253 - >seq6576,non-specific,340204,111,153,4.77815e-09,51.2544,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15759,Q#3253 - >seq6576,superfamily,340204,111,153,4.77815e-09,51.2544,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs2_gorilla,marg,CompleteHit
15760,Q#3253 - >seq6576,non-specific,336322,34,167,0.00149835,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15761,Q#3253 - >seq6576,superfamily,336322,34,167,0.00149835,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15762,Q#3253 - >seq6576,non-specific,274009,55,204,0.00179213,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15763,Q#3253 - >seq6576,superfamily,274009,55,204,0.00179213,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15764,Q#3253 - >seq6576,non-specific,179877,42,167,0.00299369,39.0486,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15765,Q#3253 - >seq6576,superfamily,179877,42,167,0.00299369,39.0486,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15766,Q#3253 - >seq6576,non-specific,273690,75,196,0.00534339,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
15767,Q#3253 - >seq6576,superfamily,355611,75,196,0.00534339,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
15768,Q#3253 - >seq6576,non-specific,335555,66,132,0.00680726,38.0104,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
15769,Q#3253 - >seq6576,superfamily,354396,66,132,0.00680726,38.0104,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
15770,Q#3253 - >seq6576,non-specific,337766,52,132,0.00823112,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
15771,Q#3253 - >seq6576,superfamily,337766,52,132,0.00823112,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs2_gorilla,marg,N-TerminusTruncated
15772,Q#3253 - >seq6576,non-specific,274008,47,243,0.00888574,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15773,Q#3253 - >seq6576,superfamily,274008,47,243,0.00888574,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15774,Q#3253 - >seq6576,non-specific,222878,53,197,0.00930068,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15775,Q#3253 - >seq6576,superfamily,222878,53,197,0.00930068,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15776,Q#3253 - >seq6576,non-specific,224117,66,150,0.00947471,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15777,Q#3253 - >seq6576,superfamily,224117,66,150,0.00947471,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
15778,Q#3258 - >seq6581,specific,238827,496,758,1.0976599999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15779,Q#3258 - >seq6581,superfamily,295487,496,758,1.0976599999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15780,Q#3258 - >seq6581,specific,333820,502,758,1.94609e-36,135.88299999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15781,Q#3258 - >seq6581,superfamily,333820,502,758,1.94609e-36,135.88299999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15782,Q#3258 - >seq6581,non-specific,238828,568,723,3.81259e-12,66.8408,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15783,Q#3258 - >seq6581,non-specific,275209,573,786,2.68315e-10,63.2456,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15784,Q#3258 - >seq6581,superfamily,275209,573,786,2.68315e-10,63.2456,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15785,Q#3258 - >seq6581,non-specific,238185,642,758,9.62248e-06,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15786,Q#3258 - >seq6581,non-specific,274009,292,444,0.000450096,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
15787,Q#3258 - >seq6581,superfamily,274009,292,444,0.000450096,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
15788,Q#3258 - >seq6581,non-specific,235175,250,455,0.00130631,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
15789,Q#3258 - >seq6581,superfamily,235175,250,455,0.00130631,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
15790,Q#3258 - >seq6581,non-specific,274009,290,464,0.00165586,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
15791,Q#3258 - >seq6581,non-specific,223496,292,486,0.00335184,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
15792,Q#3258 - >seq6581,superfamily,223496,292,486,0.00335184,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1P3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
15793,Q#3258 - >seq6581,non-specific,224117,250,487,0.0034969000000000003,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15794,Q#3258 - >seq6581,superfamily,224117,250,487,0.0034969000000000003,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs2_gorilla.marg.frame2,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1P3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
15795,Q#3259 - >seq6582,specific,197310,9,227,5.26637e-53,185.248,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15796,Q#3259 - >seq6582,superfamily,351117,9,227,5.26637e-53,185.248,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15797,Q#3259 - >seq6582,non-specific,197306,9,222,1.97405e-44,161.11,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15798,Q#3259 - >seq6582,non-specific,223780,9,220,2.7379e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15799,Q#3259 - >seq6582,non-specific,197307,9,225,3.54761e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15800,Q#3259 - >seq6582,non-specific,197320,8,220,8.01207e-19,87.1853,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15801,Q#3259 - >seq6582,non-specific,197321,7,223,9.10311e-16,78.3628,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15802,Q#3259 - >seq6582,specific,335306,10,211,3.70349e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15803,Q#3259 - >seq6582,non-specific,273186,9,220,7.69914e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15804,Q#3259 - >seq6582,non-specific,272954,9,220,6.51575e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15805,Q#3259 - >seq6582,non-specific,197336,7,220,3.45131e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15806,Q#3259 - >seq6582,non-specific,197319,8,222,2.52015e-09,59.2125,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15807,Q#3259 - >seq6582,non-specific,197322,9,221,4.224590000000001e-09,59.253,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15808,Q#3259 - >seq6582,non-specific,236970,9,216,2.0681e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15809,Q#3259 - >seq6582,non-specific,339261,107,216,0.000148293,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15810,Q#3259 - >seq6582,non-specific,197311,7,203,0.000312561,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs2_gorilla.marg.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,marg,CompleteHit
15811,Q#3260 - >seq6583,non-specific,335182,143,240,3.13714e-49,159.391,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs3_orang,pars,CompleteHit
15812,Q#3260 - >seq6583,superfamily,335182,143,240,3.13714e-49,159.391,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs3_orang,pars,CompleteHit
15813,Q#3260 - >seq6583,non-specific,340205,243,307,3.80253e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs3_orang,pars,CompleteHit
15814,Q#3260 - >seq6583,superfamily,340205,243,307,3.80253e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P3,ORF1,hs3_orang,pars,CompleteHit
15815,Q#3260 - >seq6583,non-specific,340204,98,140,1.10779e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1P3,ORF1,hs3_orang,pars,CompleteHit
15816,Q#3260 - >seq6583,superfamily,340204,98,140,1.10779e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1P3,ORF1,hs3_orang,pars,CompleteHit
15817,Q#3260 - >seq6583,non-specific,274009,82,191,0.00137801,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF1,hs3_orang,pars,BothTerminiTruncated
15818,Q#3260 - >seq6583,superfamily,274009,82,191,0.00137801,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs3_orang.pars.frame1,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P3,ORF1,hs3_orang,pars,BothTerminiTruncated
15819,Q#3265 - >seq6588,specific,238827,509,771,2.4564299999999996e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15820,Q#3265 - >seq6588,superfamily,295487,509,771,2.4564299999999996e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15821,Q#3265 - >seq6588,specific,197310,9,236,2.4571999999999994e-57,197.574,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15822,Q#3265 - >seq6588,superfamily,351117,9,236,2.4571999999999994e-57,197.574,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15823,Q#3265 - >seq6588,non-specific,197306,9,236,2.51766e-46,166.503,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15824,Q#3265 - >seq6588,specific,333820,515,771,1.5917199999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15825,Q#3265 - >seq6588,superfamily,333820,515,771,1.5917199999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15826,Q#3265 - >seq6588,non-specific,197307,9,236,1.94957e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15827,Q#3265 - >seq6588,non-specific,223780,9,238,9.704630000000001e-22,95.7431,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15828,Q#3265 - >seq6588,non-specific,197320,8,236,8.75305e-19,87.1853,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15829,Q#3265 - >seq6588,specific,335306,10,229,9.320430000000001e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15830,Q#3265 - >seq6588,non-specific,197321,7,236,2.84363e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15831,Q#3265 - >seq6588,non-specific,273186,9,237,3.9709e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15832,Q#3265 - >seq6588,non-specific,272954,9,236,3.3470199999999996e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15833,Q#3265 - >seq6588,non-specific,197336,7,235,5.0917699999999994e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15834,Q#3265 - >seq6588,non-specific,238828,581,736,9.77928e-12,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15835,Q#3265 - >seq6588,non-specific,197319,8,236,3.33326e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15836,Q#3265 - >seq6588,non-specific,197322,9,236,1.0466700000000001e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15837,Q#3265 - >seq6588,non-specific,275209,586,799,2.90607e-10,63.2456,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15838,Q#3265 - >seq6588,superfamily,275209,586,799,2.90607e-10,63.2456,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15839,Q#3265 - >seq6588,non-specific,339261,108,232,1.63553e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15840,Q#3265 - >seq6588,non-specific,197311,7,236,1.38813e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15841,Q#3265 - >seq6588,non-specific,238185,655,771,2.92777e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15842,Q#3265 - >seq6588,non-specific,236970,9,238,9.29014e-05,45.2702,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs2_gorilla,pars,CompleteHit
15843,Q#3265 - >seq6588,non-specific,197317,139,229,0.00021873400000000002,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
15844,Q#3265 - >seq6588,non-specific,274009,305,457,0.00137378,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
15845,Q#3265 - >seq6588,superfamily,274009,305,457,0.00137378,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
15846,Q#3265 - >seq6588,non-specific,274009,303,477,0.00564513,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
15847,Q#3265 - >seq6588,non-specific,235175,295,468,0.006222,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
15848,Q#3265 - >seq6588,superfamily,235175,295,468,0.006222,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs2_gorilla.pars.frame3,1909130931_L1P3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
15849,Q#3267 - >seq6590,non-specific,335182,157,254,3.12062e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15850,Q#3267 - >seq6590,superfamily,335182,157,254,3.12062e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15851,Q#3267 - >seq6590,non-specific,335182,157,254,3.12062e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15852,Q#3267 - >seq6590,non-specific,340205,257,321,3.78454e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15853,Q#3267 - >seq6590,superfamily,340205,257,321,3.78454e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15854,Q#3267 - >seq6590,non-specific,340205,257,321,3.78454e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,marg,CompleteHit
15855,Q#3267 - >seq6590,non-specific,340204,112,154,1.3892700000000003e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,marg,CompleteHit
15856,Q#3267 - >seq6590,superfamily,340204,112,154,1.3892700000000003e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,marg,CompleteHit
15857,Q#3267 - >seq6590,non-specific,340204,112,154,1.3892700000000003e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,marg,CompleteHit
15858,Q#3267 - >seq6590,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15859,Q#3267 - >seq6590,superfamily,274009,42,151,0.0006791810000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15860,Q#3267 - >seq6590,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15861,Q#3267 - >seq6590,non-specific,274008,38,164,0.0031739,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15862,Q#3267 - >seq6590,superfamily,274008,38,164,0.0031739,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15863,Q#3267 - >seq6590,non-specific,274008,38,164,0.0031739,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15864,Q#3267 - >seq6590,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15865,Q#3267 - >seq6590,superfamily,235175,54,157,0.00501044,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15866,Q#3267 - >seq6590,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,marg,BothTerminiTruncated
15867,Q#3267 - >seq6590,non-specific,313022,4,154,0.00755372,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,marg,N-TerminusTruncated
15868,Q#3267 - >seq6590,superfamily,313022,4,154,0.00755372,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,marg,N-TerminusTruncated
15869,Q#3267 - >seq6590,non-specific,313022,4,154,0.00755372,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.marg.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,marg,N-TerminusTruncated
15870,Q#3270 - >seq6593,non-specific,335182,157,254,3.12062e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15871,Q#3270 - >seq6593,superfamily,335182,157,254,3.12062e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15872,Q#3270 - >seq6593,non-specific,335182,157,254,3.12062e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15873,Q#3270 - >seq6593,non-specific,340205,257,321,3.78454e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15874,Q#3270 - >seq6593,superfamily,340205,257,321,3.78454e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15875,Q#3270 - >seq6593,non-specific,340205,257,321,3.78454e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs3_orang,pars,CompleteHit
15876,Q#3270 - >seq6593,non-specific,340204,112,154,1.3892700000000003e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,pars,CompleteHit
15877,Q#3270 - >seq6593,superfamily,340204,112,154,1.3892700000000003e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,pars,CompleteHit
15878,Q#3270 - >seq6593,non-specific,340204,112,154,1.3892700000000003e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs3_orang,pars,CompleteHit
15879,Q#3270 - >seq6593,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15880,Q#3270 - >seq6593,superfamily,274009,42,151,0.0006791810000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15881,Q#3270 - >seq6593,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15882,Q#3270 - >seq6593,non-specific,274008,38,164,0.0031739,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15883,Q#3270 - >seq6593,superfamily,274008,38,164,0.0031739,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15884,Q#3270 - >seq6593,non-specific,274008,38,164,0.0031739,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15885,Q#3270 - >seq6593,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15886,Q#3270 - >seq6593,superfamily,235175,54,157,0.00501044,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15887,Q#3270 - >seq6593,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs3_orang,pars,BothTerminiTruncated
15888,Q#3270 - >seq6593,non-specific,313022,4,154,0.00755372,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,pars,N-TerminusTruncated
15889,Q#3270 - >seq6593,superfamily,313022,4,154,0.00755372,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,pars,N-TerminusTruncated
15890,Q#3270 - >seq6593,non-specific,313022,4,154,0.00755372,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs3_orang.pars.frame3,1909130931_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs3_orang,pars,N-TerminusTruncated
15891,Q#3275 - >seq6598,non-specific,335182,157,254,3.364859999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15892,Q#3275 - >seq6598,superfamily,335182,157,254,3.364859999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15893,Q#3275 - >seq6598,non-specific,335182,157,254,3.364859999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15894,Q#3275 - >seq6598,non-specific,340205,257,321,4.0329499999999994e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15895,Q#3275 - >seq6598,superfamily,340205,257,321,4.0329499999999994e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15896,Q#3275 - >seq6598,non-specific,340205,257,321,4.0329499999999994e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15897,Q#3275 - >seq6598,non-specific,340204,112,154,1.5791099999999998e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15898,Q#3275 - >seq6598,superfamily,340204,112,154,1.5791099999999998e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15899,Q#3275 - >seq6598,non-specific,340204,112,154,1.5791099999999998e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,pars,CompleteHit
15900,Q#3275 - >seq6598,non-specific,274009,42,151,0.0006334380000000001,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15901,Q#3275 - >seq6598,superfamily,274009,42,151,0.0006334380000000001,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15902,Q#3275 - >seq6598,non-specific,274009,42,151,0.0006334380000000001,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15903,Q#3275 - >seq6598,non-specific,274008,38,164,0.00290949,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15904,Q#3275 - >seq6598,superfamily,274008,38,164,0.00290949,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15905,Q#3275 - >seq6598,non-specific,274008,38,164,0.00290949,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15906,Q#3275 - >seq6598,non-specific,235175,54,157,0.00496698,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15907,Q#3275 - >seq6598,superfamily,235175,54,157,0.00496698,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15908,Q#3275 - >seq6598,non-specific,235175,54,157,0.00496698,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
15909,Q#3275 - >seq6598,non-specific,313022,4,154,0.00656884,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
15910,Q#3275 - >seq6598,superfamily,313022,4,154,0.00656884,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
15911,Q#3275 - >seq6598,non-specific,313022,4,154,0.00656884,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
15912,Q#3278 - >seq6601,non-specific,335182,157,254,3.364859999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15913,Q#3278 - >seq6601,superfamily,335182,157,254,3.364859999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15914,Q#3278 - >seq6601,non-specific,335182,157,254,3.364859999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15915,Q#3278 - >seq6601,non-specific,340205,257,321,4.0329499999999994e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15916,Q#3278 - >seq6601,superfamily,340205,257,321,4.0329499999999994e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15917,Q#3278 - >seq6601,non-specific,340205,257,321,4.0329499999999994e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15918,Q#3278 - >seq6601,non-specific,340204,112,154,1.5791099999999998e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15919,Q#3278 - >seq6601,superfamily,340204,112,154,1.5791099999999998e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15920,Q#3278 - >seq6601,non-specific,340204,112,154,1.5791099999999998e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs4_gibbon,marg,CompleteHit
15921,Q#3278 - >seq6601,non-specific,274009,42,151,0.0006334380000000001,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15922,Q#3278 - >seq6601,superfamily,274009,42,151,0.0006334380000000001,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15923,Q#3278 - >seq6601,non-specific,274009,42,151,0.0006334380000000001,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15924,Q#3278 - >seq6601,non-specific,274008,38,164,0.00290949,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15925,Q#3278 - >seq6601,superfamily,274008,38,164,0.00290949,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15926,Q#3278 - >seq6601,non-specific,274008,38,164,0.00290949,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15927,Q#3278 - >seq6601,non-specific,235175,54,157,0.00496698,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15928,Q#3278 - >seq6601,superfamily,235175,54,157,0.00496698,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15929,Q#3278 - >seq6601,non-specific,235175,54,157,0.00496698,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
15930,Q#3278 - >seq6601,non-specific,313022,4,154,0.00656884,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,marg,N-TerminusTruncated
15931,Q#3278 - >seq6601,superfamily,313022,4,154,0.00656884,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,marg,N-TerminusTruncated
15932,Q#3278 - >seq6601,non-specific,313022,4,154,0.00656884,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs4_gibbon,marg,N-TerminusTruncated
15933,Q#3281 - >seq6604,non-specific,335182,156,253,1.0578e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15934,Q#3281 - >seq6604,superfamily,335182,156,253,1.0578e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15935,Q#3281 - >seq6604,non-specific,335182,156,253,1.0578e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15936,Q#3281 - >seq6604,non-specific,340205,256,320,1.9629100000000002e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15937,Q#3281 - >seq6604,superfamily,340205,256,320,1.9629100000000002e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15938,Q#3281 - >seq6604,non-specific,340205,256,320,1.9629100000000002e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15939,Q#3281 - >seq6604,non-specific,340204,112,153,8.6995e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15940,Q#3281 - >seq6604,superfamily,340204,112,153,8.6995e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15941,Q#3281 - >seq6604,non-specific,340204,112,153,8.6995e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,pars,CompleteHit
15942,Q#3281 - >seq6604,non-specific,274009,47,150,0.0007306360000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15943,Q#3281 - >seq6604,superfamily,274009,47,150,0.0007306360000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15944,Q#3281 - >seq6604,non-specific,274009,47,150,0.0007306360000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15945,Q#3281 - >seq6604,non-specific,274008,47,211,0.00570412,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15946,Q#3281 - >seq6604,superfamily,274008,47,211,0.00570412,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15947,Q#3281 - >seq6604,non-specific,274008,47,211,0.00570412,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
15948,Q#3281 - >seq6604,non-specific,235600,51,150,0.0091473,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
15949,Q#3281 - >seq6604,superfamily,235600,51,150,0.0091473,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
15950,Q#3281 - >seq6604,non-specific,235600,51,150,0.0091473,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
15951,Q#3284 - >seq6607,non-specific,335182,156,253,1.0578e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15952,Q#3284 - >seq6607,superfamily,335182,156,253,1.0578e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15953,Q#3284 - >seq6607,non-specific,335182,156,253,1.0578e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15954,Q#3284 - >seq6607,non-specific,340205,256,320,1.9629100000000002e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15955,Q#3284 - >seq6607,superfamily,340205,256,320,1.9629100000000002e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15956,Q#3284 - >seq6607,non-specific,340205,256,320,1.9629100000000002e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15957,Q#3284 - >seq6607,non-specific,340204,112,153,8.6995e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15958,Q#3284 - >seq6607,superfamily,340204,112,153,8.6995e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15959,Q#3284 - >seq6607,non-specific,340204,112,153,8.6995e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs5_gmonkey,marg,CompleteHit
15960,Q#3284 - >seq6607,non-specific,274009,47,150,0.0007306360000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15961,Q#3284 - >seq6607,superfamily,274009,47,150,0.0007306360000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15962,Q#3284 - >seq6607,non-specific,274009,47,150,0.0007306360000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15963,Q#3284 - >seq6607,non-specific,274008,47,211,0.00570412,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15964,Q#3284 - >seq6607,superfamily,274008,47,211,0.00570412,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15965,Q#3284 - >seq6607,non-specific,274008,47,211,0.00570412,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
15966,Q#3284 - >seq6607,non-specific,235600,51,150,0.0091473,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
15967,Q#3284 - >seq6607,superfamily,235600,51,150,0.0091473,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
15968,Q#3284 - >seq6607,non-specific,235600,51,150,0.0091473,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P2.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
15969,Q#3286 - >seq6609,non-specific,335182,157,254,2.2593200000000002e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15970,Q#3286 - >seq6609,superfamily,335182,157,254,2.2593200000000002e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15971,Q#3286 - >seq6609,non-specific,340205,257,321,3.744639999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15972,Q#3286 - >seq6609,superfamily,340205,257,321,3.744639999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15973,Q#3286 - >seq6609,non-specific,340204,112,154,8.90141e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15974,Q#3286 - >seq6609,superfamily,340204,112,154,8.90141e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs1_chimp,pars,CompleteHit
15975,Q#3286 - >seq6609,non-specific,222878,67,151,1.81195e-05,46.1609,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15976,Q#3286 - >seq6609,superfamily,222878,67,151,1.81195e-05,46.1609,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15977,Q#3286 - >seq6609,non-specific,313022,71,154,7.48914e-05,44.068999999999996,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15978,Q#3286 - >seq6609,superfamily,313022,71,154,7.48914e-05,44.068999999999996,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15979,Q#3286 - >seq6609,non-specific,235175,55,146,0.00010379,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15980,Q#3286 - >seq6609,superfamily,235175,55,146,0.00010379,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15981,Q#3286 - >seq6609,non-specific,224117,66,151,0.000305742,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15982,Q#3286 - >seq6609,superfamily,224117,66,151,0.000305742,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15983,Q#3286 - >seq6609,non-specific,235175,69,157,0.00035008,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15984,Q#3286 - >seq6609,non-specific,274008,47,244,0.00042083400000000003,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15985,Q#3286 - >seq6609,superfamily,274008,47,244,0.00042083400000000003,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15986,Q#3286 - >seq6609,non-specific,224117,71,241,0.000558065,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
15987,Q#3286 - >seq6609,superfamily,224117,71,241,0.000558065,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
15988,Q#3286 - >seq6609,non-specific,336322,36,153,0.000599226,41.3486,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15989,Q#3286 - >seq6609,superfamily,336322,36,153,0.000599226,41.3486,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15990,Q#3286 - >seq6609,non-specific,335556,66,153,0.000741071,39.8237,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15991,Q#3286 - >seq6609,superfamily,335556,66,153,0.000741071,39.8237,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15992,Q#3286 - >seq6609,non-specific,337766,52,133,0.0008331310000000001,40.6739,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15993,Q#3286 - >seq6609,superfamily,337766,52,133,0.0008331310000000001,40.6739,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15994,Q#3286 - >seq6609,non-specific,224117,50,151,0.000917089,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15995,Q#3286 - >seq6609,non-specific,335555,66,137,0.00108692,40.3216,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15996,Q#3286 - >seq6609,superfamily,354396,66,137,0.00108692,40.3216,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
15997,Q#3286 - >seq6609,non-specific,179385,61,140,0.00140183,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15998,Q#3286 - >seq6609,superfamily,179385,61,140,0.00140183,40.4086,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
15999,Q#3286 - >seq6609,non-specific,224117,66,157,0.0017019000000000001,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16000,Q#3286 - >seq6609,non-specific,222878,53,198,0.00173869,39.9977,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16001,Q#3286 - >seq6609,non-specific,224117,55,151,0.00204322,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16002,Q#3286 - >seq6609,non-specific,274765,48,128,0.00226265,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16003,Q#3286 - >seq6609,superfamily,274765,48,128,0.00226265,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16004,Q#3286 - >seq6609,non-specific,274008,56,212,0.00248775,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16005,Q#3286 - >seq6609,superfamily,274008,56,212,0.00248775,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16006,Q#3286 - >seq6609,non-specific,336322,66,168,0.00257141,39.4226,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16007,Q#3286 - >seq6609,non-specific,224117,55,151,0.00258436,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16008,Q#3286 - >seq6609,non-specific,179877,36,153,0.00322728,39.0486,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16009,Q#3286 - >seq6609,superfamily,179877,36,153,0.00322728,39.0486,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16010,Q#3286 - >seq6609,non-specific,235175,66,145,0.00420925,38.8916,PRK03918,PRK03918,N,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
16011,Q#3286 - >seq6609,non-specific,235175,69,156,0.00432072,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16012,Q#3286 - >seq6609,non-specific,274009,55,150,0.00433769,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16013,Q#3286 - >seq6609,superfamily,274009,55,150,0.00433769,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16014,Q#3286 - >seq6609,non-specific,224117,55,151,0.00500514,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16015,Q#3286 - >seq6609,non-specific,274009,50,211,0.00525207,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
16016,Q#3286 - >seq6609,non-specific,235175,56,162,0.00561118,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs1_chimp,pars,BothTerminiTruncated
16017,Q#3286 - >seq6609,non-specific,273690,75,197,0.00623851,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16018,Q#3286 - >seq6609,superfamily,355611,75,197,0.00623851,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16019,Q#3286 - >seq6609,non-specific,316375,56,151,0.0075336,36.8095,pfam13851,GAS,C,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16020,Q#3286 - >seq6609,superfamily,316375,56,151,0.0075336,36.8095,cl25894,GAS superfamily,C, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16021,Q#3286 - >seq6609,non-specific,197874,57,163,0.00920959,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
16022,Q#3286 - >seq6609,superfamily,197874,57,163,0.00920959,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs1_chimp,pars,N-TerminusTruncated
16023,Q#3286 - >seq6609,non-specific,235461,59,130,0.0095175,37.355,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16024,Q#3286 - >seq6609,superfamily,235461,59,130,0.0095175,37.355,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs1_chimp.pars.frame3,1909130931_L1P3.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs1_chimp,pars,C-TerminusTruncated
16025,Q#3287 - >seq6610,non-specific,335182,157,254,2.1179900000000002e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs3_orang,marg,CompleteHit
16026,Q#3287 - >seq6610,superfamily,335182,157,254,2.1179900000000002e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs3_orang,marg,CompleteHit
16027,Q#3287 - >seq6610,non-specific,340205,257,321,2.0684699999999995e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs3_orang,marg,CompleteHit
16028,Q#3287 - >seq6610,superfamily,340205,257,321,2.0684699999999995e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs3_orang,marg,CompleteHit
16029,Q#3287 - >seq6610,non-specific,340204,112,154,2.93342e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs3_orang,marg,CompleteHit
16030,Q#3287 - >seq6610,superfamily,340204,112,154,2.93342e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs3_orang,marg,CompleteHit
16031,Q#3287 - >seq6610,non-specific,224117,55,183,0.00184059,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16032,Q#3287 - >seq6610,superfamily,224117,55,183,0.00184059,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16033,Q#3287 - >seq6610,non-specific,224117,66,151,0.00185668,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16034,Q#3287 - >seq6610,superfamily,224117,66,151,0.00185668,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16035,Q#3287 - >seq6610,non-specific,274765,48,128,0.00348099,38.855,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs3_orang,marg,C-TerminusTruncated
16036,Q#3287 - >seq6610,superfamily,274765,48,128,0.00348099,38.855,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs3_orang,marg,C-TerminusTruncated
16037,Q#3287 - >seq6610,non-specific,179385,61,146,0.00409671,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16038,Q#3287 - >seq6610,superfamily,179385,61,146,0.00409671,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16039,Q#3287 - >seq6610,non-specific,335555,66,133,0.00429192,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16040,Q#3287 - >seq6610,superfamily,354396,66,133,0.00429192,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16041,Q#3287 - >seq6610,non-specific,235175,55,143,0.00551428,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16042,Q#3287 - >seq6610,superfamily,235175,55,143,0.00551428,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16043,Q#3287 - >seq6610,non-specific,335556,66,150,0.006111999999999999,37.1273,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16044,Q#3287 - >seq6610,superfamily,335556,66,150,0.006111999999999999,37.1273,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16045,Q#3287 - >seq6610,non-specific,222878,67,151,0.00664309,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16046,Q#3287 - >seq6610,superfamily,222878,67,151,0.00664309,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16047,Q#3287 - >seq6610,non-specific,336322,34,168,0.00735827,37.8818,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16048,Q#3287 - >seq6610,superfamily,336322,34,168,0.00735827,37.8818,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs3_orang,marg,BothTerminiTruncated
16049,Q#3287 - >seq6610,non-specific,337766,52,133,0.00879826,37.2071,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16050,Q#3287 - >seq6610,superfamily,337766,52,133,0.00879826,37.2071,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16051,Q#3287 - >seq6610,non-specific,313022,71,154,0.00883905,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16052,Q#3287 - >seq6610,superfamily,313022,71,154,0.00883905,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs3_orang,marg,N-TerminusTruncated
16053,Q#3289 - >seq6612,specific,238827,488,750,9.39931e-69,229.1,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16054,Q#3289 - >seq6612,superfamily,295487,488,750,9.39931e-69,229.1,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16055,Q#3289 - >seq6612,specific,333820,494,750,5.18091e-37,137.424,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16056,Q#3289 - >seq6612,superfamily,333820,494,750,5.18091e-37,137.424,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16057,Q#3289 - >seq6612,non-specific,238828,494,715,5.03085e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16058,Q#3289 - >seq6612,non-specific,275209,445,778,3.14978e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16059,Q#3289 - >seq6612,superfamily,275209,445,778,3.14978e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16060,Q#3289 - >seq6612,non-specific,197310,158,214,4.5225600000000006e-09,58.1317,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16061,Q#3289 - >seq6612,superfamily,351117,158,214,4.5225600000000006e-09,58.1317,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16062,Q#3289 - >seq6612,non-specific,197306,157,215,7.74333e-08,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16063,Q#3289 - >seq6612,non-specific,238185,634,750,1.14523e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs3_orang,pars,CompleteHit
16064,Q#3289 - >seq6612,non-specific,223780,168,213,0.000102007,45.2819,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16065,Q#3289 - >seq6612,non-specific,197320,162,213,0.000295617,43.6578,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16066,Q#3289 - >seq6612,non-specific,197307,168,215,0.0007922210000000001,42.2749,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame2,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs3_orang,pars,N-TerminusTruncated
16067,Q#3291 - >seq6614,specific,238827,489,734,1.1543499999999997e-64,217.929,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16068,Q#3291 - >seq6614,superfamily,295487,489,734,1.1543499999999997e-64,217.929,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16069,Q#3291 - >seq6614,specific,333820,488,734,6.3051800000000005e-37,137.424,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16070,Q#3291 - >seq6614,superfamily,333820,488,734,6.3051800000000005e-37,137.424,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16071,Q#3291 - >seq6614,non-specific,238828,544,699,2.2521099999999998e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16072,Q#3291 - >seq6614,non-specific,275209,549,762,2.60062e-10,63.2456,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16073,Q#3291 - >seq6614,superfamily,275209,549,762,2.60062e-10,63.2456,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16074,Q#3291 - >seq6614,non-specific,238185,618,734,1.79442e-06,47.3456,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16075,Q#3291 - >seq6614,specific,225881,474,674,0.00319161,40.9777,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16076,Q#3291 - >seq6614,superfamily,225881,474,674,0.00319161,40.9777,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16077,Q#3292 - >seq6615,specific,197310,9,236,3.170959999999999e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16078,Q#3292 - >seq6615,superfamily,351117,9,236,3.170959999999999e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16079,Q#3292 - >seq6615,non-specific,197306,9,236,1.23432e-50,178.829,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16080,Q#3292 - >seq6615,non-specific,197307,9,236,3.01807e-25,105.833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16081,Q#3292 - >seq6615,non-specific,223780,9,238,8.557500000000001e-25,104.988,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16082,Q#3292 - >seq6615,non-specific,197320,8,236,8.740049999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16083,Q#3292 - >seq6615,non-specific,197321,7,236,1.35439e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16084,Q#3292 - >seq6615,specific,335306,10,229,9.48085e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16085,Q#3292 - >seq6615,non-specific,272954,9,236,1.26818e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16086,Q#3292 - >seq6615,non-specific,273186,9,237,6.4276799999999996e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16087,Q#3292 - >seq6615,non-specific,197319,8,236,7.27651e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16088,Q#3292 - >seq6615,non-specific,197336,7,235,5.11846e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16089,Q#3292 - >seq6615,non-specific,197322,9,236,1.7957999999999998e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16090,Q#3292 - >seq6615,non-specific,339261,108,232,3.22362e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16091,Q#3292 - >seq6615,non-specific,236970,9,238,1.05963e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16092,Q#3292 - >seq6615,non-specific,197311,7,236,1.2784000000000001e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,pars,CompleteHit
16093,Q#3292 - >seq6615,non-specific,274009,305,457,0.00016470599999999998,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16094,Q#3292 - >seq6615,superfamily,274009,305,457,0.00016470599999999998,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16095,Q#3292 - >seq6615,non-specific,235175,295,468,0.000453359,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16096,Q#3292 - >seq6615,superfamily,235175,295,468,0.000453359,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16097,Q#3292 - >seq6615,non-specific,223496,304,499,0.000461889,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16098,Q#3292 - >seq6615,superfamily,223496,304,499,0.000461889,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1P3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16099,Q#3292 - >seq6615,non-specific,197317,139,229,0.00059868,42.5892,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16100,Q#3292 - >seq6615,non-specific,274009,303,477,0.00232766,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16101,Q#3295 - >seq6618,specific,238827,509,773,1.9930299999999995e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16102,Q#3295 - >seq6618,superfamily,295487,509,773,1.9930299999999995e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16103,Q#3295 - >seq6618,specific,197310,9,236,2.6560399999999994e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16104,Q#3295 - >seq6618,superfamily,351117,9,236,2.6560399999999994e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16105,Q#3295 - >seq6618,non-specific,197306,9,236,9.99171e-50,176.13299999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16106,Q#3295 - >seq6618,specific,333820,524,773,1.1152399999999999e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16107,Q#3295 - >seq6618,superfamily,333820,524,773,1.1152399999999999e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16108,Q#3295 - >seq6618,non-specific,197307,9,236,1.0433e-23,101.596,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16109,Q#3295 - >seq6618,non-specific,223780,9,238,1.49479e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16110,Q#3295 - >seq6618,non-specific,197320,8,236,2.24911e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16111,Q#3295 - >seq6618,specific,335306,10,229,9.985239999999999e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16112,Q#3295 - >seq6618,non-specific,197321,7,236,1.9408499999999997e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16113,Q#3295 - >seq6618,non-specific,272954,9,236,1.32388e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16114,Q#3295 - >seq6618,non-specific,273186,9,237,3.6695599999999995e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16115,Q#3295 - >seq6618,non-specific,197336,7,235,5.86949e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16116,Q#3295 - >seq6618,non-specific,197319,8,236,2.48986e-12,68.0721,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16117,Q#3295 - >seq6618,non-specific,238828,583,738,9.90164e-12,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16118,Q#3295 - >seq6618,non-specific,197322,9,236,1.89613e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16119,Q#3295 - >seq6618,non-specific,275209,588,801,3.84876e-10,62.8604,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16120,Q#3295 - >seq6618,superfamily,275209,588,801,3.84876e-10,62.8604,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16121,Q#3295 - >seq6618,non-specific,339261,108,232,2.52818e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16122,Q#3295 - >seq6618,non-specific,236970,9,238,3.641e-07,52.9742,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16123,Q#3295 - >seq6618,non-specific,197311,7,236,2.58228e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16124,Q#3295 - >seq6618,non-specific,238185,657,773,3.07969e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs5_gmonkey,marg,CompleteHit
16125,Q#3295 - >seq6618,non-specific,274009,305,457,0.00030618,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16126,Q#3295 - >seq6618,superfamily,274009,305,457,0.00030618,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16127,Q#3295 - >seq6618,non-specific,197317,139,229,0.000767488,42.5892,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16128,Q#3295 - >seq6618,non-specific,223496,304,449,0.00150372,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
16129,Q#3295 - >seq6618,superfamily,223496,304,449,0.00150372,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1P3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
16130,Q#3295 - >seq6618,non-specific,235175,295,468,0.00271915,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
16131,Q#3295 - >seq6618,superfamily,235175,295,468,0.00271915,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
16132,Q#3295 - >seq6618,non-specific,274009,303,477,0.00410853,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
16133,Q#3298 - >seq6621,non-specific,335182,156,252,7.54044e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16134,Q#3298 - >seq6621,superfamily,335182,156,252,7.54044e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16135,Q#3298 - >seq6621,non-specific,340205,255,319,1.8181799999999998e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16136,Q#3298 - >seq6621,superfamily,340205,255,319,1.8181799999999998e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16137,Q#3298 - >seq6621,non-specific,340204,111,152,2.7625e-08,49.3284,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16138,Q#3298 - >seq6621,superfamily,340204,111,152,2.7625e-08,49.3284,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs6_sqmonkey,pars,CompleteHit
16139,Q#3298 - >seq6621,non-specific,337766,51,139,0.00167751,39.5183,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
16140,Q#3298 - >seq6621,superfamily,337766,51,139,0.00167751,39.5183,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
16141,Q#3298 - >seq6621,non-specific,224117,70,237,0.0031518,39.3124,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
16142,Q#3298 - >seq6621,superfamily,224117,70,237,0.0031518,39.3124,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
16143,Q#3298 - >seq6621,non-specific,224117,54,181,0.00320713,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16144,Q#3298 - >seq6621,superfamily,224117,54,181,0.00320713,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16145,Q#3298 - >seq6621,non-specific,335556,65,148,0.00363927,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16146,Q#3298 - >seq6621,superfamily,335556,65,148,0.00363927,37.5125,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16147,Q#3298 - >seq6621,non-specific,222878,66,149,0.00382157,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16148,Q#3298 - >seq6621,superfamily,222878,66,149,0.00382157,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16149,Q#3298 - >seq6621,non-specific,335555,65,131,0.0052492,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
16150,Q#3298 - >seq6621,superfamily,354396,65,131,0.0052492,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
16151,Q#3298 - >seq6621,non-specific,274008,46,242,0.00657929,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16152,Q#3298 - >seq6621,superfamily,274008,46,242,0.00657929,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
16153,Q#3300 - >seq6623,non-specific,335182,157,253,4.10418e-46,151.687,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16154,Q#3300 - >seq6623,superfamily,335182,157,253,4.10418e-46,151.687,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16155,Q#3300 - >seq6623,non-specific,340205,256,320,1.42374e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16156,Q#3300 - >seq6623,superfamily,340205,256,320,1.42374e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16157,Q#3300 - >seq6623,non-specific,340204,112,153,2.32248e-08,49.3284,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16158,Q#3300 - >seq6623,superfamily,340204,112,153,2.32248e-08,49.3284,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs6_sqmonkey,marg,CompleteHit
16159,Q#3300 - >seq6623,non-specific,337766,52,140,0.00146277,39.9035,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
16160,Q#3300 - >seq6623,superfamily,337766,52,140,0.00146277,39.9035,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
16161,Q#3300 - >seq6623,non-specific,224117,71,238,0.00257103,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
16162,Q#3300 - >seq6623,superfamily,224117,71,238,0.00257103,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
16163,Q#3300 - >seq6623,non-specific,224117,55,182,0.00270884,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16164,Q#3300 - >seq6623,superfamily,224117,55,182,0.00270884,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16165,Q#3300 - >seq6623,non-specific,335556,66,149,0.00342436,37.8977,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16166,Q#3300 - >seq6623,superfamily,335556,66,149,0.00342436,37.8977,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16167,Q#3300 - >seq6623,non-specific,222878,67,150,0.00358075,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16168,Q#3300 - >seq6623,superfamily,222878,67,150,0.00358075,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16169,Q#3300 - >seq6623,non-specific,335555,66,132,0.00458239,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
16170,Q#3300 - >seq6623,superfamily,354396,66,132,0.00458239,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
16171,Q#3300 - >seq6623,non-specific,274008,47,243,0.00532087,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16172,Q#3300 - >seq6623,superfamily,274008,47,243,0.00532087,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs6_sqmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
16173,Q#3301 - >seq6624,specific,238827,477,738,9.151179999999998e-67,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16174,Q#3301 - >seq6624,superfamily,295487,477,738,9.151179999999998e-67,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16175,Q#3301 - >seq6624,specific,333820,483,738,1.7200200000000002e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16176,Q#3301 - >seq6624,superfamily,333820,483,738,1.7200200000000002e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16177,Q#3301 - >seq6624,non-specific,238828,483,704,6.71267e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16178,Q#3301 - >seq6624,non-specific,275209,554,766,8.12683e-08,55.5416,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16179,Q#3301 - >seq6624,superfamily,275209,554,766,8.12683e-08,55.5416,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16180,Q#3301 - >seq6624,non-specific,238185,623,738,0.000146585,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs6_sqmonkey.pars.frame1,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16181,Q#3302 - >seq6625,specific,197310,23,235,1.26482e-38,144.031,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16182,Q#3302 - >seq6625,superfamily,351117,23,235,1.26482e-38,144.031,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16183,Q#3302 - >seq6625,non-specific,197306,70,235,8.33391e-31,121.82,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16184,Q#3302 - >seq6625,non-specific,197307,24,235,3.50925e-14,73.4761,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16185,Q#3302 - >seq6625,non-specific,223780,71,237,3.76048e-13,70.7051,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16186,Q#3302 - >seq6625,non-specific,197320,71,235,1.58064e-12,68.6958,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16187,Q#3302 - >seq6625,non-specific,339261,107,231,2.54371e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1P3,ORF2,hs6_sqmonkey,pars,CompleteHit
16188,Q#3302 - >seq6625,non-specific,197321,71,235,7.85098e-08,54.4804,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16189,Q#3302 - >seq6625,non-specific,273186,71,236,2.4585e-07,53.0516,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16190,Q#3302 - >seq6625,non-specific,197322,90,235,3.25343e-07,53.475,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16191,Q#3302 - >seq6625,non-specific,335306,71,228,1.05818e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16192,Q#3302 - >seq6625,non-specific,272954,89,235,2.56413e-06,50.0741,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16193,Q#3302 - >seq6625,non-specific,197319,71,235,6.85687e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16194,Q#3302 - >seq6625,non-specific,197317,138,228,0.000149505,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16195,Q#3302 - >seq6625,non-specific,197311,71,235,0.00040496,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16196,Q#3302 - >seq6625,non-specific,236970,71,237,0.000439741,43.3442,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
16197,Q#3302 - >seq6625,non-specific,223496,231,448,0.00724794,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
16198,Q#3302 - >seq6625,superfamily,223496,231,448,0.00724794,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs6_sqmonkey.pars.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1P3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
16199,Q#3303 - >seq6626,non-specific,197310,9,66,2.82237e-13,70.4581,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16200,Q#3303 - >seq6626,superfamily,351117,9,66,2.82237e-13,70.4581,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16201,Q#3303 - >seq6626,non-specific,197306,9,128,4.01812e-11,64.4249,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16202,Q#3303 - >seq6626,non-specific,197321,7,49,1.11783e-05,47.931999999999995,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16203,Q#3303 - >seq6626,non-specific,223780,9,43,2.69315e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16204,Q#3303 - >seq6626,non-specific,197336,7,43,0.000221258,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16205,Q#3303 - >seq6626,non-specific,197307,9,43,0.00053845,42.6601,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16206,Q#3303 - >seq6626,specific,335306,10,53,0.000594773,42.6174,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16207,Q#3303 - >seq6626,non-specific,197320,8,43,0.00076616,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16208,Q#3303 - >seq6626,non-specific,273186,9,43,0.00137771,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16209,Q#3303 - >seq6626,non-specific,272954,9,43,0.00851666,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
16210,Q#3305 - >seq6628,specific,238827,518,782,3.161989999999999e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16211,Q#3305 - >seq6628,superfamily,295487,518,782,3.161989999999999e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16212,Q#3305 - >seq6628,specific,197310,9,240,8.75284e-55,190.64,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16213,Q#3305 - >seq6628,superfamily,351117,9,240,8.75284e-55,190.64,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16214,Q#3305 - >seq6628,non-specific,197306,16,240,1.6194999999999996e-46,166.888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16215,Q#3305 - >seq6628,specific,333820,524,782,2.27892e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16216,Q#3305 - >seq6628,superfamily,333820,524,782,2.27892e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16217,Q#3305 - >seq6628,non-specific,197307,4,240,2.7088399999999998e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16218,Q#3305 - >seq6628,non-specific,223780,9,242,4.85407e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16219,Q#3305 - >seq6628,non-specific,197320,9,240,4.43001e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16220,Q#3305 - >seq6628,non-specific,197321,3,240,5.993680000000001e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16221,Q#3305 - >seq6628,specific,335306,9,233,8.4514e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16222,Q#3305 - >seq6628,non-specific,273186,9,241,4.3877400000000004e-12,67.304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16223,Q#3305 - >seq6628,non-specific,272954,3,240,3.07662e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16224,Q#3305 - >seq6628,non-specific,238828,524,732,1.2471e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16225,Q#3305 - >seq6628,non-specific,197319,9,240,5.26275e-10,61.1385,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16226,Q#3305 - >seq6628,non-specific,339261,112,236,3.1318099999999998e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16227,Q#3305 - >seq6628,non-specific,197336,9,239,5.54001e-08,55.3111,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16228,Q#3305 - >seq6628,non-specific,197322,9,240,7.70475e-08,55.401,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16229,Q#3305 - >seq6628,non-specific,275209,595,810,5.77405e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
16230,Q#3305 - >seq6628,superfamily,275209,595,810,5.77405e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
16231,Q#3305 - >seq6628,non-specific,197311,27,240,3.70603e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16232,Q#3305 - >seq6628,non-specific,197317,143,233,0.000161486,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
16233,Q#3305 - >seq6628,non-specific,236970,4,242,0.000251929,44.1146,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16234,Q#3305 - >seq6628,non-specific,238185,664,782,0.00271531,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs6_sqmonkey,marg,CompleteHit
16235,Q#3305 - >seq6628,non-specific,274008,271,442,0.00723545,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
16236,Q#3305 - >seq6628,superfamily,274008,271,442,0.00723545,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs6_sqmonkey.marg.frame2,1909130931_L1P3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
16237,Q#3307 - >seq6630,non-specific,335182,157,254,4.74855e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16238,Q#3307 - >seq6630,superfamily,335182,157,254,4.74855e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16239,Q#3307 - >seq6630,non-specific,335182,157,254,4.74855e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16240,Q#3307 - >seq6630,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16241,Q#3307 - >seq6630,superfamily,340205,257,321,3.589239999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16242,Q#3307 - >seq6630,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16243,Q#3307 - >seq6630,non-specific,340204,112,154,1.1267100000000001e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16244,Q#3307 - >seq6630,superfamily,340204,112,154,1.1267100000000001e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16245,Q#3307 - >seq6630,non-specific,340204,112,154,1.1267100000000001e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,marg,CompleteHit
16246,Q#3307 - >seq6630,non-specific,337766,52,130,0.00026022,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16247,Q#3307 - >seq6630,superfamily,337766,52,130,0.00026022,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16248,Q#3307 - >seq6630,non-specific,337766,52,130,0.00026022,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16249,Q#3307 - >seq6630,non-specific,336322,36,134,0.0008588860000000001,40.9634,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16250,Q#3307 - >seq6630,superfamily,336322,36,134,0.0008588860000000001,40.9634,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16251,Q#3307 - >seq6630,non-specific,336322,36,134,0.0008588860000000001,40.9634,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16252,Q#3307 - >seq6630,non-specific,224117,66,151,0.0008934310000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16253,Q#3307 - >seq6630,superfamily,224117,66,151,0.0008934310000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16254,Q#3307 - >seq6630,non-specific,224117,66,151,0.0008934310000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16255,Q#3307 - >seq6630,non-specific,235175,55,143,0.00116828,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16256,Q#3307 - >seq6630,superfamily,235175,55,143,0.00116828,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16257,Q#3307 - >seq6630,non-specific,235175,55,143,0.00116828,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16258,Q#3307 - >seq6630,non-specific,274008,56,212,0.00134098,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16259,Q#3307 - >seq6630,superfamily,274008,56,212,0.00134098,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16260,Q#3307 - >seq6630,non-specific,274008,56,212,0.00134098,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16261,Q#3307 - >seq6630,non-specific,179385,59,146,0.00136561,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16262,Q#3307 - >seq6630,superfamily,179385,59,146,0.00136561,40.4086,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16263,Q#3307 - >seq6630,non-specific,179385,59,146,0.00136561,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16264,Q#3307 - >seq6630,non-specific,274765,48,128,0.00255906,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16265,Q#3307 - >seq6630,superfamily,274765,48,128,0.00255906,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16266,Q#3307 - >seq6630,non-specific,274765,48,128,0.00255906,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16267,Q#3307 - >seq6630,non-specific,224117,55,151,0.00378944,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16268,Q#3307 - >seq6630,non-specific,224117,55,151,0.00378944,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16269,Q#3307 - >seq6630,non-specific,222878,67,151,0.00379286,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16270,Q#3307 - >seq6630,superfamily,222878,67,151,0.00379286,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16271,Q#3307 - >seq6630,non-specific,222878,67,151,0.00379286,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16272,Q#3307 - >seq6630,non-specific,274008,47,210,0.00401396,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16273,Q#3307 - >seq6630,non-specific,274008,47,210,0.00401396,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16274,Q#3307 - >seq6630,non-specific,224117,71,241,0.00536563,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16275,Q#3307 - >seq6630,superfamily,224117,71,241,0.00536563,38.542,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16276,Q#3307 - >seq6630,non-specific,224117,71,241,0.00536563,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16277,Q#3307 - >seq6630,non-specific,313022,71,154,0.00542062,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16278,Q#3307 - >seq6630,superfamily,313022,71,154,0.00542062,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16279,Q#3307 - >seq6630,non-specific,313022,71,154,0.00542062,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16280,Q#3307 - >seq6630,non-specific,224117,56,150,0.0055074,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16281,Q#3307 - >seq6630,non-specific,224117,56,150,0.0055074,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16282,Q#3307 - >seq6630,non-specific,224117,55,204,0.00684411,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16283,Q#3307 - >seq6630,non-specific,224117,55,204,0.00684411,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16284,Q#3307 - >seq6630,non-specific,179385,66,145,0.00690899,38.0974,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16285,Q#3307 - >seq6630,non-specific,179385,66,145,0.00690899,38.0974,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16286,Q#3307 - >seq6630,non-specific,274009,55,205,0.00705794,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16287,Q#3307 - >seq6630,superfamily,274009,55,205,0.00705794,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16288,Q#3307 - >seq6630,non-specific,274009,55,205,0.00705794,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16289,Q#3307 - >seq6630,non-specific,235461,59,130,0.0071807,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16290,Q#3307 - >seq6630,superfamily,235461,59,130,0.0071807,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16291,Q#3307 - >seq6630,non-specific,235461,59,130,0.0071807,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
16292,Q#3307 - >seq6630,non-specific,336322,34,168,0.00861428,37.4966,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16293,Q#3307 - >seq6630,non-specific,336322,34,168,0.00861428,37.4966,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16294,Q#3307 - >seq6630,non-specific,224117,50,151,0.00935771,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16295,Q#3307 - >seq6630,non-specific,224117,50,151,0.00935771,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16296,Q#3307 - >seq6630,non-specific,335556,66,150,0.00936065,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16297,Q#3307 - >seq6630,superfamily,335556,66,150,0.00936065,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16298,Q#3307 - >seq6630,non-specific,335556,66,150,0.00936065,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16299,Q#3307 - >seq6630,non-specific,309330,58,157,0.00970286,36.2939,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16300,Q#3307 - >seq6630,superfamily,309330,58,157,0.00970286,36.2939,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16301,Q#3307 - >seq6630,non-specific,309330,58,157,0.00970286,36.2939,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16302,Q#3310 - >seq6633,non-specific,335182,157,254,4.74855e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16303,Q#3310 - >seq6633,superfamily,335182,157,254,4.74855e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16304,Q#3310 - >seq6633,non-specific,335182,157,254,4.74855e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16305,Q#3310 - >seq6633,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16306,Q#3310 - >seq6633,superfamily,340205,257,321,3.589239999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16307,Q#3310 - >seq6633,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16308,Q#3310 - >seq6633,non-specific,340204,112,154,1.1267100000000001e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16309,Q#3310 - >seq6633,superfamily,340204,112,154,1.1267100000000001e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16310,Q#3310 - >seq6633,non-specific,340204,112,154,1.1267100000000001e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs5_gmonkey,pars,CompleteHit
16311,Q#3310 - >seq6633,non-specific,337766,52,130,0.00026022,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16312,Q#3310 - >seq6633,superfamily,337766,52,130,0.00026022,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16313,Q#3310 - >seq6633,non-specific,337766,52,130,0.00026022,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16314,Q#3310 - >seq6633,non-specific,336322,36,134,0.0008588860000000001,40.9634,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16315,Q#3310 - >seq6633,superfamily,336322,36,134,0.0008588860000000001,40.9634,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16316,Q#3310 - >seq6633,non-specific,336322,36,134,0.0008588860000000001,40.9634,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16317,Q#3310 - >seq6633,non-specific,224117,66,151,0.0008934310000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16318,Q#3310 - >seq6633,superfamily,224117,66,151,0.0008934310000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16319,Q#3310 - >seq6633,non-specific,224117,66,151,0.0008934310000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16320,Q#3310 - >seq6633,non-specific,235175,55,143,0.00116828,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16321,Q#3310 - >seq6633,superfamily,235175,55,143,0.00116828,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16322,Q#3310 - >seq6633,non-specific,235175,55,143,0.00116828,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16323,Q#3310 - >seq6633,non-specific,274008,56,212,0.00134098,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16324,Q#3310 - >seq6633,superfamily,274008,56,212,0.00134098,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16325,Q#3310 - >seq6633,non-specific,274008,56,212,0.00134098,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16326,Q#3310 - >seq6633,non-specific,179385,59,146,0.00136561,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16327,Q#3310 - >seq6633,superfamily,179385,59,146,0.00136561,40.4086,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16328,Q#3310 - >seq6633,non-specific,179385,59,146,0.00136561,40.4086,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16329,Q#3310 - >seq6633,non-specific,274765,48,128,0.00255906,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16330,Q#3310 - >seq6633,superfamily,274765,48,128,0.00255906,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16331,Q#3310 - >seq6633,non-specific,274765,48,128,0.00255906,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16332,Q#3310 - >seq6633,non-specific,224117,55,151,0.00378944,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16333,Q#3310 - >seq6633,non-specific,224117,55,151,0.00378944,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16334,Q#3310 - >seq6633,non-specific,222878,67,151,0.00379286,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16335,Q#3310 - >seq6633,superfamily,222878,67,151,0.00379286,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16336,Q#3310 - >seq6633,non-specific,222878,67,151,0.00379286,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16337,Q#3310 - >seq6633,non-specific,274008,47,210,0.00401396,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16338,Q#3310 - >seq6633,non-specific,274008,47,210,0.00401396,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16339,Q#3310 - >seq6633,non-specific,224117,71,241,0.00536563,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16340,Q#3310 - >seq6633,superfamily,224117,71,241,0.00536563,38.542,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16341,Q#3310 - >seq6633,non-specific,224117,71,241,0.00536563,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16342,Q#3310 - >seq6633,non-specific,313022,71,154,0.00542062,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16343,Q#3310 - >seq6633,superfamily,313022,71,154,0.00542062,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16344,Q#3310 - >seq6633,non-specific,313022,71,154,0.00542062,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16345,Q#3310 - >seq6633,non-specific,224117,56,150,0.0055074,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16346,Q#3310 - >seq6633,non-specific,224117,56,150,0.0055074,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16347,Q#3310 - >seq6633,non-specific,224117,55,204,0.00684411,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16348,Q#3310 - >seq6633,non-specific,224117,55,204,0.00684411,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16349,Q#3310 - >seq6633,non-specific,179385,66,145,0.00690899,38.0974,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16350,Q#3310 - >seq6633,non-specific,179385,66,145,0.00690899,38.0974,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16351,Q#3310 - >seq6633,non-specific,274009,55,205,0.00705794,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16352,Q#3310 - >seq6633,superfamily,274009,55,205,0.00705794,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16353,Q#3310 - >seq6633,non-specific,274009,55,205,0.00705794,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16354,Q#3310 - >seq6633,non-specific,235461,59,130,0.0071807,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16355,Q#3310 - >seq6633,superfamily,235461,59,130,0.0071807,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16356,Q#3310 - >seq6633,non-specific,235461,59,130,0.0071807,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
16357,Q#3310 - >seq6633,non-specific,336322,34,168,0.00861428,37.4966,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16358,Q#3310 - >seq6633,non-specific,336322,34,168,0.00861428,37.4966,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16359,Q#3310 - >seq6633,non-specific,224117,50,151,0.00935771,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16360,Q#3310 - >seq6633,non-specific,224117,50,151,0.00935771,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16361,Q#3310 - >seq6633,non-specific,335556,66,150,0.00936065,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16362,Q#3310 - >seq6633,superfamily,335556,66,150,0.00936065,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16363,Q#3310 - >seq6633,non-specific,335556,66,150,0.00936065,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16364,Q#3310 - >seq6633,non-specific,309330,58,157,0.00970286,36.2939,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16365,Q#3310 - >seq6633,superfamily,309330,58,157,0.00970286,36.2939,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16366,Q#3310 - >seq6633,non-specific,309330,58,157,0.00970286,36.2939,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1P3.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16367,Q#3311 - >seq6634,specific,197310,9,157,3.4666599999999997e-40,148.268,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16368,Q#3311 - >seq6634,superfamily,351117,9,157,3.4666599999999997e-40,148.268,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16369,Q#3311 - >seq6634,non-specific,197306,9,154,7.95716e-30,118.738,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16370,Q#3311 - >seq6634,non-specific,197307,9,147,2.84104e-13,70.7797,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16371,Q#3311 - >seq6634,non-specific,223780,9,146,1.9021400000000002e-12,68.3939,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16372,Q#3311 - >seq6634,specific,335306,10,150,2.65885e-11,64.1886,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16373,Q#3311 - >seq6634,non-specific,197321,7,146,3.25721e-11,64.4956,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16374,Q#3311 - >seq6634,non-specific,197320,8,146,4.08056e-11,64.4586,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16375,Q#3311 - >seq6634,non-specific,197319,8,147,1.00167e-09,59.9829,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16376,Q#3311 - >seq6634,non-specific,197336,7,146,1.47753e-09,59.5483,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16377,Q#3311 - >seq6634,non-specific,272954,9,157,3.34776e-09,58.5485,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16378,Q#3311 - >seq6634,non-specific,273186,9,147,4.04547e-08,55.3628,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16379,Q#3311 - >seq6634,non-specific,197311,7,146,0.00144858,40.7381,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16380,Q#3311 - >seq6634,non-specific,197322,9,153,0.00185189,41.5338,cd09088,Ape2-like_AP-endo,C,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16381,Q#3311 - >seq6634,non-specific,236970,9,146,0.00669664,39.4922,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs3_orang.pars.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,pars,C-TerminusTruncated
16382,Q#3314 - >seq6637,specific,238827,496,758,2.30587e-68,228.715,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16383,Q#3314 - >seq6637,superfamily,295487,496,758,2.30587e-68,228.715,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16384,Q#3314 - >seq6637,specific,197310,9,222,1.4991899999999998e-54,189.87,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16385,Q#3314 - >seq6637,superfamily,351117,9,222,1.4991899999999998e-54,189.87,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16386,Q#3314 - >seq6637,non-specific,197306,9,223,8.781989999999999e-45,161.88,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16387,Q#3314 - >seq6637,specific,333820,502,758,8.456e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16388,Q#3314 - >seq6637,superfamily,333820,502,758,8.456e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16389,Q#3314 - >seq6637,non-specific,223780,9,221,1.97026e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16390,Q#3314 - >seq6637,non-specific,197307,9,223,2.3136000000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16391,Q#3314 - >seq6637,non-specific,197320,8,221,8.40801e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16392,Q#3314 - >seq6637,non-specific,197321,7,223,1.68551e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16393,Q#3314 - >seq6637,specific,335306,10,212,4.58021e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16394,Q#3314 - >seq6637,non-specific,272954,9,221,1.54347e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16395,Q#3314 - >seq6637,non-specific,273186,9,221,1.69024e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16396,Q#3314 - >seq6637,non-specific,197336,7,221,4.01965e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16397,Q#3314 - >seq6637,non-specific,238828,502,723,5.2295e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16398,Q#3314 - >seq6637,non-specific,275209,453,786,2.00097e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16399,Q#3314 - >seq6637,superfamily,275209,453,786,2.00097e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16400,Q#3314 - >seq6637,non-specific,197319,8,223,1.36933e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16401,Q#3314 - >seq6637,non-specific,197322,9,222,7.53289e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16402,Q#3314 - >seq6637,non-specific,236970,9,217,8.18343e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16403,Q#3314 - >seq6637,non-specific,238185,642,758,1.81267e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16404,Q#3314 - >seq6637,non-specific,339261,108,217,0.000116994,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs3_orang,marg,CompleteHit
16405,Q#3314 - >seq6637,non-specific,197311,7,204,0.000542336,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs3_orang.marg.frame3,1909130931_L1P3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs3_orang,marg,CompleteHit
16406,Q#3317 - >seq6640,non-specific,335182,157,254,9.254549999999999e-48,155.924,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16407,Q#3317 - >seq6640,superfamily,335182,157,254,9.254549999999999e-48,155.924,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16408,Q#3317 - >seq6640,non-specific,340205,257,321,3.02946e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16409,Q#3317 - >seq6640,superfamily,340205,257,321,3.02946e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16410,Q#3317 - >seq6640,non-specific,340204,112,154,4.13737e-09,51.6396,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16411,Q#3317 - >seq6640,superfamily,340204,112,154,4.13737e-09,51.6396,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs4_gibbon,pars,CompleteHit
16412,Q#3317 - >seq6640,non-specific,179385,61,146,0.000291078,42.3346,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16413,Q#3317 - >seq6640,superfamily,179385,61,146,0.000291078,42.3346,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16414,Q#3317 - >seq6640,non-specific,224117,66,151,0.000342458,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16415,Q#3317 - >seq6640,superfamily,224117,66,151,0.000342458,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16416,Q#3317 - >seq6640,non-specific,337766,52,133,0.000413092,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16417,Q#3317 - >seq6640,superfamily,337766,52,133,0.000413092,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16418,Q#3317 - >seq6640,non-specific,235175,55,143,0.00046302400000000003,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16419,Q#3317 - >seq6640,superfamily,235175,55,143,0.00046302400000000003,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16420,Q#3317 - >seq6640,non-specific,222878,67,151,0.000680057,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16421,Q#3317 - >seq6640,superfamily,222878,67,151,0.000680057,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16422,Q#3317 - >seq6640,non-specific,335555,66,133,0.000699537,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16423,Q#3317 - >seq6640,superfamily,354396,66,133,0.000699537,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16424,Q#3317 - >seq6640,non-specific,224117,55,151,0.000718552,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16425,Q#3317 - >seq6640,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16426,Q#3317 - >seq6640,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16427,Q#3317 - >seq6640,non-specific,274008,56,212,0.000767929,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16428,Q#3317 - >seq6640,superfamily,274008,56,212,0.000767929,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16429,Q#3317 - >seq6640,non-specific,335556,66,150,0.0009618960000000001,39.4385,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16430,Q#3317 - >seq6640,superfamily,335556,66,150,0.0009618960000000001,39.4385,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16431,Q#3317 - >seq6640,non-specific,336322,34,168,0.00105102,40.5782,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16432,Q#3317 - >seq6640,superfamily,336322,34,168,0.00105102,40.5782,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16433,Q#3317 - >seq6640,non-specific,336322,36,134,0.00124171,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16434,Q#3317 - >seq6640,non-specific,224117,71,241,0.00260694,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16435,Q#3317 - >seq6640,superfamily,224117,71,241,0.00260694,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16436,Q#3317 - >seq6640,non-specific,313022,71,154,0.00267107,39.4466,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16437,Q#3317 - >seq6640,superfamily,313022,71,154,0.00267107,39.4466,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16438,Q#3317 - >seq6640,non-specific,274008,47,244,0.00288429,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16439,Q#3317 - >seq6640,superfamily,274008,47,244,0.00288429,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16440,Q#3317 - >seq6640,non-specific,224117,66,157,0.00289382,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16441,Q#3317 - >seq6640,non-specific,224117,50,151,0.00395785,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16442,Q#3317 - >seq6640,non-specific,274009,50,150,0.004226,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16443,Q#3317 - >seq6640,superfamily,274009,50,150,0.004226,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16444,Q#3317 - >seq6640,non-specific,224117,55,151,0.00435513,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16445,Q#3317 - >seq6640,non-specific,235461,59,130,0.00438473,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16446,Q#3317 - >seq6640,superfamily,235461,59,130,0.00438473,38.5106,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16447,Q#3317 - >seq6640,non-specific,224117,55,151,0.00500514,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16448,Q#3317 - >seq6640,non-specific,224117,56,150,0.00565292,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,pars,N-TerminusTruncated
16449,Q#3317 - >seq6640,non-specific,223266,67,141,0.00691845,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16450,Q#3317 - >seq6640,superfamily,223266,67,141,0.00691845,38.0218,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16451,Q#3317 - >seq6640,non-specific,273690,75,157,0.00712177,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16452,Q#3317 - >seq6640,superfamily,355611,75,157,0.00712177,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16453,Q#3317 - >seq6640,non-specific,235600,37,131,0.00842328,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16454,Q#3317 - >seq6640,superfamily,235600,37,131,0.00842328,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
16455,Q#3317 - >seq6640,non-specific,222878,53,198,0.00863797,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16456,Q#3322 - >seq6645,specific,238827,496,758,4.4716899999999993e-69,230.25599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16457,Q#3322 - >seq6645,superfamily,295487,496,758,4.4716899999999993e-69,230.25599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16458,Q#3322 - >seq6645,specific,333820,502,758,2.70201e-37,138.194,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16459,Q#3322 - >seq6645,superfamily,333820,502,758,2.70201e-37,138.194,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16460,Q#3322 - >seq6645,non-specific,238828,502,723,2.59922e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16461,Q#3322 - >seq6645,non-specific,275209,453,786,6.342390000000001e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16462,Q#3322 - >seq6645,superfamily,275209,453,786,6.342390000000001e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16463,Q#3322 - >seq6645,non-specific,238185,642,758,1.09363e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16464,Q#3322 - >seq6645,non-specific,274009,292,444,0.000638965,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
16465,Q#3322 - >seq6645,superfamily,274009,292,444,0.000638965,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
16466,Q#3322 - >seq6645,non-specific,274009,290,464,0.00142759,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
16467,Q#3322 - >seq6645,non-specific,235175,292,455,0.00593858,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
16468,Q#3322 - >seq6645,superfamily,235175,292,455,0.00593858,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
16469,Q#3322 - >seq6645,non-specific,223496,291,436,0.00614805,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
16470,Q#3322 - >seq6645,superfamily,223496,291,436,0.00614805,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.pars.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1P3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
16471,Q#3323 - >seq6646,specific,197310,9,221,5.5755399999999995e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16472,Q#3323 - >seq6646,superfamily,351117,9,221,5.5755399999999995e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16473,Q#3323 - >seq6646,non-specific,197306,9,222,1.55786e-45,164.192,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16474,Q#3323 - >seq6646,non-specific,223780,9,220,6.092999999999999e-25,104.988,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16475,Q#3323 - >seq6646,non-specific,197307,9,222,2.25317e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16476,Q#3323 - >seq6646,non-specific,197320,8,220,6.232840000000001e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16477,Q#3323 - >seq6646,non-specific,197321,7,222,1.64529e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16478,Q#3323 - >seq6646,non-specific,272954,9,220,1.15289e-16,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16479,Q#3323 - >seq6646,specific,335306,10,211,1.33198e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16480,Q#3323 - >seq6646,non-specific,273186,9,220,4.72989e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16481,Q#3323 - >seq6646,non-specific,197319,8,222,2.00827e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16482,Q#3323 - >seq6646,non-specific,197336,7,220,2.12427e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16483,Q#3323 - >seq6646,non-specific,197322,9,221,1.12293e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16484,Q#3323 - >seq6646,non-specific,236970,9,216,3.27425e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16485,Q#3323 - >seq6646,non-specific,197311,7,203,3.76343e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16486,Q#3323 - >seq6646,non-specific,339261,108,216,0.00022167200000000001,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs4_gibbon.pars.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs4_gibbon,pars,CompleteHit
16487,Q#1 - >seq6648,specific,238827,497,759,5.701689999999998e-69,230.25599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16488,Q#1 - >seq6648,superfamily,295487,497,759,5.701689999999998e-69,230.25599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16489,Q#1 - >seq6648,specific,333820,503,759,3.72737e-37,138.194,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16490,Q#1 - >seq6648,superfamily,333820,503,759,3.72737e-37,138.194,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16491,Q#1 - >seq6648,non-specific,238828,503,724,2.6881700000000002e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16492,Q#1 - >seq6648,non-specific,275209,454,787,5.27282e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16493,Q#1 - >seq6648,superfamily,275209,454,787,5.27282e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16494,Q#1 - >seq6648,non-specific,238185,643,759,1.3671199999999999e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16495,Q#1 - >seq6648,non-specific,274009,293,445,0.000449138,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
16496,Q#1 - >seq6648,superfamily,274009,293,445,0.000449138,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
16497,Q#1 - >seq6648,non-specific,274009,291,465,0.000945535,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
16498,Q#1 - >seq6648,non-specific,223496,292,487,0.0029709,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1P3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
16499,Q#1 - >seq6648,superfamily,223496,292,487,0.0029709,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1P3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
16500,Q#1 - >seq6648,non-specific,235175,293,456,0.00348683,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
16501,Q#1 - >seq6648,superfamily,235175,293,456,0.00348683,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
16502,Q#1 - >seq6648,non-specific,224117,251,488,0.00620294,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
16503,Q#1 - >seq6648,superfamily,224117,251,488,0.00620294,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF2.hs4_gibbon.marg.frame2,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1P3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
16504,Q#2 - >seq6649,specific,197310,9,222,1.9526099999999996e-55,192.18099999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16505,Q#2 - >seq6649,superfamily,351117,9,222,1.9526099999999996e-55,192.18099999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16506,Q#2 - >seq6649,non-specific,197306,9,223,1.8854099999999998e-46,166.888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16507,Q#2 - >seq6649,non-specific,223780,9,221,2.50989e-24,103.447,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16508,Q#2 - >seq6649,non-specific,197307,9,223,1.6426900000000002e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16509,Q#2 - >seq6649,non-specific,197320,8,221,6.5171600000000005e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16510,Q#2 - >seq6649,non-specific,197321,7,223,1.5040799999999999e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16511,Q#2 - >seq6649,specific,335306,10,212,1.90268e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16512,Q#2 - >seq6649,non-specific,272954,9,221,2.0889e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16513,Q#2 - >seq6649,non-specific,273186,9,221,2.2836e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16514,Q#2 - >seq6649,non-specific,197336,7,221,3.90503e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16515,Q#2 - >seq6649,non-specific,197319,8,223,4.71457e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16516,Q#2 - >seq6649,non-specific,197322,9,222,1.15431e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16517,Q#2 - >seq6649,non-specific,236970,9,217,1.22573e-07,54.1298,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16518,Q#2 - >seq6649,non-specific,197311,7,204,8.000020000000001e-05,44.9753,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16519,Q#2 - >seq6649,non-specific,339261,108,217,0.00011822200000000001,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs4_gibbon,marg,CompleteHit
16520,Q#5 - >seq6652,non-specific,335182,157,254,9.254549999999999e-48,155.924,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16521,Q#5 - >seq6652,superfamily,335182,157,254,9.254549999999999e-48,155.924,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16522,Q#5 - >seq6652,non-specific,340205,257,321,3.02946e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16523,Q#5 - >seq6652,superfamily,340205,257,321,3.02946e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16524,Q#5 - >seq6652,non-specific,340204,112,154,4.13737e-09,51.6396,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16525,Q#5 - >seq6652,superfamily,340204,112,154,4.13737e-09,51.6396,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs4_gibbon,marg,CompleteHit
16526,Q#5 - >seq6652,non-specific,179385,61,146,0.000291078,42.3346,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16527,Q#5 - >seq6652,superfamily,179385,61,146,0.000291078,42.3346,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16528,Q#5 - >seq6652,non-specific,224117,66,151,0.000342458,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16529,Q#5 - >seq6652,superfamily,224117,66,151,0.000342458,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16530,Q#5 - >seq6652,non-specific,337766,52,133,0.000413092,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16531,Q#5 - >seq6652,superfamily,337766,52,133,0.000413092,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16532,Q#5 - >seq6652,non-specific,235175,55,143,0.00046302400000000003,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16533,Q#5 - >seq6652,superfamily,235175,55,143,0.00046302400000000003,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16534,Q#5 - >seq6652,non-specific,222878,67,151,0.000680057,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16535,Q#5 - >seq6652,superfamily,222878,67,151,0.000680057,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16536,Q#5 - >seq6652,non-specific,335555,66,133,0.000699537,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16537,Q#5 - >seq6652,superfamily,354396,66,133,0.000699537,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16538,Q#5 - >seq6652,non-specific,224117,55,151,0.000718552,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16539,Q#5 - >seq6652,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16540,Q#5 - >seq6652,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16541,Q#5 - >seq6652,non-specific,274008,56,212,0.000767929,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16542,Q#5 - >seq6652,superfamily,274008,56,212,0.000767929,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16543,Q#5 - >seq6652,non-specific,335556,66,150,0.0009618960000000001,39.4385,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16544,Q#5 - >seq6652,superfamily,335556,66,150,0.0009618960000000001,39.4385,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16545,Q#5 - >seq6652,non-specific,336322,34,168,0.00105102,40.5782,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16546,Q#5 - >seq6652,superfamily,336322,34,168,0.00105102,40.5782,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16547,Q#5 - >seq6652,non-specific,336322,36,134,0.00124171,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16548,Q#5 - >seq6652,non-specific,224117,71,241,0.00260694,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16549,Q#5 - >seq6652,superfamily,224117,71,241,0.00260694,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16550,Q#5 - >seq6652,non-specific,313022,71,154,0.00267107,39.4466,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16551,Q#5 - >seq6652,superfamily,313022,71,154,0.00267107,39.4466,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16552,Q#5 - >seq6652,non-specific,274008,47,244,0.00288429,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16553,Q#5 - >seq6652,superfamily,274008,47,244,0.00288429,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16554,Q#5 - >seq6652,non-specific,224117,66,157,0.00289382,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16555,Q#5 - >seq6652,non-specific,224117,50,151,0.00395785,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16556,Q#5 - >seq6652,non-specific,274009,50,150,0.004226,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16557,Q#5 - >seq6652,superfamily,274009,50,150,0.004226,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16558,Q#5 - >seq6652,non-specific,224117,55,151,0.00435513,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16559,Q#5 - >seq6652,non-specific,235461,59,130,0.00438473,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16560,Q#5 - >seq6652,superfamily,235461,59,130,0.00438473,38.5106,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16561,Q#5 - >seq6652,non-specific,224117,55,151,0.00500514,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16562,Q#5 - >seq6652,non-specific,224117,56,150,0.00565292,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs4_gibbon,marg,N-TerminusTruncated
16563,Q#5 - >seq6652,non-specific,223266,67,141,0.00691845,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16564,Q#5 - >seq6652,superfamily,223266,67,141,0.00691845,38.0218,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16565,Q#5 - >seq6652,non-specific,273690,75,157,0.00712177,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16566,Q#5 - >seq6652,superfamily,355611,75,157,0.00712177,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16567,Q#5 - >seq6652,non-specific,235600,37,131,0.00842328,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16568,Q#5 - >seq6652,superfamily,235600,37,131,0.00842328,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
16569,Q#5 - >seq6652,non-specific,222878,53,198,0.00863797,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16570,Q#20 - >seq6667,non-specific,335182,154,251,2.91223e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16571,Q#20 - >seq6667,superfamily,335182,154,251,2.91223e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16572,Q#20 - >seq6667,non-specific,335182,154,251,2.91223e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16573,Q#20 - >seq6667,non-specific,340205,254,318,1.3965399999999998e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16574,Q#20 - >seq6667,superfamily,340205,254,318,1.3965399999999998e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16575,Q#20 - >seq6667,non-specific,340205,254,318,1.3965399999999998e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16576,Q#20 - >seq6667,non-specific,340204,109,151,1.22165e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16577,Q#20 - >seq6667,superfamily,340204,109,151,1.22165e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16578,Q#20 - >seq6667,non-specific,340204,109,151,1.22165e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,pars,CompleteHit
16579,Q#20 - >seq6667,non-specific,274008,38,161,5.7951499999999996e-05,44.6623,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16580,Q#20 - >seq6667,superfamily,274008,38,161,5.7951499999999996e-05,44.6623,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16581,Q#20 - >seq6667,non-specific,274008,38,161,5.7951499999999996e-05,44.6623,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16582,Q#20 - >seq6667,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16583,Q#20 - >seq6667,superfamily,235175,51,154,0.000224292,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16584,Q#20 - >seq6667,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16585,Q#20 - >seq6667,non-specific,235175,52,140,0.0009571919999999999,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16586,Q#20 - >seq6667,non-specific,235175,52,140,0.0009571919999999999,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16587,Q#20 - >seq6667,non-specific,274008,3,148,0.00513133,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16588,Q#20 - >seq6667,non-specific,274008,3,148,0.00513133,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16589,Q#20 - >seq6667,non-specific,274009,30,202,0.00713602,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16590,Q#20 - >seq6667,superfamily,274009,30,202,0.00713602,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16591,Q#20 - >seq6667,non-specific,274009,30,202,0.00713602,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.pars.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,pars,BothTerminiTruncated
16592,Q#23 - >seq6670,non-specific,335182,154,251,2.91223e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16593,Q#23 - >seq6670,superfamily,335182,154,251,2.91223e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16594,Q#23 - >seq6670,non-specific,335182,154,251,2.91223e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16595,Q#23 - >seq6670,non-specific,340205,254,318,1.3965399999999998e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16596,Q#23 - >seq6670,superfamily,340205,254,318,1.3965399999999998e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16597,Q#23 - >seq6670,non-specific,340205,254,318,1.3965399999999998e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16598,Q#23 - >seq6670,non-specific,340204,109,151,1.22165e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16599,Q#23 - >seq6670,superfamily,340204,109,151,1.22165e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16600,Q#23 - >seq6670,non-specific,340204,109,151,1.22165e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs1_chimp,marg,CompleteHit
16601,Q#23 - >seq6670,non-specific,274008,38,161,5.7951499999999996e-05,44.6623,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16602,Q#23 - >seq6670,superfamily,274008,38,161,5.7951499999999996e-05,44.6623,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16603,Q#23 - >seq6670,non-specific,274008,38,161,5.7951499999999996e-05,44.6623,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16604,Q#23 - >seq6670,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16605,Q#23 - >seq6670,superfamily,235175,51,154,0.000224292,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16606,Q#23 - >seq6670,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16607,Q#23 - >seq6670,non-specific,235175,52,140,0.0009571919999999999,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16608,Q#23 - >seq6670,non-specific,235175,52,140,0.0009571919999999999,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16609,Q#23 - >seq6670,non-specific,274008,3,148,0.00513133,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16610,Q#23 - >seq6670,non-specific,274008,3,148,0.00513133,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16611,Q#23 - >seq6670,non-specific,274009,30,202,0.00713602,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16612,Q#23 - >seq6670,superfamily,274009,30,202,0.00713602,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16613,Q#23 - >seq6670,non-specific,274009,30,202,0.00713602,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs1_chimp.marg.frame3,1909130931_L1P1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs1_chimp,marg,BothTerminiTruncated
16614,Q#27 - >seq6674,non-specific,335182,154,251,2.88104e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16615,Q#27 - >seq6674,superfamily,335182,154,251,2.88104e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16616,Q#27 - >seq6674,non-specific,340205,254,318,1.44459e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16617,Q#27 - >seq6674,superfamily,340205,254,318,1.44459e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16618,Q#27 - >seq6674,non-specific,340204,109,151,1.15125e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16619,Q#27 - >seq6674,superfamily,340204,109,151,1.15125e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs2_gorilla,pars,CompleteHit
16620,Q#27 - >seq6674,non-specific,274008,38,161,4.5755200000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16621,Q#27 - >seq6674,superfamily,274008,38,161,4.5755200000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16622,Q#27 - >seq6674,non-specific,235175,51,154,0.000218481,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16623,Q#27 - >seq6674,superfamily,235175,51,154,0.000218481,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16624,Q#27 - >seq6674,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16625,Q#27 - >seq6674,non-specific,274008,3,148,0.00427463,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16626,Q#27 - >seq6674,non-specific,274009,30,202,0.00671464,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16627,Q#27 - >seq6674,superfamily,274009,30,202,0.00671464,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16628,Q#37 - >seq6684,non-specific,335182,157,254,5.70199e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16629,Q#37 - >seq6684,superfamily,335182,157,254,5.70199e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16630,Q#37 - >seq6684,non-specific,340205,257,321,1.86041e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16631,Q#37 - >seq6684,superfamily,340205,257,321,1.86041e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16632,Q#37 - >seq6684,non-specific,340204,112,154,1.14076e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16633,Q#37 - >seq6684,superfamily,340204,112,154,1.14076e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs2_gorilla,marg,CompleteHit
16634,Q#37 - >seq6684,non-specific,274009,42,151,0.000541453,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16635,Q#37 - >seq6684,superfamily,274009,42,151,0.000541453,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16636,Q#37 - >seq6684,non-specific,274008,38,164,0.00248775,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16637,Q#37 - >seq6684,superfamily,274008,38,164,0.00248775,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16638,Q#37 - >seq6684,non-specific,235175,54,157,0.00424609,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16639,Q#37 - >seq6684,superfamily,235175,54,157,0.00424609,38.8916,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16640,Q#37 - >seq6684,non-specific,274008,30,241,0.00770377,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16641,Q#50 - >seq6697,non-specific,335182,154,251,2.88104e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16642,Q#50 - >seq6697,superfamily,335182,154,251,2.88104e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16643,Q#50 - >seq6697,non-specific,340205,254,318,1.44459e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16644,Q#50 - >seq6697,superfamily,340205,254,318,1.44459e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16645,Q#50 - >seq6697,non-specific,340204,109,151,1.15125e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16646,Q#50 - >seq6697,superfamily,340204,109,151,1.15125e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs2_gorilla,marg,CompleteHit
16647,Q#50 - >seq6697,non-specific,274008,38,161,4.5755200000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16648,Q#50 - >seq6697,superfamily,274008,38,161,4.5755200000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16649,Q#50 - >seq6697,non-specific,235175,51,154,0.000218481,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16650,Q#50 - >seq6697,superfamily,235175,51,154,0.000218481,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16651,Q#50 - >seq6697,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16652,Q#50 - >seq6697,non-specific,274008,3,148,0.00427463,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16653,Q#50 - >seq6697,non-specific,274009,30,202,0.00671464,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16654,Q#50 - >seq6697,superfamily,274009,30,202,0.00671464,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs2_gorilla.marg.frame3,1909130931_L1P1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
16655,Q#51 - >seq6698,specific,238827,481,743,1.1578999999999997e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16656,Q#51 - >seq6698,superfamily,295487,481,743,1.1578999999999997e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16657,Q#51 - >seq6698,specific,333820,487,743,8.46199e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16658,Q#51 - >seq6698,superfamily,333820,487,743,8.46199e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16659,Q#51 - >seq6698,non-specific,238828,487,708,6.9682e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16660,Q#51 - >seq6698,non-specific,275209,438,771,3.1035400000000005e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16661,Q#51 - >seq6698,superfamily,275209,438,771,3.1035400000000005e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16662,Q#51 - >seq6698,non-specific,238185,627,743,6.6093e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs5_gmonkey.marg.frame2,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16663,Q#52 - >seq6699,non-specific,197310,9,71,1.5642600000000002e-14,73.9249,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16664,Q#52 - >seq6699,superfamily,351117,9,71,1.5642600000000002e-14,73.9249,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16665,Q#52 - >seq6699,non-specific,197306,9,73,2.6506599999999996e-13,70.5881,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16666,Q#52 - >seq6699,non-specific,197307,9,72,1.91911e-05,46.8973,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16667,Q#52 - >seq6699,non-specific,223780,9,43,2.21727e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16668,Q#52 - >seq6699,non-specific,197321,7,49,3.61536e-05,46.3912,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16669,Q#52 - >seq6699,specific,335306,10,74,0.000155853,44.1582,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16670,Q#52 - >seq6699,non-specific,197336,7,43,0.00018251700000000001,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16671,Q#52 - >seq6699,non-specific,197320,8,43,0.000632464,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16672,Q#52 - >seq6699,non-specific,273186,9,43,0.00113785,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16673,Q#52 - >seq6699,non-specific,272954,9,43,0.00704401,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16674,Q#52 - >seq6699,non-specific,197319,8,43,0.00990038,38.7969,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
16675,Q#55 - >seq6702,non-specific,335182,154,251,2.6432099999999997e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,pars,CompleteHit
16676,Q#55 - >seq6702,superfamily,335182,154,251,2.6432099999999997e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,pars,CompleteHit
16677,Q#55 - >seq6702,non-specific,340205,254,318,1.34119e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,pars,CompleteHit
16678,Q#55 - >seq6702,superfamily,340205,254,318,1.34119e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,pars,CompleteHit
16679,Q#55 - >seq6702,non-specific,340204,109,151,1.19772e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs0_human,pars,CompleteHit
16680,Q#55 - >seq6702,superfamily,340204,109,151,1.19772e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs0_human,pars,CompleteHit
16681,Q#55 - >seq6702,non-specific,274008,38,161,4.3035600000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16682,Q#55 - >seq6702,superfamily,274008,38,161,4.3035600000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16683,Q#55 - >seq6702,non-specific,235175,51,154,0.000218481,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16684,Q#55 - >seq6702,superfamily,235175,51,154,0.000218481,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16685,Q#55 - >seq6702,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16686,Q#55 - >seq6702,non-specific,274009,14,202,0.00358943,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16687,Q#55 - >seq6702,superfamily,274009,14,202,0.00358943,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16688,Q#55 - >seq6702,non-specific,274008,52,148,0.00707886,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.pars.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,pars,BothTerminiTruncated
16689,Q#60 - >seq6707,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16690,Q#60 - >seq6707,superfamily,335182,157,254,1.3475099999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16691,Q#60 - >seq6707,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16692,Q#60 - >seq6707,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16693,Q#60 - >seq6707,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16694,Q#60 - >seq6707,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16695,Q#60 - >seq6707,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16696,Q#60 - >seq6707,superfamily,340204,112,154,9.18373e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16697,Q#60 - >seq6707,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,pars,CompleteHit
16698,Q#60 - >seq6707,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16699,Q#60 - >seq6707,superfamily,274009,47,151,0.00016673599999999998,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16700,Q#60 - >seq6707,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16701,Q#60 - >seq6707,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16702,Q#60 - >seq6707,superfamily,274008,47,212,0.00457316,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16703,Q#60 - >seq6707,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,pars,BothTerminiTruncated
16704,Q#60 - >seq6707,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,pars,N-TerminusTruncated
16705,Q#60 - >seq6707,superfamily,313022,4,154,0.00492406,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,pars,N-TerminusTruncated
16706,Q#60 - >seq6707,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.pars.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,pars,N-TerminusTruncated
16707,Q#63 - >seq6710,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16708,Q#63 - >seq6710,superfamily,335182,157,254,1.3475099999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16709,Q#63 - >seq6710,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16710,Q#63 - >seq6710,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16711,Q#63 - >seq6710,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16712,Q#63 - >seq6710,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16713,Q#63 - >seq6710,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16714,Q#63 - >seq6710,superfamily,340204,112,154,9.18373e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16715,Q#63 - >seq6710,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs1_chimp,marg,CompleteHit
16716,Q#63 - >seq6710,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16717,Q#63 - >seq6710,superfamily,274009,47,151,0.00016673599999999998,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16718,Q#63 - >seq6710,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16719,Q#63 - >seq6710,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16720,Q#63 - >seq6710,superfamily,274008,47,212,0.00457316,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16721,Q#63 - >seq6710,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs1_chimp,marg,BothTerminiTruncated
16722,Q#63 - >seq6710,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,marg,N-TerminusTruncated
16723,Q#63 - >seq6710,superfamily,313022,4,154,0.00492406,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,marg,N-TerminusTruncated
16724,Q#63 - >seq6710,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs1_chimp.marg.frame3,1909130931_L1P2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs1_chimp,marg,N-TerminusTruncated
16725,Q#66 - >seq6713,non-specific,335182,157,254,5.70199e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16726,Q#66 - >seq6713,superfamily,335182,157,254,5.70199e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16727,Q#66 - >seq6713,non-specific,340205,257,321,1.86041e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16728,Q#66 - >seq6713,superfamily,340205,257,321,1.86041e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16729,Q#66 - >seq6713,non-specific,340204,112,154,1.14076e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16730,Q#66 - >seq6713,superfamily,340204,112,154,1.14076e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs2_gorilla,pars,CompleteHit
16731,Q#66 - >seq6713,non-specific,274009,42,151,0.000541453,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16732,Q#66 - >seq6713,superfamily,274009,42,151,0.000541453,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16733,Q#66 - >seq6713,non-specific,274008,38,164,0.00248775,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16734,Q#66 - >seq6713,superfamily,274008,38,164,0.00248775,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16735,Q#66 - >seq6713,non-specific,235175,54,157,0.00424609,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16736,Q#66 - >seq6713,superfamily,235175,54,157,0.00424609,38.8916,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16737,Q#66 - >seq6713,non-specific,274008,30,241,0.00770377,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs2_gorilla.pars.frame3,1909130931_L1P2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16738,Q#68 - >seq6715,specific,197310,59,229,7.95208e-40,147.113,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16739,Q#68 - >seq6715,superfamily,351117,59,229,7.95208e-40,147.113,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16740,Q#68 - >seq6715,non-specific,197306,61,229,9.0689e-36,135.687,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16741,Q#68 - >seq6715,non-specific,197307,61,229,6.72226e-16,78.4837,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16742,Q#68 - >seq6715,non-specific,223780,65,231,2.77395e-15,76.8683,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16743,Q#68 - >seq6715,non-specific,197320,65,229,4.44947e-13,70.2366,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16744,Q#68 - >seq6715,non-specific,197321,59,229,6.28375e-12,66.8068,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16745,Q#68 - >seq6715,non-specific,273186,64,230,1.94188e-11,65.378,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16746,Q#68 - >seq6715,non-specific,339261,101,225,4.2365600000000005e-09,55.0359,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16747,Q#68 - >seq6715,non-specific,197319,59,229,5.3429899999999996e-09,58.0569,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16748,Q#68 - >seq6715,non-specific,335306,33,222,1.00534e-08,56.4846,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,CompleteHit
16749,Q#68 - >seq6715,non-specific,272954,61,229,2.31846e-08,55.8521,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16750,Q#68 - >seq6715,non-specific,236970,61,231,2.72489e-07,52.9742,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16751,Q#68 - >seq6715,non-specific,197322,84,229,4.01175e-07,52.7046,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16752,Q#68 - >seq6715,non-specific,197311,65,229,1.24357e-06,49.9829,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16753,Q#68 - >seq6715,non-specific,197317,132,222,1.6561000000000001e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16754,Q#68 - >seq6715,non-specific,226098,131,232,0.00037788599999999997,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16755,Q#68 - >seq6715,non-specific,114219,228,371,0.00617562,40.4753,pfam05483,SCP-1,N,cl30946,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16756,Q#68 - >seq6715,superfamily,114219,228,371,0.00617562,40.4753,cl30946,SCP-1 superfamily,N, - ,Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.,L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16757,Q#68 - >seq6715,non-specific,339176,219,343,0.00719488,38.7734,pfam14335,DUF4391,N,cl20517,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16758,Q#68 - >seq6715,superfamily,339176,219,343,0.00719488,38.7734,cl20517,DUF4391 superfamily,N, - ,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1P1.ORF2.hs5_gmonkey.marg.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
16759,Q#69 - >seq6716,specific,238827,615,730,2.1268599999999998e-31,122.015,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16760,Q#69 - >seq6716,superfamily,295487,615,730,2.1268599999999998e-31,122.015,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16761,Q#69 - >seq6716,non-specific,333820,602,730,1.7874400000000002e-16,78.10300000000001,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16762,Q#69 - >seq6716,superfamily,333820,602,730,1.7874400000000002e-16,78.10300000000001,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16763,Q#69 - >seq6716,non-specific,197310,9,71,4.16344e-14,72.3841,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16764,Q#69 - >seq6716,superfamily,351117,9,71,4.16344e-14,72.3841,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16765,Q#69 - >seq6716,non-specific,197306,9,73,4.06884e-13,69.4325,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16766,Q#69 - >seq6716,non-specific,238185,614,730,8.20323e-06,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,CompleteHit
16767,Q#69 - >seq6716,non-specific,223780,9,43,1.78951e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16768,Q#69 - >seq6716,non-specific,197307,9,72,2.46208e-05,46.5121,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16769,Q#69 - >seq6716,non-specific,197321,7,49,3.5011999999999996e-05,46.006,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16770,Q#69 - >seq6716,specific,335306,10,74,0.000126584,44.1582,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16771,Q#69 - >seq6716,non-specific,197336,7,43,0.00014769299999999998,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16772,Q#69 - >seq6716,non-specific,238828,616,695,0.000254531,42.9585,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16773,Q#69 - >seq6716,non-specific,197320,8,43,0.0005122880000000001,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16774,Q#69 - >seq6716,non-specific,273186,9,43,0.000990858,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16775,Q#69 - >seq6716,non-specific,275209,614,758,0.0064563,39.3632,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16776,Q#69 - >seq6716,superfamily,275209,614,758,0.0064563,39.3632,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16777,Q#69 - >seq6716,non-specific,272954,9,43,0.00817404,38.5181,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16778,Q#70 - >seq6717,non-specific,335182,154,251,2.6432099999999997e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,marg,CompleteHit
16779,Q#70 - >seq6717,superfamily,335182,154,251,2.6432099999999997e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,marg,CompleteHit
16780,Q#70 - >seq6717,non-specific,340205,254,318,1.34119e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,marg,CompleteHit
16781,Q#70 - >seq6717,superfamily,340205,254,318,1.34119e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs0_human,marg,CompleteHit
16782,Q#70 - >seq6717,non-specific,340204,109,151,1.19772e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs0_human,marg,CompleteHit
16783,Q#70 - >seq6717,superfamily,340204,109,151,1.19772e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs0_human,marg,CompleteHit
16784,Q#70 - >seq6717,non-specific,274008,38,161,4.3035600000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16785,Q#70 - >seq6717,superfamily,274008,38,161,4.3035600000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16786,Q#70 - >seq6717,non-specific,235175,51,154,0.000218481,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16787,Q#70 - >seq6717,superfamily,235175,51,154,0.000218481,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16788,Q#70 - >seq6717,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16789,Q#70 - >seq6717,non-specific,274009,14,202,0.00358943,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16790,Q#70 - >seq6717,superfamily,274009,14,202,0.00358943,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16791,Q#70 - >seq6717,non-specific,274008,52,148,0.00707886,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs0_human.marg.frame3,1909130931_L1P1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs0_human,marg,BothTerminiTruncated
16792,Q#71 - >seq6718,specific,197310,59,229,4.969180000000001e-40,147.498,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16793,Q#71 - >seq6718,superfamily,351117,59,229,4.969180000000001e-40,147.498,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16794,Q#71 - >seq6718,non-specific,197306,61,229,2.0366899999999997e-35,134.531,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16795,Q#71 - >seq6718,specific,238827,503,609,1.6981799999999996e-34,131.259,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16796,Q#71 - >seq6718,superfamily,295487,503,609,1.6981799999999996e-34,131.259,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16797,Q#71 - >seq6718,non-specific,197307,61,229,1.5387800000000001e-15,76.9429,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16798,Q#71 - >seq6718,non-specific,223780,65,231,2.68712e-15,76.4831,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16799,Q#71 - >seq6718,non-specific,333820,509,620,6.6658600000000006e-15,73.4806,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16800,Q#71 - >seq6718,superfamily,333820,509,620,6.6658600000000006e-15,73.4806,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16801,Q#71 - >seq6718,non-specific,197320,65,229,3.51672e-13,70.2366,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16802,Q#71 - >seq6718,non-specific,197321,59,229,1.31011e-11,65.266,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16803,Q#71 - >seq6718,non-specific,273186,64,230,1.58021e-11,64.9928,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16804,Q#71 - >seq6718,non-specific,339261,101,225,2.22891e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1P1,ORF2,hs5_gmonkey,pars,CompleteHit
16805,Q#71 - >seq6718,non-specific,335306,33,222,8.02565e-09,56.4846,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,CompleteHit
16806,Q#71 - >seq6718,non-specific,197319,59,229,1.8350599999999998e-08,56.1309,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16807,Q#71 - >seq6718,non-specific,272954,61,229,2.6827099999999998e-08,55.4669,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16808,Q#71 - >seq6718,non-specific,236970,61,231,1.66052e-07,53.3594,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16809,Q#71 - >seq6718,non-specific,197322,84,229,3.16789e-07,52.7046,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16810,Q#71 - >seq6718,non-specific,197311,65,229,9.97025e-07,49.9829,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16811,Q#71 - >seq6718,non-specific,197317,132,222,1.31844e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16812,Q#71 - >seq6718,non-specific,226098,131,232,0.00030198599999999996,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
16813,Q#71 - >seq6718,non-specific,274009,298,446,0.00171618,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16814,Q#71 - >seq6718,superfamily,274009,298,446,0.00171618,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
16815,Q#71 - >seq6718,non-specific,235175,288,457,0.00325758,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16816,Q#71 - >seq6718,superfamily,235175,288,457,0.00325758,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF2.hs5_gmonkey.pars.frame1,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
16817,Q#75 - >seq6722,non-specific,335182,154,251,2.06327e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,pars,CompleteHit
16818,Q#75 - >seq6722,superfamily,335182,154,251,2.06327e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,pars,CompleteHit
16819,Q#75 - >seq6722,non-specific,340205,254,318,1.09454e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,pars,CompleteHit
16820,Q#75 - >seq6722,superfamily,340205,254,318,1.09454e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,pars,CompleteHit
16821,Q#75 - >seq6722,non-specific,340204,109,151,1.15125e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs3_orang,pars,CompleteHit
16822,Q#75 - >seq6722,superfamily,340204,109,151,1.15125e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs3_orang,pars,CompleteHit
16823,Q#75 - >seq6722,non-specific,274008,38,161,5.17199e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16824,Q#75 - >seq6722,superfamily,274008,38,161,5.17199e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16825,Q#75 - >seq6722,non-specific,235175,51,154,0.0006293630000000001,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16826,Q#75 - >seq6722,superfamily,235175,51,154,0.0006293630000000001,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16827,Q#75 - >seq6722,non-specific,235175,52,140,0.00223199,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16828,Q#75 - >seq6722,non-specific,274008,52,148,0.00648937,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,pars,BothTerminiTruncated
16829,Q#75 - >seq6722,non-specific,313022,4,151,0.00652906,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P1,ORF1,hs3_orang,pars,N-TerminusTruncated
16830,Q#75 - >seq6722,superfamily,313022,4,151,0.00652906,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs3_orang.pars.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P1,ORF1,hs3_orang,pars,N-TerminusTruncated
16831,Q#80 - >seq6727,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16832,Q#80 - >seq6727,superfamily,335182,154,251,2.201e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16833,Q#80 - >seq6727,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16834,Q#80 - >seq6727,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16835,Q#80 - >seq6727,non-specific,340204,109,151,1.07423e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16836,Q#80 - >seq6727,superfamily,340204,109,151,1.07423e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs4_gibbon,pars,CompleteHit
16837,Q#80 - >seq6727,non-specific,274008,38,161,5.30958e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16838,Q#80 - >seq6727,superfamily,274008,38,161,5.30958e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16839,Q#80 - >seq6727,non-specific,235175,51,154,0.0006293630000000001,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16840,Q#80 - >seq6727,superfamily,235175,51,154,0.0006293630000000001,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16841,Q#80 - >seq6727,non-specific,235175,52,140,0.00227128,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16842,Q#80 - >seq6727,non-specific,274008,3,148,0.00412844,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.pars.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16843,Q#81 - >seq6728,non-specific,335182,154,251,2.06327e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,marg,CompleteHit
16844,Q#81 - >seq6728,superfamily,335182,154,251,2.06327e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,marg,CompleteHit
16845,Q#81 - >seq6728,non-specific,340205,254,318,1.09454e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,marg,CompleteHit
16846,Q#81 - >seq6728,superfamily,340205,254,318,1.09454e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs3_orang,marg,CompleteHit
16847,Q#81 - >seq6728,non-specific,340204,109,151,1.15125e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs3_orang,marg,CompleteHit
16848,Q#81 - >seq6728,superfamily,340204,109,151,1.15125e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs3_orang,marg,CompleteHit
16849,Q#81 - >seq6728,non-specific,274008,38,161,5.17199e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16850,Q#81 - >seq6728,superfamily,274008,38,161,5.17199e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16851,Q#81 - >seq6728,non-specific,235175,51,154,0.0006293630000000001,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16852,Q#81 - >seq6728,superfamily,235175,51,154,0.0006293630000000001,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16853,Q#81 - >seq6728,non-specific,235175,52,140,0.00223199,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16854,Q#81 - >seq6728,non-specific,274008,52,148,0.00648937,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs3_orang,marg,BothTerminiTruncated
16855,Q#81 - >seq6728,non-specific,313022,4,151,0.00652906,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P1,ORF1,hs3_orang,marg,N-TerminusTruncated
16856,Q#81 - >seq6728,superfamily,313022,4,151,0.00652906,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs3_orang.marg.frame3,1909130931_L1P1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P1,ORF1,hs3_orang,marg,N-TerminusTruncated
16857,Q#83 - >seq6730,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16858,Q#83 - >seq6730,superfamily,335182,154,251,2.201e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16859,Q#83 - >seq6730,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16860,Q#83 - >seq6730,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16861,Q#83 - >seq6730,non-specific,340204,109,151,1.07423e-11,58.5732,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16862,Q#83 - >seq6730,superfamily,340204,109,151,1.07423e-11,58.5732,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs4_gibbon,marg,CompleteHit
16863,Q#83 - >seq6730,non-specific,274008,38,161,5.30958e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16864,Q#83 - >seq6730,superfamily,274008,38,161,5.30958e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16865,Q#83 - >seq6730,non-specific,235175,51,154,0.0006293630000000001,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16866,Q#83 - >seq6730,superfamily,235175,51,154,0.0006293630000000001,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16867,Q#83 - >seq6730,non-specific,235175,52,140,0.00227128,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16868,Q#83 - >seq6730,non-specific,274008,3,148,0.00412844,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs4_gibbon.marg.frame3,1909130931_L1P1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16869,Q#86 - >seq6733,non-specific,335182,157,254,8.960539999999999e-48,156.309,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16870,Q#86 - >seq6733,superfamily,335182,157,254,8.960539999999999e-48,156.309,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16871,Q#86 - >seq6733,non-specific,335182,157,254,8.960539999999999e-48,156.309,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16872,Q#86 - >seq6733,non-specific,340205,257,321,3.47693e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16873,Q#86 - >seq6733,superfamily,340205,257,321,3.47693e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16874,Q#86 - >seq6733,non-specific,340205,257,321,3.47693e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16875,Q#86 - >seq6733,non-specific,340204,112,154,1.17499e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16876,Q#86 - >seq6733,superfamily,340204,112,154,1.17499e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16877,Q#86 - >seq6733,non-specific,340204,112,154,1.17499e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,pars,CompleteHit
16878,Q#86 - >seq6733,non-specific,274009,42,151,0.0006851260000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16879,Q#86 - >seq6733,superfamily,274009,42,151,0.0006851260000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16880,Q#86 - >seq6733,non-specific,274009,42,151,0.0006851260000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16881,Q#86 - >seq6733,non-specific,274008,38,164,0.00337315,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16882,Q#86 - >seq6733,superfamily,274008,38,164,0.00337315,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16883,Q#86 - >seq6733,non-specific,274008,38,164,0.00337315,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16884,Q#86 - >seq6733,non-specific,313022,7,154,0.00388942,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16885,Q#86 - >seq6733,superfamily,313022,7,154,0.00388942,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16886,Q#86 - >seq6733,non-specific,313022,7,154,0.00388942,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
16887,Q#86 - >seq6733,non-specific,235175,54,157,0.00514311,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16888,Q#86 - >seq6733,superfamily,235175,54,157,0.00514311,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16889,Q#86 - >seq6733,non-specific,235175,54,157,0.00514311,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16890,Q#86 - >seq6733,non-specific,274008,28,212,0.00811605,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16891,Q#86 - >seq6733,non-specific,274008,28,212,0.00811605,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.pars.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16892,Q#90 - >seq6737,non-specific,335182,157,254,8.960539999999999e-48,156.309,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16893,Q#90 - >seq6737,superfamily,335182,157,254,8.960539999999999e-48,156.309,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16894,Q#90 - >seq6737,non-specific,335182,157,254,8.960539999999999e-48,156.309,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16895,Q#90 - >seq6737,non-specific,340205,257,321,3.47693e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16896,Q#90 - >seq6737,superfamily,340205,257,321,3.47693e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16897,Q#90 - >seq6737,non-specific,340205,257,321,3.47693e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16898,Q#90 - >seq6737,non-specific,340204,112,154,1.17499e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16899,Q#90 - >seq6737,superfamily,340204,112,154,1.17499e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16900,Q#90 - >seq6737,non-specific,340204,112,154,1.17499e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P1,ORF1,hs5_gmonkey,marg,CompleteHit
16901,Q#90 - >seq6737,non-specific,274009,42,151,0.0006851260000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16902,Q#90 - >seq6737,superfamily,274009,42,151,0.0006851260000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16903,Q#90 - >seq6737,non-specific,274009,42,151,0.0006851260000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16904,Q#90 - >seq6737,non-specific,274008,38,164,0.00337315,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16905,Q#90 - >seq6737,superfamily,274008,38,164,0.00337315,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16906,Q#90 - >seq6737,non-specific,274008,38,164,0.00337315,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16907,Q#90 - >seq6737,non-specific,313022,7,154,0.00388942,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16908,Q#90 - >seq6737,superfamily,313022,7,154,0.00388942,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16909,Q#90 - >seq6737,non-specific,313022,7,154,0.00388942,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
16910,Q#90 - >seq6737,non-specific,235175,54,157,0.00514311,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16911,Q#90 - >seq6737,superfamily,235175,54,157,0.00514311,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16912,Q#90 - >seq6737,non-specific,235175,54,157,0.00514311,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16913,Q#90 - >seq6737,non-specific,274008,28,212,0.00811605,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16914,Q#90 - >seq6737,non-specific,274008,28,212,0.00811605,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P1.ORF1.hs5_gmonkey.marg.frame3,1909130931_L1P1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16915,Q#91 - >seq6738,non-specific,335182,151,246,5.094159999999999e-34,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs2_gorilla,marg,CompleteHit
16916,Q#91 - >seq6738,superfamily,335182,151,246,5.094159999999999e-34,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs2_gorilla,marg,CompleteHit
16917,Q#91 - >seq6738,non-specific,340205,249,312,5.7030799999999995e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs2_gorilla,marg,CompleteHit
16918,Q#91 - >seq6738,superfamily,340205,249,312,5.7030799999999995e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs2_gorilla,marg,CompleteHit
16919,Q#91 - >seq6738,non-specific,214360,6,134,0.00129865,40.0988,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
16920,Q#91 - >seq6738,superfamily,214360,6,134,0.00129865,40.0988,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
16921,Q#91 - >seq6738,non-specific,224117,50,197,0.00583259,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
16922,Q#91 - >seq6738,superfamily,224117,50,197,0.00583259,38.1568,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs2_gorilla.marg.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs2_gorilla,marg,N-TerminusTruncated
16923,Q#92 - >seq6739,non-specific,335182,153,248,8.7884e-34,119.33,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs3_orang,marg,CompleteHit
16924,Q#92 - >seq6739,superfamily,335182,153,248,8.7884e-34,119.33,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs3_orang,marg,CompleteHit
16925,Q#92 - >seq6739,non-specific,340205,251,314,1.02952e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs3_orang,marg,CompleteHit
16926,Q#92 - >seq6739,superfamily,340205,251,314,1.02952e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs3_orang,marg,CompleteHit
16927,Q#92 - >seq6739,non-specific,222878,51,123,0.00139288,39.9977,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs3_orang,marg,BothTerminiTruncated
16928,Q#92 - >seq6739,superfamily,222878,51,123,0.00139288,39.9977,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs3_orang,marg,BothTerminiTruncated
16929,Q#92 - >seq6739,non-specific,224117,50,199,0.00206904,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,marg,N-TerminusTruncated
16930,Q#92 - >seq6739,superfamily,224117,50,199,0.00206904,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs3_orang,marg,N-TerminusTruncated
16931,Q#92 - >seq6739,non-specific,224117,36,200,0.00649203,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs3_orang.marg.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,marg,BothTerminiTruncated
16932,Q#95 - >seq6742,non-specific,222878,49,157,0.000166251,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16933,Q#95 - >seq6742,superfamily,222878,49,157,0.000166251,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16934,Q#95 - >seq6742,non-specific,224117,34,168,0.00134958,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16935,Q#95 - >seq6742,superfamily,224117,34,168,0.00134958,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16936,Q#95 - >seq6742,non-specific,274009,49,183,0.00495159,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,pars,N-TerminusTruncated
16937,Q#95 - >seq6742,superfamily,274009,49,183,0.00495159,38.5103,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,pars,N-TerminusTruncated
16938,Q#95 - >seq6742,non-specific,235175,48,169,0.00732741,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16939,Q#95 - >seq6742,superfamily,235175,48,169,0.00732741,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF1.hs3_orang.pars.frame3,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs3_orang,pars,BothTerminiTruncated
16940,Q#96 - >seq6743,non-specific,335182,136,231,4.77536e-35,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs3_orang.pars.frame2,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs3_orang,pars,CompleteHit
16941,Q#96 - >seq6743,superfamily,335182,136,231,4.77536e-35,122.411,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs3_orang.pars.frame2,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs3_orang,pars,CompleteHit
16942,Q#96 - >seq6743,non-specific,340205,234,297,1.76921e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs3_orang.pars.frame2,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs3_orang,pars,CompleteHit
16943,Q#96 - >seq6743,superfamily,340205,234,297,1.76921e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs3_orang.pars.frame2,1909130933_L1P4a.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs3_orang,pars,CompleteHit
16944,Q#97 - >seq6744,non-specific,335182,149,244,5.83535e-34,119.715,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,pars,CompleteHit
16945,Q#97 - >seq6744,superfamily,335182,149,244,5.83535e-34,119.715,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,pars,CompleteHit
16946,Q#97 - >seq6744,non-specific,340205,247,310,9.399079999999999e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,pars,CompleteHit
16947,Q#97 - >seq6744,superfamily,340205,247,310,9.399079999999999e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,pars,CompleteHit
16948,Q#97 - >seq6744,non-specific,222878,50,119,0.00474923,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16949,Q#97 - >seq6744,superfamily,222878,50,119,0.00474923,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16950,Q#97 - >seq6744,non-specific,224117,35,142,0.00634837,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16951,Q#97 - >seq6744,superfamily,224117,35,142,0.00634837,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs4_gibbon.pars.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1P4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
16952,Q#100 - >seq6747,non-specific,335182,137,232,1.2859100000000001e-33,118.559,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs5_gmonkey.marg.frame2,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4a,ORF1,hs5_gmonkey,marg,CompleteHit
16953,Q#100 - >seq6747,superfamily,335182,137,232,1.2859100000000001e-33,118.559,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs5_gmonkey.marg.frame2,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4a,ORF1,hs5_gmonkey,marg,CompleteHit
16954,Q#100 - >seq6747,non-specific,340205,235,298,1.0928e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs5_gmonkey.marg.frame2,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4a,ORF1,hs5_gmonkey,marg,CompleteHit
16955,Q#100 - >seq6747,superfamily,340205,235,298,1.0928e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs5_gmonkey.marg.frame2,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4a,ORF1,hs5_gmonkey,marg,CompleteHit
16956,Q#101 - >seq6748,non-specific,335182,149,244,5.83535e-34,119.715,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,marg,CompleteHit
16957,Q#101 - >seq6748,superfamily,335182,149,244,5.83535e-34,119.715,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,marg,CompleteHit
16958,Q#101 - >seq6748,non-specific,340205,247,310,9.399079999999999e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,marg,CompleteHit
16959,Q#101 - >seq6748,superfamily,340205,247,310,9.399079999999999e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs4_gibbon,marg,CompleteHit
16960,Q#101 - >seq6748,non-specific,222878,50,119,0.00474923,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16961,Q#101 - >seq6748,superfamily,222878,50,119,0.00474923,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16962,Q#101 - >seq6748,non-specific,224117,35,142,0.00634837,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16963,Q#101 - >seq6748,superfamily,224117,35,142,0.00634837,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs4_gibbon.marg.frame1,1909130933_L1P4a.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1P4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
16964,Q#106 - >seq6753,non-specific,335182,149,244,2.3838400000000003e-34,120.87100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs5_gmonkey,pars,CompleteHit
16965,Q#106 - >seq6753,superfamily,335182,149,244,2.3838400000000003e-34,120.87100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs5_gmonkey,pars,CompleteHit
16966,Q#106 - >seq6753,non-specific,340205,247,310,5.3609699999999995e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs5_gmonkey,pars,CompleteHit
16967,Q#106 - >seq6753,superfamily,340205,247,310,5.3609699999999995e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs5_gmonkey,pars,CompleteHit
16968,Q#106 - >seq6753,non-specific,222878,49,118,0.00263438,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16969,Q#106 - >seq6753,superfamily,222878,49,118,0.00263438,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs5_gmonkey.pars.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
16970,Q#108 - >seq6755,non-specific,222878,49,121,0.000642794,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs5_gmonkey.marg.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16971,Q#108 - >seq6755,superfamily,222878,49,121,0.000642794,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs5_gmonkey.marg.frame3,1909130933_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
16972,Q#114 - >seq6761,non-specific,214360,6,134,0.000256394,42.41,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
16973,Q#114 - >seq6761,superfamily,214360,6,134,0.000256394,42.41,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4a,ORF1,hs2_gorilla,pars,N-TerminusTruncated
16974,Q#114 - >seq6761,non-specific,222878,51,146,0.00342726,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16975,Q#114 - >seq6761,superfamily,222878,51,146,0.00342726,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16976,Q#114 - >seq6761,non-specific,274009,33,119,0.00701578,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16977,Q#114 - >seq6761,superfamily,274009,33,119,0.00701578,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF1.hs2_gorilla.pars.frame3,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs2_gorilla,pars,BothTerminiTruncated
16978,Q#117 - >seq6764,non-specific,335182,156,253,9.614410000000001e-48,155.924,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,pars,CompleteHit
16979,Q#117 - >seq6764,superfamily,335182,156,253,9.614410000000001e-48,155.924,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,pars,CompleteHit
16980,Q#117 - >seq6764,non-specific,340205,256,320,3.7079899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,pars,CompleteHit
16981,Q#117 - >seq6764,superfamily,340205,256,320,3.7079899999999995e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,pars,CompleteHit
16982,Q#117 - >seq6764,non-specific,340204,111,153,2.81069e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs0_human,pars,CompleteHit
16983,Q#117 - >seq6764,superfamily,340204,111,153,2.81069e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P3,ORF1,hs0_human,pars,CompleteHit
16984,Q#117 - >seq6764,non-specific,337766,51,140,0.000369423,41.8295,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs0_human,pars,N-TerminusTruncated
16985,Q#117 - >seq6764,superfamily,337766,51,140,0.000369423,41.8295,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1P3,ORF1,hs0_human,pars,N-TerminusTruncated
16986,Q#117 - >seq6764,non-specific,222878,66,150,0.000813435,40.7681,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16987,Q#117 - >seq6764,superfamily,222878,66,150,0.000813435,40.7681,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16988,Q#117 - >seq6764,non-specific,224117,54,150,0.00081449,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16989,Q#117 - >seq6764,superfamily,224117,54,150,0.00081449,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16990,Q#117 - >seq6764,non-specific,224117,65,150,0.000978038,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16991,Q#117 - >seq6764,non-specific,274008,55,211,0.00111093,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16992,Q#117 - >seq6764,superfamily,274008,55,211,0.00111093,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16993,Q#117 - >seq6764,non-specific,235175,54,142,0.00111251,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16994,Q#117 - >seq6764,superfamily,235175,54,142,0.00111251,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16995,Q#117 - >seq6764,non-specific,336322,33,167,0.00118227,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16996,Q#117 - >seq6764,superfamily,336322,33,167,0.00118227,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16997,Q#117 - >seq6764,non-specific,224117,49,150,0.00151181,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
16998,Q#117 - >seq6764,non-specific,274765,47,127,0.00169902,39.6254,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
16999,Q#117 - >seq6764,superfamily,274765,47,127,0.00169902,39.6254,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17000,Q#117 - >seq6764,non-specific,224117,70,240,0.00178378,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17001,Q#117 - >seq6764,superfamily,224117,70,240,0.00178378,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17002,Q#117 - >seq6764,non-specific,336322,35,133,0.00212813,39.4226,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17003,Q#117 - >seq6764,non-specific,335556,65,149,0.00252037,38.2829,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17004,Q#117 - >seq6764,superfamily,335556,65,149,0.00252037,38.2829,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17005,Q#117 - >seq6764,non-specific,235175,68,150,0.00316873,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17006,Q#117 - >seq6764,non-specific,274008,46,258,0.00326944,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17007,Q#117 - >seq6764,superfamily,274008,46,258,0.00326944,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17008,Q#117 - >seq6764,non-specific,337663,68,148,0.00456333,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17009,Q#117 - >seq6764,superfamily,337663,68,148,0.00456333,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17010,Q#117 - >seq6764,non-specific,224117,54,150,0.0049799,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17011,Q#117 - >seq6764,non-specific,179385,60,145,0.00498054,38.4826,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17012,Q#117 - >seq6764,superfamily,179385,60,145,0.00498054,38.4826,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17013,Q#117 - >seq6764,non-specific,274009,49,210,0.00605796,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,N-TerminusTruncated
17014,Q#117 - >seq6764,superfamily,274009,49,210,0.00605796,38.5103,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,N-TerminusTruncated
17015,Q#117 - >seq6764,non-specific,224117,55,149,0.00624299,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,N-TerminusTruncated
17016,Q#117 - >seq6764,non-specific,235461,58,129,0.0070834999999999995,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17017,Q#117 - >seq6764,superfamily,235461,58,129,0.0070834999999999995,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17018,Q#117 - >seq6764,non-specific,224117,65,156,0.00789429,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,pars,BothTerminiTruncated
17019,Q#117 - >seq6764,non-specific,235600,36,130,0.00989545,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17020,Q#117 - >seq6764,superfamily,235600,36,130,0.00989545,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs0_human.pars.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P3,ORF1,hs0_human,pars,C-TerminusTruncated
17021,Q#119 - >seq6766,non-specific,335182,157,254,1.0086600000000001e-47,155.924,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,marg,CompleteHit
17022,Q#119 - >seq6766,superfamily,335182,157,254,1.0086600000000001e-47,155.924,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,marg,CompleteHit
17023,Q#119 - >seq6766,non-specific,340205,257,321,3.86559e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,marg,CompleteHit
17024,Q#119 - >seq6766,superfamily,340205,257,321,3.86559e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P3,ORF1,hs0_human,marg,CompleteHit
17025,Q#119 - >seq6766,non-specific,340204,112,154,2.12094e-09,52.41,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs0_human,marg,CompleteHit
17026,Q#119 - >seq6766,superfamily,340204,112,154,2.12094e-09,52.41,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P3,ORF1,hs0_human,marg,CompleteHit
17027,Q#119 - >seq6766,non-specific,337766,52,141,0.000345834,41.8295,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17028,Q#119 - >seq6766,superfamily,337766,52,141,0.000345834,41.8295,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17029,Q#119 - >seq6766,non-specific,224117,55,151,0.000718552,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17030,Q#119 - >seq6766,superfamily,224117,55,151,0.000718552,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17031,Q#119 - >seq6766,non-specific,222878,67,151,0.0007295289999999999,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17032,Q#119 - >seq6766,superfamily,222878,67,151,0.0007295289999999999,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17033,Q#119 - >seq6766,non-specific,224117,66,151,0.000862832,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17034,Q#119 - >seq6766,non-specific,235175,55,143,0.000972643,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17035,Q#119 - >seq6766,superfamily,235175,55,143,0.000972643,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17036,Q#119 - >seq6766,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17037,Q#119 - >seq6766,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17038,Q#119 - >seq6766,non-specific,336322,34,168,0.000997106,40.5782,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17039,Q#119 - >seq6766,superfamily,336322,34,168,0.000997106,40.5782,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17040,Q#119 - >seq6766,non-specific,224117,50,151,0.00129932,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17041,Q#119 - >seq6766,non-specific,224117,71,241,0.00146777,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17042,Q#119 - >seq6766,superfamily,224117,71,241,0.00146777,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17043,Q#119 - >seq6766,non-specific,274765,48,128,0.0017076,39.6254,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17044,Q#119 - >seq6766,superfamily,274765,48,128,0.0017076,39.6254,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17045,Q#119 - >seq6766,non-specific,336322,36,134,0.00190852,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17046,Q#119 - >seq6766,non-specific,335556,66,150,0.00222204,38.2829,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17047,Q#119 - >seq6766,superfamily,335556,66,150,0.00222204,38.2829,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17048,Q#119 - >seq6766,non-specific,274008,47,259,0.00259836,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17049,Q#119 - >seq6766,superfamily,274008,47,259,0.00259836,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17050,Q#119 - >seq6766,non-specific,235175,69,151,0.00279459,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17051,Q#119 - >seq6766,non-specific,224117,55,151,0.00409794,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17052,Q#119 - >seq6766,non-specific,179385,61,146,0.00431658,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17053,Q#119 - >seq6766,superfamily,179385,61,146,0.00431658,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17054,Q#119 - >seq6766,non-specific,337663,69,149,0.00442526,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17055,Q#119 - >seq6766,superfamily,337663,69,149,0.00442526,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17056,Q#119 - >seq6766,non-specific,224117,56,150,0.00536563,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17057,Q#119 - >seq6766,non-specific,274009,50,211,0.00548539,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17058,Q#119 - >seq6766,superfamily,274009,50,211,0.00548539,38.5103,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17059,Q#119 - >seq6766,non-specific,224117,66,157,0.00672618,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P3,ORF1,hs0_human,marg,BothTerminiTruncated
17060,Q#119 - >seq6766,non-specific,235461,59,130,0.00693217,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17061,Q#119 - >seq6766,superfamily,235461,59,130,0.00693217,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17062,Q#119 - >seq6766,non-specific,335555,66,141,0.00938633,37.6252,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17063,Q#119 - >seq6766,superfamily,354396,66,141,0.00938633,37.6252,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1P3,ORF1,hs0_human,marg,N-TerminusTruncated
17064,Q#119 - >seq6766,non-specific,235600,37,131,0.00960242,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17065,Q#119 - >seq6766,superfamily,235600,37,131,0.00960242,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17066,Q#119 - >seq6766,non-specific,273690,75,197,0.00969916,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17067,Q#119 - >seq6766,superfamily,355611,75,197,0.00969916,37.3253,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1P3.ORF1.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1P3,ORF1,hs0_human,marg,C-TerminusTruncated
17068,Q#120 - >seq6767,specific,238827,502,747,1.6294399999999998e-60,205.988,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17069,Q#120 - >seq6767,superfamily,295487,502,747,1.6294399999999998e-60,205.988,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17070,Q#120 - >seq6767,specific,197310,30,229,1.7781900000000001e-47,169.454,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17071,Q#120 - >seq6767,superfamily,351117,30,229,1.7781900000000001e-47,169.454,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17072,Q#120 - >seq6767,non-specific,197306,25,229,1.0964499999999998e-39,147.243,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17073,Q#120 - >seq6767,specific,333820,503,747,1.0895099999999998e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17074,Q#120 - >seq6767,superfamily,333820,503,747,1.0895099999999998e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17075,Q#120 - >seq6767,non-specific,223780,20,231,1.20678e-15,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17076,Q#120 - >seq6767,non-specific,197307,25,229,5.43981e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17077,Q#120 - >seq6767,non-specific,197320,65,229,7.89679e-12,66.3846,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17078,Q#120 - >seq6767,specific,335306,23,222,2.18615e-11,64.5738,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17079,Q#120 - >seq6767,non-specific,238828,557,712,2.92031e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17080,Q#120 - >seq6767,non-specific,197321,25,229,2.92562e-11,64.8808,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17081,Q#120 - >seq6767,non-specific,273186,14,230,6.854780000000001e-10,60.7556,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17082,Q#120 - >seq6767,non-specific,339261,101,225,1.97896e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17083,Q#120 - >seq6767,non-specific,275209,562,775,9.246760000000001e-09,58.238,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17084,Q#120 - >seq6767,superfamily,275209,562,775,9.246760000000001e-09,58.238,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17085,Q#120 - >seq6767,non-specific,272954,20,229,1.0063100000000001e-08,57.3929,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17086,Q#120 - >seq6767,non-specific,197319,20,229,6.18866e-08,54.9753,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17087,Q#120 - >seq6767,non-specific,197322,84,229,6.486020000000001e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17088,Q#120 - >seq6767,non-specific,197336,20,228,4.95384e-06,49.1479,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17089,Q#120 - >seq6767,non-specific,197311,30,229,1.1465599999999999e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P3,ORF2,hs0_human,pars,CompleteHit
17090,Q#120 - >seq6767,non-specific,238185,631,747,6.12326e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P3,ORF2,hs0_human,pars,CompleteHit
17091,Q#120 - >seq6767,non-specific,197317,132,222,0.00028731599999999997,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17092,Q#120 - >seq6767,non-specific,236970,65,231,0.000893516,42.1886,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs0_human.pars.frame1,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P3,ORF2,hs0_human,pars,N-TerminusTruncated
17093,Q#125 - >seq6772,specific,238827,509,754,2.4519799999999994e-60,205.60299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17094,Q#125 - >seq6772,superfamily,295487,509,754,2.4519799999999994e-60,205.60299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17095,Q#125 - >seq6772,specific,197310,9,236,6.1175899999999986e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17096,Q#125 - >seq6772,superfamily,351117,9,236,6.1175899999999986e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17097,Q#125 - >seq6772,non-specific,197306,9,236,4.199479999999999e-49,174.207,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17098,Q#125 - >seq6772,specific,333820,510,754,1.02285e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17099,Q#125 - >seq6772,superfamily,333820,510,754,1.02285e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17100,Q#125 - >seq6772,non-specific,223780,9,238,1.1375700000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17101,Q#125 - >seq6772,non-specific,197307,9,236,1.4091999999999998e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17102,Q#125 - >seq6772,non-specific,197320,8,236,3.45776e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17103,Q#125 - >seq6772,non-specific,197321,7,236,1.00968e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17104,Q#125 - >seq6772,specific,335306,10,229,1.42958e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17105,Q#125 - >seq6772,non-specific,273186,9,237,7.96863e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17106,Q#125 - >seq6772,non-specific,272954,9,236,5.52203e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17107,Q#125 - >seq6772,non-specific,197319,8,236,5.70583e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17108,Q#125 - >seq6772,non-specific,197336,7,235,1.9098400000000003e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17109,Q#125 - >seq6772,non-specific,238828,564,719,3.16435e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,N-TerminusTruncated
17110,Q#125 - >seq6772,non-specific,197322,9,236,1.6690199999999999e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17111,Q#125 - >seq6772,non-specific,339261,108,232,2.6313200000000004e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17112,Q#125 - >seq6772,non-specific,275209,569,782,8.90347e-09,58.6232,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,N-TerminusTruncated
17113,Q#125 - >seq6772,superfamily,275209,569,782,8.90347e-09,58.6232,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,N-TerminusTruncated
17114,Q#125 - >seq6772,non-specific,236970,9,238,4.05312e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17115,Q#125 - >seq6772,non-specific,197311,7,236,7.1057000000000004e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P3,ORF2,hs0_human,marg,CompleteHit
17116,Q#125 - >seq6772,non-specific,238185,638,754,5.7950200000000006e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P3,ORF2,hs0_human,marg,CompleteHit
17117,Q#125 - >seq6772,non-specific,197317,139,229,0.000286251,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P3.ORF2.hs0_human.marg.frame3,1909130933_L1P3.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P3,ORF2,hs0_human,marg,N-TerminusTruncated
17118,Q#127 - >seq6774,non-specific,335182,153,248,5.04831e-33,117.789,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,pars,CompleteHit
17119,Q#127 - >seq6774,superfamily,335182,153,248,5.04831e-33,117.789,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,pars,CompleteHit
17120,Q#127 - >seq6774,non-specific,340205,251,314,3.9884399999999996e-30,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,pars,CompleteHit
17121,Q#127 - >seq6774,superfamily,340205,251,314,3.9884399999999996e-30,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,pars,CompleteHit
17122,Q#127 - >seq6774,non-specific,224117,50,199,0.000134161,43.5496,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
17123,Q#127 - >seq6774,superfamily,224117,50,199,0.000134161,43.5496,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
17124,Q#127 - >seq6774,non-specific,222878,51,142,0.00036463699999999996,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
17125,Q#127 - >seq6774,superfamily,222878,51,142,0.00036463699999999996,41.9237,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
17126,Q#127 - >seq6774,non-specific,224117,36,200,0.00161652,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
17127,Q#127 - >seq6774,non-specific,235175,57,194,0.00396965,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
17128,Q#127 - >seq6774,superfamily,235175,57,194,0.00396965,38.8916,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF1.hs1_chimp.pars.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
17129,Q#130 - >seq6777,non-specific,335182,150,245,3.7653299999999995e-33,117.789,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,marg,CompleteHit
17130,Q#130 - >seq6777,superfamily,335182,150,245,3.7653299999999995e-33,117.789,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,marg,CompleteHit
17131,Q#130 - >seq6777,non-specific,340205,248,311,1.77917e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,marg,CompleteHit
17132,Q#130 - >seq6777,superfamily,340205,248,311,1.77917e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs1_chimp,marg,CompleteHit
17133,Q#130 - >seq6777,non-specific,224117,50,196,0.00032915099999999997,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
17134,Q#130 - >seq6777,superfamily,224117,50,196,0.00032915099999999997,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
17135,Q#130 - >seq6777,non-specific,214360,6,133,0.00113156,40.484,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
17136,Q#130 - >seq6777,superfamily,214360,6,133,0.00113156,40.484,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
17137,Q#130 - >seq6777,non-specific,224117,36,197,0.00945423,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
17138,Q#130 - >seq6777,non-specific,222878,51,139,0.009730299999999999,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
17139,Q#130 - >seq6777,superfamily,222878,51,139,0.009730299999999999,37.3013,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs1_chimp.marg.frame3,1909130933_L1P4a.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
17140,Q#132 - >seq6779,non-specific,335182,141,235,1.83859e-32,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs2_gorilla.pars.frame1,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs2_gorilla,pars,CompleteHit
17141,Q#132 - >seq6779,superfamily,335182,141,235,1.83859e-32,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs2_gorilla.pars.frame1,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs2_gorilla,pars,CompleteHit
17142,Q#132 - >seq6779,non-specific,340205,238,301,8.08012e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs2_gorilla.pars.frame1,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs2_gorilla,pars,CompleteHit
17143,Q#132 - >seq6779,superfamily,340205,238,301,8.08012e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs2_gorilla.pars.frame1,1909130933_L1P4a.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4a,ORF1,hs2_gorilla,pars,CompleteHit
17144,Q#133 - >seq6780,non-specific,238827,500,583,6.78792e-13,68.857,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs1_chimp.marg.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
17145,Q#133 - >seq6780,superfamily,295487,500,583,6.78792e-13,68.857,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs1_chimp.marg.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
17146,Q#133 - >seq6780,non-specific,333820,500,594,1.92296e-05,46.1314,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.marg.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
17147,Q#133 - >seq6780,superfamily,333820,500,594,1.92296e-05,46.1314,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.marg.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
17148,Q#134 - >seq6781,non-specific,238827,590,660,4.1373899999999997e-07,51.9082,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs1_chimp.marg.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
17149,Q#134 - >seq6781,superfamily,295487,590,660,4.1373899999999997e-07,51.9082,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs1_chimp.marg.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
17150,Q#134 - >seq6781,non-specific,333820,591,687,0.000943191,41.1238,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.marg.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
17151,Q#134 - >seq6781,superfamily,333820,591,687,0.000943191,41.1238,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.marg.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
17152,Q#135 - >seq6782,non-specific,197310,12,231,9.78421e-07,50.8129,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4b,ORF2,hs1_chimp,pars,CompleteHit
17153,Q#135 - >seq6782,superfamily,351117,12,231,9.78421e-07,50.8129,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4b,ORF2,hs1_chimp,pars,CompleteHit
17154,Q#136 - >seq6783,non-specific,238827,492,669,7.27266e-22,95.0506,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
17155,Q#136 - >seq6783,superfamily,295487,492,669,7.27266e-22,95.0506,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
17156,Q#136 - >seq6783,non-specific,333820,492,696,1.0821400000000001e-13,70.399,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,pars,CompleteHit
17157,Q#136 - >seq6783,superfamily,333820,492,696,1.0821400000000001e-13,70.399,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,pars,CompleteHit
17158,Q#136 - >seq6783,non-specific,238828,554,668,7.17537e-05,45.2697,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs1_chimp,pars,N-TerminusTruncated
17159,Q#136 - >seq6783,non-specific,239125,329,409,0.00601984,39.6633,cd02660,Peptidase_C19D,NC,cl02553,"A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
17160,Q#136 - >seq6783,superfamily,351799,329,409,0.00601984,39.6633,cl02553,Peptidase_C19 superfamily,NC, - ,"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.",L1P4b.ORF2.hs1_chimp.pars.frame2,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
17161,Q#138 - >seq6785,non-specific,335182,59,151,2.1326999999999999e-19,79.6543,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,marg,CompleteHit
17162,Q#138 - >seq6785,superfamily,335182,59,151,2.1326999999999999e-19,79.6543,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,marg,CompleteHit
17163,Q#138 - >seq6785,non-specific,340205,154,184,4.6361800000000004e-09,51.1828,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,marg,C-TerminusTruncated
17164,Q#138 - >seq6785,superfamily,340205,154,184,4.6361800000000004e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,marg,C-TerminusTruncated
17165,Q#140 - >seq6787,non-specific,335182,59,151,1.03783e-19,80.4247,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,pars,CompleteHit
17166,Q#140 - >seq6787,superfamily,335182,59,151,1.03783e-19,80.4247,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,pars,CompleteHit
17167,Q#140 - >seq6787,non-specific,340205,154,184,4.31749e-09,51.1828,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,pars,C-TerminusTruncated
17168,Q#140 - >seq6787,superfamily,340205,154,184,4.31749e-09,51.1828,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs1_chimp.pars.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs1_chimp,pars,C-TerminusTruncated
17169,Q#141 - >seq6788,non-specific,197310,12,232,1.69306e-23,100.118,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4b,ORF2,hs1_chimp,marg,CompleteHit
17170,Q#141 - >seq6788,superfamily,351117,12,232,1.69306e-23,100.118,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4b,ORF2,hs1_chimp,marg,CompleteHit
17171,Q#141 - >seq6788,non-specific,197306,9,232,5.25894e-12,66.7361,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs1_chimp.marg.frame3,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4b,ORF2,hs1_chimp,marg,CompleteHit
17172,Q#142 - >seq6789,non-specific,197310,60,153,8.903139999999999e-06,48.1165,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs1_chimp.pars.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
17173,Q#142 - >seq6789,superfamily,351117,60,153,8.903139999999999e-06,48.1165,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs1_chimp.pars.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
17174,Q#142 - >seq6789,non-specific,197306,56,139,0.0015212,41.3129,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs1_chimp.pars.frame1,1909130934_L1P4b.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
17175,Q#145 - >seq6792,non-specific,340205,4,65,0.000678323,34.234,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs3_orang.pars.frame3,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs3_orang,pars,CompleteHit
17176,Q#145 - >seq6792,superfamily,340205,4,65,0.000678323,34.234,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs3_orang.pars.frame3,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs3_orang,pars,CompleteHit
17177,Q#147 - >seq6794,non-specific,335182,121,165,1.52504e-08,50.7643,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs3_orang.marg.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4b,ORF1,hs3_orang,marg,N-TerminusTruncated
17178,Q#147 - >seq6794,superfamily,335182,121,165,1.52504e-08,50.7643,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs3_orang.marg.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4b,ORF1,hs3_orang,marg,N-TerminusTruncated
17179,Q#147 - >seq6794,non-specific,340205,168,232,4.7379300000000007e-08,48.4864,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs3_orang.marg.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4b,ORF1,hs3_orang,marg,CompleteHit
17180,Q#147 - >seq6794,superfamily,340205,168,232,4.7379300000000007e-08,48.4864,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs3_orang.marg.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4b,ORF1,hs3_orang,marg,CompleteHit
17181,Q#150 - >seq6797,non-specific,197310,61,220,3.218e-17,82.0141,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs3_orang.pars.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4b,ORF2,hs3_orang,pars,N-TerminusTruncated
17182,Q#150 - >seq6797,superfamily,351117,61,220,3.218e-17,82.0141,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs3_orang.pars.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4b,ORF2,hs3_orang,pars,N-TerminusTruncated
17183,Q#150 - >seq6797,non-specific,197306,87,204,3.1019999999999997e-06,49.4021,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs3_orang.pars.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4b,ORF2,hs3_orang,pars,N-TerminusTruncated
17184,Q#150 - >seq6797,non-specific,197320,100,187,0.000828564,42.117,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4b.ORF2.hs3_orang.pars.frame1,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P4b,ORF2,hs3_orang,pars,BothTerminiTruncated
17185,Q#151 - >seq6798,non-specific,238827,506,563,4.2358999999999994e-07,51.523,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs3_orang.pars.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs3_orang,pars,BothTerminiTruncated
17186,Q#151 - >seq6798,superfamily,295487,506,563,4.2358999999999994e-07,51.523,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs3_orang.pars.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4b,ORF2,hs3_orang,pars,BothTerminiTruncated
17187,Q#152 - >seq6799,non-specific,238827,473,619,0.000497755,42.2782,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs3_orang.pars.frame3,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs3_orang,pars,C-TerminusTruncated
17188,Q#152 - >seq6799,superfamily,295487,473,619,0.000497755,42.2782,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs3_orang.pars.frame3,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs3_orang,pars,C-TerminusTruncated
17189,Q#153 - >seq6800,specific,238827,515,779,7.233149999999998e-33,127.022,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17190,Q#153 - >seq6800,superfamily,295487,515,779,7.233149999999998e-33,127.022,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17191,Q#153 - >seq6800,non-specific,197310,33,210,7.65471e-22,95.4961,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17192,Q#153 - >seq6800,superfamily,351117,33,210,7.65471e-22,95.4961,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17193,Q#153 - >seq6800,non-specific,197306,36,210,5.06825e-13,69.8177,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17194,Q#153 - >seq6800,non-specific,333820,521,743,1.29768e-08,55.7614,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17195,Q#153 - >seq6800,superfamily,333820,521,743,1.29768e-08,55.7614,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17196,Q#153 - >seq6800,specific,335306,33,197,0.000273731,43.3878,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4b,ORF2,hs3_orang,marg,CompleteHit
17197,Q#153 - >seq6800,non-specific,223780,33,200,0.00389078,40.2743,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4b.ORF2.hs3_orang.marg.frame2,1909130934_L1P4b.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1P4b,ORF2,hs3_orang,marg,C-TerminusTruncated
17198,Q#157 - >seq6804,non-specific,340205,255,318,3.1994199999999997e-28,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,pars,CompleteHit
17199,Q#157 - >seq6804,superfamily,340205,255,318,3.1994199999999997e-28,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,pars,CompleteHit
17200,Q#157 - >seq6804,non-specific,335182,162,252,9.9211e-20,82.3507,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,pars,CompleteHit
17201,Q#157 - >seq6804,superfamily,335182,162,252,9.9211e-20,82.3507,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,pars,CompleteHit
17202,Q#157 - >seq6804,non-specific,222878,51,123,0.00609151,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
17203,Q#157 - >seq6804,superfamily,222878,51,123,0.00609151,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
17204,Q#159 - >seq6806,non-specific,335182,152,247,8.68604e-34,119.33,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,marg,CompleteHit
17205,Q#159 - >seq6806,superfamily,335182,152,247,8.68604e-34,119.33,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,marg,CompleteHit
17206,Q#159 - >seq6806,non-specific,340205,250,313,1.27368e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,marg,CompleteHit
17207,Q#159 - >seq6806,superfamily,340205,250,313,1.27368e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,marg,CompleteHit
17208,Q#159 - >seq6806,non-specific,214360,6,136,0.00190594,39.7136,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs0_human,marg,N-TerminusTruncated
17209,Q#159 - >seq6806,superfamily,214360,6,136,0.00190594,39.7136,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4a,ORF1,hs0_human,marg,N-TerminusTruncated
17210,Q#159 - >seq6806,non-specific,222878,51,146,0.00650951,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs0_human,marg,BothTerminiTruncated
17211,Q#159 - >seq6806,superfamily,222878,51,146,0.00650951,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs0_human,marg,BothTerminiTruncated
17212,Q#159 - >seq6806,non-specific,340204,107,149,0.008734700000000001,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P4a,ORF1,hs0_human,marg,CompleteHit
17213,Q#159 - >seq6806,superfamily,340204,107,149,0.008734700000000001,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4a.ORF1.hs0_human.marg.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P4a,ORF1,hs0_human,marg,CompleteHit
17214,Q#160 - >seq6807,non-specific,223496,247,444,1.86657e-05,47.8327,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17215,Q#160 - >seq6807,superfamily,223496,247,444,1.86657e-05,47.8327,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17216,Q#160 - >seq6807,non-specific,235175,277,455,3.02859e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17217,Q#160 - >seq6807,superfamily,235175,277,455,3.02859e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17218,Q#160 - >seq6807,non-specific,313357,307,450,0.000636737,41.098,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
17219,Q#160 - >seq6807,superfamily,321788,307,450,0.000636737,41.098,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
17220,Q#160 - >seq6807,non-specific,224117,247,454,0.0007907089999999999,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17221,Q#160 - >seq6807,superfamily,224117,247,454,0.0007907089999999999,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17222,Q#160 - >seq6807,non-specific,335555,280,385,0.00202195,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1P4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
17223,Q#160 - >seq6807,superfamily,354396,280,385,0.00202195,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Flagellar,L1P4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
17224,Q#160 - >seq6807,non-specific,235175,254,436,0.00212344,41.2028,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17225,Q#160 - >seq6807,non-specific,274009,293,444,0.00246446,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17226,Q#160 - >seq6807,superfamily,274009,293,444,0.00246446,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17227,Q#160 - >seq6807,non-specific,223496,302,450,0.00322807,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17228,Q#160 - >seq6807,non-specific,224117,251,434,0.0045629,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF2.hs5_gmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17229,Q#161 - >seq6808,specific,197310,9,218,2.7522699999999995e-57,194.107,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17230,Q#161 - >seq6808,superfamily,351117,9,218,2.7522699999999995e-57,194.107,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17231,Q#161 - >seq6808,non-specific,197306,9,228,5.176369999999999e-38,141.465,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17232,Q#161 - >seq6808,non-specific,197307,9,207,1.20459e-21,94.6621,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17233,Q#161 - >seq6808,non-specific,197321,7,202,1.39108e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17234,Q#161 - >seq6808,non-specific,223780,9,228,8.724620000000001e-21,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17235,Q#161 - >seq6808,non-specific,197320,9,208,1.89076e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17236,Q#161 - >seq6808,specific,335306,10,211,5.73897e-17,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17237,Q#161 - >seq6808,non-specific,272954,9,207,1.7677e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17238,Q#161 - >seq6808,non-specific,273186,9,207,1.8999000000000004e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17239,Q#161 - >seq6808,non-specific,197319,13,218,5.734560000000001e-13,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17240,Q#161 - >seq6808,non-specific,236970,9,215,1.4190600000000002e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17241,Q#161 - >seq6808,non-specific,197336,9,194,2.13015e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17242,Q#161 - >seq6808,non-specific,197322,8,217,5.68142e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17243,Q#161 - >seq6808,non-specific,197311,30,204,3.95951e-05,44.9753,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs5_gmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17244,Q#162 - >seq6809,non-specific,318193,238,570,0.00845226,39.7163,pfam15921,CCDC158,N,cl37899,Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.,L1P4a.ORF2.hs5_gmonkey.marg.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
17245,Q#162 - >seq6809,superfamily,318193,238,570,0.00845226,39.7163,cl37899,CCDC158 superfamily,N, - ,Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.,L1P4a.ORF2.hs5_gmonkey.marg.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1P4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
17246,Q#164 - >seq6811,specific,238827,507,768,4.3531299999999995e-63,212.53599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17247,Q#164 - >seq6811,superfamily,295487,507,768,4.3531299999999995e-63,212.53599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17248,Q#164 - >seq6811,specific,197310,9,236,2.8842499999999997e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17249,Q#164 - >seq6811,superfamily,351117,9,236,2.8842499999999997e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17250,Q#164 - >seq6811,non-specific,197306,9,236,4.6055300000000003e-38,142.235,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17251,Q#164 - >seq6811,specific,333820,513,768,3.8067100000000003e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17252,Q#164 - >seq6811,superfamily,333820,513,768,3.8067100000000003e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17253,Q#164 - >seq6811,non-specific,197321,7,236,4.86342e-22,96.4672,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17254,Q#164 - >seq6811,non-specific,197307,9,236,1.5762700000000001e-21,94.6621,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17255,Q#164 - >seq6811,non-specific,197320,9,229,5.04365e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17256,Q#164 - >seq6811,non-specific,223780,9,237,5.961099999999999e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17257,Q#164 - >seq6811,specific,335306,10,229,2.07963e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17258,Q#164 - >seq6811,non-specific,273186,9,237,1.6411200000000001e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17259,Q#164 - >seq6811,non-specific,272954,9,207,9.57672e-14,72.0305,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17260,Q#164 - >seq6811,non-specific,197319,13,236,2.40833e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17261,Q#164 - >seq6811,non-specific,238828,579,720,1.6232799999999998e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
17262,Q#164 - >seq6811,non-specific,236970,9,237,1.3427700000000001e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17263,Q#164 - >seq6811,non-specific,197336,9,194,3.23376e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17264,Q#164 - >seq6811,non-specific,197322,8,223,1.27855e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17265,Q#164 - >seq6811,non-specific,275209,584,796,1.2962e-08,57.8528,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
17266,Q#164 - >seq6811,superfamily,275209,584,796,1.2962e-08,57.8528,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
17267,Q#164 - >seq6811,non-specific,197311,30,236,1.7907799999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17268,Q#164 - >seq6811,non-specific,238185,653,768,0.000171275,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17269,Q#164 - >seq6811,non-specific,235175,291,467,0.00023908599999999998,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17270,Q#164 - >seq6811,superfamily,235175,291,467,0.00023908599999999998,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17271,Q#164 - >seq6811,non-specific,223496,263,456,0.000760387,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1P4a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17272,Q#164 - >seq6811,superfamily,223496,263,456,0.000760387,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1P4a,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17273,Q#164 - >seq6811,non-specific,339261,108,232,0.00183485,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4a.ORF2.hs5_gmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P4a,ORF2,hs5_gmonkey,marg,CompleteHit
17274,Q#167 - >seq6814,non-specific,335182,151,233,3.41955e-17,75.4171,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame1,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,CompleteHit
17275,Q#167 - >seq6814,superfamily,335182,151,233,3.41955e-17,75.4171,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame1,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,CompleteHit
17276,Q#169 - >seq6816,specific,238827,456,657,1.0234e-33,128.178,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17277,Q#169 - >seq6816,superfamily,295487,456,657,1.0234e-33,128.178,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
17278,Q#169 - >seq6816,non-specific,333820,462,670,2.20103e-19,86.1921,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17279,Q#169 - >seq6816,superfamily,333820,462,670,2.20103e-19,86.1921,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17280,Q#169 - >seq6816,non-specific,238828,583,657,1.3117e-05,46.8105,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
17281,Q#169 - >seq6816,non-specific,238185,589,668,0.00295828,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs5_gmonkey.pars.frame1,1909130934_L1P4a.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4a,ORF2,hs5_gmonkey,pars,CompleteHit
17282,Q#171 - >seq6818,non-specific,197310,137,229,6.95207e-14,68.9173,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs6_sqmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
17283,Q#171 - >seq6818,superfamily,351117,137,229,6.95207e-14,68.9173,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
17284,Q#171 - >seq6818,non-specific,197306,124,229,8.26687e-09,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.pars.frame2,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
17285,Q#172 - >seq6819,specific,197310,9,195,1.41632e-30,113.6,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,CompleteHit
17286,Q#172 - >seq6819,superfamily,351117,9,195,1.41632e-30,113.6,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,CompleteHit
17287,Q#172 - >seq6819,non-specific,197306,9,155,1.09184e-22,92.9296,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17288,Q#172 - >seq6819,non-specific,197307,9,161,6.3525e-12,63.4609,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17289,Q#172 - >seq6819,non-specific,197321,7,119,4.19013e-10,58.3324,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17290,Q#172 - >seq6819,non-specific,223780,9,122,7.19793e-10,57.6083,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17291,Q#172 - >seq6819,non-specific,197320,9,140,2.24971e-09,55.9842,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17292,Q#172 - >seq6819,non-specific,273186,9,122,5.01505e-09,54.9776,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17293,Q#172 - >seq6819,non-specific,272954,9,119,1.39773e-06,47.7629,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17294,Q#172 - >seq6819,specific,335306,10,120,1.67641e-06,47.625,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17295,Q#172 - >seq6819,non-specific,197319,13,119,0.000146684,41.8785,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17296,Q#172 - >seq6819,non-specific,197336,9,125,0.00021611700000000002,41.4439,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17297,Q#172 - >seq6819,non-specific,197318,9,61,0.0009443030000000001,39.2019,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17298,Q#172 - >seq6819,non-specific,197322,8,46,0.00589125,37.2967,cd09088,Ape2-like_AP-endo,C,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.pars.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17299,Q#175 - >seq6822,specific,238827,508,771,4.0716e-43,156.297,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17300,Q#175 - >seq6822,superfamily,295487,508,771,4.0716e-43,156.297,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17301,Q#175 - >seq6822,specific,197310,9,236,3.07635e-39,145.957,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17302,Q#175 - >seq6822,superfamily,351117,9,236,3.07635e-39,145.957,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17303,Q#175 - >seq6822,non-specific,197306,9,236,6.927569999999999e-27,110.264,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17304,Q#175 - >seq6822,non-specific,333820,514,771,2.9832399999999997e-19,86.5773,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17305,Q#175 - >seq6822,superfamily,333820,514,771,2.9832399999999997e-19,86.5773,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17306,Q#175 - >seq6822,non-specific,238828,514,736,9.8459e-11,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17307,Q#175 - >seq6822,non-specific,197307,9,236,1.85167e-10,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17308,Q#175 - >seq6822,non-specific,197320,9,194,5.42749e-10,60.9918,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17309,Q#175 - >seq6822,non-specific,197321,7,236,2.8883600000000006e-09,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17310,Q#175 - >seq6822,non-specific,223780,9,194,3.43066e-09,58.7639,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17311,Q#175 - >seq6822,specific,335306,10,229,1.93555e-08,56.0994,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17312,Q#175 - >seq6822,non-specific,273186,9,237,9.31551e-06,48.4292,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17313,Q#175 - >seq6822,non-specific,275209,586,790,6.5084e-05,46.2968,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
17314,Q#175 - >seq6822,superfamily,275209,586,790,6.5084e-05,46.2968,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
17315,Q#175 - >seq6822,non-specific,238185,655,771,0.000178717,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4a,ORF2,hs6_sqmonkey,marg,CompleteHit
17316,Q#175 - >seq6822,non-specific,197336,9,87,0.00512657,39.9031,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4a.ORF2.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17317,Q#177 - >seq6824,non-specific,340205,242,279,1.09277e-13,64.2796,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.pars.frame2,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17318,Q#177 - >seq6824,superfamily,340205,242,279,1.09277e-13,64.2796,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.pars.frame2,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17319,Q#178 - >seq6825,non-specific,335182,143,238,3.97308e-34,119.715,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,pars,CompleteHit
17320,Q#178 - >seq6825,superfamily,335182,143,238,3.97308e-34,119.715,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,pars,CompleteHit
17321,Q#178 - >seq6825,non-specific,340205,241,266,1.72226e-08,50.0272,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,pars,C-TerminusTruncated
17322,Q#178 - >seq6825,superfamily,340205,241,266,1.72226e-08,50.0272,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4a,ORF1,hs0_human,pars,C-TerminusTruncated
17323,Q#178 - >seq6825,non-specific,222878,42,137,0.00378165,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs0_human,pars,BothTerminiTruncated
17324,Q#178 - >seq6825,superfamily,222878,42,137,0.00378165,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4a,ORF1,hs0_human,pars,BothTerminiTruncated
17325,Q#178 - >seq6825,non-specific,224117,41,189,0.00492385,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17326,Q#178 - >seq6825,superfamily,224117,41,189,0.00492385,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17327,Q#178 - >seq6825,non-specific,340204,98,140,0.00577462,33.9204,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P4a,ORF1,hs0_human,pars,CompleteHit
17328,Q#178 - >seq6825,superfamily,340204,98,140,0.00577462,33.9204,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P4a,ORF1,hs0_human,pars,CompleteHit
17329,Q#178 - >seq6825,non-specific,214360,3,127,0.00843031,37.4024,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17330,Q#178 - >seq6825,superfamily,214360,3,127,0.00843031,37.4024,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1P4a.ORF1.hs0_human.pars.frame3,1909130934_L1P4a.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4a,ORF1,hs0_human,pars,N-TerminusTruncated
17331,Q#180 - >seq6827,non-specific,340205,247,310,2.02324e-28,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,CompleteHit
17332,Q#180 - >seq6827,superfamily,340205,247,310,2.02324e-28,104.34,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,CompleteHit
17333,Q#180 - >seq6827,non-specific,335182,219,244,6.68872e-05,41.1343,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
17334,Q#180 - >seq6827,superfamily,335182,219,244,6.68872e-05,41.1343,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4a,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
17335,Q#180 - >seq6827,non-specific,222878,51,123,0.00375045,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
17336,Q#180 - >seq6827,superfamily,222878,51,123,0.00375045,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4a.ORF1.hs6_sqmonkey.marg.frame3,1909130934_L1P4a.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4a,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
17337,Q#181 - >seq6828,non-specific,340205,240,303,1.70622e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,marg,CompleteHit
17338,Q#181 - >seq6828,superfamily,340205,240,303,1.70622e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,marg,CompleteHit
17339,Q#181 - >seq6828,non-specific,335182,146,237,1.9592e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,marg,CompleteHit
17340,Q#181 - >seq6828,superfamily,335182,146,237,1.9592e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,marg,CompleteHit
17341,Q#183 - >seq6830,non-specific,334565,31,126,0.00435145,38.6248,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs2_gorilla.marg.frame1,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1P4d,ORF1,hs2_gorilla,marg,C-TerminusTruncated
17342,Q#183 - >seq6830,superfamily,334565,31,126,0.00435145,38.6248,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs2_gorilla.marg.frame1,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1P4d,ORF1,hs2_gorilla,marg,C-TerminusTruncated
17343,Q#184 - >seq6831,specific,197310,9,241,3.13202e-40,148.654,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17344,Q#184 - >seq6831,superfamily,351117,9,241,3.13202e-40,148.654,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17345,Q#184 - >seq6831,non-specific,197306,9,241,4.1888099999999993e-22,96.3964,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17346,Q#184 - >seq6831,non-specific,238827,522,636,3.01902e-16,78.487,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17347,Q#184 - >seq6831,superfamily,295487,522,636,3.01902e-16,78.487,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17348,Q#184 - >seq6831,specific,335306,10,234,4.12316e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17349,Q#184 - >seq6831,non-specific,197320,9,213,8.659620000000001e-13,69.081,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17350,Q#184 - >seq6831,non-specific,197307,9,241,1.81584e-09,59.2237,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17351,Q#184 - >seq6831,non-specific,197321,7,241,2.0608699999999997e-09,59.1028,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17352,Q#184 - >seq6831,non-specific,223780,9,242,2.1717399999999998e-09,59.1491,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17353,Q#184 - >seq6831,non-specific,273186,9,242,1.8267399999999999e-07,53.4368,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,marg,CompleteHit
17354,Q#184 - >seq6831,non-specific,272954,9,199,9.81717e-05,45.0665,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17355,Q#184 - >seq6831,non-specific,333820,528,640,0.000146837,43.435,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17356,Q#184 - >seq6831,superfamily,333820,528,640,0.000146837,43.435,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17357,Q#184 - >seq6831,non-specific,197336,9,92,0.00184191,41.0587,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,marg,C-TerminusTruncated
17358,Q#186 - >seq6833,non-specific,335182,146,187,5.951459999999999e-09,52.3051,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame1,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17359,Q#186 - >seq6833,superfamily,335182,146,187,5.951459999999999e-09,52.3051,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame1,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17360,Q#188 - >seq6835,non-specific,340205,238,301,5.7841999999999995e-31,110.889,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,CompleteHit
17361,Q#188 - >seq6835,superfamily,340205,238,301,5.7841999999999995e-31,110.889,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,CompleteHit
17362,Q#188 - >seq6835,non-specific,335182,193,235,7.653640000000001e-13,63.4759,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,N-TerminusTruncated
17363,Q#188 - >seq6835,superfamily,335182,193,235,7.653640000000001e-13,63.4759,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs2_gorilla,pars,N-TerminusTruncated
17364,Q#188 - >seq6835,non-specific,334565,25,120,0.00421384,38.6248,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P4d,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17365,Q#188 - >seq6835,superfamily,334565,25,120,0.00421384,38.6248,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1P4d,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17366,Q#188 - >seq6835,non-specific,224117,44,114,0.00570163,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4d,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17367,Q#188 - >seq6835,superfamily,224117,44,114,0.00570163,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF1.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1P4d,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17368,Q#190 - >seq6837,non-specific,340205,190,252,1.0302000000000001e-26,98.5624,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs3_orang.pars.frame2,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs3_orang,pars,CompleteHit
17369,Q#190 - >seq6837,superfamily,340205,190,252,1.0302000000000001e-26,98.5624,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs3_orang.pars.frame2,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs3_orang,pars,CompleteHit
17370,Q#190 - >seq6837,non-specific,335182,92,187,1.2117e-22,88.899,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs3_orang.pars.frame2,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs3_orang,pars,CompleteHit
17371,Q#190 - >seq6837,superfamily,335182,92,187,1.2117e-22,88.899,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs3_orang.pars.frame2,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs3_orang,pars,CompleteHit
17372,Q#192 - >seq6839,non-specific,238827,566,717,5.50984e-12,66.1606,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs2_gorilla.marg.frame2,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17373,Q#192 - >seq6839,superfamily,295487,566,717,5.50984e-12,66.1606,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs2_gorilla.marg.frame2,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17374,Q#192 - >seq6839,non-specific,333820,566,714,1.0040100000000001e-09,58.843,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs2_gorilla.marg.frame2,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17375,Q#192 - >seq6839,superfamily,333820,566,714,1.0040100000000001e-09,58.843,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs2_gorilla.marg.frame2,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17376,Q#193 - >seq6840,specific,197310,9,240,3.84397e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17377,Q#193 - >seq6840,superfamily,351117,9,240,3.84397e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17378,Q#193 - >seq6840,non-specific,197306,9,240,4.49415e-34,131.064,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17379,Q#193 - >seq6840,non-specific,223780,9,242,3.46796e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17380,Q#193 - >seq6840,non-specific,197320,9,233,8.452620000000002e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17381,Q#193 - >seq6840,non-specific,197307,9,240,2.54504e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17382,Q#193 - >seq6840,specific,335306,10,233,5.185740000000001e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17383,Q#193 - >seq6840,non-specific,197321,7,240,1.25502e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17384,Q#193 - >seq6840,non-specific,273186,9,241,1.0616e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17385,Q#193 - >seq6840,non-specific,197319,13,240,1.62051e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17386,Q#193 - >seq6840,non-specific,272954,9,240,1.74542e-10,62.4005,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17387,Q#193 - >seq6840,non-specific,197336,9,198,5.5056000000000005e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17388,Q#193 - >seq6840,non-specific,238827,530,589,4.5525399999999996e-07,51.523,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs2_gorilla,marg,C-TerminusTruncated
17389,Q#193 - >seq6840,superfamily,295487,530,589,4.5525399999999996e-07,51.523,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs2_gorilla,marg,C-TerminusTruncated
17390,Q#193 - >seq6840,non-specific,236970,9,242,2.27903e-06,50.2778,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17391,Q#193 - >seq6840,non-specific,339261,112,236,0.00017778599999999998,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17392,Q#193 - >seq6840,non-specific,197311,26,208,0.0008477210000000001,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs2_gorilla.marg.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,marg,CompleteHit
17393,Q#196 - >seq6843,non-specific,340205,250,312,7.392529999999999e-27,100.488,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs3_orang,marg,CompleteHit
17394,Q#196 - >seq6843,superfamily,340205,250,312,7.392529999999999e-27,100.488,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs3_orang,marg,CompleteHit
17395,Q#196 - >seq6843,non-specific,335182,151,247,2.4373e-22,89.2842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs3_orang,marg,CompleteHit
17396,Q#196 - >seq6843,superfamily,335182,151,247,2.4373e-22,89.2842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs3_orang,marg,CompleteHit
17397,Q#196 - >seq6843,non-specific,335623,50,119,0.000607634,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1P4d,ORF1,hs3_orang,marg,C-TerminusTruncated
17398,Q#196 - >seq6843,superfamily,335623,50,119,0.000607634,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1P4d,ORF1,hs3_orang,marg,C-TerminusTruncated
17399,Q#196 - >seq6843,non-specific,274008,55,217,0.0006855580000000001,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17400,Q#196 - >seq6843,superfamily,274008,55,217,0.0006855580000000001,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17401,Q#196 - >seq6843,non-specific,274008,39,144,0.00154376,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17402,Q#196 - >seq6843,superfamily,274008,39,144,0.00154376,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17403,Q#196 - >seq6843,non-specific,224117,44,239,0.00763201,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17404,Q#196 - >seq6843,superfamily,224117,44,239,0.00763201,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1P4d,ORF1,hs3_orang,marg,BothTerminiTruncated
17405,Q#196 - >seq6843,non-specific,334565,55,122,0.00937387,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1P4d,ORF1,hs3_orang,marg,C-TerminusTruncated
17406,Q#196 - >seq6843,superfamily,334565,55,122,0.00937387,37.4692,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1P4d.ORF1.hs3_orang.marg.frame1,1909130935_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1P4d,ORF1,hs3_orang,marg,C-TerminusTruncated
17407,Q#200 - >seq6847,specific,197310,7,238,6.427429999999999e-63,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17408,Q#200 - >seq6847,superfamily,351117,7,238,6.427429999999999e-63,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17409,Q#200 - >seq6847,non-specific,197306,7,238,2.69994e-37,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17410,Q#200 - >seq6847,non-specific,223780,7,240,1.48771e-23,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17411,Q#200 - >seq6847,non-specific,197320,7,231,2.0374100000000001e-22,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17412,Q#200 - >seq6847,non-specific,197307,7,238,3.2523700000000005e-22,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17413,Q#200 - >seq6847,non-specific,197321,5,238,5.8962e-20,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17414,Q#200 - >seq6847,specific,335306,8,231,6.33019e-20,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17415,Q#200 - >seq6847,non-specific,273186,7,239,2.6810800000000002e-17,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17416,Q#200 - >seq6847,non-specific,197319,11,238,4.39205e-16,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17417,Q#200 - >seq6847,non-specific,272954,7,238,1.33439e-12,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17418,Q#200 - >seq6847,non-specific,197336,7,196,5.310499999999999e-10,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17419,Q#200 - >seq6847,non-specific,197322,6,238,7.001710000000002e-08,51.9342,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17420,Q#200 - >seq6847,non-specific,236970,7,240,1.10253e-07,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17421,Q#200 - >seq6847,non-specific,339261,110,234,0.00031431,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P4d,ORF2,hs2_gorilla,pars,CompleteHit
17422,Q#200 - >seq6847,non-specific,197311,24,148,0.000434733,39.9677,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17423,Q#200 - >seq6847,non-specific,197314,5,76,0.00292681,37.7083,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs2_gorilla.pars.frame3,1909130935_L1P4d.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P4d,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17424,Q#201 - >seq6848,non-specific,238827,604,719,2.00183e-10,61.5382,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,marg,N-TerminusTruncated
17425,Q#201 - >seq6848,superfamily,295487,604,719,2.00183e-10,61.5382,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,marg,N-TerminusTruncated
17426,Q#201 - >seq6848,non-specific,333820,588,686,2.36089e-05,45.7462,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,marg,N-TerminusTruncated
17427,Q#201 - >seq6848,superfamily,333820,588,686,2.36089e-05,45.7462,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,marg,N-TerminusTruncated
17428,Q#202 - >seq6849,non-specific,335182,21,115,1.4971e-34,117.404,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,pars,CompleteHit
17429,Q#202 - >seq6849,superfamily,335182,21,115,1.4971e-34,117.404,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,pars,CompleteHit
17430,Q#202 - >seq6849,non-specific,340205,118,181,1.36732e-30,106.266,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,pars,CompleteHit
17431,Q#202 - >seq6849,superfamily,340205,118,181,1.36732e-30,106.266,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,pars,CompleteHit
17432,Q#203 - >seq6850,non-specific,238827,591,677,1.0464299999999999e-07,53.0638,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs1_chimp.pars.frame2,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17433,Q#203 - >seq6850,superfamily,295487,591,677,1.0464299999999999e-07,53.0638,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs1_chimp.pars.frame2,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17434,Q#203 - >seq6850,non-specific,333820,575,668,4.73895e-05,44.5906,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.pars.frame2,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17435,Q#203 - >seq6850,superfamily,333820,575,668,4.73895e-05,44.5906,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.pars.frame2,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17436,Q#203 - >seq6850,non-specific,238185,595,674,0.000656349,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs1_chimp.pars.frame2,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs1_chimp,pars,CompleteHit
17437,Q#206 - >seq6853,non-specific,335182,59,151,1.17956e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17438,Q#206 - >seq6853,superfamily,335182,59,151,1.17956e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17439,Q#206 - >seq6853,non-specific,335182,59,151,1.17956e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17440,Q#206 - >seq6853,non-specific,340205,154,207,2.1957e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17441,Q#206 - >seq6853,superfamily,340205,154,207,2.1957e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17442,Q#206 - >seq6853,non-specific,340205,154,207,2.1957e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,pars,CompleteHit
17443,Q#209 - >seq6856,non-specific,335182,59,151,1.17956e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17444,Q#209 - >seq6856,superfamily,335182,59,151,1.17956e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17445,Q#209 - >seq6856,non-specific,335182,59,151,1.17956e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17446,Q#209 - >seq6856,non-specific,340205,154,207,2.1957e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17447,Q#209 - >seq6856,superfamily,340205,154,207,2.1957e-18,75.8356,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17448,Q#209 - >seq6856,non-specific,340205,154,207,2.1957e-18,75.8356,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4b.ORF1.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4b,ORF1,hs0_human,marg,CompleteHit
17449,Q#211 - >seq6858,non-specific,197310,6,99,4.17434e-18,83.9401,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17450,Q#211 - >seq6858,superfamily,351117,6,99,4.17434e-18,83.9401,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17451,Q#211 - >seq6858,non-specific,197306,6,137,4.0434699999999995e-12,66.3509,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17452,Q#211 - >seq6858,non-specific,197321,4,92,8.80678e-07,50.6284,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17453,Q#211 - >seq6858,non-specific,197320,6,77,2.18682e-06,49.4358,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17454,Q#211 - >seq6858,non-specific,197307,6,81,2.14723e-05,46.5121,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17455,Q#211 - >seq6858,non-specific,223780,6,81,4.4803500000000006e-05,45.6671,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17456,Q#211 - >seq6858,specific,335306,7,78,5.52968e-05,44.9286,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17457,Q#211 - >seq6858,non-specific,273186,6,91,0.000478843,42.266000000000005,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17458,Q#211 - >seq6858,non-specific,197336,6,89,0.00122246,41.0587,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs1_chimp.pars.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17459,Q#212 - >seq6859,non-specific,238827,500,691,1.1782700000000001e-20,91.5838,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17460,Q#212 - >seq6859,superfamily,295487,500,691,1.1782700000000001e-20,91.5838,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17461,Q#212 - >seq6859,non-specific,333820,500,678,1.0364300000000001e-09,58.843,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17462,Q#212 - >seq6859,superfamily,333820,500,678,1.0364300000000001e-09,58.843,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17463,Q#212 - >seq6859,non-specific,197310,12,74,0.00244244,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17464,Q#212 - >seq6859,superfamily,351117,12,74,0.00244244,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs0_human.pars.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4b,ORF2,hs0_human,pars,C-TerminusTruncated
17465,Q#213 - >seq6860,non-specific,197310,160,218,0.00133174,41.1829,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs0_human.pars.frame2,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4b,ORF2,hs0_human,pars,N-TerminusTruncated
17466,Q#213 - >seq6860,superfamily,351117,160,218,0.00133174,41.1829,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs0_human.pars.frame2,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4b,ORF2,hs0_human,pars,N-TerminusTruncated
17467,Q#214 - >seq6861,non-specific,197310,160,218,0.00142963,41.1829,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs0_human.marg.frame2,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4b,ORF2,hs0_human,marg,N-TerminusTruncated
17468,Q#214 - >seq6861,superfamily,351117,160,218,0.00142963,41.1829,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs0_human.marg.frame2,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4b,ORF2,hs0_human,marg,N-TerminusTruncated
17469,Q#215 - >seq6862,non-specific,238827,500,691,3.90836e-21,92.7394,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17470,Q#215 - >seq6862,superfamily,295487,500,691,3.90836e-21,92.7394,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17471,Q#215 - >seq6862,non-specific,333820,485,678,5.56751e-10,59.6134,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17472,Q#215 - >seq6862,superfamily,333820,485,678,5.56751e-10,59.6134,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17473,Q#215 - >seq6862,non-specific,197310,12,74,0.00247647,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17474,Q#215 - >seq6862,superfamily,351117,12,74,0.00247647,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4b.ORF2.hs0_human.marg.frame3,1909130935_L1P4b.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4b,ORF2,hs0_human,marg,C-TerminusTruncated
17475,Q#218 - >seq6865,non-specific,335182,145,239,4.2948899999999996e-33,117.404,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,marg,CompleteHit
17476,Q#218 - >seq6865,superfamily,335182,145,239,4.2948899999999996e-33,117.404,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,marg,CompleteHit
17477,Q#218 - >seq6865,non-specific,340205,242,305,1.33276e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,marg,CompleteHit
17478,Q#218 - >seq6865,superfamily,340205,242,305,1.33276e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs1_chimp.marg.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs1_chimp,marg,CompleteHit
17479,Q#220 - >seq6867,non-specific,225747,37,114,0.000830505,40.5043,COG3206,GumC,N,cl34566,"Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell wall/membrane/envelope biogenesis]; Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane].",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4d,ORF1,hs1_chimp,marg,N-TerminusTruncated
17480,Q#220 - >seq6867,superfamily,225747,37,114,0.000830505,40.5043,cl34566,GumC superfamily,N, - ,"Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell wall/membrane/envelope biogenesis]; Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane].",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4d,ORF1,hs1_chimp,marg,N-TerminusTruncated
17481,Q#220 - >seq6867,non-specific,179385,53,118,0.00164611,39.6382,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4d,ORF1,hs1_chimp,marg,BothTerminiTruncated
17482,Q#220 - >seq6867,superfamily,179385,53,118,0.00164611,39.6382,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4d,ORF1,hs1_chimp,marg,BothTerminiTruncated
17483,Q#220 - >seq6867,non-specific,335623,49,117,0.00384374,38.3094,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P4d,ORF1,hs1_chimp,marg,C-TerminusTruncated
17484,Q#220 - >seq6867,superfamily,335623,49,117,0.00384374,38.3094,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1P4d,ORF1,hs1_chimp,marg,C-TerminusTruncated
17485,Q#220 - >seq6867,non-specific,227278,53,119,0.00825711,37.3941,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4d,ORF1,hs1_chimp,marg,C-TerminusTruncated
17486,Q#220 - >seq6867,superfamily,227278,53,119,0.00825711,37.3941,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1P4d.ORF1.hs1_chimp.marg.frame3,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4d,ORF1,hs1_chimp,marg,C-TerminusTruncated
17487,Q#221 - >seq6868,non-specific,197310,91,229,1.9140099999999996e-22,96.6517,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17488,Q#221 - >seq6868,superfamily,351117,91,229,1.9140099999999996e-22,96.6517,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17489,Q#221 - >seq6868,non-specific,238827,503,617,3.29121e-16,78.1018,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17490,Q#221 - >seq6868,superfamily,295487,503,617,3.29121e-16,78.1018,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17491,Q#221 - >seq6868,non-specific,197306,89,229,9.031050000000001e-10,59.4173,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17492,Q#221 - >seq6868,non-specific,197320,100,201,9.093200000000001e-06,47.5098,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17493,Q#221 - >seq6868,non-specific,333820,509,621,0.000119318,43.435,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17494,Q#221 - >seq6868,superfamily,333820,509,621,0.000119318,43.435,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4d,ORF2,hs1_chimp,pars,C-TerminusTruncated
17495,Q#221 - >seq6868,specific,335306,121,222,0.00179881,40.3062,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17496,Q#221 - >seq6868,non-specific,235175,280,458,0.00183147,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4d,ORF2,hs1_chimp,pars,BothTerminiTruncated
17497,Q#221 - >seq6868,superfamily,235175,280,458,0.00183147,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4d,ORF2,hs1_chimp,pars,BothTerminiTruncated
17498,Q#221 - >seq6868,non-specific,339261,102,225,0.00328714,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1P4d,ORF2,hs1_chimp,pars,CompleteHit
17499,Q#221 - >seq6868,non-specific,197311,100,197,0.00565125,38.4269,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs1_chimp.pars.frame1,1909130935_L1P4d.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4d,ORF2,hs1_chimp,pars,N-TerminusTruncated
17500,Q#223 - >seq6870,non-specific,340205,157,219,1.24171e-27,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,CompleteHit
17501,Q#223 - >seq6870,superfamily,340205,157,219,1.24171e-27,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,CompleteHit
17502,Q#223 - >seq6870,non-specific,335182,91,154,7.65229e-19,78.1135,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,N-TerminusTruncated
17503,Q#223 - >seq6870,superfamily,335182,91,154,7.65229e-19,78.1135,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,N-TerminusTruncated
17504,Q#224 - >seq6871,non-specific,340205,165,227,1.8228e-27,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,CompleteHit
17505,Q#224 - >seq6871,superfamily,340205,165,227,1.8228e-27,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,CompleteHit
17506,Q#224 - >seq6871,non-specific,335182,65,162,1.67973e-20,82.7359,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,CompleteHit
17507,Q#224 - >seq6871,superfamily,335182,65,162,1.67973e-20,82.7359,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,CompleteHit
17508,Q#225 - >seq6872,non-specific,335182,87,139,6.61481e-05,40.3639,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,N-TerminusTruncated
17509,Q#225 - >seq6872,superfamily,335182,87,139,6.61481e-05,40.3639,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.marg.frame2,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs4_gibbon,marg,N-TerminusTruncated
17510,Q#227 - >seq6874,non-specific,335182,65,94,0.00485698,35.3563,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,C-TerminusTruncated
17511,Q#227 - >seq6874,superfamily,335182,65,94,0.00485698,35.3563,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs4_gibbon.pars.frame3,1909130936_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs4_gibbon,pars,C-TerminusTruncated
17512,Q#229 - >seq6876,non-specific,238827,514,725,1.5945400000000002e-18,85.4206,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17513,Q#229 - >seq6876,superfamily,295487,514,725,1.5945400000000002e-18,85.4206,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17514,Q#229 - >seq6876,non-specific,333820,548,687,5.987180000000001e-13,68.0878,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,N-TerminusTruncated
17515,Q#229 - >seq6876,superfamily,333820,548,687,5.987180000000001e-13,68.0878,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,N-TerminusTruncated
17516,Q#229 - >seq6876,non-specific,238828,550,687,5.14465e-07,51.818000000000005,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,N-TerminusTruncated
17517,Q#229 - >seq6876,non-specific,275209,550,686,0.00513369,40.1336,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,BothTerminiTruncated
17518,Q#229 - >seq6876,superfamily,275209,550,686,0.00513369,40.1336,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4d.ORF2.hs3_orang.marg.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs3_orang,marg,BothTerminiTruncated
17519,Q#231 - >seq6878,non-specific,238827,474,525,2.38872e-12,66.931,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17520,Q#231 - >seq6878,superfamily,295487,474,525,2.38872e-12,66.931,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17521,Q#231 - >seq6878,non-specific,197310,6,38,0.00413981,39.6421,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17522,Q#231 - >seq6878,superfamily,351117,6,38,0.00413981,39.6421,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17523,Q#231 - >seq6878,non-specific,274009,231,432,0.0049777,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4d,ORF2,hs3_orang,pars,BothTerminiTruncated
17524,Q#231 - >seq6878,superfamily,274009,231,432,0.0049777,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF2.hs3_orang.pars.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4d,ORF2,hs3_orang,pars,BothTerminiTruncated
17525,Q#232 - >seq6879,specific,197310,33,224,2.5514900000000002e-36,137.09799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17526,Q#232 - >seq6879,superfamily,351117,33,224,2.5514900000000002e-36,137.09799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17527,Q#232 - >seq6879,non-specific,238827,567,753,9.526069999999999e-23,97.3618,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,N-TerminusTruncated
17528,Q#232 - >seq6879,superfamily,295487,567,753,9.526069999999999e-23,97.3618,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,N-TerminusTruncated
17529,Q#232 - >seq6879,non-specific,197306,33,224,1.09038e-17,83.2996,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17530,Q#232 - >seq6879,non-specific,333820,566,753,6.319290000000001e-16,76.5622,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,N-TerminusTruncated
17531,Q#232 - >seq6879,superfamily,333820,566,753,6.319290000000001e-16,76.5622,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,N-TerminusTruncated
17532,Q#232 - >seq6879,non-specific,197320,56,187,1.26485e-07,53.673,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4d,ORF2,hs3_orang,pars,BothTerminiTruncated
17533,Q#232 - >seq6879,non-specific,238828,568,703,2.00236e-06,49.5068,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,N-TerminusTruncated
17534,Q#232 - >seq6879,specific,335306,33,188,0.00040649800000000004,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17535,Q#232 - >seq6879,non-specific,236970,51,182,0.0009055310000000001,42.1886,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17536,Q#232 - >seq6879,non-specific,197307,33,187,0.00195508,40.7341,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17537,Q#232 - >seq6879,non-specific,275209,570,702,0.00196768,41.2892,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,BothTerminiTruncated
17538,Q#232 - >seq6879,superfamily,275209,570,702,0.00196768,41.2892,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs3_orang,pars,BothTerminiTruncated
17539,Q#232 - >seq6879,non-specific,223780,47,187,0.00239614,40.6595,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4d,ORF2,hs3_orang,pars,C-TerminusTruncated
17540,Q#232 - >seq6879,non-specific,197321,34,217,0.00391471,39.8428,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.pars.frame2,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4d,ORF2,hs3_orang,pars,CompleteHit
17541,Q#234 - >seq6881,specific,197310,9,241,1.9057000000000002e-52,183.707,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17542,Q#234 - >seq6881,superfamily,351117,9,241,1.9057000000000002e-52,183.707,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17543,Q#234 - >seq6881,non-specific,197306,9,241,1.36691e-30,121.04899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17544,Q#234 - >seq6881,non-specific,197320,9,199,1.55544e-17,83.3333,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17545,Q#234 - >seq6881,non-specific,197307,9,234,6.9305e-16,78.4837,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17546,Q#234 - >seq6881,non-specific,197321,7,234,1.6737900000000002e-14,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17547,Q#234 - >seq6881,non-specific,223780,9,199,1.76473e-14,74.5571,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17548,Q#234 - >seq6881,specific,335306,10,200,1.81125e-13,70.7369,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17549,Q#234 - >seq6881,non-specific,238827,524,575,3.73075e-12,66.931,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17550,Q#234 - >seq6881,superfamily,295487,524,575,3.73075e-12,66.931,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17551,Q#234 - >seq6881,non-specific,273186,9,242,1.7593500000000002e-10,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17552,Q#234 - >seq6881,non-specific,236970,9,194,2.23688e-08,56.441,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17553,Q#234 - >seq6881,non-specific,197319,13,241,5.251580000000001e-08,54.9753,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,CompleteHit
17554,Q#234 - >seq6881,non-specific,272954,9,199,9.382419999999999e-08,54.3113,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17555,Q#234 - >seq6881,non-specific,197336,9,158,6.15462e-05,45.6811,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17556,Q#234 - >seq6881,non-specific,197311,42,151,0.004007,39.5825,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs3_orang.marg.frame3,1909130936_L1P4d.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs3_orang,marg,C-TerminusTruncated
17557,Q#237 - >seq6884,non-specific,340205,2,50,5.079919999999999e-16,64.2796,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4e,ORF1,hs6_sqmonkey,marg,CompleteHit
17558,Q#237 - >seq6884,superfamily,340205,2,50,5.079919999999999e-16,64.2796,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4e,ORF1,hs6_sqmonkey,marg,CompleteHit
17559,Q#238 - >seq6885,non-specific,197310,110,203,0.00749251,37.3309,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs6_sqmonkey.pars.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
17560,Q#238 - >seq6885,superfamily,351117,110,203,0.00749251,37.3309,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.pars.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
17561,Q#240 - >seq6887,specific,197310,9,225,1.4222799999999999e-32,122.46,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,CompleteHit
17562,Q#240 - >seq6887,superfamily,351117,9,225,1.4222799999999999e-32,122.46,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,CompleteHit
17563,Q#240 - >seq6887,non-specific,197306,9,135,2.2437200000000003e-22,94.8556,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17564,Q#240 - >seq6887,non-specific,223780,9,152,2.51146e-09,57.2231,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17565,Q#240 - >seq6887,non-specific,197336,9,135,3.79583e-09,56.8519,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17566,Q#240 - >seq6887,non-specific,197320,9,117,2.0638799999999996e-08,54.4434,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17567,Q#240 - >seq6887,non-specific,197321,7,94,3.30988e-08,54.0952,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17568,Q#240 - >seq6887,non-specific,197307,9,136,8.78525e-08,52.6753,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17569,Q#240 - >seq6887,specific,335306,10,148,4.3000100000000004e-07,50.3214,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17570,Q#240 - >seq6887,non-specific,273186,9,140,2.73968e-06,48.044,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17571,Q#240 - >seq6887,non-specific,197319,13,136,0.000586245,41.1081,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17572,Q#240 - >seq6887,non-specific,272954,9,43,0.000601993,40.8293,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17573,Q#240 - >seq6887,non-specific,197318,9,53,0.00137213,39.9723,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P4e.ORF2.hs6_sqmonkey.pars.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
17574,Q#241 - >seq6888,specific,197310,9,226,5.43402e-31,120.919,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,CompleteHit
17575,Q#241 - >seq6888,superfamily,351117,9,226,5.43402e-31,120.919,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,CompleteHit
17576,Q#241 - >seq6888,non-specific,197306,9,135,2.9329400000000005e-22,96.0112,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17577,Q#241 - >seq6888,non-specific,197336,9,135,7.479919999999999e-09,56.8519,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17578,Q#241 - >seq6888,non-specific,197321,7,141,7.58643e-09,56.7916,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17579,Q#241 - >seq6888,non-specific,197307,9,140,8.43957e-09,56.5273,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17580,Q#241 - >seq6888,non-specific,223780,9,153,2.2949599999999995e-08,55.2971,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17581,Q#241 - >seq6888,non-specific,197320,9,117,3.4609699999999994e-08,54.8286,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17582,Q#241 - >seq6888,specific,335306,10,149,2.5833e-07,51.8622,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17583,Q#241 - >seq6888,non-specific,273186,9,140,2.40582e-06,49.1996,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17584,Q#241 - >seq6888,non-specific,238827,503,646,1.65779e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17585,Q#241 - >seq6888,superfamily,295487,503,646,1.65779e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17586,Q#241 - >seq6888,non-specific,272954,9,141,9.37543e-05,44.2961,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17587,Q#241 - >seq6888,non-specific,333820,503,650,9.94208e-05,43.435,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17588,Q#241 - >seq6888,superfamily,333820,503,650,9.94208e-05,43.435,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17589,Q#241 - >seq6888,non-specific,197319,13,135,0.0010743,41.1081,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17590,Q#241 - >seq6888,non-specific,197318,9,53,0.00261018,39.9723,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P4e.ORF2.hs6_sqmonkey.marg.frame3,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17591,Q#242 - >seq6889,non-specific,238827,499,593,4.63575e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs6_sqmonkey.marg.frame2,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17592,Q#242 - >seq6889,superfamily,295487,499,593,4.63575e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs6_sqmonkey.marg.frame2,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4e,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
17593,Q#245 - >seq6892,non-specific,335182,90,151,4.57658e-21,83.8915,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs0_human.pars.frame3,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs0_human,pars,N-TerminusTruncated
17594,Q#245 - >seq6892,superfamily,335182,90,151,4.57658e-21,83.8915,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs0_human.pars.frame3,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs0_human,pars,N-TerminusTruncated
17595,Q#245 - >seq6892,non-specific,340205,155,198,2.3293900000000002e-14,65.4352,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs0_human.pars.frame3,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs0_human,pars,C-TerminusTruncated
17596,Q#245 - >seq6892,superfamily,340205,155,198,2.3293900000000002e-14,65.4352,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs0_human.pars.frame3,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs0_human,pars,C-TerminusTruncated
17597,Q#247 - >seq6894,non-specific,197310,153,206,0.00339457,39.2569,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
17598,Q#247 - >seq6894,superfamily,351117,153,206,0.00339457,39.2569,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
17599,Q#249 - >seq6896,non-specific,340205,37,80,5.87788e-13,57.7312,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs6_sqmonkey.pars.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
17600,Q#249 - >seq6896,superfamily,340205,37,80,5.87788e-13,57.7312,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs6_sqmonkey.pars.frame1,1909130937_L1P4e.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
17601,Q#252 - >seq6899,non-specific,197310,26,134,4.501600000000001e-11,63.9097,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs3_orang.marg.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4e,ORF2,hs3_orang,marg,C-TerminusTruncated
17602,Q#252 - >seq6899,superfamily,351117,26,134,4.501600000000001e-11,63.9097,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.marg.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,marg,C-TerminusTruncated
17603,Q#252 - >seq6899,non-specific,197306,35,132,0.000113723,44.7797,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.marg.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,marg,C-TerminusTruncated
17604,Q#253 - >seq6900,specific,238827,539,806,3.18957e-48,170.935,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17605,Q#253 - >seq6900,superfamily,295487,539,806,3.18957e-48,170.935,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17606,Q#253 - >seq6900,non-specific,333820,545,806,1.40016e-18,84.6513,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17607,Q#253 - >seq6900,superfamily,333820,545,806,1.40016e-18,84.6513,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17608,Q#253 - >seq6900,non-specific,238828,631,758,7.13255e-07,51.4328,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs3_orang,marg,N-TerminusTruncated
17609,Q#253 - >seq6900,non-specific,197310,7,249,6.21871e-06,48.5017,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17610,Q#253 - >seq6900,superfamily,351117,7,249,6.21871e-06,48.5017,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,marg,CompleteHit
17611,Q#254 - >seq6901,non-specific,197310,1,115,2.04337e-13,70.4581,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs3_orang.pars.frame3,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17612,Q#254 - >seq6901,superfamily,351117,1,115,2.04337e-13,70.4581,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.pars.frame3,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17613,Q#254 - >seq6901,non-specific,197306,1,129,8.486830000000001e-07,50.9429,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.pars.frame3,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17614,Q#255 - >seq6902,non-specific,238827,521,706,6.74314e-16,77.3314,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17615,Q#255 - >seq6902,superfamily,295487,521,706,6.74314e-16,77.3314,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17616,Q#255 - >seq6902,non-specific,333820,613,691,7.5688499999999995e-06,47.287,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17617,Q#255 - >seq6902,superfamily,333820,613,691,7.5688499999999995e-06,47.287,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17618,Q#255 - >seq6902,non-specific,238828,613,691,0.000591253,42.1881,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17619,Q#255 - >seq6902,non-specific,197310,165,210,0.000978774,41.5681,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17620,Q#255 - >seq6902,superfamily,351117,165,210,0.000978774,41.5681,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,pars,N-TerminusTruncated
17621,Q#256 - >seq6903,non-specific,238827,466,517,1.0523e-12,68.0866,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17622,Q#256 - >seq6903,superfamily,295487,466,517,1.0523e-12,68.0866,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17623,Q#256 - >seq6903,non-specific,197310,29,165,0.000332751,42.7237,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17624,Q#256 - >seq6903,superfamily,351117,29,165,0.000332751,42.7237,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17625,Q#256 - >seq6903,non-specific,197306,31,163,0.0006205609999999999,42.0833,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17626,Q#256 - >seq6903,non-specific,333820,472,509,0.00903721,38.0422,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17627,Q#256 - >seq6903,superfamily,333820,472,509,0.00903721,38.0422,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs3_orang.pars.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs3_orang,pars,C-TerminusTruncated
17628,Q#259 - >seq6906,non-specific,335182,180,269,6.09632e-19,80.8099,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs3_orang,marg,N-TerminusTruncated
17629,Q#259 - >seq6906,superfamily,335182,180,269,6.09632e-19,80.8099,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs3_orang,marg,N-TerminusTruncated
17630,Q#259 - >seq6906,non-specific,340205,302,355,2.44507e-14,66.976,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs3_orang,marg,CompleteHit
17631,Q#259 - >seq6906,superfamily,340205,302,355,2.44507e-14,66.976,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs3_orang.marg.frame1,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs3_orang,marg,CompleteHit
17632,Q#261 - >seq6908,non-specific,340205,186,243,9.79643e-19,77.3764,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4e,ORF1,hs3_orang,pars,CompleteHit
17633,Q#261 - >seq6908,superfamily,340205,186,243,9.79643e-19,77.3764,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4e,ORF1,hs3_orang,pars,CompleteHit
17634,Q#261 - >seq6908,non-specific,335182,134,178,3.58024e-10,55.3867,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4e,ORF1,hs3_orang,pars,N-TerminusTruncated
17635,Q#261 - >seq6908,superfamily,335182,134,178,3.58024e-10,55.3867,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs3_orang.pars.frame2,1909130937_L1P4e.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4e,ORF1,hs3_orang,pars,N-TerminusTruncated
17636,Q#264 - >seq6911,non-specific,335182,153,237,5.0579199999999995e-21,86.2026,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs0_human,marg,CompleteHit
17637,Q#264 - >seq6911,superfamily,335182,153,237,5.0579199999999995e-21,86.2026,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs0_human,marg,CompleteHit
17638,Q#264 - >seq6911,non-specific,340205,241,329,4.2171199999999997e-13,63.5092,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs0_human,marg,CompleteHit
17639,Q#264 - >seq6911,superfamily,340205,241,329,4.2171199999999997e-13,63.5092,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs0_human,marg,CompleteHit
17640,Q#265 - >seq6912,specific,238827,506,767,3.25379e-57,196.358,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,CompleteHit
17641,Q#265 - >seq6912,superfamily,295487,506,767,3.25379e-57,196.358,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,CompleteHit
17642,Q#265 - >seq6912,specific,197310,9,235,1.7610999999999997e-41,152.12,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17643,Q#265 - >seq6912,superfamily,351117,9,235,1.7610999999999997e-41,152.12,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17644,Q#265 - >seq6912,non-specific,197306,9,235,2.7618e-29,117.197,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17645,Q#265 - >seq6912,non-specific,333820,512,767,2.4319e-26,106.60799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,CompleteHit
17646,Q#265 - >seq6912,superfamily,333820,512,767,2.4319e-26,106.60799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,CompleteHit
17647,Q#265 - >seq6912,non-specific,197307,9,235,5.7313e-11,63.8461,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17648,Q#265 - >seq6912,non-specific,223780,9,236,6.39189e-10,60.6899,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17649,Q#265 - >seq6912,non-specific,197320,9,193,6.60841e-09,57.525,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1P4e,ORF2,hs0_human,pars,C-TerminusTruncated
17650,Q#265 - >seq6912,non-specific,273186,9,236,2.81436e-07,52.6664,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17651,Q#265 - >seq6912,non-specific,197321,7,235,9.0149e-07,51.0136,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17652,Q#265 - >seq6912,specific,335306,10,228,3.12834e-06,49.1658,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17653,Q#265 - >seq6912,non-specific,238828,578,732,5.1522500000000005e-06,48.3513,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,N-TerminusTruncated
17654,Q#265 - >seq6912,non-specific,197319,9,235,0.00107379,41.8785,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs0_human,pars,CompleteHit
17655,Q#265 - >seq6912,non-specific,238185,654,767,0.00719657,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs0_human.pars.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs0_human,pars,CompleteHit
17656,Q#267 - >seq6914,specific,238827,502,721,1.64724e-38,143.201,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17657,Q#267 - >seq6914,superfamily,295487,502,721,1.64724e-38,143.201,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17658,Q#267 - >seq6914,non-specific,333820,508,689,4.6067e-19,85.8069,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17659,Q#267 - >seq6914,superfamily,333820,508,689,4.6067e-19,85.8069,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17660,Q#267 - >seq6914,non-specific,197310,4,217,4.06594e-17,81.6289,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17661,Q#267 - >seq6914,superfamily,351117,4,217,4.06594e-17,81.6289,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17662,Q#267 - >seq6914,non-specific,238828,534,689,1.44917e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17663,Q#267 - >seq6914,non-specific,275209,539,753,0.000108228,45.5264,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17664,Q#267 - >seq6914,superfamily,275209,539,753,0.000108228,45.5264,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17665,Q#267 - >seq6914,non-specific,238185,609,723,0.000876707,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,marg,CompleteHit
17666,Q#268 - >seq6915,non-specific,238827,462,500,1.5492000000000001e-07,53.0638,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17667,Q#268 - >seq6915,superfamily,295487,462,500,1.5492000000000001e-07,53.0638,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17668,Q#268 - >seq6915,non-specific,235175,247,421,0.00026007,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17669,Q#268 - >seq6915,superfamily,235175,247,421,0.00026007,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17670,Q#268 - >seq6915,non-specific,274009,254,410,0.00509337,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17671,Q#268 - >seq6915,superfamily,274009,254,410,0.00509337,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17672,Q#270 - >seq6917,non-specific,238827,562,670,1.86409e-20,90.8134,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17673,Q#270 - >seq6917,superfamily,295487,562,670,1.86409e-20,90.8134,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17674,Q#270 - >seq6917,non-specific,333820,544,638,8.672830000000001e-08,53.065,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17675,Q#270 - >seq6917,superfamily,333820,544,638,8.672830000000001e-08,53.065,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17676,Q#270 - >seq6917,non-specific,197310,1,64,1.54833e-06,50.4277,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17677,Q#270 - >seq6917,superfamily,351117,1,64,1.54833e-06,50.4277,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17678,Q#270 - >seq6917,non-specific,238828,546,638,0.00873595,38.7213,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17679,Q#272 - >seq6919,specific,238827,446,551,9.24868e-29,115.081,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17680,Q#272 - >seq6919,superfamily,295487,446,551,9.24868e-29,115.081,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17681,Q#272 - >seq6919,non-specific,333820,452,597,3.7989899999999995e-13,68.8582,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17682,Q#272 - >seq6919,superfamily,333820,452,597,3.7989899999999995e-13,68.8582,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17683,Q#272 - >seq6919,non-specific,197310,101,169,5.04969e-09,57.7465,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17684,Q#272 - >seq6919,superfamily,351117,101,169,5.04969e-09,57.7465,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17685,Q#272 - >seq6919,non-specific,235175,233,405,0.00022560900000000001,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
17686,Q#272 - >seq6919,superfamily,235175,233,405,0.00022560900000000001,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
17687,Q#272 - >seq6919,non-specific,274009,246,394,0.00814454,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17688,Q#272 - >seq6919,superfamily,274009,246,394,0.00814454,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1P4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17689,Q#273 - >seq6920,non-specific,235175,243,420,0.00122816,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4.ORF2.hs3_orang.marg.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4,ORF2,hs3_orang,marg,BothTerminiTruncated
17690,Q#273 - >seq6920,superfamily,235175,243,420,0.00122816,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4.ORF2.hs3_orang.marg.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P4,ORF2,hs3_orang,marg,BothTerminiTruncated
17691,Q#273 - >seq6920,non-specific,335609,324,432,0.00892793,37.913000000000004,pfam04079,SMC_ScpB, - ,cl00612,"Segregation and condensation complex subunit ScpB; This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerizes and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies.",L1P4.ORF2.hs3_orang.marg.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4,ORF2,hs3_orang,marg,CompleteHit
17692,Q#273 - >seq6920,superfamily,351177,324,432,0.00892793,37.913000000000004,cl00612,SMC_ScpB superfamily, - , - ,"Segregation and condensation complex subunit ScpB; This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerizes and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies.",L1P4.ORF2.hs3_orang.marg.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4,ORF2,hs3_orang,marg,CompleteHit
17693,Q#274 - >seq6921,non-specific,197310,50,123,0.00200643,40.7977,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs3_orang.marg.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4,ORF2,hs3_orang,marg,BothTerminiTruncated
17694,Q#274 - >seq6921,superfamily,351117,50,123,0.00200643,40.7977,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs3_orang.marg.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs3_orang,marg,BothTerminiTruncated
17695,Q#275 - >seq6922,specific,238827,482,731,1.37439e-57,197.899,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,CompleteHit
17696,Q#275 - >seq6922,superfamily,295487,482,731,1.37439e-57,197.899,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,CompleteHit
17697,Q#275 - >seq6922,specific,333820,483,731,1.98896e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,CompleteHit
17698,Q#275 - >seq6922,superfamily,333820,483,731,1.98896e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,CompleteHit
17699,Q#275 - >seq6922,non-specific,197310,5,212,3.7846499999999997e-14,73.1545,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4,ORF2,hs3_orang,marg,CompleteHit
17700,Q#275 - >seq6922,superfamily,351117,5,212,3.7846499999999997e-14,73.1545,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs3_orang,marg,CompleteHit
17701,Q#275 - >seq6922,non-specific,238828,536,692,8.50891e-14,71.8484,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,N-TerminusTruncated
17702,Q#275 - >seq6922,non-specific,275209,541,759,1.63552e-08,57.8528,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,N-TerminusTruncated
17703,Q#275 - >seq6922,superfamily,275209,541,759,1.63552e-08,57.8528,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,N-TerminusTruncated
17704,Q#275 - >seq6922,non-specific,238185,611,696,0.00129035,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs3_orang.marg.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs3_orang,marg,CompleteHit
17705,Q#276 - >seq6923,non-specific,197310,1,175,3.54908e-20,90.4885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs3_orang.pars.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4,ORF2,hs3_orang,pars,CompleteHit
17706,Q#276 - >seq6923,superfamily,351117,1,175,3.54908e-20,90.4885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs3_orang.pars.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs3_orang,pars,CompleteHit
17707,Q#276 - >seq6923,non-specific,197306,1,175,9.75781e-06,47.8613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs3_orang.pars.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs3_orang,pars,CompleteHit
17708,Q#276 - >seq6923,non-specific,197320,67,160,0.0017211,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4.ORF2.hs3_orang.pars.frame3,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17709,Q#277 - >seq6924,non-specific,197310,24,68,0.00424832,39.6421,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs3_orang.pars.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4,ORF2,hs3_orang,pars,BothTerminiTruncated
17710,Q#277 - >seq6924,superfamily,351117,24,68,0.00424832,39.6421,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs3_orang.pars.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs3_orang,pars,BothTerminiTruncated
17711,Q#277 - >seq6924,non-specific,227608,157,299,0.00457476,41.0663,COG5283,COG5283,N,cl34972,"Phage-related tail protein  [Mobilome: prophages, transposons]; Phage-related tail protein [Function unknown].",L1P4.ORF2.hs3_orang.pars.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17712,Q#277 - >seq6924,superfamily,227608,157,299,0.00457476,41.0663,cl34972,COG5283 superfamily,N, - ,"Phage-related tail protein  [Mobilome: prophages, transposons]; Phage-related tail protein [Function unknown].",L1P4.ORF2.hs3_orang.pars.frame2,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17713,Q#278 - >seq6925,specific,238827,434,678,4.436939999999999e-57,196.358,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,CompleteHit
17714,Q#278 - >seq6925,superfamily,295487,434,678,4.436939999999999e-57,196.358,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,CompleteHit
17715,Q#278 - >seq6925,specific,333820,435,678,3.5323e-30,117.779,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,CompleteHit
17716,Q#278 - >seq6925,superfamily,333820,435,678,3.5323e-30,117.779,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,CompleteHit
17717,Q#278 - >seq6925,non-specific,238828,488,643,8.20721e-12,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17718,Q#278 - >seq6925,non-specific,275209,493,706,4.41048e-07,53.2304,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17719,Q#278 - >seq6925,superfamily,275209,493,706,4.41048e-07,53.2304,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs3_orang.pars.frame1,1909130937_L1P4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs3_orang,pars,N-TerminusTruncated
17720,Q#279 - >seq6926,non-specific,197310,4,184,0.00155378,41.1829,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs2_gorilla.marg.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17721,Q#279 - >seq6926,superfamily,351117,4,184,0.00155378,41.1829,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs2_gorilla.marg.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17722,Q#281 - >seq6928,non-specific,197310,173,229,1.135e-05,47.7313,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs2_gorilla.marg.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17723,Q#281 - >seq6928,superfamily,351117,173,229,1.135e-05,47.7313,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs2_gorilla.marg.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
17724,Q#281 - >seq6928,non-specific,275075,416,482,0.00592634,39.522,TIGR04239,rhombo_GlpG,C,cl37404,"rhomboid family protease GlpG; GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain.",L1P4.ORF2.hs2_gorilla.marg.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
17725,Q#281 - >seq6928,superfamily,275075,416,482,0.00592634,39.522,cl37404,rhombo_GlpG superfamily,C, - ,"rhomboid family protease GlpG; GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain.",L1P4.ORF2.hs2_gorilla.marg.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
17726,Q#282 - >seq6929,specific,238827,328,571,5.3275499999999996e-30,118.163,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs2_gorilla,pars,CompleteHit
17727,Q#282 - >seq6929,superfamily,295487,328,571,5.3275499999999996e-30,118.163,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs2_gorilla,pars,CompleteHit
17728,Q#282 - >seq6929,non-specific,333820,334,554,2.27179e-12,66.1618,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs2_gorilla,pars,CompleteHit
17729,Q#282 - >seq6929,superfamily,333820,334,554,2.27179e-12,66.1618,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs2_gorilla,pars,CompleteHit
17730,Q#283 - >seq6930,non-specific,238827,466,578,5.82096e-12,65.7754,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17731,Q#283 - >seq6930,superfamily,295487,466,578,5.82096e-12,65.7754,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17732,Q#283 - >seq6930,non-specific,333820,448,522,3.1288400000000003e-06,48.0574,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
17733,Q#283 - >seq6930,superfamily,333820,448,522,3.1288400000000003e-06,48.0574,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
17734,Q#283 - >seq6930,non-specific,197310,29,80,3.53036e-05,45.8053,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17735,Q#283 - >seq6930,superfamily,351117,29,80,3.53036e-05,45.8053,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17736,Q#284 - >seq6931,non-specific,275075,260,326,0.00440067,39.522,TIGR04239,rhombo_GlpG,C,cl37404,"rhomboid family protease GlpG; GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain.",L1P4.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1P4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17737,Q#284 - >seq6931,superfamily,275075,260,326,0.00440067,39.522,cl37404,rhombo_GlpG superfamily,C, - ,"rhomboid family protease GlpG; GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain.",L1P4.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1P4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17738,Q#285 - >seq6932,specific,238827,443,705,3.4579299999999998e-47,168.238,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17739,Q#285 - >seq6932,superfamily,295487,443,705,3.4579299999999998e-47,168.238,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17740,Q#285 - >seq6932,non-specific,333820,449,705,5.565150000000001e-20,88.5033,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17741,Q#285 - >seq6932,superfamily,333820,449,705,5.565150000000001e-20,88.5033,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17742,Q#286 - >seq6933,non-specific,197310,50,166,0.000583926,42.7237,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs1_chimp.marg.frame2,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4,ORF2,hs1_chimp,marg,N-TerminusTruncated
17743,Q#286 - >seq6933,superfamily,351117,50,166,0.000583926,42.7237,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs1_chimp.marg.frame2,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs1_chimp,marg,N-TerminusTruncated
17744,Q#287 - >seq6934,non-specific,197310,5,209,1.3639e-13,71.6137,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17745,Q#287 - >seq6934,superfamily,351117,5,209,1.3639e-13,71.6137,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17746,Q#287 - >seq6934,non-specific,238827,602,625,4.788719999999999e-06,48.8266,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17747,Q#287 - >seq6934,superfamily,295487,602,625,4.788719999999999e-06,48.8266,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17748,Q#287 - >seq6934,non-specific,333820,586,625,0.00401392,39.583,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17749,Q#287 - >seq6934,superfamily,333820,586,625,0.00401392,39.583,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17750,Q#287 - >seq6934,non-specific,197306,5,209,0.00490297,39.7721,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs1_chimp,marg,CompleteHit
17751,Q#287 - >seq6934,non-specific,235175,275,358,0.00906193,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17752,Q#287 - >seq6934,superfamily,235175,275,358,0.00906193,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4,ORF2,hs1_chimp,marg,BothTerminiTruncated
17753,Q#288 - >seq6935,non-specific,197310,85,171,6.46236e-12,66.2209,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs1_chimp.pars.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4,ORF2,hs1_chimp,pars,N-TerminusTruncated
17754,Q#288 - >seq6935,superfamily,351117,85,171,6.46236e-12,66.2209,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs1_chimp.pars.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs1_chimp,pars,N-TerminusTruncated
17755,Q#288 - >seq6935,non-specific,238827,617,682,2.80655e-07,52.2934,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs1_chimp.pars.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs1_chimp,pars,N-TerminusTruncated
17756,Q#288 - >seq6935,superfamily,295487,617,682,2.80655e-07,52.2934,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs1_chimp.pars.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs1_chimp,pars,N-TerminusTruncated
17757,Q#288 - >seq6935,non-specific,197306,1,171,0.0006560030000000001,42.4685,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs1_chimp.pars.frame3,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs1_chimp,pars,CompleteHit
17758,Q#290 - >seq6937,specific,238827,426,629,1.5821099999999998e-48,171.705,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,C-TerminusTruncated
17759,Q#290 - >seq6937,superfamily,295487,426,629,1.5821099999999998e-48,171.705,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,C-TerminusTruncated
17760,Q#290 - >seq6937,non-specific,333820,432,627,4.96116e-25,103.141,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,C-TerminusTruncated
17761,Q#290 - >seq6937,superfamily,333820,432,627,4.96116e-25,103.141,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,C-TerminusTruncated
17762,Q#290 - >seq6937,non-specific,238828,432,627,1.59117e-09,59.1368,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,CompleteHit
17763,Q#290 - >seq6937,non-specific,275209,502,586,0.000669465,42.83,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,BothTerminiTruncated
17764,Q#290 - >seq6937,superfamily,275209,502,586,0.000669465,42.83,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,BothTerminiTruncated
17765,Q#290 - >seq6937,specific,225881,398,595,0.0023111,40.9777,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,BothTerminiTruncated
17766,Q#290 - >seq6937,superfamily,225881,398,595,0.0023111,40.9777,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,BothTerminiTruncated
17767,Q#290 - >seq6937,non-specific,238185,564,632,0.00406861,37.7156,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4,ORF2,hs1_chimp,pars,C-TerminusTruncated
17768,Q#292 - >seq6939,non-specific,340205,114,157,6.34369e-11,58.8868,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF2.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF2,hs0_human,marg,N-TerminusTruncated
17769,Q#292 - >seq6939,superfamily,340205,114,157,6.34369e-11,58.8868,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF2.hs0_human.marg.frame2,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF2,hs0_human,marg,N-TerminusTruncated
17770,Q#293 - >seq6940,specific,238827,736,1000,2.77738e-44,159.764,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs0_human,marg,CompleteHit
17771,Q#293 - >seq6940,superfamily,295487,736,1000,2.77738e-44,159.764,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs0_human,marg,CompleteHit
17772,Q#293 - >seq6940,specific,197310,220,451,4.10284e-39,145.572,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17773,Q#293 - >seq6940,superfamily,351117,220,451,4.10284e-39,145.572,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17774,Q#293 - >seq6940,non-specific,197306,220,451,3.5993699999999996e-28,114.116,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17775,Q#293 - >seq6940,non-specific,333820,742,1000,1.0658e-17,82.3401,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs0_human,marg,CompleteHit
17776,Q#293 - >seq6940,superfamily,333820,742,1000,1.0658e-17,82.3401,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs0_human,marg,CompleteHit
17777,Q#293 - >seq6940,non-specific,335182,2,72,2.07223e-17,78.4987,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF2,hs0_human,marg,N-TerminusTruncated
17778,Q#293 - >seq6940,superfamily,335182,2,72,2.07223e-17,78.4987,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF2,hs0_human,marg,N-TerminusTruncated
17779,Q#293 - >seq6940,non-specific,197307,220,451,4.45287e-12,67.3129,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17780,Q#293 - >seq6940,non-specific,223780,220,408,9.165470000000001e-10,60.6899,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs0_human,marg,C-TerminusTruncated
17781,Q#293 - >seq6940,non-specific,197320,220,408,3.36687e-09,59.0658,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs0_human,marg,C-TerminusTruncated
17782,Q#293 - >seq6940,non-specific,197321,218,408,1.0169700000000001e-08,57.562,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17783,Q#293 - >seq6940,specific,335306,221,444,5.80537e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17784,Q#293 - >seq6940,non-specific,273186,220,452,6.738769999999999e-08,54.9776,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4e.ORF2.hs0_human.marg.frame1,1909130937_L1P4e.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs0_human,marg,CompleteHit
17785,Q#295 - >seq6942,specific,238827,485,751,1.2407899999999998e-54,189.424,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17786,Q#295 - >seq6942,superfamily,295487,485,751,1.2407899999999998e-54,189.424,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17787,Q#295 - >seq6942,non-specific,333820,491,751,2.1322199999999998e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17788,Q#295 - >seq6942,superfamily,333820,491,751,2.1322199999999998e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17789,Q#295 - >seq6942,non-specific,238828,491,711,1.63144e-08,56.0552,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs2_gorilla,marg,CompleteHit
17790,Q#295 - >seq6942,non-specific,235175,270,444,0.000344516,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
17791,Q#295 - >seq6942,superfamily,235175,270,444,0.000344516,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
17792,Q#296 - >seq6943,specific,238827,531,795,2.0181699999999998e-48,171.705,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17793,Q#296 - >seq6943,superfamily,295487,531,795,2.0181699999999998e-48,171.705,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17794,Q#296 - >seq6943,specific,197310,7,243,2.6355899999999998e-27,111.289,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17795,Q#296 - >seq6943,superfamily,351117,7,243,2.6355899999999998e-27,111.289,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17796,Q#296 - >seq6943,non-specific,333820,537,795,3.5816e-18,83.4957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17797,Q#296 - >seq6943,superfamily,333820,537,795,3.5816e-18,83.4957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17798,Q#296 - >seq6943,non-specific,197306,7,243,1.6863499999999998e-14,74.0548,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs2_gorilla,marg,CompleteHit
17799,Q#298 - >seq6945,specific,238827,472,730,4.5410800000000004e-36,135.882,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs2_gorilla,pars,CompleteHit
17800,Q#298 - >seq6945,superfamily,295487,472,730,4.5410800000000004e-36,135.882,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs2_gorilla,pars,CompleteHit
17801,Q#298 - >seq6945,non-specific,333820,478,730,5.86442e-11,62.3098,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs2_gorilla,pars,CompleteHit
17802,Q#298 - >seq6945,superfamily,333820,478,730,5.86442e-11,62.3098,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs2_gorilla.pars.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs2_gorilla,pars,CompleteHit
17803,Q#300 - >seq6947,non-specific,238827,580,789,2.33185e-25,104.681,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs6_sqmonkey,marg,CompleteHit
17804,Q#300 - >seq6947,superfamily,295487,580,789,2.33185e-25,104.681,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs6_sqmonkey,marg,CompleteHit
17805,Q#300 - >seq6947,non-specific,333820,579,789,3.71295e-18,82.7253,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs6_sqmonkey,marg,CompleteHit
17806,Q#300 - >seq6947,superfamily,333820,579,789,3.71295e-18,82.7253,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs6_sqmonkey,marg,CompleteHit
17807,Q#300 - >seq6947,non-specific,238828,631,789,0.000682416,41.8029,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4d.ORF2.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
17808,Q#305 - >seq6952,non-specific,335182,127,222,1.2986600000000002e-26,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs6_sqmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs6_sqmonkey,marg,CompleteHit
17809,Q#305 - >seq6952,superfamily,335182,127,222,1.2986600000000002e-26,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs6_sqmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs6_sqmonkey,marg,CompleteHit
17810,Q#305 - >seq6952,non-specific,340205,225,287,3.2379600000000004e-25,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs6_sqmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs6_sqmonkey,marg,CompleteHit
17811,Q#305 - >seq6952,superfamily,340205,225,287,3.2379600000000004e-25,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs6_sqmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4d,ORF1,hs6_sqmonkey,marg,CompleteHit
17812,Q#306 - >seq6953,non-specific,237177,29,121,0.00228347,38.991,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1P4d.ORF1.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1P4d,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
17813,Q#306 - >seq6953,superfamily,237177,29,121,0.00228347,38.991,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1P4d.ORF1.hs6_sqmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1P4d,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
17814,Q#307 - >seq6954,non-specific,335182,24,119,8.15685e-28,100.07,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs6_sqmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs6_sqmonkey,pars,CompleteHit
17815,Q#307 - >seq6954,superfamily,335182,24,119,8.15685e-28,100.07,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs6_sqmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs6_sqmonkey,pars,CompleteHit
17816,Q#307 - >seq6954,non-specific,340205,122,184,2.5083900000000002e-26,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs6_sqmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs6_sqmonkey,pars,CompleteHit
17817,Q#307 - >seq6954,superfamily,340205,122,184,2.5083900000000002e-26,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs6_sqmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs6_sqmonkey,pars,CompleteHit
17818,Q#311 - >seq6958,non-specific,197310,98,160,0.000224815,43.4941,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs5_gmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4d,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17819,Q#311 - >seq6958,superfamily,351117,98,160,0.000224815,43.4941,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.marg.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
17820,Q#312 - >seq6959,specific,197310,11,274,2.0592e-30,120.149,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17821,Q#312 - >seq6959,superfamily,351117,11,274,2.0592e-30,120.149,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17822,Q#312 - >seq6959,non-specific,238827,565,785,1.41156e-23,100.05799999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17823,Q#312 - >seq6959,superfamily,295487,565,785,1.41156e-23,100.05799999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17824,Q#312 - >seq6959,non-specific,197306,11,274,1.12745e-16,80.218,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17825,Q#312 - >seq6959,specific,335306,12,267,1.36301e-08,56.0994,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17826,Q#312 - >seq6959,non-specific,333820,583,738,5.51813e-08,53.4502,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
17827,Q#312 - >seq6959,superfamily,333820,583,738,5.51813e-08,53.4502,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
17828,Q#312 - >seq6959,non-specific,235175,306,524,0.000526916,43.8992,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
17829,Q#312 - >seq6959,superfamily,235175,306,524,0.000526916,43.8992,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1P4d,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
17830,Q#312 - >seq6959,non-specific,197307,11,267,0.0009182239999999999,41.8897,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4d,ORF2,hs5_gmonkey,marg,CompleteHit
17831,Q#312 - >seq6959,non-specific,197321,9,84,0.00543541,39.4576,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4d,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
17832,Q#313 - >seq6960,non-specific,197310,84,136,0.00170222,39.2569,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs5_gmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17833,Q#313 - >seq6960,superfamily,351117,84,136,0.00170222,39.2569,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
17834,Q#314 - >seq6961,specific,197310,27,232,1.25788e-29,114.37100000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4d,ORF2,hs5_gmonkey,pars,CompleteHit
17835,Q#314 - >seq6961,superfamily,351117,27,232,1.25788e-29,114.37100000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,pars,CompleteHit
17836,Q#314 - >seq6961,non-specific,197306,28,232,1.99039e-15,75.2104,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,pars,CompleteHit
17837,Q#314 - >seq6961,specific,335306,27,225,1.13527e-05,46.0842,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs5_gmonkey,pars,CompleteHit
17838,Q#317 - >seq6964,non-specific,340205,267,331,4.94978e-22,87.7768,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,marg,CompleteHit
17839,Q#317 - >seq6964,superfamily,340205,267,331,4.94978e-22,87.7768,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,marg,CompleteHit
17840,Q#317 - >seq6964,non-specific,335182,167,264,1.59299e-18,79.2691,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,marg,CompleteHit
17841,Q#317 - >seq6964,superfamily,335182,167,264,1.59299e-18,79.2691,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.marg.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,marg,CompleteHit
17842,Q#318 - >seq6965,non-specific,340205,248,292,2.31861e-13,63.5092,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
17843,Q#318 - >seq6965,superfamily,340205,248,292,2.31861e-13,63.5092,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame3,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
17844,Q#319 - >seq6966,non-specific,335182,206,231,0.000278885,39.2083,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
17845,Q#319 - >seq6966,superfamily,335182,206,231,0.000278885,39.2083,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame2,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
17846,Q#320 - >seq6967,non-specific,335182,134,188,7.71539e-13,63.0907,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
17847,Q#320 - >seq6967,superfamily,335182,134,188,7.71539e-13,63.0907,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs5_gmonkey.pars.frame1,1909130937_L1P4d.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
17848,Q#321 - >seq6968,non-specific,197310,9,229,2.88136e-24,102.43,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17849,Q#321 - >seq6968,superfamily,351117,9,229,2.88136e-24,102.43,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17850,Q#321 - >seq6968,non-specific,197306,9,235,9.20165e-19,86.7664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17851,Q#321 - >seq6968,specific,335306,10,201,1.7522099999999999e-12,68.0406,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17852,Q#321 - >seq6968,non-specific,197307,9,158,9.52098e-10,60.3793,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17853,Q#321 - >seq6968,non-specific,223780,9,158,1.18854e-06,51.0599,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17854,Q#321 - >seq6968,non-specific,197321,7,94,2.9198700000000002e-06,49.858000000000004,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17855,Q#321 - >seq6968,non-specific,197320,9,165,1.7263900000000003e-05,47.5098,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17856,Q#321 - >seq6968,non-specific,197336,9,91,0.000215824,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17857,Q#321 - >seq6968,non-specific,273186,9,158,0.0006561410000000001,42.6512,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17858,Q#321 - >seq6968,non-specific,197319,13,158,0.00934335,39.1821,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4d.ORF2.hs4_gibbon.marg.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,marg,C-TerminusTruncated
17859,Q#322 - >seq6969,non-specific,235175,257,465,0.00026424799999999997,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17860,Q#322 - >seq6969,superfamily,235175,257,465,0.00026424799999999997,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17861,Q#322 - >seq6969,non-specific,224117,255,386,0.0007540530000000001,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17862,Q#322 - >seq6969,superfamily,224117,255,386,0.0007540530000000001,43.5496,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17863,Q#322 - >seq6969,non-specific,187803,249,447,0.00104035,42.9151,cd09672,Cas8a1_I-A,NC,cl21533,"CRISPR/Cas system-associated protein Cas8a1; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family",L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17864,Q#322 - >seq6969,superfamily,328778,249,447,0.00104035,42.9151,cl21533,Cas8a1_I-A superfamily,NC, - ,"CRISPR/Cas system-associated protein Cas8a1; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family",L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17865,Q#322 - >seq6969,non-specific,235175,252,487,0.00116679,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,BothTerminiTruncated
17866,Q#322 - >seq6969,non-specific,179877,293,465,0.0017897000000000002,42.1302,PRK04778,PRK04778,N,cl32064,septation ring formation regulator EzrA; Provisional,L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1P4d,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17867,Q#322 - >seq6969,superfamily,179877,293,465,0.0017897000000000002,42.1302,cl32064,PRK04778 superfamily,N, - ,septation ring formation regulator EzrA; Provisional,L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1P4d,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17868,Q#322 - >seq6969,non-specific,224117,252,445,0.00406227,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1P4d.ORF2.hs4_gibbon.marg.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1P4d,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17869,Q#323 - >seq6970,specific,238827,489,744,7.3211499999999995e-31,121.244,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs4_gibbon.marg.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17870,Q#323 - >seq6970,superfamily,295487,489,744,7.3211499999999995e-31,121.244,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs4_gibbon.marg.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17871,Q#323 - >seq6970,non-specific,333820,506,715,1.93211e-15,75.4066,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.marg.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17872,Q#323 - >seq6970,superfamily,333820,506,715,1.93211e-15,75.4066,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.marg.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs4_gibbon,marg,CompleteHit
17873,Q#323 - >seq6970,non-specific,238828,563,718,1.18063e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4d.ORF2.hs4_gibbon.marg.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4d,ORF2,hs4_gibbon,marg,N-TerminusTruncated
17874,Q#324 - >seq6971,non-specific,197310,6,103,4.15755e-18,83.9401,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17875,Q#324 - >seq6971,superfamily,351117,6,103,4.15755e-18,83.9401,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17876,Q#324 - >seq6971,non-specific,197306,6,225,1.32058e-12,67.8917,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,CompleteHit
17877,Q#324 - >seq6971,non-specific,238827,500,544,9.735299999999999e-09,56.1454,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17878,Q#324 - >seq6971,superfamily,295487,500,544,9.735299999999999e-09,56.1454,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17879,Q#324 - >seq6971,non-specific,197321,4,88,5.13413e-08,54.4804,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17880,Q#324 - >seq6971,non-specific,197307,6,77,2.18158e-07,52.2901,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17881,Q#324 - >seq6971,non-specific,197336,6,85,2.15242e-06,49.5331,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17882,Q#324 - >seq6971,non-specific,223780,6,77,2.15558e-06,49.5191,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17883,Q#324 - >seq6971,specific,335306,7,74,5.953759999999999e-06,47.625,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17884,Q#324 - >seq6971,non-specific,274008,252,400,1.4104200000000001e-05,48.5143,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17885,Q#324 - >seq6971,superfamily,274008,252,400,1.4104200000000001e-05,48.5143,cl37069,SMC_prok_B superfamily,C, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17886,Q#324 - >seq6971,non-specific,273186,6,87,3.55397e-05,45.7328,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17887,Q#324 - >seq6971,non-specific,197320,6,94,0.00021899299999999998,43.2726,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17888,Q#324 - >seq6971,non-specific,272954,6,73,0.00109909,41.2145,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17889,Q#324 - >seq6971,non-specific,214017,291,414,0.00166199,39.6764,cd12924,iSH2_PIK3R1,N,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17890,Q#324 - >seq6971,superfamily,355389,291,414,0.00166199,39.6764,cl25402,iSH2_PI3K_IA_R superfamily,N, - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17891,Q#324 - >seq6971,non-specific,313357,305,399,0.0044605,38.7868,pfam10112,Halogen_Hydrol,NC,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF2,hs4_gibbon,pars,BothTerminiTruncated
17892,Q#324 - >seq6971,superfamily,321788,305,399,0.0044605,38.7868,cl02059,Halogen_Hydrol superfamily,NC, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF2,hs4_gibbon,pars,BothTerminiTruncated
17893,Q#324 - >seq6971,non-specific,333820,506,536,0.00695395,38.0422,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17894,Q#324 - >seq6971,superfamily,333820,506,536,0.00695395,38.0422,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4d,ORF2,hs4_gibbon,pars,C-TerminusTruncated
17895,Q#324 - >seq6971,non-specific,214019,291,414,0.00759938,37.7542,cd12926,iSH2_PIK3R2,N,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects.",L1P4d.ORF2.hs4_gibbon.pars.frame3,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17896,Q#325 - >seq6972,non-specific,238827,530,679,5.88358e-12,65.3902,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs4_gibbon.pars.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17897,Q#325 - >seq6972,superfamily,295487,530,679,5.88358e-12,65.3902,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs4_gibbon.pars.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17898,Q#325 - >seq6972,non-specific,333820,536,672,2.37796e-07,51.138999999999996,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.pars.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17899,Q#325 - >seq6972,superfamily,333820,536,672,2.37796e-07,51.138999999999996,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs4_gibbon.pars.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17900,Q#325 - >seq6972,non-specific,238828,507,631,0.000256203,42.9585,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4d.ORF2.hs4_gibbon.pars.frame2,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4d,ORF2,hs4_gibbon,pars,BothTerminiTruncated
17901,Q#326 - >seq6973,non-specific,197310,88,207,2.03861e-11,64.2949,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17902,Q#326 - >seq6973,superfamily,351117,88,207,2.03861e-11,64.2949,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17903,Q#326 - >seq6973,non-specific,197306,88,213,4.4333400000000006e-08,54.4097,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17904,Q#326 - >seq6973,non-specific,197320,97,196,0.00229455,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs4_gibbon.pars.frame1,1909130937_L1P4d.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P4d,ORF2,hs4_gibbon,pars,N-TerminusTruncated
17905,Q#327 - >seq6974,non-specific,197310,5,53,1.50035e-05,46.9609,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4e,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17906,Q#327 - >seq6974,superfamily,351117,5,53,1.50035e-05,46.9609,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4e,ORF2,hs2_gorilla,pars,C-TerminusTruncated
17907,Q#327 - >seq6974,non-specific,238827,537,620,0.000311556,43.0486,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4e,ORF2,hs2_gorilla,pars,BothTerminiTruncated
17908,Q#327 - >seq6974,superfamily,295487,537,620,0.000311556,43.0486,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4e,ORF2,hs2_gorilla,pars,BothTerminiTruncated
17909,Q#329 - >seq6976,non-specific,335182,134,231,1.0937799999999999e-32,116.24799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs0_human.pars.frame1,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs0_human,pars,CompleteHit
17910,Q#329 - >seq6976,superfamily,335182,134,231,1.0937799999999999e-32,116.24799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs0_human.pars.frame1,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs0_human,pars,CompleteHit
17911,Q#329 - >seq6976,non-specific,340205,234,296,7.655770000000001e-26,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs0_human.pars.frame1,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs0_human,pars,CompleteHit
17912,Q#329 - >seq6976,superfamily,340205,234,296,7.655770000000001e-26,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs0_human.pars.frame1,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4d,ORF1,hs0_human,pars,CompleteHit
17913,Q#331 - >seq6978,non-specific,318299,44,115,0.00168793,38.3567,pfam16043,DUF4795,N,cl23731,Domain of unknown function (DUF4795); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 285 and 978 amino acids in length.,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF1,hs0_human,pars,N-TerminusTruncated
17914,Q#331 - >seq6978,superfamily,318299,44,115,0.00168793,38.3567,cl23731,DUF4795 superfamily,N, - ,Domain of unknown function (DUF4795); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 285 and 978 amino acids in length.,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF1,hs0_human,pars,N-TerminusTruncated
17915,Q#331 - >seq6978,non-specific,222878,47,117,0.0057685,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF1,hs0_human,pars,BothTerminiTruncated
17916,Q#331 - >seq6978,superfamily,222878,47,117,0.0057685,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF1,hs0_human,pars,BothTerminiTruncated
17917,Q#331 - >seq6978,non-specific,338178,22,120,0.00606895,37.2066,pfam11932,DUF3450,C,cl26418,Protein of unknown function (DUF3450); This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length.,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF1,hs0_human,pars,C-TerminusTruncated
17918,Q#331 - >seq6978,superfamily,338178,22,120,0.00606895,37.2066,cl26418,DUF3450 superfamily,C, - ,Protein of unknown function (DUF3450); This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length.,L1P4d.ORF1.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4d,ORF1,hs0_human,pars,C-TerminusTruncated
17919,Q#332 - >seq6979,non-specific,197310,80,212,6.25791e-22,95.4961,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4e,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17920,Q#332 - >seq6979,superfamily,351117,80,212,6.25791e-22,95.4961,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17921,Q#332 - >seq6979,non-specific,197306,80,211,7.72462e-12,65.9657,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs2_gorilla,pars,N-TerminusTruncated
17922,Q#332 - >seq6979,non-specific,197320,90,176,2.48092e-05,46.7394,cd09086,ExoIII-like_AP-endo,NC,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs2_gorilla.pars.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1P4e,ORF2,hs2_gorilla,pars,BothTerminiTruncated
17923,Q#335 - >seq6982,non-specific,335182,159,242,2.2217599999999998e-26,100.455,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs2_gorilla.marg.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs2_gorilla,marg,CompleteHit
17924,Q#335 - >seq6982,superfamily,335182,159,242,2.2217599999999998e-26,100.455,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs2_gorilla.marg.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1P4e,ORF1,hs2_gorilla,marg,CompleteHit
17925,Q#335 - >seq6982,non-specific,340204,100,143,0.000887667,36.6168,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4e.ORF1.hs2_gorilla.marg.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1P4e,ORF1,hs2_gorilla,marg,CompleteHit
17926,Q#335 - >seq6982,superfamily,340204,100,143,0.000887667,36.6168,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P4e.ORF1.hs2_gorilla.marg.frame2,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1P4e,ORF1,hs2_gorilla,marg,CompleteHit
17927,Q#336 - >seq6983,non-specific,340205,274,318,4.48349e-06,43.4788,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs2_gorilla,marg,N-TerminusTruncated
17928,Q#336 - >seq6983,superfamily,340205,274,318,4.48349e-06,43.4788,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs2_gorilla.marg.frame1,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs2_gorilla,marg,N-TerminusTruncated
17929,Q#337 - >seq6984,non-specific,335182,160,243,4.2625100000000004e-26,99.2994,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs2_gorilla,pars,CompleteHit
17930,Q#337 - >seq6984,superfamily,335182,160,243,4.2625100000000004e-26,99.2994,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs2_gorilla,pars,CompleteHit
17931,Q#337 - >seq6984,non-specific,340205,246,294,1.52793e-08,50.4124,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17932,Q#337 - >seq6984,superfamily,340205,246,294,1.52793e-08,50.4124,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P4e,ORF1,hs2_gorilla,pars,C-TerminusTruncated
17933,Q#337 - >seq6984,non-specific,274475,52,119,0.00230918,39.2816,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4e,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17934,Q#337 - >seq6984,superfamily,274475,52,119,0.00230918,39.2816,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1P4e,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17935,Q#337 - >seq6984,non-specific,274008,49,193,0.00588507,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4e,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17936,Q#337 - >seq6984,superfamily,274008,49,193,0.00588507,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P4e.ORF1.hs2_gorilla.pars.frame3,1909130937_L1P4e.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P4e,ORF1,hs2_gorilla,pars,BothTerminiTruncated
17937,Q#339 - >seq6986,non-specific,227709,375,642,0.0076787999999999995,40.2595,COG5422,ROM1,C,cl34999,"RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].",L1P4e.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4e,ORF2,hs1_chimp,marg,C-TerminusTruncated
17938,Q#339 - >seq6986,superfamily,227709,375,642,0.0076787999999999995,40.2595,cl34999,ROM1 superfamily,C, - ,"RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].",L1P4e.ORF2.hs1_chimp.marg.frame3,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4e,ORF2,hs1_chimp,marg,C-TerminusTruncated
17939,Q#341 - >seq6988,specific,238827,527,796,5.254899999999999e-52,181.72,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17940,Q#341 - >seq6988,superfamily,295487,527,796,5.254899999999999e-52,181.72,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17941,Q#341 - >seq6988,specific,197310,8,242,4.9050499999999996e-30,119.37799999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17942,Q#341 - >seq6988,superfamily,351117,8,242,4.9050499999999996e-30,119.37799999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17943,Q#341 - >seq6988,non-specific,197306,8,242,3.4101e-23,99.478,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17944,Q#341 - >seq6988,non-specific,333820,533,796,3.2481e-22,95.0517,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17945,Q#341 - >seq6988,superfamily,333820,533,796,3.2481e-22,95.0517,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17946,Q#341 - >seq6988,specific,335306,8,235,1.02423e-08,56.8698,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17947,Q#341 - >seq6988,non-specific,197320,9,199,8.42718e-08,54.4434,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs1_chimp,marg,C-TerminusTruncated
17948,Q#341 - >seq6988,non-specific,197321,8,199,2.4560900000000002e-06,49.858000000000004,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17949,Q#341 - >seq6988,non-specific,223780,8,199,4.11806e-06,49.5191,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs1_chimp,marg,C-TerminusTruncated
17950,Q#341 - >seq6988,non-specific,197307,8,207,4.7231099999999996e-06,49.2085,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1P4e,ORF2,hs1_chimp,marg,CompleteHit
17951,Q#341 - >seq6988,non-specific,238828,603,735,5.3259e-06,48.7364,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,marg,N-TerminusTruncated
17952,Q#341 - >seq6988,non-specific,197319,8,149,0.0009129610000000001,42.2637,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P4e.ORF2.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4e,ORF2,hs1_chimp,marg,C-TerminusTruncated
17953,Q#343 - >seq6990,non-specific,197310,48,220,3.54036e-21,93.1849,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4e,ORF2,hs1_chimp,pars,N-TerminusTruncated
17954,Q#343 - >seq6990,superfamily,351117,48,220,3.54036e-21,93.1849,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,pars,N-TerminusTruncated
17955,Q#343 - >seq6990,non-specific,197306,46,220,1.96554e-14,73.6696,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,pars,N-TerminusTruncated
17956,Q#343 - >seq6990,non-specific,238827,553,642,1.4936700000000002e-06,49.9822,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs1_chimp,pars,BothTerminiTruncated
17957,Q#343 - >seq6990,superfamily,295487,553,642,1.4936700000000002e-06,49.9822,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs1_chimp,pars,BothTerminiTruncated
17958,Q#343 - >seq6990,non-specific,333820,553,632,9.95514e-05,43.8202,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs1_chimp,pars,BothTerminiTruncated
17959,Q#343 - >seq6990,superfamily,333820,553,632,9.95514e-05,43.8202,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.pars.frame2,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4e,ORF2,hs1_chimp,pars,BothTerminiTruncated
17960,Q#344 - >seq6991,specific,238827,472,729,1.69417e-33,128.563,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,pars,CompleteHit
17961,Q#344 - >seq6991,superfamily,295487,472,729,1.69417e-33,128.563,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,pars,CompleteHit
17962,Q#344 - >seq6991,non-specific,333820,478,729,2.98404e-10,60.3838,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,pars,CompleteHit
17963,Q#344 - >seq6991,superfamily,333820,478,729,2.98404e-10,60.3838,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1P4e,ORF2,hs1_chimp,pars,CompleteHit
17964,Q#344 - >seq6991,non-specific,197310,12,47,0.00266796,40.4125,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4e,ORF2,hs1_chimp,pars,C-TerminusTruncated
17965,Q#344 - >seq6991,superfamily,351117,12,47,0.00266796,40.4125,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4e.ORF2.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4e,ORF2,hs1_chimp,pars,C-TerminusTruncated
17966,Q#347 - >seq6994,non-specific,335182,167,241,1.03414e-24,96.2178,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,marg,N-TerminusTruncated
17967,Q#347 - >seq6994,superfamily,335182,167,241,1.03414e-24,96.2178,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,marg,N-TerminusTruncated
17968,Q#347 - >seq6994,non-specific,340205,273,327,2.40294e-15,69.6724,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,marg,CompleteHit
17969,Q#347 - >seq6994,superfamily,340205,273,327,2.40294e-15,69.6724,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs1_chimp.marg.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,marg,CompleteHit
17970,Q#350 - >seq6997,non-specific,335182,151,248,1.3235999999999997e-31,113.93700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs0_human,marg,CompleteHit
17971,Q#350 - >seq6997,superfamily,335182,151,248,1.3235999999999997e-31,113.93700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4d.ORF1.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs0_human,marg,CompleteHit
17972,Q#350 - >seq6997,non-specific,340205,251,313,2.15595e-26,98.9475,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs0_human,marg,CompleteHit
17973,Q#350 - >seq6997,superfamily,340205,251,313,2.15595e-26,98.9475,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4d.ORF1.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P4d,ORF1,hs0_human,marg,CompleteHit
17974,Q#353 - >seq7000,non-specific,197310,6,61,0.00014931700000000002,40.7977,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4d,ORF2,hs0_human,pars,C-TerminusTruncated
17975,Q#353 - >seq7000,superfamily,351117,6,61,0.00014931700000000002,40.7977,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs0_human.pars.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs0_human,pars,C-TerminusTruncated
17976,Q#354 - >seq7001,non-specific,197310,48,104,2.7059699999999996e-06,45.4201,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs0_human.pars.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1P4d,ORF2,hs0_human,pars,C-TerminusTruncated
17977,Q#354 - >seq7001,superfamily,351117,48,104,2.7059699999999996e-06,45.4201,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs0_human.pars.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1P4d,ORF2,hs0_human,pars,C-TerminusTruncated
17978,Q#355 - >seq7002,non-specific,238827,626,737,1.47305e-12,67.7014,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs0_human.marg.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs0_human,marg,N-TerminusTruncated
17979,Q#355 - >seq7002,superfamily,295487,626,737,1.47305e-12,67.7014,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs0_human.marg.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs0_human,marg,N-TerminusTruncated
17980,Q#355 - >seq7002,non-specific,333820,540,737,7.20426e-06,47.287,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs0_human.marg.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs0_human,marg,CompleteHit
17981,Q#355 - >seq7002,superfamily,333820,540,737,7.20426e-06,47.287,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs0_human.marg.frame2,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4d,ORF2,hs0_human,marg,CompleteHit
17982,Q#356 - >seq7003,specific,197310,9,239,2.5093299999999997e-43,157.513,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17983,Q#356 - >seq7003,superfamily,351117,9,239,2.5093299999999997e-43,157.513,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17984,Q#356 - >seq7003,non-specific,197306,9,239,7.90057e-20,89.4628,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17985,Q#356 - >seq7003,non-specific,238827,515,571,7.19296e-11,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs0_human,marg,C-TerminusTruncated
17986,Q#356 - >seq7003,superfamily,295487,515,571,7.19296e-11,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs0_human,marg,C-TerminusTruncated
17987,Q#356 - >seq7003,non-specific,197307,9,239,4.15051e-09,58.0681,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17988,Q#356 - >seq7003,specific,335306,10,213,1.80489e-08,55.7142,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17989,Q#356 - >seq7003,non-specific,223780,9,240,1.75878e-07,53.3711,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17990,Q#356 - >seq7003,non-specific,197320,9,211,2.46558e-07,52.9026,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17991,Q#356 - >seq7003,non-specific,197321,7,239,2.62388e-06,49.858000000000004,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17992,Q#356 - >seq7003,non-specific,272954,9,210,0.00170014,41.2145,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P4d,ORF2,hs0_human,marg,CompleteHit
17993,Q#356 - >seq7003,non-specific,333820,521,572,0.00939704,38.0422,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs0_human,marg,C-TerminusTruncated
17994,Q#356 - >seq7003,superfamily,333820,521,572,0.00939704,38.0422,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4d.ORF2.hs0_human.marg.frame3,1909130937_L1P4d.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1P4d,ORF2,hs0_human,marg,C-TerminusTruncated
17995,Q#357 - >seq7004,non-specific,335182,118,215,2.22653e-25,96.9882,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,pars,CompleteHit
17996,Q#357 - >seq7004,superfamily,335182,118,215,2.22653e-25,96.9882,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P4e.ORF1.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,pars,CompleteHit
17997,Q#357 - >seq7004,non-specific,340205,218,291,3.3237999999999996e-18,76.9912,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,pars,CompleteHit
17998,Q#357 - >seq7004,superfamily,340205,218,291,3.3237999999999996e-18,76.9912,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P4e.ORF1.hs1_chimp.pars.frame1,1909130937_L1P4e.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1P4e,ORF1,hs1_chimp,pars,CompleteHit
17999,Q#363 - >seq7010,non-specific,335182,155,251,2.6825e-40,136.664,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18000,Q#363 - >seq7010,superfamily,335182,155,251,2.6825e-40,136.664,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18001,Q#363 - >seq7010,non-specific,340205,254,317,3.8479599999999997e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18002,Q#363 - >seq7010,superfamily,340205,254,317,3.8479599999999997e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18003,Q#363 - >seq7010,non-specific,340204,110,152,5.2647900000000004e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18004,Q#363 - >seq7010,superfamily,340204,110,152,5.2647900000000004e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs3_orang,pars,CompleteHit
18005,Q#363 - >seq7010,non-specific,222878,51,149,0.0006882339999999999,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18006,Q#363 - >seq7010,superfamily,222878,51,149,0.0006882339999999999,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18007,Q#363 - >seq7010,non-specific,224117,50,201,0.000713748,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18008,Q#363 - >seq7010,superfamily,224117,50,201,0.000713748,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18009,Q#363 - >seq7010,non-specific,275316,51,148,0.00113716,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18010,Q#363 - >seq7010,superfamily,275316,51,148,0.00113716,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs3_orang,pars,BothTerminiTruncated
18011,Q#363 - >seq7010,non-specific,224117,47,201,0.00259319,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.pars.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs3_orang,pars,N-TerminusTruncated
18012,Q#365 - >seq7012,non-specific,335182,153,249,4.0483099999999997e-39,133.582,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18013,Q#365 - >seq7012,superfamily,335182,153,249,4.0483099999999997e-39,133.582,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18014,Q#365 - >seq7012,non-specific,340205,252,315,6.13614e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18015,Q#365 - >seq7012,superfamily,340205,252,315,6.13614e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18016,Q#365 - >seq7012,non-specific,340204,109,150,1.2576800000000001e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18017,Q#365 - >seq7012,superfamily,340204,109,150,1.2576800000000001e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs2_gorilla,marg,CompleteHit
18018,Q#365 - >seq7012,non-specific,275316,61,147,0.00600635,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18019,Q#365 - >seq7012,superfamily,275316,61,147,0.00600635,38.0776,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18020,Q#367 - >seq7014,non-specific,335182,155,251,2.6899399999999998e-40,136.664,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18021,Q#367 - >seq7014,superfamily,335182,155,251,2.6899399999999998e-40,136.664,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18022,Q#367 - >seq7014,non-specific,340205,254,317,4.22594e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18023,Q#367 - >seq7014,superfamily,340205,254,317,4.22594e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18024,Q#367 - >seq7014,non-specific,340204,110,152,5.12855e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18025,Q#367 - >seq7014,superfamily,340204,110,152,5.12855e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs3_orang,marg,CompleteHit
18026,Q#367 - >seq7014,non-specific,224117,50,201,0.000663528,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18027,Q#367 - >seq7014,superfamily,224117,50,201,0.000663528,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18028,Q#367 - >seq7014,non-specific,222878,51,149,0.000685904,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18029,Q#367 - >seq7014,superfamily,222878,51,149,0.000685904,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18030,Q#367 - >seq7014,non-specific,275316,51,148,0.00115335,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18031,Q#367 - >seq7014,superfamily,275316,51,148,0.00115335,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs3_orang,marg,BothTerminiTruncated
18032,Q#367 - >seq7014,non-specific,224117,47,201,0.00253974,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs3_orang,marg,N-TerminusTruncated
18033,Q#367 - >seq7014,superfamily,224117,47,201,0.00253974,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs3_orang.marg.frame3,1909130938_L1PA12.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs3_orang,marg,N-TerminusTruncated
18034,Q#369 - >seq7016,non-specific,340204,110,147,5.78362e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18035,Q#369 - >seq7016,superfamily,340204,110,147,5.78362e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18036,Q#369 - >seq7016,non-specific,340204,110,147,5.78362e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18037,Q#369 - >seq7016,non-specific,224117,51,171,0.000156058,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18038,Q#369 - >seq7016,superfamily,224117,51,171,0.000156058,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18039,Q#369 - >seq7016,non-specific,224117,51,171,0.000156058,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18040,Q#369 - >seq7016,non-specific,222878,51,176,0.00022810900000000002,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18041,Q#369 - >seq7016,superfamily,222878,51,176,0.00022810900000000002,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18042,Q#369 - >seq7016,non-specific,222878,51,176,0.00022810900000000002,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18043,Q#369 - >seq7016,non-specific,224117,50,164,0.000278306,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18044,Q#369 - >seq7016,non-specific,224117,50,164,0.000278306,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18045,Q#369 - >seq7016,non-specific,275316,51,148,0.000968523,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18046,Q#369 - >seq7016,superfamily,275316,51,148,0.000968523,40.774,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18047,Q#369 - >seq7016,non-specific,275316,51,148,0.000968523,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18048,Q#369 - >seq7016,non-specific,336734,72,152,0.0023956999999999997,36.0047,pfam07544,Med9, - ,cl06533,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18049,Q#369 - >seq7016,superfamily,336734,72,152,0.0023956999999999997,36.0047,cl06533,Med9 superfamily, - , - ,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18050,Q#369 - >seq7016,non-specific,336734,72,152,0.0023956999999999997,36.0047,pfam07544,Med9, - ,cl06533,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18051,Q#369 - >seq7016,non-specific,274009,51,149,0.00320689,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18052,Q#369 - >seq7016,superfamily,274009,51,149,0.00320689,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18053,Q#369 - >seq7016,non-specific,274009,51,149,0.00320689,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18054,Q#369 - >seq7016,non-specific,224117,51,147,0.00342298,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18055,Q#369 - >seq7016,non-specific,224117,51,147,0.00342298,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18056,Q#369 - >seq7016,non-specific,197874,73,148,0.00709733,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18057,Q#369 - >seq7016,superfamily,197874,73,148,0.00709733,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18058,Q#369 - >seq7016,non-specific,197874,73,148,0.00709733,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18059,Q#369 - >seq7016,non-specific,225288,41,164,0.00747087,37.7616,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18060,Q#369 - >seq7016,superfamily,331991,41,164,0.00747087,37.7616,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18061,Q#369 - >seq7016,non-specific,225288,41,164,0.00747087,37.7616,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA12.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18062,Q#370 - >seq7017,non-specific,340204,110,147,5.78362e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18063,Q#370 - >seq7017,superfamily,340204,110,147,5.78362e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18064,Q#370 - >seq7017,non-specific,340204,110,147,5.78362e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18065,Q#370 - >seq7017,non-specific,224117,51,171,0.000156058,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18066,Q#370 - >seq7017,superfamily,224117,51,171,0.000156058,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18067,Q#370 - >seq7017,non-specific,224117,51,171,0.000156058,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18068,Q#370 - >seq7017,non-specific,222878,51,176,0.00022810900000000002,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18069,Q#370 - >seq7017,superfamily,222878,51,176,0.00022810900000000002,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18070,Q#370 - >seq7017,non-specific,222878,51,176,0.00022810900000000002,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18071,Q#370 - >seq7017,non-specific,224117,50,164,0.000278306,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18072,Q#370 - >seq7017,non-specific,224117,50,164,0.000278306,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18073,Q#370 - >seq7017,non-specific,275316,51,148,0.000968523,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18074,Q#370 - >seq7017,superfamily,275316,51,148,0.000968523,40.774,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18075,Q#370 - >seq7017,non-specific,275316,51,148,0.000968523,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18076,Q#370 - >seq7017,non-specific,336734,72,152,0.0023956999999999997,36.0047,pfam07544,Med9, - ,cl06533,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18077,Q#370 - >seq7017,superfamily,336734,72,152,0.0023956999999999997,36.0047,cl06533,Med9 superfamily, - , - ,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18078,Q#370 - >seq7017,non-specific,336734,72,152,0.0023956999999999997,36.0047,pfam07544,Med9, - ,cl06533,"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18079,Q#370 - >seq7017,non-specific,274009,51,149,0.00320689,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18080,Q#370 - >seq7017,superfamily,274009,51,149,0.00320689,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18081,Q#370 - >seq7017,non-specific,274009,51,149,0.00320689,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18082,Q#370 - >seq7017,non-specific,224117,51,147,0.00342298,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18083,Q#370 - >seq7017,non-specific,224117,51,147,0.00342298,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18084,Q#370 - >seq7017,non-specific,197874,73,148,0.00709733,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18085,Q#370 - >seq7017,superfamily,197874,73,148,0.00709733,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18086,Q#370 - >seq7017,non-specific,197874,73,148,0.00709733,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA12,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18087,Q#370 - >seq7017,non-specific,225288,41,164,0.00747087,37.7616,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18088,Q#370 - >seq7017,superfamily,331991,41,164,0.00747087,37.7616,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18089,Q#370 - >seq7017,non-specific,225288,41,164,0.00747087,37.7616,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA12.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18090,Q#372 - >seq7019,non-specific,335182,140,236,5.75056e-41,137.819,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs4_gibbon.marg.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18091,Q#372 - >seq7019,superfamily,335182,140,236,5.75056e-41,137.819,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs4_gibbon.marg.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18092,Q#372 - >seq7019,non-specific,340205,239,302,1.29342e-31,112.815,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs4_gibbon.marg.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18093,Q#372 - >seq7019,superfamily,340205,239,302,1.29342e-31,112.815,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs4_gibbon.marg.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,marg,CompleteHit
18094,Q#373 - >seq7020,non-specific,340204,110,146,2.51921e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18095,Q#373 - >seq7020,superfamily,340204,110,146,2.51921e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18096,Q#373 - >seq7020,non-specific,235175,48,141,0.00154621,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18097,Q#373 - >seq7020,superfamily,235175,48,141,0.00154621,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18098,Q#373 - >seq7020,non-specific,224117,33,159,0.00256562,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18099,Q#373 - >seq7020,superfamily,224117,33,159,0.00256562,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18100,Q#373 - >seq7020,non-specific,224117,33,147,0.00345004,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18101,Q#373 - >seq7020,non-specific,274008,48,148,0.00365457,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18102,Q#373 - >seq7020,superfamily,274008,48,148,0.00365457,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18103,Q#373 - >seq7020,non-specific,337766,54,128,0.00368188,38.3627,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18104,Q#373 - >seq7020,superfamily,337766,54,128,0.00368188,38.3627,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18105,Q#373 - >seq7020,non-specific,225288,41,148,0.00484829,38.532,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18106,Q#373 - >seq7020,superfamily,331991,41,148,0.00484829,38.532,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA13,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18107,Q#373 - >seq7020,non-specific,313299,74,128,0.00617759,35.2556,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA13,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18108,Q#373 - >seq7020,superfamily,313299,74,128,0.00617759,35.2556,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA13,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18109,Q#375 - >seq7022,non-specific,335182,155,251,3.00837e-39,133.967,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18110,Q#375 - >seq7022,superfamily,335182,155,251,3.00837e-39,133.967,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18111,Q#375 - >seq7022,non-specific,340205,254,317,1.8158899999999999e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18112,Q#375 - >seq7022,superfamily,340205,254,317,1.8158899999999999e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18113,Q#375 - >seq7022,non-specific,340204,110,152,1.92404e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18114,Q#375 - >seq7022,superfamily,340204,110,152,1.92404e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs5_gmonkey,pars,CompleteHit
18115,Q#375 - >seq7022,non-specific,222878,51,140,0.000751441,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18116,Q#375 - >seq7022,superfamily,222878,51,140,0.000751441,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18117,Q#375 - >seq7022,non-specific,224117,50,201,0.0008351010000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18118,Q#375 - >seq7022,superfamily,224117,50,201,0.0008351010000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18119,Q#375 - >seq7022,non-specific,275316,51,148,0.00139062,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18120,Q#375 - >seq7022,superfamily,275316,51,148,0.00139062,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18121,Q#378 - >seq7025,non-specific,335182,140,236,5.75056e-41,137.819,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs4_gibbon.pars.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18122,Q#378 - >seq7025,superfamily,335182,140,236,5.75056e-41,137.819,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs4_gibbon.pars.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18123,Q#378 - >seq7025,non-specific,340205,239,302,1.29342e-31,112.815,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs4_gibbon.pars.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18124,Q#378 - >seq7025,superfamily,340205,239,302,1.29342e-31,112.815,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs4_gibbon.pars.frame2,1909130938_L1PA12.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs4_gibbon,pars,CompleteHit
18125,Q#386 - >seq7033,non-specific,335182,156,252,1.25851e-44,147.835,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18126,Q#386 - >seq7033,superfamily,335182,156,252,1.25851e-44,147.835,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18127,Q#386 - >seq7033,non-specific,340205,256,319,1.2744799999999998e-30,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18128,Q#386 - >seq7033,superfamily,340205,256,319,1.2744799999999998e-30,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18129,Q#386 - >seq7033,non-specific,340204,112,153,2.42805e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18130,Q#386 - >seq7033,superfamily,340204,112,153,2.42805e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs6_sqmonkey,marg,CompleteHit
18131,Q#388 - >seq7035,non-specific,335182,156,252,1.0576e-42,142.827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18132,Q#388 - >seq7035,superfamily,335182,156,252,1.0576e-42,142.827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18133,Q#388 - >seq7035,non-specific,335182,156,252,1.0576e-42,142.827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18134,Q#388 - >seq7035,non-specific,340205,256,319,1.0724899999999999e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18135,Q#388 - >seq7035,superfamily,340205,256,319,1.0724899999999999e-29,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18136,Q#388 - >seq7035,non-specific,340205,256,319,1.0724899999999999e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,pars,CompleteHit
18137,Q#388 - >seq7035,non-specific,340204,112,153,3.96718e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,pars,CompleteHit
18138,Q#388 - >seq7035,superfamily,340204,112,153,3.96718e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,pars,CompleteHit
18139,Q#388 - >seq7035,non-specific,340204,112,153,3.96718e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,pars,CompleteHit
18140,Q#388 - >seq7035,non-specific,222878,53,196,0.00417153,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,pars,BothTerminiTruncated
18141,Q#388 - >seq7035,superfamily,222878,53,196,0.00417153,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,pars,BothTerminiTruncated
18142,Q#388 - >seq7035,non-specific,222878,53,196,0.00417153,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.pars.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,pars,BothTerminiTruncated
18143,Q#391 - >seq7038,non-specific,335182,156,252,1.0576e-42,142.827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18144,Q#391 - >seq7038,superfamily,335182,156,252,1.0576e-42,142.827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18145,Q#391 - >seq7038,non-specific,335182,156,252,1.0576e-42,142.827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18146,Q#391 - >seq7038,non-specific,340205,256,319,1.0724899999999999e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18147,Q#391 - >seq7038,superfamily,340205,256,319,1.0724899999999999e-29,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18148,Q#391 - >seq7038,non-specific,340205,256,319,1.0724899999999999e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs0_human,marg,CompleteHit
18149,Q#391 - >seq7038,non-specific,340204,112,153,3.96718e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,marg,CompleteHit
18150,Q#391 - >seq7038,superfamily,340204,112,153,3.96718e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,marg,CompleteHit
18151,Q#391 - >seq7038,non-specific,340204,112,153,3.96718e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs0_human,marg,CompleteHit
18152,Q#391 - >seq7038,non-specific,222878,53,196,0.00417153,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,marg,BothTerminiTruncated
18153,Q#391 - >seq7038,superfamily,222878,53,196,0.00417153,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,marg,BothTerminiTruncated
18154,Q#391 - >seq7038,non-specific,222878,53,196,0.00417153,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs0_human.marg.frame3,1909130938_L1PA11.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs0_human,marg,BothTerminiTruncated
18155,Q#393 - >seq7040,non-specific,335182,138,234,4.78853e-39,132.812,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs1_chimp.pars.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,pars,CompleteHit
18156,Q#393 - >seq7040,superfamily,335182,138,234,4.78853e-39,132.812,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs1_chimp.pars.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,pars,CompleteHit
18157,Q#393 - >seq7040,non-specific,340205,237,300,2.4726e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs1_chimp.pars.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,pars,CompleteHit
18158,Q#393 - >seq7040,superfamily,340205,237,300,2.4726e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs1_chimp.pars.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,pars,CompleteHit
18159,Q#394 - >seq7041,non-specific,222878,56,176,0.000333311,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs1_chimp,pars,BothTerminiTruncated
18160,Q#394 - >seq7041,superfamily,222878,56,176,0.000333311,41.9237,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs1_chimp,pars,BothTerminiTruncated
18161,Q#394 - >seq7041,non-specific,224117,64,164,0.00202717,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs1_chimp,pars,BothTerminiTruncated
18162,Q#394 - >seq7041,superfamily,224117,64,164,0.00202717,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs1_chimp,pars,BothTerminiTruncated
18163,Q#396 - >seq7043,non-specific,335182,138,234,4.9085199999999995e-39,132.812,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,marg,CompleteHit
18164,Q#396 - >seq7043,superfamily,335182,138,234,4.9085199999999995e-39,132.812,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,marg,CompleteHit
18165,Q#396 - >seq7043,non-specific,340205,237,300,2.7783e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,marg,CompleteHit
18166,Q#396 - >seq7043,superfamily,340205,237,300,2.7783e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA12,ORF1,hs1_chimp,marg,CompleteHit
18167,Q#397 - >seq7044,non-specific,222878,56,176,0.000329435,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs1_chimp,marg,BothTerminiTruncated
18168,Q#397 - >seq7044,superfamily,222878,56,176,0.000329435,41.9237,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs1_chimp,marg,BothTerminiTruncated
18169,Q#397 - >seq7044,non-specific,224117,64,164,0.00200351,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs1_chimp,marg,BothTerminiTruncated
18170,Q#397 - >seq7044,superfamily,224117,64,164,0.00200351,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs1_chimp,marg,BothTerminiTruncated
18171,Q#399 - >seq7046,non-specific,335182,153,249,6.78109e-39,132.812,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18172,Q#399 - >seq7046,superfamily,335182,153,249,6.78109e-39,132.812,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18173,Q#399 - >seq7046,non-specific,340205,252,315,5.13072e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18174,Q#399 - >seq7046,superfamily,340205,252,315,5.13072e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18175,Q#399 - >seq7046,non-specific,340204,109,150,1.35428e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18176,Q#399 - >seq7046,superfamily,340204,109,150,1.35428e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs2_gorilla,pars,CompleteHit
18177,Q#399 - >seq7046,non-specific,275316,61,147,0.00523812,38.4628,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18178,Q#399 - >seq7046,superfamily,275316,61,147,0.00523812,38.4628,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18179,Q#400 - >seq7047,non-specific,335182,155,251,3.00837e-39,133.967,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18180,Q#400 - >seq7047,superfamily,335182,155,251,3.00837e-39,133.967,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18181,Q#400 - >seq7047,non-specific,340205,254,317,1.8158899999999999e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18182,Q#400 - >seq7047,superfamily,340205,254,317,1.8158899999999999e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18183,Q#400 - >seq7047,non-specific,340204,110,152,1.92404e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18184,Q#400 - >seq7047,superfamily,340204,110,152,1.92404e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs5_gmonkey,marg,CompleteHit
18185,Q#400 - >seq7047,non-specific,222878,51,140,0.000751441,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18186,Q#400 - >seq7047,superfamily,222878,51,140,0.000751441,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18187,Q#400 - >seq7047,non-specific,224117,50,201,0.0008351010000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18188,Q#400 - >seq7047,superfamily,224117,50,201,0.0008351010000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18189,Q#400 - >seq7047,non-specific,275316,51,148,0.00139062,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18190,Q#400 - >seq7047,superfamily,275316,51,148,0.00139062,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18191,Q#403 - >seq7050,non-specific,335182,140,236,2.35917e-41,138.975,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs3_orang.pars.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18192,Q#403 - >seq7050,superfamily,335182,140,236,2.35917e-41,138.975,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs3_orang.pars.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18193,Q#403 - >seq7050,non-specific,340205,239,303,1.16052e-28,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs3_orang.pars.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18194,Q#403 - >seq7050,superfamily,340205,239,303,1.16052e-28,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs3_orang.pars.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18195,Q#405 - >seq7052,non-specific,340204,110,146,2.5286100000000002e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18196,Q#405 - >seq7052,superfamily,340204,110,146,2.5286100000000002e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18197,Q#405 - >seq7052,non-specific,225288,41,148,0.00036451400000000003,41.9988,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18198,Q#405 - >seq7052,superfamily,331991,41,148,0.00036451400000000003,41.9988,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18199,Q#405 - >seq7052,non-specific,235175,48,141,0.0009792919999999999,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18200,Q#405 - >seq7052,superfamily,235175,48,141,0.0009792919999999999,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18201,Q#405 - >seq7052,non-specific,274008,48,148,0.0026653000000000002,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18202,Q#405 - >seq7052,superfamily,274008,48,148,0.0026653000000000002,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18203,Q#405 - >seq7052,non-specific,313299,55,128,0.00291987,36.4112,pfam10046,BLOC1_2, - ,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18204,Q#405 - >seq7052,superfamily,313299,55,128,0.00291987,36.4112,cl10824,BLOC1_2 superfamily, - , - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,pars,CompleteHit
18205,Q#405 - >seq7052,non-specific,224428,3,131,0.00447035,38.6404,COG1511,YhgE,C,cl34288,"Uncharacterized membrane protein YhgE, phage infection protein (PIP) family [Function unknown]; Predicted membrane protein [Function unknown].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,pars,C-TerminusTruncated
18206,Q#405 - >seq7052,superfamily,224428,3,131,0.00447035,38.6404,cl34288,YhgE superfamily,C, - ,"Uncharacterized membrane protein YhgE, phage infection protein (PIP) family [Function unknown]; Predicted membrane protein [Function unknown].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,pars,C-TerminusTruncated
18207,Q#405 - >seq7052,non-specific,224117,33,147,0.00455021,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,N-TerminusTruncated
18208,Q#405 - >seq7052,superfamily,224117,33,147,0.00455021,38.542,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs3_orang,pars,N-TerminusTruncated
18209,Q#405 - >seq7052,non-specific,224117,47,159,0.00921057,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.pars.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,pars,BothTerminiTruncated
18210,Q#406 - >seq7053,non-specific,335182,140,236,2.42005e-41,138.975,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs3_orang.marg.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18211,Q#406 - >seq7053,superfamily,335182,140,236,2.42005e-41,138.975,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs3_orang.marg.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18212,Q#406 - >seq7053,non-specific,340205,239,303,1.1957799999999998e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs3_orang.marg.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18213,Q#406 - >seq7053,superfamily,340205,239,303,1.1957799999999998e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs3_orang.marg.frame1,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18214,Q#408 - >seq7055,non-specific,340204,110,146,2.2103e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18215,Q#408 - >seq7055,superfamily,340204,110,146,2.2103e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18216,Q#408 - >seq7055,non-specific,225288,41,148,0.00035084300000000004,41.9988,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18217,Q#408 - >seq7055,superfamily,331991,41,148,0.00035084300000000004,41.9988,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18218,Q#408 - >seq7055,non-specific,235175,48,141,0.000926295,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18219,Q#408 - >seq7055,superfamily,235175,48,141,0.000926295,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18220,Q#408 - >seq7055,non-specific,274008,48,148,0.00245613,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18221,Q#408 - >seq7055,superfamily,274008,48,148,0.00245613,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18222,Q#408 - >seq7055,non-specific,313299,55,128,0.00273627,36.4112,pfam10046,BLOC1_2, - ,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18223,Q#408 - >seq7055,superfamily,313299,55,128,0.00273627,36.4112,cl10824,BLOC1_2 superfamily, - , - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,marg,CompleteHit
18224,Q#408 - >seq7055,non-specific,224117,33,147,0.00419289,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,N-TerminusTruncated
18225,Q#408 - >seq7055,superfamily,224117,33,147,0.00419289,38.9272,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs3_orang,marg,N-TerminusTruncated
18226,Q#408 - >seq7055,non-specific,224428,3,131,0.00449381,38.6404,COG1511,YhgE,C,cl34288,"Uncharacterized membrane protein YhgE, phage infection protein (PIP) family [Function unknown]; Predicted membrane protein [Function unknown].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,marg,C-TerminusTruncated
18227,Q#408 - >seq7055,superfamily,224428,3,131,0.00449381,38.6404,cl34288,YhgE superfamily,C, - ,"Uncharacterized membrane protein YhgE, phage infection protein (PIP) family [Function unknown]; Predicted membrane protein [Function unknown].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA13,ORF1,hs3_orang,marg,C-TerminusTruncated
18228,Q#408 - >seq7055,non-specific,224117,47,159,0.00848685,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs3_orang.marg.frame3,1909130938_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs3_orang,marg,BothTerminiTruncated
18229,Q#410 - >seq7057,non-specific,335182,154,250,2.5126200000000003e-42,142.05700000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18230,Q#410 - >seq7057,superfamily,335182,154,250,2.5126200000000003e-42,142.05700000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18231,Q#410 - >seq7057,non-specific,340205,253,317,1.3651199999999998e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18232,Q#410 - >seq7057,superfamily,340205,253,317,1.3651199999999998e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18233,Q#410 - >seq7057,non-specific,340204,110,151,2.83457e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18234,Q#410 - >seq7057,superfamily,340204,110,151,2.83457e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs4_gibbon,pars,CompleteHit
18235,Q#410 - >seq7057,non-specific,224117,33,200,0.00210397,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18236,Q#410 - >seq7057,superfamily,224117,33,200,0.00210397,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18237,Q#410 - >seq7057,non-specific,224117,51,147,0.00333819,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18238,Q#410 - >seq7057,superfamily,224117,51,147,0.00333819,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18239,Q#410 - >seq7057,non-specific,235175,51,141,0.0051208,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18240,Q#410 - >seq7057,superfamily,235175,51,141,0.0051208,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18241,Q#410 - >seq7057,non-specific,222878,52,194,0.00628119,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18242,Q#410 - >seq7057,superfamily,222878,52,194,0.00628119,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18243,Q#410 - >seq7057,non-specific,275316,52,148,0.00833896,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18244,Q#410 - >seq7057,superfamily,275316,52,148,0.00833896,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA13,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18245,Q#413 - >seq7060,non-specific,335182,154,250,2.5030399999999998e-42,142.05700000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18246,Q#413 - >seq7060,superfamily,335182,154,250,2.5030399999999998e-42,142.05700000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18247,Q#413 - >seq7060,non-specific,340205,253,317,1.3588299999999998e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18248,Q#413 - >seq7060,superfamily,340205,253,317,1.3588299999999998e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18249,Q#413 - >seq7060,non-specific,340204,110,151,3.2401799999999998e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18250,Q#413 - >seq7060,superfamily,340204,110,151,3.2401799999999998e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs4_gibbon,marg,CompleteHit
18251,Q#413 - >seq7060,non-specific,224117,33,200,0.00231999,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18252,Q#413 - >seq7060,superfamily,224117,33,200,0.00231999,39.6976,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18253,Q#413 - >seq7060,non-specific,224117,51,147,0.00391126,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18254,Q#413 - >seq7060,superfamily,224117,51,147,0.00391126,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18255,Q#413 - >seq7060,non-specific,235175,51,141,0.00574405,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18256,Q#413 - >seq7060,superfamily,235175,51,141,0.00574405,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18257,Q#413 - >seq7060,non-specific,222878,52,194,0.00634442,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18258,Q#413 - >seq7060,superfamily,222878,52,194,0.00634442,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18259,Q#413 - >seq7060,non-specific,275316,52,148,0.00842321,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18260,Q#413 - >seq7060,superfamily,275316,52,148,0.00842321,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA13,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18261,Q#416 - >seq7063,non-specific,335182,155,251,4.067959999999999e-42,141.286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18262,Q#416 - >seq7063,superfamily,335182,155,251,4.067959999999999e-42,141.286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18263,Q#416 - >seq7063,non-specific,340205,254,318,3.09841e-30,109.348,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18264,Q#416 - >seq7063,superfamily,340205,254,318,3.09841e-30,109.348,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18265,Q#416 - >seq7063,non-specific,340204,110,152,7.79552e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18266,Q#416 - >seq7063,superfamily,340204,110,152,7.79552e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs6_sqmonkey,pars,CompleteHit
18267,Q#416 - >seq7063,non-specific,224117,33,201,0.0026808000000000005,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
18268,Q#416 - >seq7063,superfamily,224117,33,201,0.0026808000000000005,39.3124,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
18269,Q#417 - >seq7064,non-specific,335182,140,236,6.82539e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18270,Q#417 - >seq7064,superfamily,335182,140,236,6.82539e-43,143.21200000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18271,Q#417 - >seq7064,non-specific,340205,239,303,1.7423299999999998e-29,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18272,Q#417 - >seq7064,superfamily,340205,239,303,1.7423299999999998e-29,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA13,ORF1,hs6_sqmonkey,marg,CompleteHit
18273,Q#420 - >seq7067,non-specific,335182,153,249,7.28613e-42,140.901,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18274,Q#420 - >seq7067,superfamily,335182,153,249,7.28613e-42,140.901,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18275,Q#420 - >seq7067,non-specific,340205,252,316,1.1266199999999998e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18276,Q#420 - >seq7067,superfamily,340205,252,316,1.1266199999999998e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18277,Q#420 - >seq7067,non-specific,340204,109,150,2.35931e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18278,Q#420 - >seq7067,superfamily,340204,109,150,2.35931e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs2_gorilla,marg,CompleteHit
18279,Q#420 - >seq7067,non-specific,224117,31,199,0.000663528,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18280,Q#420 - >seq7067,superfamily,224117,31,199,0.000663528,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18281,Q#420 - >seq7067,non-specific,222878,51,193,0.00318649,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18282,Q#420 - >seq7067,superfamily,222878,51,193,0.00318649,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18283,Q#420 - >seq7067,non-specific,337766,53,127,0.00500608,37.9775,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18284,Q#420 - >seq7067,superfamily,337766,53,127,0.00500608,37.9775,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18285,Q#423 - >seq7070,non-specific,335182,153,249,6.93368e-42,140.901,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18286,Q#423 - >seq7070,superfamily,335182,153,249,6.93368e-42,140.901,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18287,Q#423 - >seq7070,non-specific,340205,252,316,1.1435799999999999e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18288,Q#423 - >seq7070,superfamily,340205,252,316,1.1435799999999999e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18289,Q#423 - >seq7070,non-specific,340204,109,150,2.21076e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18290,Q#423 - >seq7070,superfamily,340204,109,150,2.21076e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs2_gorilla,pars,CompleteHit
18291,Q#423 - >seq7070,non-specific,224117,31,199,0.000570641,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18292,Q#423 - >seq7070,superfamily,224117,31,199,0.000570641,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18293,Q#423 - >seq7070,non-specific,222878,51,193,0.00315388,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18294,Q#423 - >seq7070,superfamily,222878,51,193,0.00315388,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18295,Q#423 - >seq7070,non-specific,337766,53,127,0.00478475,37.9775,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18296,Q#423 - >seq7070,superfamily,337766,53,127,0.00478475,37.9775,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA13.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA13,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18297,Q#424 - >seq7071,non-specific,335182,155,252,1.2539199999999998e-39,134.35299999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18298,Q#424 - >seq7071,superfamily,335182,155,252,1.2539199999999998e-39,134.35299999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18299,Q#424 - >seq7071,non-specific,340204,110,152,1.8367e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18300,Q#424 - >seq7071,superfamily,340204,110,152,1.8367e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18301,Q#424 - >seq7071,non-specific,224117,47,202,0.000103354,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
18302,Q#424 - >seq7071,superfamily,224117,47,202,0.000103354,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
18303,Q#424 - >seq7071,non-specific,224117,48,202,0.00019277,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18304,Q#424 - >seq7071,non-specific,222878,49,149,0.0008141610000000001,40.7681,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18305,Q#424 - >seq7071,superfamily,222878,49,149,0.0008141610000000001,40.7681,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18306,Q#424 - >seq7071,non-specific,274008,48,181,0.0062518,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18307,Q#424 - >seq7071,superfamily,274008,48,181,0.0062518,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18308,Q#424 - >seq7071,non-specific,275316,51,148,0.0068028,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18309,Q#424 - >seq7071,superfamily,275316,51,148,0.0068028,38.0776,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA12,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18310,Q#427 - >seq7074,non-specific,335182,155,252,5.91915e-40,135.50799999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18311,Q#427 - >seq7074,superfamily,335182,155,252,5.91915e-40,135.50799999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18312,Q#427 - >seq7074,non-specific,340205,255,319,2.41399e-30,109.348,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18313,Q#427 - >seq7074,superfamily,340205,255,319,2.41399e-30,109.348,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18314,Q#427 - >seq7074,non-specific,340204,110,152,7.22326e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18315,Q#427 - >seq7074,superfamily,340204,110,152,7.22326e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs6_sqmonkey,marg,CompleteHit
18316,Q#427 - >seq7074,non-specific,224117,47,202,0.000101767,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18317,Q#427 - >seq7074,superfamily,224117,47,202,0.000101767,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
18318,Q#427 - >seq7074,non-specific,224117,48,202,0.00018,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18319,Q#427 - >seq7074,non-specific,222878,49,149,0.000745452,40.7681,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18320,Q#427 - >seq7074,superfamily,222878,49,149,0.000745452,40.7681,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18321,Q#427 - >seq7074,non-specific,275316,51,148,0.00213883,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18322,Q#427 - >seq7074,superfamily,275316,51,148,0.00213883,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18323,Q#427 - >seq7074,non-specific,274008,48,181,0.00557783,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18324,Q#427 - >seq7074,superfamily,274008,48,181,0.00557783,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA12.ORF1.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18325,Q#428 - >seq7075,specific,238827,477,722,8.531029999999999e-61,207.144,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18326,Q#428 - >seq7075,superfamily,295487,477,722,8.531029999999999e-61,207.144,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18327,Q#428 - >seq7075,specific,333820,474,722,5.38976e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18328,Q#428 - >seq7075,superfamily,333820,474,722,5.38976e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18329,Q#428 - >seq7075,non-specific,238828,474,719,4.42605e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18330,Q#428 - >seq7075,non-specific,275209,526,750,8.16953e-07,52.46,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
18331,Q#428 - >seq7075,superfamily,275209,526,750,8.16953e-07,52.46,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
18332,Q#428 - >seq7075,non-specific,238185,606,722,0.000131814,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18333,Q#428 - >seq7075,specific,311990,1190,1208,0.000261599,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18334,Q#428 - >seq7075,superfamily,311990,1190,1208,0.000261599,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18335,Q#428 - >seq7075,specific,225881,474,689,0.00245309,41.3629,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
18336,Q#428 - >seq7075,superfamily,225881,474,689,0.00245309,41.3629,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
18337,Q#430 - >seq7077,specific,197310,9,236,6.817219999999998e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18338,Q#430 - >seq7077,superfamily,351117,9,236,6.817219999999998e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18339,Q#430 - >seq7077,non-specific,197306,9,236,1.26437e-47,170.355,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18340,Q#430 - >seq7077,non-specific,197307,9,236,3.79271e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18341,Q#430 - >seq7077,non-specific,223780,9,237,6.19679e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18342,Q#430 - >seq7077,non-specific,197320,8,229,9.72087e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18343,Q#430 - >seq7077,non-specific,197321,7,236,4.9530399999999995e-19,87.9928,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18344,Q#430 - >seq7077,specific,335306,10,229,1.78557e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18345,Q#430 - >seq7077,non-specific,273186,9,237,1.78627e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18346,Q#430 - >seq7077,non-specific,272954,9,236,3.4927100000000003e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18347,Q#430 - >seq7077,non-specific,197319,8,236,1.3348499999999999e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18348,Q#430 - >seq7077,non-specific,197336,7,229,5.12519e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18349,Q#430 - >seq7077,non-specific,197322,9,236,1.3289799999999998e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18350,Q#430 - >seq7077,non-specific,339261,108,232,8.49105e-08,51.5691,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18351,Q#430 - >seq7077,non-specific,236970,9,237,8.90314e-08,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18352,Q#430 - >seq7077,non-specific,197311,7,236,8.117760000000001e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs6_sqmonkey.pars.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,pars,CompleteHit
18353,Q#432 - >seq7079,non-specific,340205,244,300,5.15756e-21,84.31,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18354,Q#432 - >seq7079,superfamily,340205,244,300,5.15756e-21,84.31,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs6_sqmonkey,pars,CompleteHit
18355,Q#433 - >seq7080,specific,238827,487,576,1.2263099999999998e-29,117.777,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs6_sqmonkey.marg.frame2,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
18356,Q#433 - >seq7080,superfamily,295487,487,576,1.2263099999999998e-29,117.777,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs6_sqmonkey.marg.frame2,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
18357,Q#433 - >seq7080,non-specific,333820,484,587,6.36857e-14,71.1694,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.marg.frame2,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
18358,Q#433 - >seq7080,superfamily,333820,484,587,6.36857e-14,71.1694,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.marg.frame2,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
18359,Q#436 - >seq7083,non-specific,335182,154,250,3.0475099999999994e-42,141.671,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18360,Q#436 - >seq7083,superfamily,335182,154,250,3.0475099999999994e-42,141.671,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18361,Q#436 - >seq7083,non-specific,340205,253,317,9.94921e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18362,Q#436 - >seq7083,superfamily,340205,253,317,9.94921e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18363,Q#436 - >seq7083,non-specific,340204,110,151,1.76926e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18364,Q#436 - >seq7083,superfamily,340204,110,151,1.76926e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs1_chimp,pars,CompleteHit
18365,Q#436 - >seq7083,non-specific,224117,51,200,0.00134903,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs1_chimp,pars,N-TerminusTruncated
18366,Q#436 - >seq7083,superfamily,224117,51,200,0.00134903,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs1_chimp,pars,N-TerminusTruncated
18367,Q#436 - >seq7083,non-specific,222878,52,194,0.00628119,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs1_chimp,pars,BothTerminiTruncated
18368,Q#436 - >seq7083,superfamily,222878,52,194,0.00628119,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs1_chimp,pars,BothTerminiTruncated
18369,Q#439 - >seq7086,non-specific,335182,154,250,3.2028699999999996e-42,141.671,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18370,Q#439 - >seq7086,superfamily,335182,154,250,3.2028699999999996e-42,141.671,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18371,Q#439 - >seq7086,non-specific,340205,253,317,9.39631e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18372,Q#439 - >seq7086,superfamily,340205,253,317,9.39631e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18373,Q#439 - >seq7086,non-specific,340204,110,151,2.06255e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18374,Q#439 - >seq7086,superfamily,340204,110,151,2.06255e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs1_chimp,marg,CompleteHit
18375,Q#439 - >seq7086,non-specific,224117,51,200,0.00148786,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs1_chimp,marg,N-TerminusTruncated
18376,Q#439 - >seq7086,superfamily,224117,51,200,0.00148786,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs1_chimp,marg,N-TerminusTruncated
18377,Q#439 - >seq7086,non-specific,222878,52,194,0.00651336,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs1_chimp,marg,BothTerminiTruncated
18378,Q#439 - >seq7086,superfamily,222878,52,194,0.00651336,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs1_chimp,marg,BothTerminiTruncated
18379,Q#442 - >seq7089,specific,197310,9,236,4.674759999999999e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18380,Q#442 - >seq7089,superfamily,351117,9,236,4.674759999999999e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18381,Q#442 - >seq7089,non-specific,197306,9,236,1.09431e-47,170.355,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18382,Q#442 - >seq7089,specific,238827,639,758,6.67611e-28,112.77,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
18383,Q#442 - >seq7089,superfamily,295487,639,758,6.67611e-28,112.77,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
18384,Q#442 - >seq7089,non-specific,197307,9,236,1.0809e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18385,Q#442 - >seq7089,non-specific,197320,8,229,1.00079e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18386,Q#442 - >seq7089,non-specific,223780,9,237,2.99467e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18387,Q#442 - >seq7089,non-specific,197321,7,236,1.21228e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18388,Q#442 - >seq7089,specific,335306,10,229,1.83677e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18389,Q#442 - >seq7089,non-specific,273186,9,237,4.4073e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18390,Q#442 - >seq7089,non-specific,272954,9,236,2.3950999999999998e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18391,Q#442 - >seq7089,non-specific,333820,642,758,2.35854e-12,66.547,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
18392,Q#442 - >seq7089,superfamily,333820,642,758,2.35854e-12,66.547,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
18393,Q#442 - >seq7089,non-specific,197336,7,229,5.27456e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18394,Q#442 - >seq7089,non-specific,197319,8,236,1.36125e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18395,Q#442 - >seq7089,non-specific,197322,9,236,1.3687600000000001e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18396,Q#442 - >seq7089,non-specific,339261,108,232,1.92118e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18397,Q#442 - >seq7089,non-specific,236970,9,237,4.338430000000001e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18398,Q#442 - >seq7089,non-specific,197311,7,236,9.86378e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18399,Q#442 - >seq7089,non-specific,238828,597,755,3.56417e-05,46.4253,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
18400,Q#442 - >seq7089,non-specific,238185,632,758,3.83896e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18401,Q#442 - >seq7089,specific,311990,1226,1244,0.000579629,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18402,Q#442 - >seq7089,superfamily,311990,1226,1244,0.000579629,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs6_sqmonkey,marg,CompleteHit
18403,Q#442 - >seq7089,non-specific,235175,294,463,0.00111234,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
18404,Q#442 - >seq7089,superfamily,235175,294,463,0.00111234,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
18405,Q#442 - >seq7089,non-specific,223496,304,499,0.00238842,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA12,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
18406,Q#442 - >seq7089,superfamily,223496,304,499,0.00238842,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA12.ORF2.hs6_sqmonkey.marg.frame3,1909130938_L1PA12.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA12,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
18407,Q#443 - >seq7090,non-specific,335182,146,242,4.06793e-45,148.99,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18408,Q#443 - >seq7090,superfamily,335182,146,242,4.06793e-45,148.99,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18409,Q#443 - >seq7090,non-specific,340205,246,309,8.85002e-31,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18410,Q#443 - >seq7090,superfamily,340205,246,309,8.85002e-31,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18411,Q#443 - >seq7090,non-specific,340204,102,143,1.68621e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18412,Q#443 - >seq7090,superfamily,340204,102,143,1.68621e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs6_sqmonkey.pars.frame1,1909130938_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA11,ORF1,hs6_sqmonkey,pars,CompleteHit
18413,Q#447 - >seq7094,non-specific,335182,157,253,8.584659999999999e-45,148.605,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18414,Q#447 - >seq7094,superfamily,335182,157,253,8.584659999999999e-45,148.605,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18415,Q#447 - >seq7094,non-specific,340205,256,320,7.50403e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18416,Q#447 - >seq7094,superfamily,340205,256,320,7.50403e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18417,Q#447 - >seq7094,non-specific,340204,112,154,4.06414e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18418,Q#447 - >seq7094,superfamily,340204,112,154,4.06414e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs2_gorilla,marg,CompleteHit
18419,Q#447 - >seq7094,non-specific,310226,53,204,0.000791559,41.0614,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18420,Q#447 - >seq7094,superfamily,310226,53,204,0.000791559,41.0614,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18421,Q#450 - >seq7097,non-specific,335182,147,243,2.19015e-45,149.761,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18422,Q#450 - >seq7097,superfamily,335182,147,243,2.19015e-45,149.761,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18423,Q#450 - >seq7097,non-specific,340205,246,310,5.4906299999999995e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18424,Q#450 - >seq7097,superfamily,340205,246,310,5.4906299999999995e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18425,Q#450 - >seq7097,non-specific,340204,102,144,3.67188e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18426,Q#450 - >seq7097,superfamily,340204,102,144,3.67188e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs3_orang,pars,CompleteHit
18427,Q#450 - >seq7097,non-specific,310226,43,194,0.00851494,37.5946,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,pars,BothTerminiTruncated
18428,Q#450 - >seq7097,superfamily,310226,43,194,0.00851494,37.5946,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,pars,BothTerminiTruncated
18429,Q#450 - >seq7097,non-specific,313493,1,117,0.00977009,37.2742,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,pars,BothTerminiTruncated
18430,Q#450 - >seq7097,superfamily,313493,1,117,0.00977009,37.2742,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs3_orang.pars.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,pars,BothTerminiTruncated
18431,Q#453 - >seq7100,non-specific,335182,157,253,8.584659999999999e-45,148.605,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18432,Q#453 - >seq7100,superfamily,335182,157,253,8.584659999999999e-45,148.605,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18433,Q#453 - >seq7100,non-specific,340205,256,320,6.4730299999999995e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18434,Q#453 - >seq7100,superfamily,340205,256,320,6.4730299999999995e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18435,Q#453 - >seq7100,non-specific,340204,112,154,6.137800000000001e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18436,Q#453 - >seq7100,superfamily,340204,112,154,6.137800000000001e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs3_orang,marg,CompleteHit
18437,Q#453 - >seq7100,non-specific,313493,1,127,0.00251939,39.2002,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,marg,BothTerminiTruncated
18438,Q#453 - >seq7100,superfamily,313493,1,127,0.00251939,39.2002,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,marg,BothTerminiTruncated
18439,Q#453 - >seq7100,non-specific,310226,53,204,0.00887992,37.5946,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,marg,BothTerminiTruncated
18440,Q#453 - >seq7100,superfamily,310226,53,204,0.00887992,37.5946,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs3_orang.marg.frame3,1909130938_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs3_orang,marg,BothTerminiTruncated
18441,Q#456 - >seq7103,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18442,Q#456 - >seq7103,superfamily,335182,157,254,2.5720400000000002e-47,155.153,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18443,Q#456 - >seq7103,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18444,Q#456 - >seq7103,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18445,Q#456 - >seq7103,superfamily,340205,257,321,6.16117e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18446,Q#456 - >seq7103,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18447,Q#456 - >seq7103,non-specific,340204,112,154,1.94116e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18448,Q#456 - >seq7103,superfamily,340204,112,154,1.94116e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18449,Q#456 - >seq7103,non-specific,340204,112,154,1.94116e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,pars,CompleteHit
18450,Q#456 - >seq7103,non-specific,224117,56,183,0.00286876,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18451,Q#456 - >seq7103,superfamily,224117,56,183,0.00286876,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18452,Q#456 - >seq7103,non-specific,224117,56,183,0.00286876,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18453,Q#456 - >seq7103,non-specific,222878,53,198,0.00406819,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18454,Q#456 - >seq7103,superfamily,222878,53,198,0.00406819,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18455,Q#456 - >seq7103,non-specific,222878,53,198,0.00406819,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18456,Q#456 - >seq7103,non-specific,313493,9,127,0.00994545,37.2742,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18457,Q#456 - >seq7103,superfamily,313493,9,127,0.00994545,37.2742,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18458,Q#456 - >seq7103,non-specific,313493,9,127,0.00994545,37.2742,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18459,Q#459 - >seq7106,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18460,Q#459 - >seq7106,superfamily,335182,157,254,2.5720400000000002e-47,155.153,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18461,Q#459 - >seq7106,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18462,Q#459 - >seq7106,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18463,Q#459 - >seq7106,superfamily,340205,257,321,6.16117e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18464,Q#459 - >seq7106,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18465,Q#459 - >seq7106,non-specific,340204,112,154,1.94116e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18466,Q#459 - >seq7106,superfamily,340204,112,154,1.94116e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18467,Q#459 - >seq7106,non-specific,340204,112,154,1.94116e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs4_gibbon,marg,CompleteHit
18468,Q#459 - >seq7106,non-specific,224117,56,183,0.00286876,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18469,Q#459 - >seq7106,superfamily,224117,56,183,0.00286876,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18470,Q#459 - >seq7106,non-specific,224117,56,183,0.00286876,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18471,Q#459 - >seq7106,non-specific,222878,53,198,0.00406819,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18472,Q#459 - >seq7106,superfamily,222878,53,198,0.00406819,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18473,Q#459 - >seq7106,non-specific,222878,53,198,0.00406819,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18474,Q#459 - >seq7106,non-specific,313493,9,127,0.00994545,37.2742,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18475,Q#459 - >seq7106,superfamily,313493,9,127,0.00994545,37.2742,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18476,Q#459 - >seq7106,non-specific,313493,9,127,0.00994545,37.2742,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA10,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18477,Q#460 - >seq7107,non-specific,335182,156,252,1.92071e-45,150.14600000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18478,Q#460 - >seq7107,superfamily,335182,156,252,1.92071e-45,150.14600000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18479,Q#460 - >seq7107,non-specific,340205,255,319,2.1843800000000002e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18480,Q#460 - >seq7107,superfamily,340205,255,319,2.1843800000000002e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18481,Q#460 - >seq7107,non-specific,340204,111,153,1.9482600000000003e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18482,Q#460 - >seq7107,superfamily,340204,111,153,1.9482600000000003e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs5_gmonkey,pars,CompleteHit
18483,Q#460 - >seq7107,non-specific,222878,52,196,0.00547312,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA10,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18484,Q#460 - >seq7107,superfamily,222878,52,196,0.00547312,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs5_gmonkey.pars.frame1,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA10,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18485,Q#466 - >seq7113,non-specific,335182,157,253,1.8798199999999998e-44,147.44899999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18486,Q#466 - >seq7113,superfamily,335182,157,253,1.8798199999999998e-44,147.44899999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18487,Q#466 - >seq7113,non-specific,340205,256,320,1.0857399999999999e-30,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18488,Q#466 - >seq7113,superfamily,340205,256,320,1.0857399999999999e-30,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18489,Q#466 - >seq7113,non-specific,340204,112,154,4.52755e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18490,Q#466 - >seq7113,superfamily,340204,112,154,4.52755e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs2_gorilla,pars,CompleteHit
18491,Q#466 - >seq7113,non-specific,310226,53,204,0.000791559,41.0614,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18492,Q#466 - >seq7113,superfamily,310226,53,204,0.000791559,41.0614,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18493,Q#467 - >seq7114,non-specific,335182,156,252,1.78825e-42,142.442,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18494,Q#467 - >seq7114,superfamily,335182,156,252,1.78825e-42,142.442,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18495,Q#467 - >seq7114,non-specific,340205,256,319,2.47754e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18496,Q#467 - >seq7114,superfamily,340205,256,319,2.47754e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18497,Q#467 - >seq7114,non-specific,340204,112,153,3.19639e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18498,Q#467 - >seq7114,superfamily,340204,112,153,3.19639e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs5_gmonkey,marg,CompleteHit
18499,Q#467 - >seq7114,non-specific,222878,53,196,0.00635179,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18500,Q#467 - >seq7114,superfamily,222878,53,196,0.00635179,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs5_gmonkey.marg.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18501,Q#469 - >seq7116,non-specific,238827,433,523,2.7363600000000003e-19,87.3466,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
18502,Q#469 - >seq7116,superfamily,295487,433,523,2.7363600000000003e-19,87.3466,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
18503,Q#469 - >seq7116,non-specific,197310,82,167,4.60637e-13,69.6877,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18504,Q#469 - >seq7116,superfamily,351117,82,167,4.60637e-13,69.6877,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18505,Q#469 - >seq7116,non-specific,197306,78,164,0.00010528200000000001,44.7797,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18506,Q#469 - >seq7116,non-specific,197307,67,164,0.000194433,44.2009,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18507,Q#469 - >seq7116,non-specific,333820,439,523,0.00383143,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
18508,Q#469 - >seq7116,superfamily,333820,439,523,0.00383143,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.pars.frame3,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
18509,Q#470 - >seq7117,specific,238827,503,764,1.8419799999999997e-30,120.089,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18510,Q#470 - >seq7117,superfamily,295487,503,764,1.8419799999999997e-30,120.089,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18511,Q#470 - >seq7117,non-specific,197310,8,214,2.5046700000000002e-14,73.5397,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18512,Q#470 - >seq7117,superfamily,351117,8,214,2.5046700000000002e-14,73.5397,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18513,Q#470 - >seq7117,non-specific,333820,509,732,1.8351099999999999e-09,58.0726,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18514,Q#470 - >seq7117,superfamily,333820,509,732,1.8351099999999999e-09,58.0726,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18515,Q#470 - >seq7117,non-specific,197306,8,214,6.319619999999999e-08,54.7949,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs5_gmonkey.marg.frame1,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs5_gmonkey,marg,CompleteHit
18516,Q#471 - >seq7118,non-specific,238827,592,622,2.39931e-07,52.6786,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs5_gmonkey.marg.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
18517,Q#471 - >seq7118,superfamily,295487,592,622,2.39931e-07,52.6786,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs5_gmonkey.marg.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
18518,Q#471 - >seq7118,non-specific,333820,576,622,3.03796e-05,45.7462,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.marg.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
18519,Q#471 - >seq7118,superfamily,333820,576,622,3.03796e-05,45.7462,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.marg.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
18520,Q#473 - >seq7120,non-specific,197310,46,138,0.00127038,41.1829,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs0_human.pars.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18521,Q#473 - >seq7120,superfamily,351117,46,138,0.00127038,41.1829,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs0_human.pars.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18522,Q#474 - >seq7121,specific,238827,404,515,1.0824999999999999e-33,128.94799999999998,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs0_human.pars.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs0_human,pars,C-TerminusTruncated
18523,Q#474 - >seq7121,superfamily,295487,404,515,1.0824999999999999e-33,128.94799999999998,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs0_human.pars.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs0_human,pars,C-TerminusTruncated
18524,Q#474 - >seq7121,non-specific,333820,410,520,5.92237e-14,70.7842,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.pars.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs0_human,pars,C-TerminusTruncated
18525,Q#474 - >seq7121,superfamily,333820,410,520,5.92237e-14,70.7842,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.pars.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs0_human,pars,C-TerminusTruncated
18526,Q#476 - >seq7123,specific,238827,563,675,2.69057e-27,110.459,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18527,Q#476 - >seq7123,superfamily,295487,563,675,2.69057e-27,110.459,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18528,Q#476 - >seq7123,non-specific,333820,545,654,7.0458299999999996e-15,73.4806,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18529,Q#476 - >seq7123,superfamily,333820,545,654,7.0458299999999996e-15,73.4806,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18530,Q#476 - >seq7123,non-specific,197310,85,164,5.8651800000000004e-08,54.2797,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18531,Q#476 - >seq7123,superfamily,351117,85,164,5.8651800000000004e-08,54.2797,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18532,Q#476 - >seq7123,non-specific,238828,556,645,1.05645e-05,47.5809,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,N-TerminusTruncated
18533,Q#476 - >seq7123,non-specific,238185,564,649,0.00118379,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs0_human.pars.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P4,ORF2,hs0_human,pars,CompleteHit
18534,Q#477 - >seq7124,specific,238827,450,618,5.2701799999999995e-31,121.62899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs0_human,marg,C-TerminusTruncated
18535,Q#477 - >seq7124,superfamily,295487,450,618,5.2701799999999995e-31,121.62899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs0_human,marg,C-TerminusTruncated
18536,Q#477 - >seq7124,non-specific,333820,456,618,7.85258e-16,76.5622,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs0_human,marg,C-TerminusTruncated
18537,Q#477 - >seq7124,superfamily,333820,456,618,7.85258e-16,76.5622,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1P4,ORF2,hs0_human,marg,C-TerminusTruncated
18538,Q#477 - >seq7124,non-specific,197310,51,127,4.23558e-05,45.8053,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1P4,ORF2,hs0_human,marg,BothTerminiTruncated
18539,Q#477 - >seq7124,superfamily,351117,51,127,4.23558e-05,45.8053,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs0_human,marg,BothTerminiTruncated
18540,Q#477 - >seq7124,non-specific,197306,53,123,0.00231877,40.5425,cd08372,EEP,NC,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs0_human.marg.frame2,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1P4,ORF2,hs0_human,marg,BothTerminiTruncated
18541,Q#478 - >seq7125,non-specific,129705,219,483,0.00650859,40.3374,TIGR00618,sbcc,NC,cl31020,"exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4.ORF2.hs0_human.marg.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4,ORF2,hs0_human,marg,BothTerminiTruncated
18542,Q#478 - >seq7125,superfamily,129705,219,483,0.00650859,40.3374,cl31020,sbcc superfamily,NC, - ,"exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P4.ORF2.hs0_human.marg.frame3,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1P4,ORF2,hs0_human,marg,BothTerminiTruncated
18543,Q#479 - >seq7126,non-specific,335182,156,252,4.515369999999999e-44,146.679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18544,Q#479 - >seq7126,superfamily,335182,156,252,4.515369999999999e-44,146.679,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18545,Q#479 - >seq7126,non-specific,340205,255,319,3.7443199999999993e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18546,Q#479 - >seq7126,superfamily,340205,255,319,3.7443199999999993e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18547,Q#479 - >seq7126,non-specific,340204,111,153,3.3426200000000003e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18548,Q#479 - >seq7126,superfamily,340204,111,153,3.3426200000000003e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA10,ORF1,hs1_chimp,pars,CompleteHit
18549,Q#479 - >seq7126,non-specific,310226,52,203,0.00166919,39.9058,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF1,hs1_chimp,pars,BothTerminiTruncated
18550,Q#479 - >seq7126,superfamily,310226,52,203,0.00166919,39.9058,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs1_chimp.pars.frame1,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF1,hs1_chimp,pars,BothTerminiTruncated
18551,Q#483 - >seq7130,non-specific,335182,157,253,7.26797e-44,145.909,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18552,Q#483 - >seq7130,superfamily,335182,157,253,7.26797e-44,145.909,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18553,Q#483 - >seq7130,non-specific,340205,256,320,4.1984299999999995e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18554,Q#483 - >seq7130,superfamily,340205,256,320,4.1984299999999995e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18555,Q#483 - >seq7130,non-specific,340204,112,154,3.16114e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18556,Q#483 - >seq7130,superfamily,340204,112,154,3.16114e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1PA10,ORF1,hs1_chimp,marg,CompleteHit
18557,Q#483 - >seq7130,non-specific,310226,53,204,0.00163457,39.9058,pfam05478,Prominin,NC,cl25943,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF1,hs1_chimp,marg,BothTerminiTruncated
18558,Q#483 - >seq7130,superfamily,310226,53,204,0.00163457,39.9058,cl25943,Prominin superfamily,NC, - ,"Prominin; The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration.",L1PA10.ORF1.hs1_chimp.marg.frame2,1909130938_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF1,hs1_chimp,marg,BothTerminiTruncated
18559,Q#485 - >seq7132,non-specific,238827,542,727,2.01896e-17,82.339,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs0_human,marg,N-TerminusTruncated
18560,Q#485 - >seq7132,superfamily,295487,542,727,2.01896e-17,82.339,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs0_human,marg,N-TerminusTruncated
18561,Q#485 - >seq7132,non-specific,197310,1,203,1.50816e-15,77.0065,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1P4,ORF2,hs0_human,marg,CompleteHit
18562,Q#485 - >seq7132,superfamily,351117,1,203,1.50816e-15,77.0065,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1P4,ORF2,hs0_human,marg,CompleteHit
18563,Q#485 - >seq7132,non-specific,333820,549,705,1.66993e-10,61.1542,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs0_human,marg,N-TerminusTruncated
18564,Q#485 - >seq7132,superfamily,333820,549,705,1.66993e-10,61.1542,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs0_human.marg.frame1,1909130938_L1P4.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1P4,ORF2,hs0_human,marg,N-TerminusTruncated
18565,Q#486 - >seq7133,non-specific,335182,157,253,2.05736e-45,150.14600000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18566,Q#486 - >seq7133,superfamily,335182,157,253,2.05736e-45,150.14600000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18567,Q#486 - >seq7133,non-specific,340205,256,320,2.52862e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18568,Q#486 - >seq7133,superfamily,340205,256,320,2.52862e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18569,Q#486 - >seq7133,non-specific,340204,112,154,1.7371600000000002e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18570,Q#486 - >seq7133,superfamily,340204,112,154,1.7371600000000002e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Trimerization,L1PA10,ORF1,hs5_gmonkey,marg,CompleteHit
18571,Q#486 - >seq7133,non-specific,313493,2,127,0.00519777,38.0446,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18572,Q#486 - >seq7133,superfamily,313493,2,127,0.00519777,38.0446,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18573,Q#486 - >seq7133,non-specific,222878,53,197,0.00579699,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA10,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18574,Q#486 - >seq7133,superfamily,222878,53,197,0.00579699,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs5_gmonkey.marg.frame2,1909130938_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA10,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18575,Q#487 - >seq7134,non-specific,238827,506,672,5.327649999999999e-22,95.4358,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18576,Q#487 - >seq7134,superfamily,295487,506,672,5.327649999999999e-22,95.4358,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18577,Q#487 - >seq7134,non-specific,333820,505,640,5.14067e-10,59.6134,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18578,Q#487 - >seq7134,superfamily,333820,505,640,5.14067e-10,59.6134,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18579,Q#487 - >seq7134,non-specific,238828,506,629,2.98131e-07,52.2032,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
18580,Q#487 - >seq7134,non-specific,238185,562,674,0.00639906,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P4.ORF2.hs5_gmonkey.pars.frame2,1909130938_L1P4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1P4,ORF2,hs5_gmonkey,pars,CompleteHit
18581,Q#489 - >seq7136,non-specific,335182,156,252,1.82186e-43,145.138,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18582,Q#489 - >seq7136,superfamily,335182,156,252,1.82186e-43,145.138,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18583,Q#489 - >seq7136,non-specific,340205,256,319,1.11865e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18584,Q#489 - >seq7136,superfamily,340205,256,319,1.11865e-29,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18585,Q#489 - >seq7136,non-specific,340204,112,153,2.8974400000000002e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18586,Q#489 - >seq7136,superfamily,340204,112,153,2.8974400000000002e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs2_gorilla.marg.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs2_gorilla,marg,CompleteHit
18587,Q#492 - >seq7139,non-specific,335182,156,252,3.8028499999999993e-44,146.679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18588,Q#492 - >seq7139,superfamily,335182,156,252,3.8028499999999993e-44,146.679,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18589,Q#492 - >seq7139,non-specific,335182,156,252,3.8028499999999993e-44,146.679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18590,Q#492 - >seq7139,non-specific,340205,256,319,1.01745e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18591,Q#492 - >seq7139,superfamily,340205,256,319,1.01745e-29,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18592,Q#492 - >seq7139,non-specific,340205,256,319,1.01745e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18593,Q#492 - >seq7139,non-specific,340204,112,153,3.66745e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18594,Q#492 - >seq7139,superfamily,340204,112,153,3.66745e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18595,Q#492 - >seq7139,non-specific,340204,112,153,3.66745e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.pars.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,pars,CompleteHit
18596,Q#494 - >seq7141,non-specific,335182,156,252,3.8028499999999993e-44,146.679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18597,Q#494 - >seq7141,superfamily,335182,156,252,3.8028499999999993e-44,146.679,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18598,Q#494 - >seq7141,non-specific,335182,156,252,3.8028499999999993e-44,146.679,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18599,Q#494 - >seq7141,non-specific,340205,256,319,1.01745e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18600,Q#494 - >seq7141,superfamily,340205,256,319,1.01745e-29,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18601,Q#494 - >seq7141,non-specific,340205,256,319,1.01745e-29,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18602,Q#494 - >seq7141,non-specific,340204,112,153,3.66745e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18603,Q#494 - >seq7141,superfamily,340204,112,153,3.66745e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18604,Q#494 - >seq7141,non-specific,340204,112,153,3.66745e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs3_orang.marg.frame3,1909130938_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs3_orang,marg,CompleteHit
18605,Q#497 - >seq7144,non-specific,335182,155,251,2.3299500000000002e-42,142.05700000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18606,Q#497 - >seq7144,superfamily,335182,155,251,2.3299500000000002e-42,142.05700000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18607,Q#497 - >seq7144,non-specific,340205,255,318,1.68018e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18608,Q#497 - >seq7144,superfamily,340205,255,318,1.68018e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18609,Q#497 - >seq7144,non-specific,340204,111,152,3.15564e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18610,Q#497 - >seq7144,superfamily,340204,111,152,3.15564e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs4_gibbon,pars,CompleteHit
18611,Q#497 - >seq7144,non-specific,222878,52,195,0.00708262,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18612,Q#497 - >seq7144,superfamily,222878,52,195,0.00708262,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs4_gibbon.pars.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18613,Q#500 - >seq7147,non-specific,335182,156,252,2.71611e-42,142.05700000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18614,Q#500 - >seq7147,superfamily,335182,156,252,2.71611e-42,142.05700000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18615,Q#500 - >seq7147,non-specific,340205,256,319,1.90319e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18616,Q#500 - >seq7147,superfamily,340205,256,319,1.90319e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18617,Q#500 - >seq7147,non-specific,340204,112,153,2.45201e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18618,Q#500 - >seq7147,superfamily,340204,112,153,2.45201e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs4_gibbon,marg,CompleteHit
18619,Q#500 - >seq7147,non-specific,222878,53,196,0.00640765,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18620,Q#500 - >seq7147,superfamily,222878,53,196,0.00640765,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs4_gibbon.marg.frame3,1909130938_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18621,Q#503 - >seq7150,non-specific,335182,156,252,1.78825e-42,142.442,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18622,Q#503 - >seq7150,superfamily,335182,156,252,1.78825e-42,142.442,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18623,Q#503 - >seq7150,non-specific,340205,256,319,2.47754e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18624,Q#503 - >seq7150,superfamily,340205,256,319,2.47754e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18625,Q#503 - >seq7150,non-specific,340204,112,153,3.19639e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18626,Q#503 - >seq7150,superfamily,340204,112,153,3.19639e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs5_gmonkey,pars,CompleteHit
18627,Q#503 - >seq7150,non-specific,222878,53,196,0.00635179,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18628,Q#503 - >seq7150,superfamily,222878,53,196,0.00635179,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA11.ORF1.hs5_gmonkey.pars.frame3,1909130938_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18629,Q#511 - >seq7158,non-specific,335182,157,253,9.50397e-44,145.909,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18630,Q#511 - >seq7158,superfamily,335182,157,253,9.50397e-44,145.909,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18631,Q#511 - >seq7158,non-specific,340205,256,320,3.7379299999999997e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18632,Q#511 - >seq7158,superfamily,340205,256,320,3.7379299999999997e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18633,Q#511 - >seq7158,non-specific,340204,112,154,1.9352e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18634,Q#511 - >seq7158,superfamily,340204,112,154,1.9352e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs6_sqmonkey,pars,CompleteHit
18635,Q#511 - >seq7158,non-specific,313493,9,127,0.00322645,38.815,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18636,Q#511 - >seq7158,superfamily,313493,9,127,0.00322645,38.815,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs6_sqmonkey.pars.frame3,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA10,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18637,Q#512 - >seq7159,non-specific,335182,158,254,1.34453e-43,145.523,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18638,Q#512 - >seq7159,superfamily,335182,158,254,1.34453e-43,145.523,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18639,Q#512 - >seq7159,non-specific,340205,257,321,3.93361e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18640,Q#512 - >seq7159,superfamily,340205,257,321,3.93361e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18641,Q#512 - >seq7159,non-specific,340204,113,155,2.1624400000000001e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18642,Q#512 - >seq7159,superfamily,340204,113,155,2.1624400000000001e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PA10,ORF1,hs6_sqmonkey,marg,CompleteHit
18643,Q#512 - >seq7159,non-specific,313493,10,128,0.00335877,38.815,pfam10267,Tmemb_cc2,NC,cl24036,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18644,Q#512 - >seq7159,superfamily,313493,10,128,0.00335877,38.815,cl24036,Tmemb_cc2 superfamily,NC, - ,Predicted transmembrane and coiled-coil 2 protein; This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.,L1PA10.ORF1.hs6_sqmonkey.marg.frame1,1909130938_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18645,Q#513 - >seq7160,non-specific,340204,112,153,1.35122e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18646,Q#513 - >seq7160,superfamily,340204,112,153,1.35122e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18647,Q#513 - >seq7160,non-specific,224117,69,149,0.000701401,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18648,Q#513 - >seq7160,superfamily,224117,69,149,0.000701401,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18649,Q#513 - >seq7160,non-specific,333788,30,138,0.00219143,39.1306,pfam00038,Filament,N,cl25641,Intermediate filament protein; Intermediate filament protein.  ,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA11,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18650,Q#513 - >seq7160,superfamily,333788,30,138,0.00219143,39.1306,cl25641,Filament superfamily,N, - ,Intermediate filament protein; Intermediate filament protein.  ,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA11,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18651,Q#513 - >seq7160,non-specific,235175,56,143,0.00308772,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18652,Q#513 - >seq7160,superfamily,235175,56,143,0.00308772,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18653,Q#513 - >seq7160,non-specific,224117,54,149,0.00311357,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18654,Q#513 - >seq7160,non-specific,224117,55,146,0.00377091,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18655,Q#513 - >seq7160,non-specific,274009,52,149,0.00829062,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18656,Q#513 - >seq7160,superfamily,274009,52,149,0.00829062,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18657,Q#513 - >seq7160,non-specific,225288,55,145,0.0087995,37.7616,COG2433,COG2433,NC,cl27170,"Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]; Uncharacterized conserved protein [Function unknown].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18658,Q#513 - >seq7160,superfamily,331991,55,145,0.0087995,37.7616,cl27170,DUF460 superfamily,NC, - ,Protein of unknown function (DUF460); Archaeal protein of unknown function.,L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18659,Q#513 - >seq7160,non-specific,224117,54,149,0.00940178,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF1.hs2_gorilla.pars.frame3,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18660,Q#517 - >seq7164,non-specific,335182,147,244,2.3220099999999997e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,pars,CompleteHit
18661,Q#517 - >seq7164,superfamily,335182,147,244,2.3220099999999997e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,pars,CompleteHit
18662,Q#517 - >seq7164,non-specific,340205,247,311,3.2307499999999996e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,pars,CompleteHit
18663,Q#517 - >seq7164,superfamily,340205,247,311,3.2307499999999996e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,pars,CompleteHit
18664,Q#517 - >seq7164,non-specific,340204,102,144,1.56092e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs0_human,pars,CompleteHit
18665,Q#517 - >seq7164,superfamily,340204,102,144,1.56092e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA10,ORF1,hs0_human,pars,CompleteHit
18666,Q#517 - >seq7164,non-specific,224117,46,173,0.0007418430000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18667,Q#517 - >seq7164,superfamily,224117,46,173,0.0007418430000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18668,Q#517 - >seq7164,non-specific,224117,44,194,0.00127443,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,pars,N-TerminusTruncated
18669,Q#517 - >seq7164,non-specific,222878,43,188,0.00212878,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18670,Q#517 - >seq7164,superfamily,222878,43,188,0.00212878,39.6125,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18671,Q#517 - >seq7164,non-specific,274008,56,154,0.00902074,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18672,Q#517 - >seq7164,superfamily,274008,56,154,0.00902074,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF1.hs0_human.pars.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,pars,BothTerminiTruncated
18673,Q#520 - >seq7167,non-specific,335182,157,254,1.56254e-45,150.531,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,marg,CompleteHit
18674,Q#520 - >seq7167,superfamily,335182,157,254,1.56254e-45,150.531,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,marg,CompleteHit
18675,Q#520 - >seq7167,non-specific,340205,257,321,5.231119999999999e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,marg,CompleteHit
18676,Q#520 - >seq7167,superfamily,340205,257,321,5.231119999999999e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA10,ORF1,hs0_human,marg,CompleteHit
18677,Q#520 - >seq7167,non-specific,340204,112,154,2.98948e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs0_human,marg,CompleteHit
18678,Q#520 - >seq7167,superfamily,340204,112,154,2.98948e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA10,ORF1,hs0_human,marg,CompleteHit
18679,Q#520 - >seq7167,non-specific,224117,56,183,0.00108216,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,marg,BothTerminiTruncated
18680,Q#520 - >seq7167,superfamily,224117,56,183,0.00108216,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA10,ORF1,hs0_human,marg,BothTerminiTruncated
18681,Q#520 - >seq7167,non-specific,224117,54,204,0.00187291,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF1,hs0_human,marg,N-TerminusTruncated
18682,Q#520 - >seq7167,non-specific,222878,53,198,0.00304681,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF1,hs0_human,marg,BothTerminiTruncated
18683,Q#520 - >seq7167,superfamily,222878,53,198,0.00304681,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA10.ORF1.hs0_human.marg.frame3,1909130938_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF1,hs0_human,marg,BothTerminiTruncated
18684,Q#523 - >seq7170,non-specific,335182,156,252,2.3067899999999998e-43,144.753,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18685,Q#523 - >seq7170,superfamily,335182,156,252,2.3067899999999998e-43,144.753,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18686,Q#523 - >seq7170,non-specific,335182,156,252,2.3067899999999998e-43,144.753,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18687,Q#523 - >seq7170,non-specific,340205,256,319,1.2693800000000002e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18688,Q#523 - >seq7170,superfamily,340205,256,319,1.2693800000000002e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18689,Q#523 - >seq7170,non-specific,340205,256,319,1.2693800000000002e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18690,Q#523 - >seq7170,non-specific,340204,112,153,3.1651499999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18691,Q#523 - >seq7170,superfamily,340204,112,153,3.1651499999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18692,Q#523 - >seq7170,non-specific,340204,112,153,3.1651499999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.pars.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,pars,CompleteHit
18693,Q#526 - >seq7173,non-specific,335182,156,252,2.3067899999999998e-43,144.753,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18694,Q#526 - >seq7173,superfamily,335182,156,252,2.3067899999999998e-43,144.753,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18695,Q#526 - >seq7173,non-specific,335182,156,252,2.3067899999999998e-43,144.753,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18696,Q#526 - >seq7173,non-specific,340205,256,319,1.2693800000000002e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18697,Q#526 - >seq7173,superfamily,340205,256,319,1.2693800000000002e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18698,Q#526 - >seq7173,non-specific,340205,256,319,1.2693800000000002e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18699,Q#526 - >seq7173,non-specific,340204,112,153,3.1651499999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18700,Q#526 - >seq7173,superfamily,340204,112,153,3.1651499999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18701,Q#526 - >seq7173,non-specific,340204,112,153,3.1651499999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA11.ORF1.hs1_chimp.marg.frame3,1909130938_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA11,ORF1,hs1_chimp,marg,CompleteHit
18702,Q#527 - >seq7174,non-specific,335182,143,235,8.7622e-42,140.131,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18703,Q#527 - >seq7174,superfamily,335182,143,235,8.7622e-42,140.131,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA11.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18704,Q#527 - >seq7174,non-specific,340205,239,302,1.60405e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18705,Q#527 - >seq7174,superfamily,340205,239,302,1.60405e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA11.ORF1.hs2_gorilla.pars.frame1,1909130938_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA11,ORF1,hs2_gorilla,pars,CompleteHit
18706,Q#529 - >seq7176,non-specific,335182,155,252,2.5795300000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18707,Q#529 - >seq7176,superfamily,335182,155,252,2.5795300000000003e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18708,Q#529 - >seq7176,non-specific,340205,255,318,5.989629999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18709,Q#529 - >seq7176,superfamily,340205,255,318,5.989629999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18710,Q#529 - >seq7176,non-specific,340204,110,152,4.6035e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18711,Q#529 - >seq7176,superfamily,340204,110,152,4.6035e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs2_gorilla,marg,CompleteHit
18712,Q#529 - >seq7176,non-specific,224117,47,202,0.000226732,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18713,Q#529 - >seq7176,superfamily,224117,47,202,0.000226732,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs2_gorilla,marg,N-TerminusTruncated
18714,Q#529 - >seq7176,non-specific,224117,50,202,0.00027477400000000004,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18715,Q#529 - >seq7176,non-specific,222878,51,149,0.00061187,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18716,Q#529 - >seq7176,superfamily,222878,51,149,0.00061187,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18717,Q#529 - >seq7176,non-specific,275316,51,148,0.00133826,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18718,Q#529 - >seq7176,superfamily,275316,51,148,0.00133826,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs2_gorilla.marg.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs2_gorilla,marg,BothTerminiTruncated
18719,Q#530 - >seq7177,non-specific,335182,140,236,5.773159999999999e-40,135.50799999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs3_orang.pars.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18720,Q#530 - >seq7177,superfamily,335182,140,236,5.773159999999999e-40,135.50799999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs3_orang.pars.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18721,Q#530 - >seq7177,non-specific,340205,239,302,7.268489999999998e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs3_orang.pars.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18722,Q#530 - >seq7177,superfamily,340205,239,302,7.268489999999998e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs3_orang.pars.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18723,Q#531 - >seq7178,non-specific,340204,110,149,1.74786e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18724,Q#531 - >seq7178,superfamily,340204,110,149,1.74786e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs3_orang,pars,CompleteHit
18725,Q#531 - >seq7178,non-specific,222878,51,140,0.00023777,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18726,Q#531 - >seq7178,superfamily,222878,51,140,0.00023777,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18727,Q#531 - >seq7178,non-specific,224117,50,160,0.0006839589999999999,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18728,Q#531 - >seq7178,superfamily,224117,50,160,0.0006839589999999999,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18729,Q#531 - >seq7178,non-specific,235175,40,141,0.00154042,40.0472,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,pars,C-TerminusTruncated
18730,Q#531 - >seq7178,superfamily,235175,40,141,0.00154042,40.0472,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,pars,C-TerminusTruncated
18731,Q#531 - >seq7178,non-specific,275316,51,148,0.00191209,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18732,Q#531 - >seq7178,superfamily,275316,51,148,0.00191209,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs3_orang,pars,BothTerminiTruncated
18733,Q#531 - >seq7178,non-specific,313299,64,128,0.00267981,36.4112,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA14,ORF1,hs3_orang,pars,N-TerminusTruncated
18734,Q#531 - >seq7178,superfamily,313299,64,128,0.00267981,36.4112,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA14,ORF1,hs3_orang,pars,N-TerminusTruncated
18735,Q#531 - >seq7178,non-specific,197874,51,148,0.00534707,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs3_orang,pars,N-TerminusTruncated
18736,Q#531 - >seq7178,superfamily,197874,51,148,0.00534707,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs3_orang.pars.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs3_orang,pars,N-TerminusTruncated
18737,Q#532 - >seq7179,non-specific,335182,140,236,5.773159999999999e-40,135.50799999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs3_orang.marg.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18738,Q#532 - >seq7179,superfamily,335182,140,236,5.773159999999999e-40,135.50799999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs3_orang.marg.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18739,Q#532 - >seq7179,non-specific,340205,239,302,7.268489999999998e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs3_orang.marg.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18740,Q#532 - >seq7179,superfamily,340205,239,302,7.268489999999998e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs3_orang.marg.frame1,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18741,Q#535 - >seq7182,non-specific,335182,152,248,6.19334e-39,133.197,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18742,Q#535 - >seq7182,superfamily,335182,152,248,6.19334e-39,133.197,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18743,Q#535 - >seq7182,non-specific,340205,251,314,1.72633e-31,112.815,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18744,Q#535 - >seq7182,superfamily,340205,251,314,1.72633e-31,112.815,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18745,Q#535 - >seq7182,non-specific,340204,108,149,1.9131700000000002e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18746,Q#535 - >seq7182,superfamily,340204,108,149,1.9131700000000002e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs4_gibbon,pars,CompleteHit
18747,Q#535 - >seq7182,non-specific,224117,36,198,9.453659999999999e-05,43.9348,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA14,ORF1,hs4_gibbon,pars,C-TerminusTruncated
18748,Q#535 - >seq7182,superfamily,224117,36,198,9.453659999999999e-05,43.9348,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA14,ORF1,hs4_gibbon,pars,C-TerminusTruncated
18749,Q#535 - >seq7182,non-specific,222878,49,139,9.64735e-05,43.8497,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18750,Q#535 - >seq7182,superfamily,222878,49,139,9.64735e-05,43.8497,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18751,Q#535 - >seq7182,non-specific,275316,49,146,0.000625633,41.1592,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18752,Q#535 - >seq7182,superfamily,275316,49,146,0.000625633,41.1592,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs4_gibbon,pars,BothTerminiTruncated
18753,Q#535 - >seq7182,non-specific,226883,69,180,0.00266252,39.2805,COG4477,EzrA,N,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA14,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18754,Q#535 - >seq7182,superfamily,226883,69,180,0.00266252,39.2805,cl34766,EzrA superfamily,N, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA14,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18755,Q#535 - >seq7182,non-specific,197874,49,145,0.008793299999999999,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA14,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18756,Q#535 - >seq7182,superfamily,197874,49,145,0.008793299999999999,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs4_gibbon.pars.frame1,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA14,ORF1,hs4_gibbon,pars,N-TerminusTruncated
18757,Q#539 - >seq7186,non-specific,335182,154,250,7.07383e-39,132.812,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18758,Q#539 - >seq7186,superfamily,335182,154,250,7.07383e-39,132.812,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18759,Q#539 - >seq7186,non-specific,340205,253,316,1.50098e-31,112.815,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18760,Q#539 - >seq7186,superfamily,340205,253,316,1.50098e-31,112.815,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18761,Q#539 - >seq7186,non-specific,340204,110,151,1.79686e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18762,Q#539 - >seq7186,superfamily,340204,110,151,1.79686e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs4_gibbon,marg,CompleteHit
18763,Q#539 - >seq7186,non-specific,222878,51,141,9.5056e-05,43.8497,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18764,Q#539 - >seq7186,superfamily,222878,51,141,9.5056e-05,43.8497,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18765,Q#539 - >seq7186,non-specific,224117,50,200,0.00025254,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18766,Q#539 - >seq7186,superfamily,224117,50,200,0.00025254,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18767,Q#539 - >seq7186,non-specific,275316,51,148,0.000457512,41.9296,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18768,Q#539 - >seq7186,superfamily,275316,51,148,0.000457512,41.9296,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs4_gibbon,marg,BothTerminiTruncated
18769,Q#539 - >seq7186,non-specific,226883,71,182,0.00233811,39.2805,COG4477,EzrA,N,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA14,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18770,Q#539 - >seq7186,superfamily,226883,71,182,0.00233811,39.2805,cl34766,EzrA superfamily,N, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA14,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18771,Q#539 - >seq7186,non-specific,197874,51,147,0.00819348,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18772,Q#539 - >seq7186,superfamily,197874,51,147,0.00819348,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs4_gibbon.marg.frame3,1909130939_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs4_gibbon,marg,N-TerminusTruncated
18773,Q#541 - >seq7188,non-specific,340204,110,149,1.74786e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18774,Q#541 - >seq7188,superfamily,340204,110,149,1.74786e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs3_orang,marg,CompleteHit
18775,Q#541 - >seq7188,non-specific,222878,51,140,0.00023777,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18776,Q#541 - >seq7188,superfamily,222878,51,140,0.00023777,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18777,Q#541 - >seq7188,non-specific,224117,50,160,0.0006839589999999999,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18778,Q#541 - >seq7188,superfamily,224117,50,160,0.0006839589999999999,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18779,Q#541 - >seq7188,non-specific,235175,40,141,0.00154042,40.0472,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,marg,C-TerminusTruncated
18780,Q#541 - >seq7188,superfamily,235175,40,141,0.00154042,40.0472,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs3_orang,marg,C-TerminusTruncated
18781,Q#541 - >seq7188,non-specific,275316,51,148,0.00191209,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18782,Q#541 - >seq7188,superfamily,275316,51,148,0.00191209,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs3_orang,marg,BothTerminiTruncated
18783,Q#541 - >seq7188,non-specific,313299,64,128,0.00267981,36.4112,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA14,ORF1,hs3_orang,marg,N-TerminusTruncated
18784,Q#541 - >seq7188,superfamily,313299,64,128,0.00267981,36.4112,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA14,ORF1,hs3_orang,marg,N-TerminusTruncated
18785,Q#541 - >seq7188,non-specific,197874,51,148,0.00534707,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs3_orang,marg,N-TerminusTruncated
18786,Q#541 - >seq7188,superfamily,197874,51,148,0.00534707,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs3_orang.marg.frame3,1909130939_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs3_orang,marg,N-TerminusTruncated
18787,Q#545 - >seq7192,non-specific,335182,155,252,2.5795300000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18788,Q#545 - >seq7192,superfamily,335182,155,252,2.5795300000000003e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18789,Q#545 - >seq7192,non-specific,340205,255,318,5.989629999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18790,Q#545 - >seq7192,superfamily,340205,255,318,5.989629999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18791,Q#545 - >seq7192,non-specific,340204,110,152,4.6035e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18792,Q#545 - >seq7192,superfamily,340204,110,152,4.6035e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs2_gorilla,pars,CompleteHit
18793,Q#545 - >seq7192,non-specific,224117,47,202,0.000226732,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18794,Q#545 - >seq7192,superfamily,224117,47,202,0.000226732,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs2_gorilla,pars,N-TerminusTruncated
18795,Q#545 - >seq7192,non-specific,224117,50,202,0.00027477400000000004,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18796,Q#545 - >seq7192,non-specific,222878,51,149,0.00061187,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18797,Q#545 - >seq7192,superfamily,222878,51,149,0.00061187,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18798,Q#545 - >seq7192,non-specific,275316,51,148,0.00133826,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18799,Q#545 - >seq7192,superfamily,275316,51,148,0.00133826,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs2_gorilla.pars.frame3,1909130939_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18800,Q#548 - >seq7195,non-specific,335182,153,249,4.32611e-42,141.286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,pars,CompleteHit
18801,Q#548 - >seq7195,superfamily,335182,153,249,4.32611e-42,141.286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,pars,CompleteHit
18802,Q#548 - >seq7195,non-specific,340205,252,316,8.78493e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,pars,CompleteHit
18803,Q#548 - >seq7195,superfamily,340205,252,316,8.78493e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,pars,CompleteHit
18804,Q#548 - >seq7195,non-specific,340204,109,150,2.36806e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs0_human,pars,CompleteHit
18805,Q#548 - >seq7195,superfamily,340204,109,150,2.36806e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA13,ORF1,hs0_human,pars,CompleteHit
18806,Q#548 - >seq7195,non-specific,224117,24,199,0.00138931,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF1,hs0_human,pars,N-TerminusTruncated
18807,Q#548 - >seq7195,superfamily,224117,24,199,0.00138931,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs0_human,pars,N-TerminusTruncated
18808,Q#548 - >seq7195,non-specific,222878,51,193,0.0069426,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs0_human,pars,BothTerminiTruncated
18809,Q#548 - >seq7195,superfamily,222878,51,193,0.0069426,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs0_human.pars.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF1,hs0_human,pars,BothTerminiTruncated
18810,Q#551 - >seq7198,non-specific,335182,153,249,4.54669e-42,141.286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,marg,CompleteHit
18811,Q#551 - >seq7198,superfamily,335182,153,249,4.54669e-42,141.286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,marg,CompleteHit
18812,Q#551 - >seq7198,non-specific,340205,252,316,8.74747e-30,108.19200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,marg,CompleteHit
18813,Q#551 - >seq7198,superfamily,340205,252,316,8.74747e-30,108.19200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA13,ORF1,hs0_human,marg,CompleteHit
18814,Q#551 - >seq7198,non-specific,340204,109,150,2.65435e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs0_human,marg,CompleteHit
18815,Q#551 - >seq7198,superfamily,340204,109,150,2.65435e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA13,ORF1,hs0_human,marg,CompleteHit
18816,Q#551 - >seq7198,non-specific,224117,24,199,0.00155931,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF1,hs0_human,marg,N-TerminusTruncated
18817,Q#551 - >seq7198,superfamily,224117,24,199,0.00155931,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF1,hs0_human,marg,N-TerminusTruncated
18818,Q#551 - >seq7198,non-specific,222878,51,193,0.00726269,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs0_human,marg,BothTerminiTruncated
18819,Q#551 - >seq7198,superfamily,222878,51,193,0.00726269,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA13.ORF1.hs0_human.marg.frame3,1909130939_L1PA13.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF1,hs0_human,marg,BothTerminiTruncated
18820,Q#553 - >seq7200,non-specific,335182,155,252,2.9649099999999997e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18821,Q#553 - >seq7200,superfamily,335182,155,252,2.9649099999999997e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18822,Q#553 - >seq7200,non-specific,335182,155,252,2.9649099999999997e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18823,Q#553 - >seq7200,non-specific,340205,255,318,6.314619999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18824,Q#553 - >seq7200,superfamily,340205,255,318,6.314619999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18825,Q#553 - >seq7200,non-specific,340205,255,318,6.314619999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18826,Q#553 - >seq7200,non-specific,340204,110,152,2.81745e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18827,Q#553 - >seq7200,superfamily,340204,110,152,2.81745e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18828,Q#553 - >seq7200,non-specific,340204,110,152,2.81745e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,pars,CompleteHit
18829,Q#553 - >seq7200,non-specific,224117,47,202,4.8211800000000005e-05,45.0904,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18830,Q#553 - >seq7200,superfamily,224117,47,202,4.8211800000000005e-05,45.0904,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18831,Q#553 - >seq7200,non-specific,224117,47,202,4.8211800000000005e-05,45.0904,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18832,Q#553 - >seq7200,non-specific,224117,50,202,0.00014775200000000002,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18833,Q#553 - >seq7200,non-specific,224117,50,202,0.00014775200000000002,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18834,Q#553 - >seq7200,non-specific,222878,51,149,0.000457834,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18835,Q#553 - >seq7200,superfamily,222878,51,149,0.000457834,41.5385,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18836,Q#553 - >seq7200,non-specific,222878,51,149,0.000457834,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18837,Q#553 - >seq7200,non-specific,275316,51,149,0.00102936,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18838,Q#553 - >seq7200,superfamily,275316,51,149,0.00102936,40.774,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18839,Q#553 - >seq7200,non-specific,275316,51,149,0.00102936,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,pars,BothTerminiTruncated
18840,Q#553 - >seq7200,non-specific,197874,51,154,0.00653099,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18841,Q#553 - >seq7200,superfamily,197874,51,154,0.00653099,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18842,Q#553 - >seq7200,non-specific,197874,51,154,0.00653099,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.pars.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,pars,N-TerminusTruncated
18843,Q#556 - >seq7203,non-specific,335182,155,252,2.9649099999999997e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18844,Q#556 - >seq7203,superfamily,335182,155,252,2.9649099999999997e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18845,Q#556 - >seq7203,non-specific,335182,155,252,2.9649099999999997e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18846,Q#556 - >seq7203,non-specific,340205,255,318,6.314619999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18847,Q#556 - >seq7203,superfamily,340205,255,318,6.314619999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18848,Q#556 - >seq7203,non-specific,340205,255,318,6.314619999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18849,Q#556 - >seq7203,non-specific,340204,110,152,2.81745e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18850,Q#556 - >seq7203,superfamily,340204,110,152,2.81745e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18851,Q#556 - >seq7203,non-specific,340204,110,152,2.81745e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs1_chimp,marg,CompleteHit
18852,Q#556 - >seq7203,non-specific,224117,47,202,4.8211800000000005e-05,45.0904,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18853,Q#556 - >seq7203,superfamily,224117,47,202,4.8211800000000005e-05,45.0904,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18854,Q#556 - >seq7203,non-specific,224117,47,202,4.8211800000000005e-05,45.0904,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18855,Q#556 - >seq7203,non-specific,224117,50,202,0.00014775200000000002,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18856,Q#556 - >seq7203,non-specific,224117,50,202,0.00014775200000000002,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18857,Q#556 - >seq7203,non-specific,222878,51,149,0.000457834,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18858,Q#556 - >seq7203,superfamily,222878,51,149,0.000457834,41.5385,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18859,Q#556 - >seq7203,non-specific,222878,51,149,0.000457834,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18860,Q#556 - >seq7203,non-specific,275316,51,149,0.00102936,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18861,Q#556 - >seq7203,superfamily,275316,51,149,0.00102936,40.774,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18862,Q#556 - >seq7203,non-specific,275316,51,149,0.00102936,40.774,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs1_chimp,marg,BothTerminiTruncated
18863,Q#556 - >seq7203,non-specific,197874,51,154,0.00653099,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18864,Q#556 - >seq7203,superfamily,197874,51,154,0.00653099,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18865,Q#556 - >seq7203,non-specific,197874,51,154,0.00653099,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA14.ORF1.hs1_chimp.marg.frame3,1909130939_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA14,ORF1,hs1_chimp,marg,N-TerminusTruncated
18866,Q#560 - >seq7207,non-specific,335182,155,251,1.9309099999999998e-38,132.041,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18867,Q#560 - >seq7207,superfamily,335182,155,251,1.9309099999999998e-38,132.041,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18868,Q#560 - >seq7207,non-specific,340205,254,317,1.03635e-31,113.2,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18869,Q#560 - >seq7207,superfamily,340205,254,317,1.03635e-31,113.2,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18870,Q#560 - >seq7207,non-specific,340204,110,152,1.33802e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18871,Q#560 - >seq7207,superfamily,340204,110,152,1.33802e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs5_gmonkey,marg,CompleteHit
18872,Q#560 - >seq7207,non-specific,222878,51,140,0.000164106,43.0793,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18873,Q#560 - >seq7207,superfamily,222878,51,140,0.000164106,43.0793,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18874,Q#560 - >seq7207,non-specific,224117,50,201,0.000599454,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18875,Q#560 - >seq7207,superfamily,224117,50,201,0.000599454,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18876,Q#560 - >seq7207,non-specific,275316,51,148,0.000655157,41.1592,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18877,Q#560 - >seq7207,superfamily,275316,51,148,0.000655157,41.1592,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
18878,Q#560 - >seq7207,non-specific,226883,71,183,0.00161751,40.0509,COG4477,EzrA,N,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA14,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
18879,Q#560 - >seq7207,superfamily,226883,71,183,0.00161751,40.0509,cl34766,EzrA superfamily,N, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA14,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
18880,Q#560 - >seq7207,non-specific,235175,40,149,0.00700869,38.1212,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
18881,Q#560 - >seq7207,superfamily,235175,40,149,0.00700869,38.1212,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA14.ORF1.hs5_gmonkey.marg.frame3,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
18882,Q#564 - >seq7211,non-specific,335182,152,248,6.145959999999999e-38,130.501,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18883,Q#564 - >seq7211,superfamily,335182,152,248,6.145959999999999e-38,130.501,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18884,Q#564 - >seq7211,non-specific,340205,251,314,1.02223e-30,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18885,Q#564 - >seq7211,superfamily,340205,251,314,1.02223e-30,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18886,Q#564 - >seq7211,non-specific,340204,107,149,3.82668e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18887,Q#564 - >seq7211,superfamily,340204,107,149,3.82668e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs5_gmonkey,pars,CompleteHit
18888,Q#564 - >seq7211,non-specific,222878,45,137,0.000110436,43.4645,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18889,Q#564 - >seq7211,superfamily,222878,45,137,0.000110436,43.4645,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18890,Q#564 - >seq7211,non-specific,275316,48,145,0.00149338,40.0036,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18891,Q#564 - >seq7211,superfamily,275316,48,145,0.00149338,40.0036,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18892,Q#564 - >seq7211,non-specific,224117,46,198,0.00180065,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18893,Q#564 - >seq7211,superfamily,224117,46,198,0.00180065,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA14,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
18894,Q#564 - >seq7211,non-specific,226883,68,180,0.00642183,38.1249,COG4477,EzrA,N,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA14,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
18895,Q#564 - >seq7211,superfamily,226883,68,180,0.00642183,38.1249,cl34766,EzrA superfamily,N, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PA14.ORF1.hs5_gmonkey.pars.frame1,1909130940_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA14,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
18896,Q#565 - >seq7212,non-specific,335182,155,249,3.4628300000000002e-31,112.781,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs1_chimp.marg.frame3,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs1_chimp,marg,CompleteHit
18897,Q#565 - >seq7212,superfamily,335182,155,249,3.4628300000000002e-31,112.781,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs1_chimp.marg.frame3,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs1_chimp,marg,CompleteHit
18898,Q#566 - >seq7213,non-specific,335182,145,240,4.7141699999999993e-32,114.70700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,marg,CompleteHit
18899,Q#566 - >seq7213,superfamily,335182,145,240,4.7141699999999993e-32,114.70700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,marg,CompleteHit
18900,Q#566 - >seq7213,non-specific,340205,243,306,1.30953e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,marg,CompleteHit
18901,Q#566 - >seq7213,superfamily,340205,243,306,1.30953e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,marg,CompleteHit
18902,Q#566 - >seq7213,non-specific,100796,44,131,0.00228627,39.4996,PRK01156,PRK01156,NC,cl30905,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,marg,BothTerminiTruncated
18903,Q#566 - >seq7213,superfamily,100796,44,131,0.00228627,39.4996,cl30905,PRK01156 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,marg,BothTerminiTruncated
18904,Q#566 - >seq7213,non-specific,222878,47,139,0.0027624000000000004,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF1,hs3_orang,marg,BothTerminiTruncated
18905,Q#566 - >seq7213,superfamily,222878,47,139,0.0027624000000000004,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF1,hs3_orang,marg,BothTerminiTruncated
18906,Q#566 - >seq7213,non-specific,336866,45,117,0.00702356,36.0334,pfam07926,TPR_MLP1_2,N,cl25510,"TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.",L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,marg,N-TerminusTruncated
18907,Q#566 - >seq7213,superfamily,336866,45,117,0.00702356,36.0334,cl25510,TPR_MLP1_2 superfamily,N, - ,"TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.",L1PA15-16.ORF1.hs3_orang.marg.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,marg,N-TerminusTruncated
18908,Q#567 - >seq7214,non-specific,224117,26,119,0.00148589,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF1.hs2_gorilla.pars.frame1,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15-16,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18909,Q#567 - >seq7214,superfamily,224117,26,119,0.00148589,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF1.hs2_gorilla.pars.frame1,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA15-16,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18910,Q#567 - >seq7214,non-specific,100796,18,121,0.00184927,39.4996,PRK01156,PRK01156,NC,cl30905,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs2_gorilla.pars.frame1,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA15-16,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18911,Q#567 - >seq7214,superfamily,100796,18,121,0.00184927,39.4996,cl30905,PRK01156 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs2_gorilla.pars.frame1,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA15-16,ORF1,hs2_gorilla,pars,BothTerminiTruncated
18912,Q#569 - >seq7216,non-specific,340205,233,296,9.208e-31,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs2_gorilla.pars.frame3,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs2_gorilla,pars,CompleteHit
18913,Q#569 - >seq7216,superfamily,340205,233,296,9.208e-31,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs2_gorilla.pars.frame3,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs2_gorilla,pars,CompleteHit
18914,Q#569 - >seq7216,non-specific,335182,140,230,1.13838e-28,105.463,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs2_gorilla.pars.frame3,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs2_gorilla,pars,CompleteHit
18915,Q#569 - >seq7216,superfamily,335182,140,230,1.13838e-28,105.463,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs2_gorilla.pars.frame3,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs2_gorilla,pars,CompleteHit
18916,Q#571 - >seq7218,non-specific,340205,153,216,3.4386099999999995e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs2_gorilla.marg.frame2,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs2_gorilla,marg,CompleteHit
18917,Q#571 - >seq7218,superfamily,340205,153,216,3.4386099999999995e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs2_gorilla.marg.frame2,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs2_gorilla,marg,CompleteHit
18918,Q#571 - >seq7218,non-specific,335182,60,150,2.4300599999999997e-30,107.774,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs2_gorilla.marg.frame2,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs2_gorilla,marg,CompleteHit
18919,Q#571 - >seq7218,superfamily,335182,60,150,2.4300599999999997e-30,107.774,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs2_gorilla.marg.frame2,1909130941_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA15-16,ORF1,hs2_gorilla,marg,CompleteHit
18920,Q#575 - >seq7222,non-specific,335182,148,242,2.8105599999999996e-30,110.085,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,pars,CompleteHit
18921,Q#575 - >seq7222,superfamily,335182,148,242,2.8105599999999996e-30,110.085,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,pars,CompleteHit
18922,Q#575 - >seq7222,non-specific,340205,245,308,1.81574e-29,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,pars,CompleteHit
18923,Q#575 - >seq7222,superfamily,340205,245,308,1.81574e-29,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs3_orang,pars,CompleteHit
18924,Q#575 - >seq7222,non-specific,227355,50,297,0.0019398,39.676,COG5022,COG5022,NC,cl34868,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,pars,BothTerminiTruncated
18925,Q#575 - >seq7222,superfamily,227355,50,297,0.0019398,39.676,cl34868,COG5022 superfamily,NC, - ,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15-16,ORF1,hs3_orang,pars,BothTerminiTruncated
18926,Q#575 - >seq7222,non-specific,337766,49,134,0.00719783,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA15-16,ORF1,hs3_orang,pars,N-TerminusTruncated
18927,Q#575 - >seq7222,superfamily,337766,49,134,0.00719783,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA15-16,ORF1,hs3_orang,pars,N-TerminusTruncated
18928,Q#575 - >seq7222,non-specific,235175,53,166,0.00730251,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF1,hs3_orang,pars,C-TerminusTruncated
18929,Q#575 - >seq7222,superfamily,235175,53,166,0.00730251,37.736,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs3_orang.pars.frame3,1909130941_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF1,hs3_orang,pars,C-TerminusTruncated
18930,Q#579 - >seq7226,non-specific,340205,237,292,2.79329e-19,79.6876,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs1_chimp.marg.frame1,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs1_chimp,marg,CompleteHit
18931,Q#579 - >seq7226,superfamily,340205,237,292,2.79329e-19,79.6876,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs1_chimp.marg.frame1,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs1_chimp,marg,CompleteHit
18932,Q#580 - >seq7227,non-specific,335182,155,252,4.09358e-40,136.279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs0_human,marg,CompleteHit
18933,Q#580 - >seq7227,superfamily,335182,155,252,4.09358e-40,136.279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs0_human,marg,CompleteHit
18934,Q#580 - >seq7227,non-specific,340205,255,318,1.4988399999999997e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs0_human,marg,CompleteHit
18935,Q#580 - >seq7227,superfamily,340205,255,318,1.4988399999999997e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs0_human,marg,CompleteHit
18936,Q#580 - >seq7227,non-specific,340204,110,152,5.1451e-08,48.558,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs0_human,marg,CompleteHit
18937,Q#580 - >seq7227,superfamily,340204,110,152,5.1451e-08,48.558,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs0_human,marg,CompleteHit
18938,Q#580 - >seq7227,non-specific,224117,22,202,1.56634e-05,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs0_human,marg,N-TerminusTruncated
18939,Q#580 - >seq7227,superfamily,224117,22,202,1.56634e-05,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs0_human,marg,N-TerminusTruncated
18940,Q#580 - >seq7227,non-specific,224117,50,202,6.589479999999999e-05,44.7052,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs0_human,marg,BothTerminiTruncated
18941,Q#580 - >seq7227,non-specific,222878,51,149,0.00123105,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs0_human,marg,BothTerminiTruncated
18942,Q#580 - >seq7227,superfamily,222878,51,149,0.00123105,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs0_human,marg,BothTerminiTruncated
18943,Q#580 - >seq7227,non-specific,275316,51,149,0.00144289,40.0036,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs0_human,marg,BothTerminiTruncated
18944,Q#580 - >seq7227,superfamily,275316,51,149,0.00144289,40.0036,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs0_human.marg.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs0_human,marg,BothTerminiTruncated
18945,Q#581 - >seq7228,non-specific,340205,248,303,4.7398199999999994e-20,81.9988,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs1_chimp.pars.frame2,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs1_chimp,pars,CompleteHit
18946,Q#581 - >seq7228,superfamily,340205,248,303,4.7398199999999994e-20,81.9988,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs1_chimp.pars.frame2,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA15-16,ORF1,hs1_chimp,pars,CompleteHit
18947,Q#583 - >seq7230,non-specific,335182,154,250,2.0040099999999997e-39,134.35299999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18948,Q#583 - >seq7230,superfamily,335182,154,250,2.0040099999999997e-39,134.35299999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18949,Q#583 - >seq7230,non-specific,335182,154,250,2.0040099999999997e-39,134.35299999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18950,Q#583 - >seq7230,non-specific,340205,253,316,6.667679999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18951,Q#583 - >seq7230,superfamily,340205,253,316,6.667679999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18952,Q#583 - >seq7230,non-specific,340205,253,316,6.667679999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18953,Q#583 - >seq7230,non-specific,340204,110,151,5.2977700000000006e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18954,Q#583 - >seq7230,superfamily,340204,110,151,5.2977700000000006e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18955,Q#583 - >seq7230,non-specific,340204,110,151,5.2977700000000006e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA14,ORF1,hs6_sqmonkey,pars,CompleteHit
18956,Q#583 - >seq7230,non-specific,224117,50,200,0.00033691699999999995,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18957,Q#583 - >seq7230,superfamily,224117,50,200,0.00033691699999999995,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18958,Q#583 - >seq7230,non-specific,224117,50,200,0.00033691699999999995,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18959,Q#583 - >seq7230,non-specific,222878,51,141,0.00126166,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18960,Q#583 - >seq7230,superfamily,222878,51,141,0.00126166,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18961,Q#583 - >seq7230,non-specific,222878,51,141,0.00126166,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18962,Q#583 - >seq7230,non-specific,275316,51,148,0.00192192,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18963,Q#583 - >seq7230,superfamily,275316,51,148,0.00192192,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18964,Q#583 - >seq7230,non-specific,275316,51,148,0.00192192,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.pars.frame1,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
18965,Q#587 - >seq7234,non-specific,335182,154,250,2.0040099999999997e-39,134.35299999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18966,Q#587 - >seq7234,superfamily,335182,154,250,2.0040099999999997e-39,134.35299999999998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18967,Q#587 - >seq7234,non-specific,335182,154,250,2.0040099999999997e-39,134.35299999999998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18968,Q#587 - >seq7234,non-specific,340205,253,316,6.667679999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18969,Q#587 - >seq7234,superfamily,340205,253,316,6.667679999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18970,Q#587 - >seq7234,non-specific,340205,253,316,6.667679999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18971,Q#587 - >seq7234,non-specific,340204,110,151,5.2977700000000006e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18972,Q#587 - >seq7234,superfamily,340204,110,151,5.2977700000000006e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18973,Q#587 - >seq7234,non-specific,340204,110,151,5.2977700000000006e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA14,ORF1,hs6_sqmonkey,marg,CompleteHit
18974,Q#587 - >seq7234,non-specific,224117,50,200,0.00033691699999999995,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18975,Q#587 - >seq7234,superfamily,224117,50,200,0.00033691699999999995,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18976,Q#587 - >seq7234,non-specific,224117,50,200,0.00033691699999999995,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18977,Q#587 - >seq7234,non-specific,222878,51,141,0.00126166,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18978,Q#587 - >seq7234,superfamily,222878,51,141,0.00126166,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18979,Q#587 - >seq7234,non-specific,222878,51,141,0.00126166,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18980,Q#587 - >seq7234,non-specific,275316,51,148,0.00192192,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18981,Q#587 - >seq7234,superfamily,275316,51,148,0.00192192,39.6184,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18982,Q#587 - >seq7234,non-specific,275316,51,148,0.00192192,39.6184,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA14.ORF1.hs6_sqmonkey.marg.frame3,1909130941_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA14,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
18983,Q#589 - >seq7236,non-specific,335182,136,233,6.8474e-41,137.819,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA14,ORF1,hs0_human,pars,CompleteHit
18984,Q#589 - >seq7236,superfamily,335182,136,233,6.8474e-41,137.819,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA14,ORF1,hs0_human,pars,CompleteHit
18985,Q#589 - >seq7236,non-specific,340205,236,299,2.72052e-31,111.65899999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA14,ORF1,hs0_human,pars,CompleteHit
18986,Q#589 - >seq7236,superfamily,340205,236,299,2.72052e-31,111.65899999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA14,ORF1,hs0_human,pars,CompleteHit
18987,Q#589 - >seq7236,non-specific,340204,109,133,0.00551233,34.3056,pfam17489,Tnp_22_trimer,N,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA14,ORF1,hs0_human,pars,N-TerminusTruncated
18988,Q#589 - >seq7236,superfamily,340204,109,133,0.00551233,34.3056,cl38761,Tnp_22_trimer superfamily,N, - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA14.ORF1.hs0_human.pars.frame2,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA14,ORF1,hs0_human,pars,N-TerminusTruncated
18989,Q#590 - >seq7237,non-specific,222878,47,171,0.00021678599999999998,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18990,Q#590 - >seq7237,superfamily,222878,47,171,0.00021678599999999998,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18991,Q#590 - >seq7237,non-specific,274008,29,133,0.00411169,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18992,Q#590 - >seq7237,superfamily,274008,29,133,0.00411169,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18993,Q#590 - >seq7237,non-specific,313299,60,124,0.0056356,35.2556,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA14,ORF1,hs0_human,pars,N-TerminusTruncated
18994,Q#590 - >seq7237,superfamily,313299,60,124,0.0056356,35.2556,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA14,ORF1,hs0_human,pars,N-TerminusTruncated
18995,Q#590 - >seq7237,non-specific,224117,29,118,0.00851461,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18996,Q#590 - >seq7237,superfamily,224117,29,118,0.00851461,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF1.hs0_human.pars.frame3,1909130941_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF1,hs0_human,pars,BothTerminiTruncated
18997,Q#593 - >seq7240,non-specific,335182,142,237,1.06091e-33,118.945,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs1_chimp.pars.frame1,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs1_chimp,pars,CompleteHit
18998,Q#593 - >seq7240,superfamily,335182,142,237,1.06091e-33,118.945,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs1_chimp.pars.frame1,1909130941_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs1_chimp,pars,CompleteHit
18999,Q#596 - >seq7243,non-specific,335182,149,245,1.07786e-34,122.02600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,marg,CompleteHit
19000,Q#596 - >seq7243,superfamily,335182,149,245,1.07786e-34,122.02600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,marg,CompleteHit
19001,Q#596 - >seq7243,non-specific,340205,248,311,7.8871600000000005e-28,102.8,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,marg,CompleteHit
19002,Q#596 - >seq7243,superfamily,340205,248,311,7.8871600000000005e-28,102.8,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,marg,CompleteHit
19003,Q#596 - >seq7243,non-specific,100796,48,129,0.00476007,38.7292,PRK01156,PRK01156,NC,cl30905,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs0_human,marg,BothTerminiTruncated
19004,Q#596 - >seq7243,superfamily,100796,48,129,0.00476007,38.7292,cl30905,PRK01156 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs0_human,marg,BothTerminiTruncated
19005,Q#596 - >seq7243,non-specific,222878,51,121,0.00965984,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF1,hs0_human,marg,BothTerminiTruncated
19006,Q#596 - >seq7243,superfamily,222878,51,121,0.00965984,37.3013,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF1,hs0_human,marg,BothTerminiTruncated
19007,Q#596 - >seq7243,non-specific,336866,49,121,0.00972252,35.6482,pfam07926,TPR_MLP1_2,N,cl25510,"TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.",L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs0_human,marg,N-TerminusTruncated
19008,Q#596 - >seq7243,superfamily,336866,49,121,0.00972252,35.6482,cl25510,TPR_MLP1_2 superfamily,N, - ,"TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.",L1PA15-16.ORF1.hs0_human.marg.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF1,hs0_human,marg,N-TerminusTruncated
19009,Q#599 - >seq7246,non-specific,335182,154,249,4.0777499999999997e-36,125.87799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19010,Q#599 - >seq7246,superfamily,335182,154,249,4.0777499999999997e-36,125.87799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19011,Q#599 - >seq7246,non-specific,340205,252,315,1.53641e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19012,Q#599 - >seq7246,superfamily,340205,252,315,1.53641e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19013,Q#599 - >seq7246,non-specific,222878,51,141,1.27473e-05,46.5461,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19014,Q#599 - >seq7246,superfamily,222878,51,141,1.27473e-05,46.5461,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19015,Q#599 - >seq7246,non-specific,340204,110,151,4.74035e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19016,Q#599 - >seq7246,superfamily,340204,110,151,4.74035e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs1_chimp,pars,CompleteHit
19017,Q#599 - >seq7246,non-specific,224117,51,147,0.0006013230000000001,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19018,Q#599 - >seq7246,superfamily,224117,51,147,0.0006013230000000001,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19019,Q#599 - >seq7246,non-specific,274009,51,147,0.00393635,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19020,Q#599 - >seq7246,superfamily,274009,51,147,0.00393635,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs1_chimp.pars.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,pars,BothTerminiTruncated
19021,Q#602 - >seq7249,non-specific,335182,148,236,3.3342199999999995e-32,115.09299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame1,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19022,Q#602 - >seq7249,superfamily,335182,148,236,3.3342199999999995e-32,115.09299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame1,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19023,Q#602 - >seq7249,non-specific,340205,239,302,7.03863e-28,102.8,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame1,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19024,Q#602 - >seq7249,superfamily,340205,239,302,7.03863e-28,102.8,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame1,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19025,Q#604 - >seq7251,non-specific,222878,51,141,3.3789300000000004e-06,48.0869,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19026,Q#604 - >seq7251,superfamily,222878,51,141,3.3789300000000004e-06,48.0869,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19027,Q#604 - >seq7251,non-specific,340204,110,151,1.1454800000000001e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19028,Q#604 - >seq7251,superfamily,340204,110,151,1.1454800000000001e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs5_gmonkey,pars,CompleteHit
19029,Q#604 - >seq7251,non-specific,224117,51,147,0.00101346,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19030,Q#604 - >seq7251,superfamily,224117,51,147,0.00101346,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19031,Q#604 - >seq7251,non-specific,274009,51,147,0.00160338,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19032,Q#604 - >seq7251,superfamily,274009,51,147,0.00160338,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19033,Q#604 - >seq7251,non-specific,224117,51,122,0.00513672,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs5_gmonkey.pars.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19034,Q#607 - >seq7254,non-specific,335182,154,249,4.0777499999999997e-36,125.87799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19035,Q#607 - >seq7254,superfamily,335182,154,249,4.0777499999999997e-36,125.87799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19036,Q#607 - >seq7254,non-specific,340205,252,315,1.53641e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19037,Q#607 - >seq7254,superfamily,340205,252,315,1.53641e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19038,Q#607 - >seq7254,non-specific,222878,51,141,1.27473e-05,46.5461,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19039,Q#607 - >seq7254,superfamily,222878,51,141,1.27473e-05,46.5461,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19040,Q#607 - >seq7254,non-specific,340204,110,151,4.74035e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19041,Q#607 - >seq7254,superfamily,340204,110,151,4.74035e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs1_chimp,marg,CompleteHit
19042,Q#607 - >seq7254,non-specific,224117,51,147,0.0006013230000000001,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19043,Q#607 - >seq7254,superfamily,224117,51,147,0.0006013230000000001,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19044,Q#607 - >seq7254,non-specific,274009,51,147,0.00393635,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19045,Q#607 - >seq7254,superfamily,274009,51,147,0.00393635,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF1.hs1_chimp.marg.frame3,1909130943_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs1_chimp,marg,BothTerminiTruncated
19046,Q#609 - >seq7256,non-specific,335182,154,249,4.9395e-36,125.493,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19047,Q#609 - >seq7256,superfamily,335182,154,249,4.9395e-36,125.493,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19048,Q#609 - >seq7256,non-specific,340205,252,315,2.26944e-29,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19049,Q#609 - >seq7256,superfamily,340205,252,315,2.26944e-29,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19050,Q#609 - >seq7256,non-specific,222878,51,141,1.30899e-05,46.5461,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19051,Q#609 - >seq7256,superfamily,222878,51,141,1.30899e-05,46.5461,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19052,Q#609 - >seq7256,non-specific,340204,110,151,0.000116003,38.928000000000004,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19053,Q#609 - >seq7256,superfamily,340204,110,151,0.000116003,38.928000000000004,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA15,ORF1,hs5_gmonkey,marg,CompleteHit
19054,Q#609 - >seq7256,non-specific,224117,33,200,0.00136529,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19055,Q#609 - >seq7256,superfamily,224117,33,200,0.00136529,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs5_gmonkey.marg.frame3,1909130943_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19056,Q#611 - >seq7258,non-specific,335182,63,120,3.00888e-15,68.8687,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,pars,C-TerminusTruncated
19057,Q#611 - >seq7258,superfamily,335182,63,120,3.00888e-15,68.8687,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame3,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs0_human,pars,C-TerminusTruncated
19058,Q#616 - >seq7263,non-specific,335182,150,246,8.740339999999999e-32,114.322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,marg,CompleteHit
19059,Q#616 - >seq7263,superfamily,335182,150,246,8.740339999999999e-32,114.322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,marg,CompleteHit
19060,Q#616 - >seq7263,non-specific,340205,249,312,2.33499e-30,109.73299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,marg,CompleteHit
19061,Q#616 - >seq7263,superfamily,340205,249,312,2.33499e-30,109.73299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,marg,CompleteHit
19062,Q#616 - >seq7263,non-specific,275056,58,128,0.00925513,36.5245,TIGR04211,SH3_and_anchor,NC,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA15-16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19063,Q#616 - >seq7263,superfamily,275056,58,128,0.00925513,36.5245,cl25512,SH3_and_anchor superfamily,NC, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA15-16.ORF1.hs4_gibbon.marg.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA15-16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19064,Q#617 - >seq7264,non-specific,335182,150,246,7.0819e-32,114.322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,pars,CompleteHit
19065,Q#617 - >seq7264,superfamily,335182,150,246,7.0819e-32,114.322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,pars,CompleteHit
19066,Q#617 - >seq7264,non-specific,340205,249,312,1.0244999999999999e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,pars,CompleteHit
19067,Q#617 - >seq7264,superfamily,340205,249,312,1.0244999999999999e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs4_gibbon,pars,CompleteHit
19068,Q#617 - >seq7264,non-specific,275056,58,128,0.00869669,36.5245,TIGR04211,SH3_and_anchor,NC,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA15-16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19069,Q#617 - >seq7264,superfamily,275056,58,128,0.00869669,36.5245,cl25512,SH3_and_anchor superfamily,NC, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA15-16.ORF1.hs4_gibbon.pars.frame3,1909130943_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA15-16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19070,Q#618 - >seq7265,specific,238827,483,745,4.135909999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19071,Q#618 - >seq7265,superfamily,295487,483,745,4.135909999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19072,Q#618 - >seq7265,specific,333820,489,713,1.7066e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19073,Q#618 - >seq7265,superfamily,333820,489,713,1.7066e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19074,Q#618 - >seq7265,non-specific,238828,489,710,3.60525e-14,72.6188,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19075,Q#618 - >seq7265,non-specific,275209,440,769,9.419319999999999e-08,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19076,Q#618 - >seq7265,superfamily,275209,440,769,9.419319999999999e-08,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19077,Q#618 - >seq7265,specific,225881,401,653,0.00103714,42.1333,COG3344,YkfC,C,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
19078,Q#618 - >seq7265,superfamily,225881,401,653,0.00103714,42.1333,cl34590,YkfC superfamily,C, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
19079,Q#618 - >seq7265,non-specific,238185,629,714,0.0011193,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame2,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19080,Q#619 - >seq7266,specific,197310,7,233,1.1073e-55,192.56599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19081,Q#619 - >seq7266,superfamily,351117,7,233,1.1073e-55,192.56599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19082,Q#619 - >seq7266,non-specific,197306,7,233,6.48356e-38,141.85,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19083,Q#619 - >seq7266,non-specific,223780,7,234,4.21784e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19084,Q#619 - >seq7266,non-specific,197307,7,233,8.35476e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19085,Q#619 - >seq7266,non-specific,197320,7,218,9.1087e-21,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19086,Q#619 - >seq7266,non-specific,197321,5,233,7.072779999999999e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19087,Q#619 - >seq7266,specific,335306,8,226,2.1684e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19088,Q#619 - >seq7266,non-specific,273186,7,234,1.4539500000000002e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19089,Q#619 - >seq7266,non-specific,197319,11,233,1.0562799999999999e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19090,Q#619 - >seq7266,non-specific,272954,7,191,3.8084e-14,73.1861,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
19091,Q#619 - >seq7266,non-specific,236970,7,218,6.06123e-11,64.145,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19092,Q#619 - >seq7266,non-specific,197336,7,191,3.10434e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19093,Q#619 - >seq7266,non-specific,197311,28,233,3.73711e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19094,Q#619 - >seq7266,non-specific,197318,7,145,0.00106441,41.8983,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
19095,Q#619 - >seq7266,non-specific,339261,106,229,0.00385363,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs6_sqmonkey.pars.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs6_sqmonkey,pars,CompleteHit
19096,Q#622 - >seq7269,specific,238827,507,776,2.4703299999999997e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19097,Q#622 - >seq7269,superfamily,295487,507,776,2.4703299999999997e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19098,Q#622 - >seq7269,specific,197310,7,233,1.87211e-55,192.56599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19099,Q#622 - >seq7269,superfamily,351117,7,233,1.87211e-55,192.56599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19100,Q#622 - >seq7269,non-specific,197306,7,233,1.3258899999999999e-36,138.38299999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19101,Q#622 - >seq7269,specific,333820,513,776,7.083399999999999e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19102,Q#622 - >seq7269,superfamily,333820,513,776,7.083399999999999e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19103,Q#622 - >seq7269,non-specific,223780,7,234,3.2866799999999994e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19104,Q#622 - >seq7269,non-specific,197320,7,218,1.8962400000000002e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19105,Q#622 - >seq7269,non-specific,197307,7,233,6.1482e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19106,Q#622 - >seq7269,non-specific,197321,5,233,1.2334500000000002e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19107,Q#622 - >seq7269,specific,335306,8,226,2.6615900000000003e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19108,Q#622 - >seq7269,non-specific,273186,7,234,6.707839999999999e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19109,Q#622 - >seq7269,non-specific,197319,11,233,9.338879999999998e-13,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19110,Q#622 - >seq7269,non-specific,238828,513,739,1.0722100000000001e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19111,Q#622 - >seq7269,non-specific,272954,7,191,1.15125e-12,69.3341,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
19112,Q#622 - >seq7269,non-specific,236970,7,218,4.724609999999999e-10,61.4486,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19113,Q#622 - >seq7269,non-specific,197336,7,191,3.81718e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19114,Q#622 - >seq7269,non-specific,275209,463,800,1.85915e-07,54.386,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19115,Q#622 - >seq7269,superfamily,275209,463,800,1.85915e-07,54.386,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19116,Q#622 - >seq7269,non-specific,197311,28,233,9.036370000000001e-05,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19117,Q#622 - >seq7269,non-specific,235175,288,466,0.00239652,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
19118,Q#622 - >seq7269,superfamily,235175,288,466,0.00239652,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
19119,Q#622 - >seq7269,non-specific,197318,7,145,0.00289054,40.7427,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
19120,Q#622 - >seq7269,non-specific,224117,207,464,0.00464427,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
19121,Q#622 - >seq7269,superfamily,224117,207,464,0.00464427,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15-16,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
19122,Q#622 - >seq7269,non-specific,238185,658,743,0.00538405,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19123,Q#622 - >seq7269,non-specific,339261,106,229,0.00542447,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19124,Q#622 - >seq7269,non-specific,139971,5,233,0.00743776,39.292,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1PA15-16.ORF2.hs6_sqmonkey.marg.frame3,1909130943_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF2,hs6_sqmonkey,marg,CompleteHit
19125,Q#623 - >seq7270,non-specific,340205,156,219,1.8084799999999998e-27,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame1,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs0_human,pars,CompleteHit
19126,Q#623 - >seq7270,superfamily,340205,156,219,1.8084799999999998e-27,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame1,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs0_human,pars,CompleteHit
19127,Q#623 - >seq7270,non-specific,335182,107,153,1.86005e-13,63.8611,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame1,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs0_human,pars,N-TerminusTruncated
19128,Q#623 - >seq7270,superfamily,335182,107,153,1.86005e-13,63.8611,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs0_human.pars.frame1,1909130943_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs0_human,pars,N-TerminusTruncated
19129,Q#625 - >seq7272,non-specific,335182,154,250,2.69955e-33,118.559,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19130,Q#625 - >seq7272,superfamily,335182,154,250,2.69955e-33,118.559,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19131,Q#625 - >seq7272,non-specific,340205,253,316,6.593789999999999e-30,108.57799999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19132,Q#625 - >seq7272,superfamily,340205,253,316,6.593789999999999e-30,108.57799999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19133,Q#625 - >seq7272,non-specific,222878,50,122,0.000115385,43.4645,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19134,Q#625 - >seq7272,superfamily,222878,50,122,0.000115385,43.4645,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19135,Q#625 - >seq7272,non-specific,340204,109,151,0.00288463,35.076,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19136,Q#625 - >seq7272,superfamily,340204,109,151,0.00288463,35.076,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs6_sqmonkey.pars.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PA15,ORF1,hs6_sqmonkey,pars,CompleteHit
19137,Q#628 - >seq7275,non-specific,335182,141,237,6.778459999999998e-33,117.01899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs6_sqmonkey.marg.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,marg,CompleteHit
19138,Q#628 - >seq7275,superfamily,335182,141,237,6.778459999999998e-33,117.01899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs6_sqmonkey.marg.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,marg,CompleteHit
19139,Q#628 - >seq7275,non-specific,340205,240,303,1.08541e-28,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs6_sqmonkey.marg.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,marg,CompleteHit
19140,Q#628 - >seq7275,superfamily,340205,240,303,1.08541e-28,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs6_sqmonkey.marg.frame1,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15,ORF1,hs6_sqmonkey,marg,CompleteHit
19141,Q#630 - >seq7277,non-specific,222878,51,123,5.3089399999999994e-05,44.6201,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs6_sqmonkey.marg.frame3,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19142,Q#630 - >seq7277,superfamily,222878,51,123,5.3089399999999994e-05,44.6201,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs6_sqmonkey.marg.frame3,1909130945_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19143,Q#631 - >seq7278,non-specific,335182,150,246,4.06894e-40,136.279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,marg,CompleteHit
19144,Q#631 - >seq7278,superfamily,335182,150,246,4.06894e-40,136.279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,marg,CompleteHit
19145,Q#631 - >seq7278,non-specific,340205,249,312,6.15497e-29,105.881,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,marg,CompleteHit
19146,Q#631 - >seq7278,superfamily,340205,249,312,6.15497e-29,105.881,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,marg,CompleteHit
19147,Q#631 - >seq7278,non-specific,222878,49,121,0.00049931,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs0_human,marg,BothTerminiTruncated
19148,Q#631 - >seq7278,superfamily,222878,49,121,0.00049931,41.5385,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs0_human.marg.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF1,hs0_human,marg,BothTerminiTruncated
19149,Q#635 - >seq7282,non-specific,335182,151,247,2.9227099999999997e-39,133.967,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,pars,CompleteHit
19150,Q#635 - >seq7282,superfamily,335182,151,247,2.9227099999999997e-39,133.967,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,pars,CompleteHit
19151,Q#635 - >seq7282,non-specific,340205,250,313,1.23064e-28,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,pars,CompleteHit
19152,Q#635 - >seq7282,superfamily,340205,250,313,1.23064e-28,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15,ORF1,hs0_human,pars,CompleteHit
19153,Q#635 - >seq7282,non-specific,222878,49,144,5.21881e-05,44.6201,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs0_human,pars,BothTerminiTruncated
19154,Q#635 - >seq7282,superfamily,222878,49,144,5.21881e-05,44.6201,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF1,hs0_human,pars,BothTerminiTruncated
19155,Q#635 - >seq7282,non-specific,340204,108,148,0.00057922,37.001999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs0_human,pars,CompleteHit
19156,Q#635 - >seq7282,superfamily,340204,108,148,0.00057922,37.001999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA15,ORF1,hs0_human,pars,CompleteHit
19157,Q#635 - >seq7282,non-specific,224117,31,197,0.00719346,38.1568,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF1,hs0_human,pars,N-TerminusTruncated
19158,Q#635 - >seq7282,superfamily,224117,31,197,0.00719346,38.1568,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF1.hs0_human.pars.frame3,1909130946_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF1,hs0_human,pars,N-TerminusTruncated
19159,Q#637 - >seq7284,non-specific,335182,135,231,1.63838e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs1_chimp.marg.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,marg,CompleteHit
19160,Q#637 - >seq7284,superfamily,335182,135,231,1.63838e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs1_chimp.marg.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,marg,CompleteHit
19161,Q#637 - >seq7284,non-specific,340205,234,297,5.186019999999999e-31,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs1_chimp.marg.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,marg,CompleteHit
19162,Q#637 - >seq7284,superfamily,340205,234,297,5.186019999999999e-31,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs1_chimp.marg.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,marg,CompleteHit
19163,Q#639 - >seq7286,non-specific,222878,51,153,0.0008792339999999999,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs1_chimp.marg.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs1_chimp,marg,BothTerminiTruncated
19164,Q#639 - >seq7286,superfamily,222878,51,153,0.0008792339999999999,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs1_chimp.marg.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs1_chimp,marg,BothTerminiTruncated
19165,Q#639 - >seq7286,non-specific,235505,35,154,0.00194831,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PA16.ORF1.hs1_chimp.marg.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA16,ORF1,hs1_chimp,marg,BothTerminiTruncated
19166,Q#639 - >seq7286,superfamily,235505,35,154,0.00194831,39.4686,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PA16.ORF1.hs1_chimp.marg.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs1_chimp,marg,BothTerminiTruncated
19167,Q#640 - >seq7287,non-specific,335182,135,231,1.63838e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs1_chimp.pars.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,pars,CompleteHit
19168,Q#640 - >seq7287,superfamily,335182,135,231,1.63838e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs1_chimp.pars.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,pars,CompleteHit
19169,Q#640 - >seq7287,non-specific,340205,234,297,5.186019999999999e-31,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs1_chimp.pars.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,pars,CompleteHit
19170,Q#640 - >seq7287,superfamily,340205,234,297,5.186019999999999e-31,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs1_chimp.pars.frame2,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs1_chimp,pars,CompleteHit
19171,Q#642 - >seq7289,non-specific,222878,51,153,0.0008792339999999999,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs1_chimp.pars.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs1_chimp,pars,BothTerminiTruncated
19172,Q#642 - >seq7289,superfamily,222878,51,153,0.0008792339999999999,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs1_chimp.pars.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs1_chimp,pars,BothTerminiTruncated
19173,Q#642 - >seq7289,non-specific,235505,35,154,0.00194831,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PA16.ORF1.hs1_chimp.pars.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA16,ORF1,hs1_chimp,pars,BothTerminiTruncated
19174,Q#642 - >seq7289,superfamily,235505,35,154,0.00194831,39.4686,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PA16.ORF1.hs1_chimp.pars.frame3,1909130947_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs1_chimp,pars,BothTerminiTruncated
19175,Q#643 - >seq7290,non-specific,335182,144,232,6.54151e-33,117.01899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19176,Q#643 - >seq7290,superfamily,335182,144,232,6.54151e-33,117.01899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19177,Q#643 - >seq7290,non-specific,340205,235,298,5.95499e-32,113.585,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19178,Q#643 - >seq7290,superfamily,340205,235,298,5.95499e-32,113.585,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19179,Q#644 - >seq7291,non-specific,222878,51,156,5.04892e-05,44.6201,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs0_human,marg,BothTerminiTruncated
19180,Q#644 - >seq7291,superfamily,222878,51,156,5.04892e-05,44.6201,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs0_human,marg,BothTerminiTruncated
19181,Q#644 - >seq7291,non-specific,224117,36,167,0.000708815,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,BothTerminiTruncated
19182,Q#644 - >seq7291,superfamily,224117,36,167,0.000708815,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs0_human,marg,BothTerminiTruncated
19183,Q#644 - >seq7291,non-specific,237177,51,145,0.00115399,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19184,Q#644 - >seq7291,superfamily,237177,51,145,0.00115399,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19185,Q#644 - >seq7291,non-specific,224117,48,167,0.00266283,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,BothTerminiTruncated
19186,Q#644 - >seq7291,non-specific,274009,38,232,0.00636108,38.1251,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,N-TerminusTruncated
19187,Q#644 - >seq7291,superfamily,274009,38,232,0.00636108,38.1251,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,N-TerminusTruncated
19188,Q#644 - >seq7291,non-specific,235175,42,168,0.00675266,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19189,Q#644 - >seq7291,superfamily,235175,42,168,0.00675266,37.736,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19190,Q#644 - >seq7291,non-specific,336322,44,122,0.00964147,37.1114,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19191,Q#644 - >seq7291,superfamily,336322,44,122,0.00964147,37.1114,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA16.ORF1.hs0_human.marg.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA16,ORF1,hs0_human,marg,C-TerminusTruncated
19192,Q#646 - >seq7293,non-specific,335182,134,228,1.0668200000000001e-32,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs5_gmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,marg,CompleteHit
19193,Q#646 - >seq7293,superfamily,335182,134,228,1.0668200000000001e-32,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs5_gmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,marg,CompleteHit
19194,Q#646 - >seq7293,non-specific,340205,231,294,1.65471e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs5_gmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,marg,CompleteHit
19195,Q#646 - >seq7293,superfamily,340205,231,294,1.65471e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs5_gmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,marg,CompleteHit
19196,Q#647 - >seq7294,non-specific,222878,51,156,0.000302153,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19197,Q#647 - >seq7294,superfamily,222878,51,156,0.000302153,41.9237,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19198,Q#647 - >seq7294,non-specific,222878,51,156,0.000302153,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19199,Q#647 - >seq7294,non-specific,224117,36,165,0.00064359,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19200,Q#647 - >seq7294,superfamily,224117,36,165,0.00064359,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19201,Q#647 - >seq7294,non-specific,224117,36,165,0.00064359,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
19202,Q#647 - >seq7294,non-specific,214360,6,136,0.00580942,38.1728,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19203,Q#647 - >seq7294,superfamily,214360,6,136,0.00580942,38.1728,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19204,Q#647 - >seq7294,non-specific,214360,6,136,0.00580942,38.1728,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19205,Q#648 - >seq7295,non-specific,222878,51,156,0.000302153,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19206,Q#648 - >seq7295,superfamily,222878,51,156,0.000302153,41.9237,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19207,Q#648 - >seq7295,non-specific,222878,51,156,0.000302153,41.9237,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19208,Q#648 - >seq7295,non-specific,224117,36,165,0.00064359,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19209,Q#648 - >seq7295,superfamily,224117,36,165,0.00064359,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19210,Q#648 - >seq7295,non-specific,224117,36,165,0.00064359,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19211,Q#648 - >seq7295,non-specific,214360,6,136,0.00580942,38.1728,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
19212,Q#648 - >seq7295,superfamily,214360,6,136,0.00580942,38.1728,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
19213,Q#648 - >seq7295,non-specific,214360,6,136,0.00580942,38.1728,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1PA16.ORF1.hs5_gmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
19214,Q#650 - >seq7297,non-specific,224117,36,144,0.000310737,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19215,Q#650 - >seq7297,superfamily,224117,36,144,0.000310737,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19216,Q#650 - >seq7297,non-specific,340204,107,148,0.000347872,37.3872,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19217,Q#650 - >seq7297,superfamily,340204,107,148,0.000347872,37.3872,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA16,ORF1,hs6_sqmonkey,pars,CompleteHit
19218,Q#650 - >seq7297,non-specific,222878,51,140,0.00050735,41.5385,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19219,Q#650 - >seq7297,superfamily,222878,51,140,0.00050735,41.5385,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19220,Q#650 - >seq7297,non-specific,224117,33,144,0.00413703,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19221,Q#650 - >seq7297,non-specific,237177,51,144,0.00595943,37.8354,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA16,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19222,Q#650 - >seq7297,superfamily,237177,51,144,0.00595943,37.8354,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA16.ORF1.hs6_sqmonkey.pars.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA16,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19223,Q#652 - >seq7299,non-specific,335182,134,229,1.1173199999999999e-35,123.95200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs6_sqmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,marg,CompleteHit
19224,Q#652 - >seq7299,superfamily,335182,134,229,1.1173199999999999e-35,123.95200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs6_sqmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,marg,CompleteHit
19225,Q#652 - >seq7299,non-specific,340205,232,295,8.90887e-32,112.815,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs6_sqmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,marg,CompleteHit
19226,Q#652 - >seq7299,superfamily,340205,232,295,8.90887e-32,112.815,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs6_sqmonkey.marg.frame2,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs6_sqmonkey,marg,CompleteHit
19227,Q#653 - >seq7300,non-specific,222878,51,142,0.000197938,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19228,Q#653 - >seq7300,superfamily,222878,51,142,0.000197938,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19229,Q#653 - >seq7300,non-specific,183703,48,243,0.00159633,39.5621,PRK12724,PRK12724,C,cl32815,flagellar biosynthesis regulator FlhF; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19230,Q#653 - >seq7300,superfamily,183703,48,243,0.00159633,39.5621,cl32815,PRK12724 superfamily,C, - ,flagellar biosynthesis regulator FlhF; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19231,Q#653 - >seq7300,non-specific,224117,51,167,0.00272872,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19232,Q#653 - >seq7300,superfamily,224117,51,167,0.00272872,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19233,Q#653 - >seq7300,non-specific,224117,36,146,0.00313803,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19234,Q#653 - >seq7300,non-specific,224117,33,167,0.00548695,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19235,Q#653 - >seq7300,non-specific,235175,42,168,0.00564535,38.1212,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19236,Q#653 - >seq7300,superfamily,235175,42,168,0.00564535,38.1212,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA16.ORF1.hs6_sqmonkey.marg.frame3,1909130948_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19237,Q#654 - >seq7301,non-specific,335182,134,230,4.280140000000001e-37,127.419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs0_human.pars.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,pars,CompleteHit
19238,Q#654 - >seq7301,superfamily,335182,134,230,4.280140000000001e-37,127.419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs0_human.pars.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,pars,CompleteHit
19239,Q#654 - >seq7301,non-specific,340205,233,296,5.35769e-32,113.2,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs0_human.pars.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,pars,CompleteHit
19240,Q#654 - >seq7301,superfamily,340205,233,296,5.35769e-32,113.2,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs0_human.pars.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,pars,CompleteHit
19241,Q#655 - >seq7302,non-specific,222878,51,156,5.04892e-05,44.6201,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs0_human,pars,BothTerminiTruncated
19242,Q#655 - >seq7302,superfamily,222878,51,156,5.04892e-05,44.6201,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs0_human,pars,BothTerminiTruncated
19243,Q#655 - >seq7302,non-specific,224117,36,167,0.000708815,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,BothTerminiTruncated
19244,Q#655 - >seq7302,superfamily,224117,36,167,0.000708815,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs0_human,pars,BothTerminiTruncated
19245,Q#655 - >seq7302,non-specific,237177,51,145,0.00115399,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19246,Q#655 - >seq7302,superfamily,237177,51,145,0.00115399,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19247,Q#655 - >seq7302,non-specific,224117,48,167,0.00266283,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,BothTerminiTruncated
19248,Q#655 - >seq7302,non-specific,274009,38,232,0.00636108,38.1251,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,N-TerminusTruncated
19249,Q#655 - >seq7302,superfamily,274009,38,232,0.00636108,38.1251,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,N-TerminusTruncated
19250,Q#655 - >seq7302,non-specific,235175,42,168,0.00675266,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19251,Q#655 - >seq7302,superfamily,235175,42,168,0.00675266,37.736,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19252,Q#655 - >seq7302,non-specific,336322,44,122,0.00964147,37.1114,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19253,Q#655 - >seq7302,superfamily,336322,44,122,0.00964147,37.1114,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA16.ORF1.hs0_human.pars.frame3,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA16,ORF1,hs0_human,pars,C-TerminusTruncated
19254,Q#657 - >seq7304,non-specific,335182,134,230,4.280140000000001e-37,127.419,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs0_human.marg.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,marg,CompleteHit
19255,Q#657 - >seq7304,superfamily,335182,134,230,4.280140000000001e-37,127.419,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs0_human.marg.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,marg,CompleteHit
19256,Q#657 - >seq7304,non-specific,340205,233,296,5.35769e-32,113.2,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs0_human.marg.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,marg,CompleteHit
19257,Q#657 - >seq7304,superfamily,340205,233,296,5.35769e-32,113.2,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs0_human.marg.frame2,1909130948_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs0_human,marg,CompleteHit
19258,Q#658 - >seq7305,non-specific,335182,134,228,1.0668200000000001e-32,115.863,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs5_gmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,pars,CompleteHit
19259,Q#658 - >seq7305,superfamily,335182,134,228,1.0668200000000001e-32,115.863,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs5_gmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,pars,CompleteHit
19260,Q#658 - >seq7305,non-specific,340205,231,294,1.65471e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs5_gmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,pars,CompleteHit
19261,Q#658 - >seq7305,superfamily,340205,231,294,1.65471e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs5_gmonkey.pars.frame2,1909130948_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs5_gmonkey,pars,CompleteHit
19262,Q#661 - >seq7308,non-specific,340205,225,288,2.26206e-30,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,CompleteHit
19263,Q#661 - >seq7308,superfamily,340205,225,288,2.26206e-30,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,CompleteHit
19264,Q#661 - >seq7308,non-specific,335182,193,222,2.51441e-06,44.9863,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,N-TerminusTruncated
19265,Q#661 - >seq7308,superfamily,335182,193,222,2.51441e-06,44.9863,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,N-TerminusTruncated
19266,Q#662 - >seq7309,non-specific,335182,133,213,1.0650799999999999e-20,84.2766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame2,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19267,Q#662 - >seq7309,superfamily,335182,133,213,1.0650799999999999e-20,84.2766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame2,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19268,Q#663 - >seq7310,non-specific,340205,243,306,2.17776e-29,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19269,Q#663 - >seq7310,superfamily,340205,243,306,2.17776e-29,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19270,Q#663 - >seq7310,non-specific,335182,211,240,4.2078699999999996e-06,44.6011,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,N-TerminusTruncated
19271,Q#663 - >seq7310,superfamily,335182,211,240,4.2078699999999996e-06,44.6011,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA16,ORF1,hs4_gibbon,marg,N-TerminusTruncated
19272,Q#663 - >seq7310,non-specific,222878,48,118,0.00171672,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19273,Q#663 - >seq7310,superfamily,222878,48,118,0.00171672,39.6125,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19274,Q#663 - >seq7310,non-specific,275056,54,125,0.0021569000000000002,38.4505,TIGR04211,SH3_and_anchor,NC,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19275,Q#663 - >seq7310,superfamily,275056,54,125,0.0021569000000000002,38.4505,cl25512,SH3_and_anchor superfamily,NC, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19276,Q#663 - >seq7310,non-specific,274008,47,125,0.00236328,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19277,Q#663 - >seq7310,superfamily,274008,47,125,0.00236328,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19278,Q#663 - >seq7310,non-specific,227278,46,118,0.00521496,38.1645,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs4_gibbon,marg,C-TerminusTruncated
19279,Q#663 - >seq7310,superfamily,227278,46,118,0.00521496,38.1645,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs4_gibbon,marg,C-TerminusTruncated
19280,Q#663 - >seq7310,non-specific,313299,47,118,0.00850605,34.8704,pfam10046,BLOC1_2, - ,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19281,Q#663 - >seq7310,superfamily,313299,47,118,0.00850605,34.8704,cl10824,BLOC1_2 superfamily, - , - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs4_gibbon,marg,CompleteHit
19282,Q#663 - >seq7310,non-specific,224117,47,228,0.00968654,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19283,Q#663 - >seq7310,superfamily,224117,47,228,0.00968654,37.3864,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.marg.frame3,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19284,Q#664 - >seq7311,non-specific,335182,61,157,2.9247899999999996e-37,126.26299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs2_gorilla.pars.frame1,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA16,ORF1,hs2_gorilla,pars,CompleteHit
19285,Q#664 - >seq7311,superfamily,335182,61,157,2.9247899999999996e-37,126.26299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs2_gorilla.pars.frame1,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA16,ORF1,hs2_gorilla,pars,CompleteHit
19286,Q#664 - >seq7311,non-specific,340205,160,223,5.5527599999999994e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs2_gorilla.pars.frame1,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA16,ORF1,hs2_gorilla,pars,CompleteHit
19287,Q#664 - >seq7311,superfamily,340205,160,223,5.5527599999999994e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs2_gorilla.pars.frame1,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA16,ORF1,hs2_gorilla,pars,CompleteHit
19288,Q#667 - >seq7314,non-specific,335182,56,152,1.73471e-35,121.256,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs2_gorilla.marg.frame2,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs2_gorilla,marg,CompleteHit
19289,Q#667 - >seq7314,superfamily,335182,56,152,1.73471e-35,121.256,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs2_gorilla.marg.frame2,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs2_gorilla,marg,CompleteHit
19290,Q#667 - >seq7314,non-specific,340205,155,218,4.62e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs2_gorilla.marg.frame2,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs2_gorilla,marg,CompleteHit
19291,Q#667 - >seq7314,superfamily,340205,155,218,4.62e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs2_gorilla.marg.frame2,1909130948_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs2_gorilla,marg,CompleteHit
19292,Q#671 - >seq7318,non-specific,222878,51,155,0.000170383,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs3_orang,pars,BothTerminiTruncated
19293,Q#671 - >seq7318,superfamily,222878,51,155,0.000170383,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF1,hs3_orang,pars,BothTerminiTruncated
19294,Q#671 - >seq7318,non-specific,184156,90,161,0.00208567,38.5543,PRK13575,PRK13575,C,cl28986,3-dehydroquinate dehydratase; Provisional,L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs3_orang,pars,C-TerminusTruncated
19295,Q#671 - >seq7318,superfamily,355862,90,161,0.00208567,38.5543,cl28986,Aldolase_Class_I superfamily,C, - ,"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.",L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA16,ORF1,hs3_orang,pars,C-TerminusTruncated
19296,Q#671 - >seq7318,non-specific,224117,36,166,0.00304459,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs3_orang,pars,BothTerminiTruncated
19297,Q#671 - >seq7318,superfamily,224117,36,166,0.00304459,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs3_orang,pars,BothTerminiTruncated
19298,Q#671 - >seq7318,non-specific,224117,47,166,0.00623975,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.pars.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF1,hs3_orang,pars,BothTerminiTruncated
19299,Q#673 - >seq7320,non-specific,335182,134,230,1.31889e-36,126.26299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs3_orang.marg.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,marg,CompleteHit
19300,Q#673 - >seq7320,superfamily,335182,134,230,1.31889e-36,126.26299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs3_orang.marg.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,marg,CompleteHit
19301,Q#673 - >seq7320,non-specific,340205,233,296,2.8137299999999997e-30,108.57799999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs3_orang.marg.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,marg,CompleteHit
19302,Q#673 - >seq7320,superfamily,340205,233,296,2.8137299999999997e-30,108.57799999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs3_orang.marg.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,marg,CompleteHit
19303,Q#674 - >seq7321,non-specific,222878,51,155,0.000170383,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs3_orang,marg,BothTerminiTruncated
19304,Q#674 - >seq7321,superfamily,222878,51,155,0.000170383,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF1,hs3_orang,marg,BothTerminiTruncated
19305,Q#674 - >seq7321,non-specific,184156,90,161,0.00208567,38.5543,PRK13575,PRK13575,C,cl28986,3-dehydroquinate dehydratase; Provisional,L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs3_orang,marg,C-TerminusTruncated
19306,Q#674 - >seq7321,superfamily,355862,90,161,0.00208567,38.5543,cl28986,Aldolase_Class_I superfamily,C, - ,"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.",L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA16,ORF1,hs3_orang,marg,C-TerminusTruncated
19307,Q#674 - >seq7321,non-specific,224117,36,166,0.00304459,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs3_orang,marg,BothTerminiTruncated
19308,Q#674 - >seq7321,superfamily,224117,36,166,0.00304459,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF1,hs3_orang,marg,BothTerminiTruncated
19309,Q#674 - >seq7321,non-specific,224117,47,166,0.00623975,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs3_orang.marg.frame3,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF1,hs3_orang,marg,BothTerminiTruncated
19310,Q#675 - >seq7322,non-specific,274008,45,120,4.19747e-05,44.6623,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19311,Q#675 - >seq7322,superfamily,274008,45,120,4.19747e-05,44.6623,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19312,Q#675 - >seq7322,non-specific,224117,45,119,0.00033779400000000004,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19313,Q#675 - >seq7322,superfamily,224117,45,119,0.00033779400000000004,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19314,Q#675 - >seq7322,non-specific,309330,46,117,0.0006448830000000001,39.7607,pfam04156,IncA,NC,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19315,Q#675 - >seq7322,superfamily,309330,46,117,0.0006448830000000001,39.7607,cl25897,IncA superfamily,NC, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19316,Q#675 - >seq7322,non-specific,188306,47,110,0.00186165,39.5238,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19317,Q#675 - >seq7322,superfamily,188306,47,110,0.00186165,39.5238,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19318,Q#675 - >seq7322,non-specific,222878,45,113,0.00198439,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19319,Q#675 - >seq7322,superfamily,222878,45,113,0.00198439,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19320,Q#675 - >seq7322,non-specific,224117,39,117,0.00427557,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19321,Q#675 - >seq7322,non-specific,235600,44,119,0.00496637,37.9848,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1PA16,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19322,Q#675 - >seq7322,superfamily,235600,44,119,0.00496637,37.9848,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1PA16,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19323,Q#675 - >seq7322,non-specific,224117,38,113,0.00551243,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19324,Q#675 - >seq7322,non-specific,235175,48,117,0.00630761,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19325,Q#675 - >seq7322,superfamily,235175,48,117,0.00630761,38.1212,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19326,Q#675 - >seq7322,non-specific,274009,47,119,0.00720156,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19327,Q#675 - >seq7322,superfamily,274009,47,119,0.00720156,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19328,Q#675 - >seq7322,non-specific,235600,12,106,0.00784834,37.5996,PRK05771,PRK05771,NC,cl35381,V-type ATP synthase subunit I; Validated,L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase,L1PA16,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19329,Q#675 - >seq7322,non-specific,274008,47,117,0.00896817,37.3435,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF1.hs4_gibbon.pars.frame1,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19330,Q#676 - >seq7323,non-specific,335182,131,211,1.21803e-20,84.2766,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame2,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,CompleteHit
19331,Q#676 - >seq7323,superfamily,335182,131,211,1.21803e-20,84.2766,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs4_gibbon.pars.frame2,1909130948_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs4_gibbon,pars,CompleteHit
19332,Q#677 - >seq7324,non-specific,335182,134,230,1.31889e-36,126.26299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs3_orang.pars.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,pars,CompleteHit
19333,Q#677 - >seq7324,superfamily,335182,134,230,1.31889e-36,126.26299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA16.ORF1.hs3_orang.pars.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,pars,CompleteHit
19334,Q#677 - >seq7324,non-specific,340205,233,296,2.8137299999999997e-30,108.57799999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs3_orang.pars.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,pars,CompleteHit
19335,Q#677 - >seq7324,superfamily,340205,233,296,2.8137299999999997e-30,108.57799999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA16.ORF1.hs3_orang.pars.frame2,1909130948_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA16,ORF1,hs3_orang,pars,CompleteHit
19336,Q#679 - >seq7326,non-specific,340205,246,309,4.15022e-28,103.57,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs2_gorilla.marg.frame3,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs2_gorilla,marg,CompleteHit
19337,Q#679 - >seq7326,superfamily,340205,246,309,4.15022e-28,103.57,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs2_gorilla.marg.frame3,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs2_gorilla,marg,CompleteHit
19338,Q#679 - >seq7326,non-specific,335182,156,243,2.76573e-26,99.6846,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs2_gorilla.marg.frame3,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs2_gorilla,marg,CompleteHit
19339,Q#679 - >seq7326,superfamily,335182,156,243,2.76573e-26,99.6846,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs2_gorilla.marg.frame3,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs2_gorilla,marg,CompleteHit
19340,Q#680 - >seq7327,non-specific,335182,140,234,3.62477e-34,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs3_orang.pars.frame1,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs3_orang,pars,CompleteHit
19341,Q#680 - >seq7327,superfamily,335182,140,234,3.62477e-34,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs3_orang.pars.frame1,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs3_orang,pars,CompleteHit
19342,Q#680 - >seq7327,non-specific,340205,237,300,5.16006e-29,105.49600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs3_orang.pars.frame1,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs3_orang,pars,CompleteHit
19343,Q#680 - >seq7327,superfamily,340205,237,300,5.16006e-29,105.49600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs3_orang.pars.frame1,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs3_orang,pars,CompleteHit
19344,Q#684 - >seq7331,non-specific,335182,149,243,2.91047e-33,117.789,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs3_orang,marg,CompleteHit
19345,Q#684 - >seq7331,superfamily,335182,149,243,2.91047e-33,117.789,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs3_orang,marg,CompleteHit
19346,Q#684 - >seq7331,non-specific,340205,246,309,1.30638e-29,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs3_orang,marg,CompleteHit
19347,Q#684 - >seq7331,superfamily,340205,246,309,1.30638e-29,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs3_orang,marg,CompleteHit
19348,Q#684 - >seq7331,non-specific,335623,49,119,0.00175968,39.0798,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA17,ORF1,hs3_orang,marg,C-TerminusTruncated
19349,Q#684 - >seq7331,superfamily,335623,49,119,0.00175968,39.0798,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA17,ORF1,hs3_orang,marg,C-TerminusTruncated
19350,Q#684 - >seq7331,non-specific,274008,48,173,0.00443565,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,marg,BothTerminiTruncated
19351,Q#684 - >seq7331,superfamily,274008,48,173,0.00443565,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,marg,BothTerminiTruncated
19352,Q#684 - >seq7331,non-specific,222878,23,143,0.00677248,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs3_orang,marg,BothTerminiTruncated
19353,Q#684 - >seq7331,superfamily,222878,23,143,0.00677248,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs3_orang.marg.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs3_orang,marg,BothTerminiTruncated
19354,Q#686 - >seq7333,non-specific,335623,49,119,0.00041869,41.0058,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs3_orang,pars,C-TerminusTruncated
19355,Q#686 - >seq7333,superfamily,335623,49,119,0.00041869,41.0058,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs3_orang,pars,C-TerminusTruncated
19356,Q#686 - >seq7333,non-specific,274386,1,156,0.000692381,40.805,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19357,Q#686 - >seq7333,superfamily,274386,1,156,0.000692381,40.805,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19358,Q#686 - >seq7333,non-specific,222878,23,141,0.00101717,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19359,Q#686 - >seq7333,superfamily,222878,23,141,0.00101717,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19360,Q#686 - >seq7333,non-specific,274008,48,141,0.00319949,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19361,Q#686 - >seq7333,superfamily,274008,48,141,0.00319949,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19362,Q#686 - >seq7333,non-specific,309330,25,145,0.00511822,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs3_orang,pars,N-TerminusTruncated
19363,Q#686 - >seq7333,superfamily,309330,25,145,0.00511822,37.0643,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF1,hs3_orang,pars,N-TerminusTruncated
19364,Q#686 - >seq7333,non-specific,274009,21,119,0.00721077,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19365,Q#686 - >seq7333,superfamily,274009,21,119,0.00721077,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs3_orang.pars.frame3,1909130955_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs3_orang,pars,BothTerminiTruncated
19366,Q#688 - >seq7335,non-specific,340205,235,298,1.04798e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs1_chimp.marg.frame2,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs1_chimp,marg,CompleteHit
19367,Q#688 - >seq7335,superfamily,340205,235,298,1.04798e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs1_chimp.marg.frame2,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs1_chimp,marg,CompleteHit
19368,Q#688 - >seq7335,non-specific,335182,139,232,2.2826e-28,105.07700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.marg.frame2,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs1_chimp,marg,CompleteHit
19369,Q#688 - >seq7335,superfamily,335182,139,232,2.2826e-28,105.07700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.marg.frame2,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs1_chimp,marg,CompleteHit
19370,Q#689 - >seq7336,non-specific,335182,142,236,1.29715e-31,113.552,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19371,Q#689 - >seq7336,superfamily,335182,142,236,1.29715e-31,113.552,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19372,Q#689 - >seq7336,non-specific,340205,239,302,6.02194e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19373,Q#689 - >seq7336,superfamily,340205,239,302,6.02194e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19374,Q#689 - >seq7336,non-specific,274008,23,179,0.00199694,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19375,Q#689 - >seq7336,superfamily,274008,23,179,0.00199694,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19376,Q#689 - >seq7336,non-specific,340204,101,140,0.0072411,33.9204,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19377,Q#689 - >seq7336,superfamily,340204,101,140,0.0072411,33.9204,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA17.ORF1.hs2_gorilla.pars.frame2,1909130955_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA17,ORF1,hs2_gorilla,pars,CompleteHit
19378,Q#691 - >seq7338,non-specific,222878,24,140,0.0043422,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,marg,BothTerminiTruncated
19379,Q#691 - >seq7338,superfamily,222878,24,140,0.0043422,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,marg,BothTerminiTruncated
19380,Q#691 - >seq7338,non-specific,335336,49,133,0.00570573,36.9806,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF1,hs1_chimp,marg,C-TerminusTruncated
19381,Q#691 - >seq7338,superfamily,355101,49,133,0.00570573,36.9806,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF1,hs1_chimp,marg,C-TerminusTruncated
19382,Q#691 - >seq7338,non-specific,274008,29,141,0.009853200000000001,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs1_chimp,marg,BothTerminiTruncated
19383,Q#691 - >seq7338,superfamily,274008,29,141,0.009853200000000001,37.3435,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs1_chimp.marg.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs1_chimp,marg,BothTerminiTruncated
19384,Q#693 - >seq7340,non-specific,335182,149,227,2.6463999999999998e-14,67.3279,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs1_chimp,pars,CompleteHit
19385,Q#693 - >seq7340,superfamily,335182,149,227,2.6463999999999998e-14,67.3279,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs1_chimp,pars,CompleteHit
19386,Q#693 - >seq7340,non-specific,274008,29,186,0.00038586699999999997,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs1_chimp,pars,BothTerminiTruncated
19387,Q#693 - >seq7340,superfamily,274008,29,186,0.00038586699999999997,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs1_chimp,pars,BothTerminiTruncated
19388,Q#693 - >seq7340,non-specific,237177,50,176,0.0009203989999999999,40.5318,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19389,Q#693 - >seq7340,superfamily,237177,50,176,0.0009203989999999999,40.5318,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19390,Q#693 - >seq7340,non-specific,188306,48,194,0.00130864,39.909,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19391,Q#693 - >seq7340,superfamily,188306,48,194,0.00130864,39.909,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19392,Q#693 - >seq7340,non-specific,335336,49,144,0.00198399,38.1362,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19393,Q#693 - >seq7340,superfamily,355101,49,144,0.00198399,38.1362,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF1,hs1_chimp,pars,C-TerminusTruncated
19394,Q#693 - >seq7340,non-specific,222878,24,139,0.00330531,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,pars,BothTerminiTruncated
19395,Q#693 - >seq7340,superfamily,222878,24,139,0.00330531,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs1_chimp,pars,BothTerminiTruncated
19396,Q#693 - >seq7340,non-specific,274008,48,173,0.00637223,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs1_chimp.pars.frame3,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs1_chimp,pars,BothTerminiTruncated
19397,Q#695 - >seq7342,non-specific,340205,235,298,9.96819e-28,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame1,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs1_chimp,pars,CompleteHit
19398,Q#695 - >seq7342,superfamily,340205,235,298,9.96819e-28,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame1,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs1_chimp,pars,CompleteHit
19399,Q#695 - >seq7342,non-specific,335182,191,232,2.91568e-09,53.4607,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame1,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs1_chimp,pars,N-TerminusTruncated
19400,Q#695 - >seq7342,superfamily,335182,191,232,2.91568e-09,53.4607,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs1_chimp.pars.frame1,1909130955_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs1_chimp,pars,N-TerminusTruncated
19401,Q#698 - >seq7345,non-specific,335182,155,245,5.43156e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,marg,CompleteHit
19402,Q#698 - >seq7345,superfamily,335182,155,245,5.43156e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,marg,CompleteHit
19403,Q#698 - >seq7345,non-specific,340205,248,311,6.902069999999999e-27,100.103,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,marg,CompleteHit
19404,Q#698 - >seq7345,superfamily,340205,248,311,6.902069999999999e-27,100.103,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,marg,CompleteHit
19405,Q#698 - >seq7345,non-specific,335623,48,118,0.00140928,39.465,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19406,Q#698 - >seq7345,superfamily,335623,48,118,0.00140928,39.465,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19407,Q#698 - >seq7345,non-specific,237177,49,230,0.00440852,38.2206,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19408,Q#698 - >seq7345,superfamily,237177,49,230,0.00440852,38.2206,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19409,Q#698 - >seq7345,non-specific,222878,22,145,0.00499026,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19410,Q#698 - >seq7345,superfamily,222878,22,145,0.00499026,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19411,Q#698 - >seq7345,non-specific,183703,47,180,0.00542245,38.0213,PRK12724,PRK12724,C,cl32815,flagellar biosynthesis regulator FlhF; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19412,Q#698 - >seq7345,superfamily,183703,47,180,0.00542245,38.0213,cl32815,PRK12724 superfamily,C, - ,flagellar biosynthesis regulator FlhF; Provisional,L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA17,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
19413,Q#698 - >seq7345,non-specific,224117,49,164,0.00905075,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19414,Q#698 - >seq7345,superfamily,224117,49,164,0.00905075,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19415,Q#698 - >seq7345,non-specific,274008,47,178,0.00992709,37.3435,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19416,Q#698 - >seq7345,superfamily,274008,47,178,0.00992709,37.3435,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
19417,Q#701 - >seq7348,non-specific,335182,155,239,1.4333899999999999e-16,73.4911,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19418,Q#701 - >seq7348,superfamily,335182,155,239,1.4333899999999999e-16,73.4911,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19419,Q#701 - >seq7348,non-specific,335623,48,118,0.000956105,39.8502,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19420,Q#701 - >seq7348,superfamily,335623,48,118,0.000956105,39.8502,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19421,Q#701 - >seq7348,non-specific,237177,49,175,0.00169269,39.7614,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19422,Q#701 - >seq7348,superfamily,237177,49,175,0.00169269,39.7614,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19423,Q#701 - >seq7348,non-specific,224117,49,178,0.00242668,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19424,Q#701 - >seq7348,superfamily,224117,49,178,0.00242668,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19425,Q#701 - >seq7348,non-specific,222878,22,145,0.00268267,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19426,Q#701 - >seq7348,superfamily,222878,22,145,0.00268267,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19427,Q#701 - >seq7348,non-specific,274008,47,178,0.00273325,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19428,Q#701 - >seq7348,superfamily,274008,47,178,0.00273325,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19429,Q#701 - >seq7348,non-specific,183703,47,180,0.00309711,38.7917,PRK12724,PRK12724,C,cl32815,flagellar biosynthesis regulator FlhF; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19430,Q#701 - >seq7348,superfamily,183703,47,180,0.00309711,38.7917,cl32815,PRK12724 superfamily,C, - ,flagellar biosynthesis regulator FlhF; Provisional,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA17,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
19431,Q#701 - >seq7348,non-specific,274008,50,196,0.00605784,38.1139,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
19432,Q#701 - >seq7348,superfamily,274008,50,196,0.00605784,38.1139,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
19433,Q#701 - >seq7348,non-specific,224117,49,197,0.00916706,37.3864,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19434,Q#701 - >seq7348,superfamily,224117,49,197,0.00916706,37.3864,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19435,Q#701 - >seq7348,non-specific,340204,106,144,0.00974327,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19436,Q#701 - >seq7348,superfamily,340204,106,144,0.00974327,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19437,Q#701 - >seq7348,non-specific,274386,1,153,0.00986878,37.3382,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19438,Q#701 - >seq7348,superfamily,274386,1,153,0.00986878,37.3382,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PA17.ORF1.hs6_sqmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
19439,Q#702 - >seq7349,non-specific,340205,235,298,4.2117099999999995e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19440,Q#702 - >seq7349,superfamily,340205,235,298,4.2117099999999995e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,CompleteHit
19441,Q#702 - >seq7349,non-specific,335182,202,232,4.97661e-07,46.9123,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
19442,Q#702 - >seq7349,superfamily,335182,202,232,4.97661e-07,46.9123,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs6_sqmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
19443,Q#704 - >seq7351,non-specific,340205,253,316,4.1884399999999993e-29,106.266,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,CompleteHit
19444,Q#704 - >seq7351,superfamily,340205,253,316,4.1884399999999993e-29,106.266,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,CompleteHit
19445,Q#704 - >seq7351,non-specific,335182,218,250,5.30543e-07,46.9123,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19446,Q#704 - >seq7351,superfamily,335182,218,250,5.30543e-07,46.9123,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
19447,Q#705 - >seq7352,non-specific,335182,153,223,1.0894200000000001e-13,65.7871,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
19448,Q#705 - >seq7352,superfamily,335182,153,223,1.0894200000000001e-13,65.7871,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.marg.frame2,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA17,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
19449,Q#706 - >seq7353,non-specific,335182,139,209,1.70553e-13,65.0167,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
19450,Q#706 - >seq7353,superfamily,335182,139,209,1.70553e-13,65.0167,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame2,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
19451,Q#708 - >seq7355,non-specific,274008,29,120,0.00033038699999999997,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs4_gibbon.pars.frame2,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19452,Q#708 - >seq7355,superfamily,274008,29,120,0.00033038699999999997,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs4_gibbon.pars.frame2,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF1,hs4_gibbon,pars,BothTerminiTruncated
19453,Q#708 - >seq7355,non-specific,335623,21,119,0.00377859,38.3094,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs4_gibbon.pars.frame2,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19454,Q#708 - >seq7355,superfamily,335623,21,119,0.00377859,38.3094,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA17.ORF1.hs4_gibbon.pars.frame2,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other,L1PA17,ORF1,hs4_gibbon,pars,C-TerminusTruncated
19455,Q#709 - >seq7356,non-specific,335182,137,231,1.9596099999999998e-32,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs4_gibbon.pars.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,pars,CompleteHit
19456,Q#709 - >seq7356,superfamily,335182,137,231,1.9596099999999998e-32,115.478,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs4_gibbon.pars.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,pars,CompleteHit
19457,Q#709 - >seq7356,non-specific,340205,234,297,2.15521e-28,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs4_gibbon.pars.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,pars,CompleteHit
19458,Q#709 - >seq7356,superfamily,340205,234,297,2.15521e-28,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs4_gibbon.pars.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,pars,CompleteHit
19459,Q#710 - >seq7357,non-specific,224117,50,132,0.00159101,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs5_gmonkey.pars.frame3,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19460,Q#710 - >seq7357,superfamily,224117,50,132,0.00159101,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF1.hs5_gmonkey.pars.frame3,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA17,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
19461,Q#712 - >seq7359,non-specific,335182,149,243,6.7892e-32,114.322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,marg,CompleteHit
19462,Q#712 - >seq7359,superfamily,335182,149,243,6.7892e-32,114.322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,marg,CompleteHit
19463,Q#712 - >seq7359,non-specific,340205,246,309,1.2106e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,marg,CompleteHit
19464,Q#712 - >seq7359,superfamily,340205,246,309,1.2106e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs4_gibbon,marg,CompleteHit
19465,Q#712 - >seq7359,non-specific,274008,29,120,0.00503911,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19466,Q#712 - >seq7359,superfamily,274008,29,120,0.00503911,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs4_gibbon.marg.frame3,1909130958_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs4_gibbon,marg,BothTerminiTruncated
19467,Q#713 - >seq7360,non-specific,340205,239,302,4.30368e-29,105.881,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,CompleteHit
19468,Q#713 - >seq7360,superfamily,340205,239,302,4.30368e-29,105.881,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,CompleteHit
19469,Q#713 - >seq7360,non-specific,335182,204,236,6.21753e-07,46.9123,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
19470,Q#713 - >seq7360,superfamily,335182,204,236,6.21753e-07,46.9123,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs5_gmonkey.pars.frame1,1909130958_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
19471,Q#716 - >seq7363,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19472,Q#716 - >seq7363,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19473,Q#716 - >seq7363,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19474,Q#716 - >seq7363,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19475,Q#716 - >seq7363,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19476,Q#716 - >seq7363,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19477,Q#716 - >seq7363,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19478,Q#716 - >seq7363,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19479,Q#716 - >seq7363,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,marg,CompleteHit
19480,Q#716 - >seq7363,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19481,Q#716 - >seq7363,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19482,Q#716 - >seq7363,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19483,Q#716 - >seq7363,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19484,Q#716 - >seq7363,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19485,Q#716 - >seq7363,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19486,Q#716 - >seq7363,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19487,Q#716 - >seq7363,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19488,Q#716 - >seq7363,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19489,Q#716 - >seq7363,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19490,Q#716 - >seq7363,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19491,Q#716 - >seq7363,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19492,Q#716 - >seq7363,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19493,Q#716 - >seq7363,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19494,Q#716 - >seq7363,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19495,Q#716 - >seq7363,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
19496,Q#716 - >seq7363,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
19497,Q#716 - >seq7363,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
19498,Q#716 - >seq7363,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19499,Q#716 - >seq7363,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19500,Q#716 - >seq7363,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
19501,Q#716 - >seq7363,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19502,Q#716 - >seq7363,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19503,Q#716 - >seq7363,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19504,Q#716 - >seq7363,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19505,Q#716 - >seq7363,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19506,Q#717 - >seq7364,non-specific,130141,277,387,0.00598205,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs2_gorilla.pars.frame1,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
19507,Q#717 - >seq7364,superfamily,130141,277,387,0.00598205,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs2_gorilla.pars.frame1,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
19508,Q#719 - >seq7366,specific,238827,510,772,2.813779999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19509,Q#719 - >seq7366,superfamily,295487,510,772,2.813779999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19510,Q#719 - >seq7366,specific,197310,9,236,7.4864599999999995e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19511,Q#719 - >seq7366,superfamily,351117,9,236,7.4864599999999995e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19512,Q#719 - >seq7366,non-specific,197306,9,236,1.29167e-55,193.082,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19513,Q#719 - >seq7366,specific,333820,516,772,2.00715e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19514,Q#719 - >seq7366,superfamily,333820,516,772,2.00715e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19515,Q#719 - >seq7366,non-specific,197307,9,236,8.652849999999999e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19516,Q#719 - >seq7366,non-specific,223780,9,238,2.5109300000000002e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19517,Q#719 - >seq7366,non-specific,197320,8,236,2.41317e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19518,Q#719 - >seq7366,non-specific,197321,7,236,2.86828e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19519,Q#719 - >seq7366,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19520,Q#719 - >seq7366,non-specific,273186,9,237,1.07384e-17,83.8676,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19521,Q#719 - >seq7366,non-specific,272954,9,236,3.27562e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19522,Q#719 - >seq7366,non-specific,197319,8,236,6.8901e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19523,Q#719 - >seq7366,non-specific,197336,7,235,1.58841e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19524,Q#719 - >seq7366,non-specific,238828,516,737,4.03331e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19525,Q#719 - >seq7366,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19526,Q#719 - >seq7366,non-specific,236970,9,238,3.4747e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19527,Q#719 - >seq7366,non-specific,275209,467,800,1.98136e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19528,Q#719 - >seq7366,superfamily,275209,467,800,1.98136e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19529,Q#719 - >seq7366,non-specific,339261,108,232,1.68056e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19530,Q#719 - >seq7366,non-specific,197317,139,229,8.10573e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
19531,Q#719 - >seq7366,non-specific,197311,7,236,2.41717e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19532,Q#719 - >seq7366,non-specific,238185,656,772,0.00019203799999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19533,Q#719 - >seq7366,non-specific,274009,305,453,0.000279386,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
19534,Q#719 - >seq7366,superfamily,274009,305,453,0.000279386,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
19535,Q#719 - >seq7366,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
19536,Q#719 - >seq7366,non-specific,197314,7,236,0.00272008,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19537,Q#719 - >seq7366,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19538,Q#719 - >seq7366,non-specific,235175,301,469,0.00527011,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
19539,Q#719 - >seq7366,superfamily,235175,301,469,0.00527011,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
19540,Q#719 - >seq7366,non-specific,224117,311,428,0.00897753,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
19541,Q#719 - >seq7366,superfamily,224117,311,428,0.00897753,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
19542,Q#719 - >seq7366,specific,311990,1241,1259,0.00901839,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19543,Q#719 - >seq7366,superfamily,311990,1241,1259,0.00901839,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs2_gorilla,pars,CompleteHit
19544,Q#720 - >seq7367,non-specific,130141,277,387,0.00598205,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs2_gorilla.marg.frame1,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
19545,Q#720 - >seq7367,superfamily,130141,277,387,0.00598205,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs2_gorilla.marg.frame1,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
19546,Q#721 - >seq7368,specific,238827,510,772,2.813779999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19547,Q#721 - >seq7368,superfamily,295487,510,772,2.813779999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19548,Q#721 - >seq7368,specific,197310,9,236,7.4864599999999995e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19549,Q#721 - >seq7368,superfamily,351117,9,236,7.4864599999999995e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19550,Q#721 - >seq7368,non-specific,197306,9,236,1.29167e-55,193.082,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19551,Q#721 - >seq7368,specific,333820,516,772,2.00715e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19552,Q#721 - >seq7368,superfamily,333820,516,772,2.00715e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19553,Q#721 - >seq7368,non-specific,197307,9,236,8.652849999999999e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19554,Q#721 - >seq7368,non-specific,223780,9,238,2.5109300000000002e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19555,Q#721 - >seq7368,non-specific,197320,8,236,2.41317e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19556,Q#721 - >seq7368,non-specific,197321,7,236,2.86828e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19557,Q#721 - >seq7368,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19558,Q#721 - >seq7368,non-specific,273186,9,237,1.07384e-17,83.8676,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19559,Q#721 - >seq7368,non-specific,272954,9,236,3.27562e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19560,Q#721 - >seq7368,non-specific,197319,8,236,6.8901e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19561,Q#721 - >seq7368,non-specific,197336,7,235,1.58841e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19562,Q#721 - >seq7368,non-specific,238828,516,737,4.03331e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19563,Q#721 - >seq7368,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19564,Q#721 - >seq7368,non-specific,236970,9,238,3.4747e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19565,Q#721 - >seq7368,non-specific,275209,467,800,1.98136e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19566,Q#721 - >seq7368,superfamily,275209,467,800,1.98136e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19567,Q#721 - >seq7368,non-specific,339261,108,232,1.68056e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19568,Q#721 - >seq7368,non-specific,197317,139,229,8.10573e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
19569,Q#721 - >seq7368,non-specific,197311,7,236,2.41717e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19570,Q#721 - >seq7368,non-specific,238185,656,772,0.00019203799999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19571,Q#721 - >seq7368,non-specific,274009,305,453,0.000279386,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
19572,Q#721 - >seq7368,superfamily,274009,305,453,0.000279386,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
19573,Q#721 - >seq7368,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
19574,Q#721 - >seq7368,non-specific,197314,7,236,0.00272008,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19575,Q#721 - >seq7368,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19576,Q#721 - >seq7368,non-specific,235175,301,469,0.00527011,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
19577,Q#721 - >seq7368,superfamily,235175,301,469,0.00527011,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
19578,Q#721 - >seq7368,non-specific,224117,311,428,0.00897753,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
19579,Q#721 - >seq7368,superfamily,224117,311,428,0.00897753,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
19580,Q#721 - >seq7368,specific,311990,1241,1259,0.00901839,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19581,Q#721 - >seq7368,superfamily,311990,1241,1259,0.00901839,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs2_gorilla.marg.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs2_gorilla,marg,CompleteHit
19582,Q#727 - >seq7374,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19583,Q#727 - >seq7374,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19584,Q#727 - >seq7374,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19585,Q#727 - >seq7374,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19586,Q#727 - >seq7374,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19587,Q#727 - >seq7374,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,marg,CompleteHit
19588,Q#727 - >seq7374,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,marg,CompleteHit
19589,Q#727 - >seq7374,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,marg,CompleteHit
19590,Q#727 - >seq7374,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,marg,CompleteHit
19591,Q#727 - >seq7374,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19592,Q#727 - >seq7374,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19593,Q#727 - >seq7374,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19594,Q#727 - >seq7374,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19595,Q#727 - >seq7374,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19596,Q#727 - >seq7374,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19597,Q#727 - >seq7374,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19598,Q#727 - >seq7374,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19599,Q#727 - >seq7374,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19600,Q#727 - >seq7374,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19601,Q#727 - >seq7374,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19602,Q#727 - >seq7374,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19603,Q#727 - >seq7374,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19604,Q#727 - >seq7374,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19605,Q#727 - >seq7374,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19606,Q#727 - >seq7374,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,marg,N-TerminusTruncated
19607,Q#727 - >seq7374,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,marg,N-TerminusTruncated
19608,Q#727 - >seq7374,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,marg,N-TerminusTruncated
19609,Q#727 - >seq7374,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19610,Q#727 - >seq7374,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19611,Q#727 - >seq7374,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,marg,C-TerminusTruncated
19612,Q#727 - >seq7374,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19613,Q#727 - >seq7374,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19614,Q#727 - >seq7374,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19615,Q#727 - >seq7374,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19616,Q#727 - >seq7374,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.marg.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,marg,BothTerminiTruncated
19617,Q#729 - >seq7376,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19618,Q#729 - >seq7376,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19619,Q#729 - >seq7376,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19620,Q#729 - >seq7376,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19621,Q#729 - >seq7376,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19622,Q#729 - >seq7376,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs0_human,pars,CompleteHit
19623,Q#729 - >seq7376,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,pars,CompleteHit
19624,Q#729 - >seq7376,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,pars,CompleteHit
19625,Q#729 - >seq7376,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs0_human,pars,CompleteHit
19626,Q#729 - >seq7376,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19627,Q#729 - >seq7376,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19628,Q#729 - >seq7376,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19629,Q#729 - >seq7376,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19630,Q#729 - >seq7376,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19631,Q#729 - >seq7376,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19632,Q#729 - >seq7376,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19633,Q#729 - >seq7376,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19634,Q#729 - >seq7376,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19635,Q#729 - >seq7376,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19636,Q#729 - >seq7376,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19637,Q#729 - >seq7376,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19638,Q#729 - >seq7376,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19639,Q#729 - >seq7376,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19640,Q#729 - >seq7376,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19641,Q#729 - >seq7376,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,pars,N-TerminusTruncated
19642,Q#729 - >seq7376,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,pars,N-TerminusTruncated
19643,Q#729 - >seq7376,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs0_human,pars,N-TerminusTruncated
19644,Q#729 - >seq7376,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19645,Q#729 - >seq7376,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19646,Q#729 - >seq7376,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs0_human,pars,C-TerminusTruncated
19647,Q#729 - >seq7376,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19648,Q#729 - >seq7376,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19649,Q#729 - >seq7376,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19650,Q#729 - >seq7376,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19651,Q#729 - >seq7376,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs0_human.pars.frame3,1909130959_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs0_human,pars,BothTerminiTruncated
19652,Q#730 - >seq7377,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19653,Q#730 - >seq7377,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19654,Q#730 - >seq7377,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19655,Q#730 - >seq7377,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19656,Q#730 - >seq7377,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19657,Q#730 - >seq7377,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19658,Q#730 - >seq7377,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19659,Q#730 - >seq7377,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19660,Q#730 - >seq7377,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs2_gorilla,pars,CompleteHit
19661,Q#730 - >seq7377,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19662,Q#730 - >seq7377,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19663,Q#730 - >seq7377,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19664,Q#730 - >seq7377,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19665,Q#730 - >seq7377,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19666,Q#730 - >seq7377,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19667,Q#730 - >seq7377,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19668,Q#730 - >seq7377,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19669,Q#730 - >seq7377,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19670,Q#730 - >seq7377,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19671,Q#730 - >seq7377,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19672,Q#730 - >seq7377,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19673,Q#730 - >seq7377,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19674,Q#730 - >seq7377,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19675,Q#730 - >seq7377,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19676,Q#730 - >seq7377,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
19677,Q#730 - >seq7377,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
19678,Q#730 - >seq7377,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
19679,Q#730 - >seq7377,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19680,Q#730 - >seq7377,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19681,Q#730 - >seq7377,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
19682,Q#730 - >seq7377,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19683,Q#730 - >seq7377,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19684,Q#730 - >seq7377,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19685,Q#730 - >seq7377,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19686,Q#730 - >seq7377,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs2_gorilla.pars.frame3,1909130959_L1PA2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19687,Q#732 - >seq7379,non-specific,335182,141,211,4.681580000000001e-15,69.2539,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.pars.frame1,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs0_human,pars,C-TerminusTruncated
19688,Q#732 - >seq7379,superfamily,335182,141,211,4.681580000000001e-15,69.2539,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.pars.frame1,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA17,ORF1,hs0_human,pars,C-TerminusTruncated
19689,Q#735 - >seq7382,non-specific,335182,140,211,2.85636e-18,78.1135,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.marg.frame1,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs0_human,marg,C-TerminusTruncated
19690,Q#735 - >seq7382,superfamily,335182,140,211,2.85636e-18,78.1135,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.marg.frame1,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA17,ORF1,hs0_human,marg,C-TerminusTruncated
19691,Q#737 - >seq7384,non-specific,340205,245,308,4.482909999999999e-31,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,marg,CompleteHit
19692,Q#737 - >seq7384,superfamily,340205,245,308,4.482909999999999e-31,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,marg,CompleteHit
19693,Q#737 - >seq7384,non-specific,335182,212,242,8.713700000000001e-07,46.5271,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,marg,N-TerminusTruncated
19694,Q#737 - >seq7384,superfamily,335182,212,242,8.713700000000001e-07,46.5271,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,marg,N-TerminusTruncated
19695,Q#737 - >seq7384,non-specific,222878,21,119,0.00373614,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs0_human,marg,BothTerminiTruncated
19696,Q#737 - >seq7384,superfamily,222878,21,119,0.00373614,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF1,hs0_human,marg,BothTerminiTruncated
19697,Q#737 - >seq7384,non-specific,274008,46,125,0.00534453,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,marg,BothTerminiTruncated
19698,Q#737 - >seq7384,superfamily,274008,46,125,0.00534453,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,marg,BothTerminiTruncated
19699,Q#737 - >seq7384,non-specific,274008,27,126,0.00771241,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,marg,BothTerminiTruncated
19700,Q#737 - >seq7384,non-specific,179877,42,119,0.00969852,37.1226,PRK04778,PRK04778,C,cl32064,septation ring formation regulator EzrA; Provisional,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA17,ORF1,hs0_human,marg,C-TerminusTruncated
19701,Q#737 - >seq7384,superfamily,179877,42,119,0.00969852,37.1226,cl32064,PRK04778 superfamily,C, - ,septation ring formation regulator EzrA; Provisional,L1PA17.ORF1.hs0_human.marg.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA17,ORF1,hs0_human,marg,C-TerminusTruncated
19702,Q#738 - >seq7385,non-specific,340205,246,309,1.62153e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,pars,CompleteHit
19703,Q#738 - >seq7385,superfamily,340205,246,309,1.62153e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,pars,CompleteHit
19704,Q#738 - >seq7385,non-specific,335182,201,243,3.14798e-07,47.6827,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,pars,N-TerminusTruncated
19705,Q#738 - >seq7385,superfamily,335182,201,243,3.14798e-07,47.6827,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA17,ORF1,hs0_human,pars,N-TerminusTruncated
19706,Q#738 - >seq7385,non-specific,222878,23,121,0.00406136,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs0_human,pars,BothTerminiTruncated
19707,Q#738 - >seq7385,superfamily,222878,23,121,0.00406136,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF1,hs0_human,pars,BothTerminiTruncated
19708,Q#738 - >seq7385,non-specific,274008,48,127,0.00634406,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,pars,BothTerminiTruncated
19709,Q#738 - >seq7385,superfamily,274008,48,127,0.00634406,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,pars,BothTerminiTruncated
19710,Q#738 - >seq7385,non-specific,274008,29,128,0.00875652,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF1.hs0_human.pars.frame3,1909130959_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF1,hs0_human,pars,BothTerminiTruncated
19711,Q#740 - >seq7387,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19712,Q#740 - >seq7387,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19713,Q#740 - >seq7387,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19714,Q#740 - >seq7387,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19715,Q#740 - >seq7387,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19716,Q#740 - >seq7387,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19717,Q#740 - >seq7387,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19718,Q#740 - >seq7387,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19719,Q#740 - >seq7387,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,pars,CompleteHit
19720,Q#740 - >seq7387,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19721,Q#740 - >seq7387,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19722,Q#740 - >seq7387,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19723,Q#740 - >seq7387,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19724,Q#740 - >seq7387,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19725,Q#740 - >seq7387,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19726,Q#740 - >seq7387,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19727,Q#740 - >seq7387,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19728,Q#740 - >seq7387,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19729,Q#740 - >seq7387,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19730,Q#740 - >seq7387,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19731,Q#740 - >seq7387,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19732,Q#740 - >seq7387,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19733,Q#740 - >seq7387,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19734,Q#740 - >seq7387,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19735,Q#740 - >seq7387,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,pars,N-TerminusTruncated
19736,Q#740 - >seq7387,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,pars,N-TerminusTruncated
19737,Q#740 - >seq7387,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,pars,N-TerminusTruncated
19738,Q#740 - >seq7387,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19739,Q#740 - >seq7387,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19740,Q#740 - >seq7387,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,pars,C-TerminusTruncated
19741,Q#740 - >seq7387,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19742,Q#740 - >seq7387,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19743,Q#740 - >seq7387,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19744,Q#740 - >seq7387,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19745,Q#740 - >seq7387,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.pars.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,pars,BothTerminiTruncated
19746,Q#743 - >seq7390,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19747,Q#743 - >seq7390,superfamily,335182,154,251,1.77447e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19748,Q#743 - >seq7390,non-specific,335182,154,251,1.77447e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19749,Q#743 - >seq7390,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19750,Q#743 - >seq7390,superfamily,340205,254,318,7.2471199999999996e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19751,Q#743 - >seq7390,non-specific,340205,254,318,7.2471199999999996e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19752,Q#743 - >seq7390,specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19753,Q#743 - >seq7390,superfamily,340204,109,151,1.2191300000000002e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19754,Q#743 - >seq7390,non-specific,340204,109,151,1.2191300000000002e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA2,ORF1,hs1_chimp,marg,CompleteHit
19755,Q#743 - >seq7390,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19756,Q#743 - >seq7390,superfamily,335623,34,146,0.0007983069999999999,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19757,Q#743 - >seq7390,non-specific,335623,34,146,0.0007983069999999999,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19758,Q#743 - >seq7390,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19759,Q#743 - >seq7390,superfamily,337663,48,139,0.00142584,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19760,Q#743 - >seq7390,non-specific,337663,48,139,0.00142584,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19761,Q#743 - >seq7390,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19762,Q#743 - >seq7390,superfamily,235175,52,140,0.00199268,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19763,Q#743 - >seq7390,non-specific,235175,52,140,0.00199268,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19764,Q#743 - >seq7390,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19765,Q#743 - >seq7390,superfamily,274008,39,209,0.00249218,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19766,Q#743 - >seq7390,non-specific,274008,39,209,0.00249218,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19767,Q#743 - >seq7390,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19768,Q#743 - >seq7390,superfamily,316375,34,136,0.0066006,37.1947,cl25894,GAS superfamily,NC, - ,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19769,Q#743 - >seq7390,non-specific,316375,34,136,0.0066006,37.1947,pfam13851,GAS,NC,cl25894,"Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_GAS,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19770,Q#743 - >seq7390,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,marg,N-TerminusTruncated
19771,Q#743 - >seq7390,superfamily,313022,21,151,0.00670243,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,marg,N-TerminusTruncated
19772,Q#743 - >seq7390,non-specific,313022,21,151,0.00670243,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA2,ORF1,hs1_chimp,marg,N-TerminusTruncated
19773,Q#743 - >seq7390,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19774,Q#743 - >seq7390,superfamily,355611,53,194,0.00720908,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19775,Q#743 - >seq7390,non-specific,273690,53,194,0.00720908,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA2,ORF1,hs1_chimp,marg,C-TerminusTruncated
19776,Q#743 - >seq7390,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19777,Q#743 - >seq7390,superfamily,335556,47,130,0.00789922,36.7421,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19778,Q#743 - >seq7390,non-specific,335556,47,130,0.00789922,36.7421,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19779,Q#743 - >seq7390,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19780,Q#743 - >seq7390,non-specific,235175,34,148,0.00900276,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF1.hs1_chimp.marg.frame3,1909130959_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF1,hs1_chimp,marg,BothTerminiTruncated
19781,Q#747 - >seq7394,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19782,Q#747 - >seq7394,superfamily,335182,154,251,3.9370899999999993e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19783,Q#747 - >seq7394,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19784,Q#747 - >seq7394,non-specific,340205,254,318,6.872510000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19785,Q#747 - >seq7394,superfamily,340205,254,318,6.872510000000001e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19786,Q#747 - >seq7394,non-specific,340205,254,318,6.872510000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19787,Q#747 - >seq7394,non-specific,340204,109,151,2.32986e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19788,Q#747 - >seq7394,superfamily,340204,109,151,2.32986e-13,63.5808,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19789,Q#747 - >seq7394,non-specific,340204,109,151,2.32986e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,pars,CompleteHit
19790,Q#747 - >seq7394,non-specific,235175,52,140,0.000581764,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19791,Q#747 - >seq7394,superfamily,235175,52,140,0.000581764,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19792,Q#747 - >seq7394,non-specific,235175,52,140,0.000581764,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19793,Q#747 - >seq7394,non-specific,335623,52,146,0.000756605,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19794,Q#747 - >seq7394,superfamily,335623,52,146,0.000756605,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19795,Q#747 - >seq7394,non-specific,335623,52,146,0.000756605,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19796,Q#747 - >seq7394,non-specific,273690,53,194,0.00218663,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19797,Q#747 - >seq7394,superfamily,355611,53,194,0.00218663,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19798,Q#747 - >seq7394,non-specific,273690,53,194,0.00218663,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19799,Q#747 - >seq7394,non-specific,235316,51,172,0.00271617,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19800,Q#747 - >seq7394,superfamily,235316,51,172,0.00271617,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19801,Q#747 - >seq7394,non-specific,235316,51,172,0.00271617,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19802,Q#747 - >seq7394,non-specific,274008,38,161,0.00574555,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19803,Q#747 - >seq7394,superfamily,274008,38,161,0.00574555,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19804,Q#747 - >seq7394,non-specific,274008,38,161,0.00574555,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19805,Q#747 - >seq7394,non-specific,274008,39,209,0.00643319,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19806,Q#747 - >seq7394,non-specific,274008,39,209,0.00643319,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,BothTerminiTruncated
19807,Q#747 - >seq7394,non-specific,274256,17,262,0.00774345,37.8596,TIGR02680,TIGR02680,C,cl37155,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19808,Q#747 - >seq7394,superfamily,274256,17,262,0.00774345,37.8596,cl37155,TIGR02680 superfamily,C, - ,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19809,Q#747 - >seq7394,non-specific,274256,17,262,0.00774345,37.8596,TIGR02680,TIGR02680,C,cl37155,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19810,Q#747 - >seq7394,non-specific,235175,30,154,0.00783162,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19811,Q#747 - >seq7394,non-specific,235175,30,154,0.00783162,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.pars.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,pars,C-TerminusTruncated
19812,Q#750 - >seq7397,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19813,Q#750 - >seq7397,superfamily,335182,154,251,3.9370899999999993e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19814,Q#750 - >seq7397,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19815,Q#750 - >seq7397,non-specific,340205,254,318,6.872510000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19816,Q#750 - >seq7397,superfamily,340205,254,318,6.872510000000001e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19817,Q#750 - >seq7397,non-specific,340205,254,318,6.872510000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19818,Q#750 - >seq7397,non-specific,340204,109,151,2.32986e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19819,Q#750 - >seq7397,superfamily,340204,109,151,2.32986e-13,63.5808,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19820,Q#750 - >seq7397,non-specific,340204,109,151,2.32986e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs1_chimp,marg,CompleteHit
19821,Q#750 - >seq7397,non-specific,235175,52,140,0.000581764,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19822,Q#750 - >seq7397,superfamily,235175,52,140,0.000581764,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19823,Q#750 - >seq7397,non-specific,235175,52,140,0.000581764,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19824,Q#750 - >seq7397,non-specific,335623,52,146,0.000756605,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19825,Q#750 - >seq7397,superfamily,335623,52,146,0.000756605,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19826,Q#750 - >seq7397,non-specific,335623,52,146,0.000756605,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19827,Q#750 - >seq7397,non-specific,273690,53,194,0.00218663,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19828,Q#750 - >seq7397,superfamily,355611,53,194,0.00218663,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19829,Q#750 - >seq7397,non-specific,273690,53,194,0.00218663,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19830,Q#750 - >seq7397,non-specific,235316,51,172,0.00271617,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19831,Q#750 - >seq7397,superfamily,235316,51,172,0.00271617,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19832,Q#750 - >seq7397,non-specific,235316,51,172,0.00271617,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19833,Q#750 - >seq7397,non-specific,274008,38,161,0.00574555,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19834,Q#750 - >seq7397,superfamily,274008,38,161,0.00574555,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19835,Q#750 - >seq7397,non-specific,274008,38,161,0.00574555,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19836,Q#750 - >seq7397,non-specific,274008,39,209,0.00643319,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19837,Q#750 - >seq7397,non-specific,274008,39,209,0.00643319,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,BothTerminiTruncated
19838,Q#750 - >seq7397,non-specific,274256,17,262,0.00774345,37.8596,TIGR02680,TIGR02680,C,cl37155,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19839,Q#750 - >seq7397,superfamily,274256,17,262,0.00774345,37.8596,cl37155,TIGR02680 superfamily,C, - ,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19840,Q#750 - >seq7397,non-specific,274256,17,262,0.00774345,37.8596,TIGR02680,TIGR02680,C,cl37155,"TIGR02680 family protein; Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved]",L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19841,Q#750 - >seq7397,non-specific,235175,30,154,0.00783162,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19842,Q#750 - >seq7397,non-specific,235175,30,154,0.00783162,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs1_chimp.marg.frame3,1909131001_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs1_chimp,marg,C-TerminusTruncated
19843,Q#751 - >seq7398,non-specific,335182,153,250,1.22382e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19844,Q#751 - >seq7398,superfamily,335182,153,250,1.22382e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19845,Q#751 - >seq7398,non-specific,335182,153,250,1.22382e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19846,Q#751 - >seq7398,non-specific,340205,253,317,1.1307899999999999e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19847,Q#751 - >seq7398,superfamily,340205,253,317,1.1307899999999999e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19848,Q#751 - >seq7398,non-specific,340205,253,317,1.1307899999999999e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19849,Q#751 - >seq7398,non-specific,340204,108,150,8.600389999999999e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19850,Q#751 - >seq7398,superfamily,340204,108,150,8.600389999999999e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19851,Q#751 - >seq7398,non-specific,340204,108,150,8.600389999999999e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,marg,CompleteHit
19852,Q#751 - >seq7398,non-specific,235175,50,153,0.000164168,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,marg,BothTerminiTruncated
19853,Q#751 - >seq7398,superfamily,235175,50,153,0.000164168,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,marg,BothTerminiTruncated
19854,Q#751 - >seq7398,non-specific,235175,50,153,0.000164168,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,marg,BothTerminiTruncated
19855,Q#751 - >seq7398,non-specific,235175,42,139,0.000820658,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,marg,BothTerminiTruncated
19856,Q#751 - >seq7398,non-specific,235175,42,139,0.000820658,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,marg,BothTerminiTruncated
19857,Q#751 - >seq7398,non-specific,313022,25,150,0.00866739,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,marg,N-TerminusTruncated
19858,Q#751 - >seq7398,superfamily,313022,25,150,0.00866739,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,marg,N-TerminusTruncated
19859,Q#751 - >seq7398,non-specific,313022,25,150,0.00866739,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.marg.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,marg,N-TerminusTruncated
19860,Q#756 - >seq7403,non-specific,335182,153,250,1.22382e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19861,Q#756 - >seq7403,superfamily,335182,153,250,1.22382e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19862,Q#756 - >seq7403,non-specific,335182,153,250,1.22382e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19863,Q#756 - >seq7403,non-specific,340205,253,317,1.1307899999999999e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19864,Q#756 - >seq7403,superfamily,340205,253,317,1.1307899999999999e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19865,Q#756 - >seq7403,non-specific,340205,253,317,1.1307899999999999e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19866,Q#756 - >seq7403,non-specific,340204,108,150,8.600389999999999e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19867,Q#756 - >seq7403,superfamily,340204,108,150,8.600389999999999e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19868,Q#756 - >seq7403,non-specific,340204,108,150,8.600389999999999e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs1_chimp,pars,CompleteHit
19869,Q#756 - >seq7403,non-specific,235175,50,153,0.000164168,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,pars,BothTerminiTruncated
19870,Q#756 - >seq7403,superfamily,235175,50,153,0.000164168,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,pars,BothTerminiTruncated
19871,Q#756 - >seq7403,non-specific,235175,50,153,0.000164168,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,pars,BothTerminiTruncated
19872,Q#756 - >seq7403,non-specific,235175,42,139,0.000820658,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,pars,BothTerminiTruncated
19873,Q#756 - >seq7403,non-specific,235175,42,139,0.000820658,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs1_chimp,pars,BothTerminiTruncated
19874,Q#756 - >seq7403,non-specific,313022,25,150,0.00866739,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,pars,N-TerminusTruncated
19875,Q#756 - >seq7403,superfamily,313022,25,150,0.00866739,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,pars,N-TerminusTruncated
19876,Q#756 - >seq7403,non-specific,313022,25,150,0.00866739,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs1_chimp.pars.frame3,1909131002_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs1_chimp,pars,N-TerminusTruncated
19877,Q#757 - >seq7404,non-specific,335182,154,251,1.7366599999999996e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19878,Q#757 - >seq7404,superfamily,335182,154,251,1.7366599999999996e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19879,Q#757 - >seq7404,non-specific,335182,154,251,1.7366599999999996e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19880,Q#757 - >seq7404,non-specific,340205,254,318,1.1198199999999999e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19881,Q#757 - >seq7404,superfamily,340205,254,318,1.1198199999999999e-33,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19882,Q#757 - >seq7404,non-specific,340205,254,318,1.1198199999999999e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19883,Q#757 - >seq7404,non-specific,340204,109,151,8.81352e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19884,Q#757 - >seq7404,superfamily,340204,109,151,8.81352e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19885,Q#757 - >seq7404,non-specific,340204,109,151,8.81352e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,marg,CompleteHit
19886,Q#757 - >seq7404,non-specific,274008,38,161,4.49611e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19887,Q#757 - >seq7404,superfamily,274008,38,161,4.49611e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19888,Q#757 - >seq7404,non-specific,274008,38,161,4.49611e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19889,Q#757 - >seq7404,non-specific,235175,51,154,0.000602458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19890,Q#757 - >seq7404,superfamily,235175,51,154,0.000602458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19891,Q#757 - >seq7404,non-specific,235175,51,154,0.000602458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19892,Q#757 - >seq7404,non-specific,235175,52,140,0.00219339,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19893,Q#757 - >seq7404,non-specific,235175,52,140,0.00219339,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19894,Q#757 - >seq7404,non-specific,274008,3,148,0.00368693,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19895,Q#757 - >seq7404,non-specific,274008,3,148,0.00368693,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.marg.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,marg,BothTerminiTruncated
19896,Q#762 - >seq7409,non-specific,335182,154,251,1.7366599999999996e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19897,Q#762 - >seq7409,superfamily,335182,154,251,1.7366599999999996e-48,157.85,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19898,Q#762 - >seq7409,non-specific,335182,154,251,1.7366599999999996e-48,157.85,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19899,Q#762 - >seq7409,non-specific,340205,254,318,1.1198199999999999e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19900,Q#762 - >seq7409,superfamily,340205,254,318,1.1198199999999999e-33,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19901,Q#762 - >seq7409,non-specific,340205,254,318,1.1198199999999999e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19902,Q#762 - >seq7409,non-specific,340204,109,151,8.81352e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19903,Q#762 - >seq7409,superfamily,340204,109,151,8.81352e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19904,Q#762 - >seq7409,non-specific,340204,109,151,8.81352e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs3_orang,pars,CompleteHit
19905,Q#762 - >seq7409,non-specific,274008,38,161,4.49611e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19906,Q#762 - >seq7409,superfamily,274008,38,161,4.49611e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19907,Q#762 - >seq7409,non-specific,274008,38,161,4.49611e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19908,Q#762 - >seq7409,non-specific,235175,51,154,0.000602458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19909,Q#762 - >seq7409,superfamily,235175,51,154,0.000602458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19910,Q#762 - >seq7409,non-specific,235175,51,154,0.000602458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19911,Q#762 - >seq7409,non-specific,235175,52,140,0.00219339,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19912,Q#762 - >seq7409,non-specific,235175,52,140,0.00219339,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19913,Q#762 - >seq7409,non-specific,274008,3,148,0.00368693,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19914,Q#762 - >seq7409,non-specific,274008,3,148,0.00368693,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs3_orang.pars.frame3,1909131003_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs3_orang,pars,BothTerminiTruncated
19915,Q#765 - >seq7412,non-specific,335182,153,250,1.2777100000000002e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19916,Q#765 - >seq7412,superfamily,335182,153,250,1.2777100000000002e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19917,Q#765 - >seq7412,non-specific,335182,153,250,1.2777100000000002e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19918,Q#765 - >seq7412,non-specific,340205,253,317,8.96345e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19919,Q#765 - >seq7412,superfamily,340205,253,317,8.96345e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19920,Q#765 - >seq7412,non-specific,340205,253,317,8.96345e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19921,Q#765 - >seq7412,non-specific,340204,109,150,7.08627e-10,53.5656,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19922,Q#765 - >seq7412,superfamily,340204,109,150,7.08627e-10,53.5656,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19923,Q#765 - >seq7412,non-specific,340204,109,150,7.08627e-10,53.5656,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,pars,CompleteHit
19924,Q#765 - >seq7412,non-specific,235175,51,153,0.00283467,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19925,Q#765 - >seq7412,superfamily,235175,51,153,0.00283467,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19926,Q#765 - >seq7412,non-specific,235175,51,153,0.00283467,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19927,Q#765 - >seq7412,non-specific,274009,34,201,0.00505744,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19928,Q#765 - >seq7412,superfamily,274009,34,201,0.00505744,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19929,Q#765 - >seq7412,non-specific,274009,34,201,0.00505744,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19930,Q#765 - >seq7412,non-specific,274008,39,208,0.00914189,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19931,Q#765 - >seq7412,superfamily,274008,39,208,0.00914189,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19932,Q#765 - >seq7412,non-specific,274008,39,208,0.00914189,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.pars.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,pars,BothTerminiTruncated
19933,Q#768 - >seq7415,non-specific,335182,153,250,1.2777100000000002e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19934,Q#768 - >seq7415,superfamily,335182,153,250,1.2777100000000002e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19935,Q#768 - >seq7415,non-specific,335182,153,250,1.2777100000000002e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19936,Q#768 - >seq7415,non-specific,340205,253,317,8.96345e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19937,Q#768 - >seq7415,superfamily,340205,253,317,8.96345e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19938,Q#768 - >seq7415,non-specific,340205,253,317,8.96345e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19939,Q#768 - >seq7415,non-specific,340204,109,150,7.08627e-10,53.5656,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19940,Q#768 - >seq7415,superfamily,340204,109,150,7.08627e-10,53.5656,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19941,Q#768 - >seq7415,non-specific,340204,109,150,7.08627e-10,53.5656,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs2_gorilla,marg,CompleteHit
19942,Q#768 - >seq7415,non-specific,235175,51,153,0.00283467,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19943,Q#768 - >seq7415,superfamily,235175,51,153,0.00283467,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19944,Q#768 - >seq7415,non-specific,235175,51,153,0.00283467,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19945,Q#768 - >seq7415,non-specific,274009,34,201,0.00505744,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19946,Q#768 - >seq7415,superfamily,274009,34,201,0.00505744,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19947,Q#768 - >seq7415,non-specific,274009,34,201,0.00505744,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19948,Q#768 - >seq7415,non-specific,274008,39,208,0.00914189,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19949,Q#768 - >seq7415,superfamily,274008,39,208,0.00914189,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19950,Q#768 - >seq7415,non-specific,274008,39,208,0.00914189,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs2_gorilla.marg.frame3,1909131003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs2_gorilla,marg,BothTerminiTruncated
19951,Q#769 - >seq7416,specific,238827,512,774,5.625099999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19952,Q#769 - >seq7416,superfamily,295487,512,774,5.625099999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19953,Q#769 - >seq7416,specific,197310,9,238,5.837849999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19954,Q#769 - >seq7416,superfamily,351117,9,238,5.837849999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19955,Q#769 - >seq7416,non-specific,197306,9,238,2.03712e-55,192.696,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19956,Q#769 - >seq7416,specific,333820,518,774,3.04608e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19957,Q#769 - >seq7416,superfamily,333820,518,774,3.04608e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19958,Q#769 - >seq7416,non-specific,197307,9,238,3.0913400000000003e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19959,Q#769 - >seq7416,non-specific,223780,9,240,1.7707999999999998e-24,104.21700000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19960,Q#769 - >seq7416,non-specific,197321,7,238,6.354430000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19961,Q#769 - >seq7416,non-specific,197320,8,238,9.37075e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19962,Q#769 - >seq7416,non-specific,273186,9,239,1.14676e-19,89.6456,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19963,Q#769 - >seq7416,specific,335306,10,231,3.85404e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19964,Q#769 - >seq7416,non-specific,272954,9,238,1.47943e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19965,Q#769 - >seq7416,non-specific,197319,8,238,1.48047e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19966,Q#769 - >seq7416,non-specific,197336,7,237,8.44903e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19967,Q#769 - >seq7416,non-specific,238828,518,739,2.47893e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19968,Q#769 - >seq7416,non-specific,197322,9,238,5.06928e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19969,Q#769 - >seq7416,non-specific,275209,469,802,4.6527099999999994e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19970,Q#769 - >seq7416,superfamily,275209,469,802,4.6527099999999994e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19971,Q#769 - >seq7416,non-specific,339261,110,234,2.0723800000000002e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19972,Q#769 - >seq7416,non-specific,236970,9,240,2.82974e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19973,Q#769 - >seq7416,non-specific,197311,7,238,2.9113e-08,55.3757,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19974,Q#769 - >seq7416,non-specific,197317,141,231,2.39101e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
19975,Q#769 - >seq7416,non-specific,238185,658,774,0.000181425,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19976,Q#769 - >seq7416,non-specific,197314,7,194,0.000477101,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
19977,Q#769 - >seq7416,non-specific,226098,140,241,0.000496289,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
19978,Q#769 - >seq7416,non-specific,197318,9,238,0.000842302,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19979,Q#769 - >seq7416,non-specific,274009,307,455,0.00101202,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
19980,Q#769 - >seq7416,superfamily,274009,307,455,0.00101202,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
19981,Q#769 - >seq7416,specific,311990,1243,1261,0.00205633,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19982,Q#769 - >seq7416,superfamily,311990,1243,1261,0.00205633,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19983,Q#769 - >seq7416,non-specific,235175,297,466,0.0038909999999999995,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
19984,Q#769 - >seq7416,superfamily,235175,297,466,0.0038909999999999995,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
19985,Q#769 - >seq7416,non-specific,274008,159,502,0.00433825,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
19986,Q#769 - >seq7416,superfamily,274008,159,502,0.00433825,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
19987,Q#769 - >seq7416,non-specific,239569,527,750,0.00899948,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,marg,CompleteHit
19988,Q#769 - >seq7416,non-specific,293702,339,453,0.008999700000000001,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
19989,Q#769 - >seq7416,superfamily,293702,339,453,0.008999700000000001,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
19990,Q#772 - >seq7419,specific,238827,510,772,5.6054899999999996e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19991,Q#772 - >seq7419,superfamily,295487,510,772,5.6054899999999996e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19992,Q#772 - >seq7419,specific,197310,9,236,2.60739e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19993,Q#772 - >seq7419,superfamily,351117,9,236,2.60739e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19994,Q#772 - >seq7419,non-specific,197306,9,236,2.16312e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19995,Q#772 - >seq7419,specific,333820,516,772,3.0703299999999996e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19996,Q#772 - >seq7419,superfamily,333820,516,772,3.0703299999999996e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19997,Q#772 - >seq7419,non-specific,197307,9,236,6.37519e-26,108.14399999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19998,Q#772 - >seq7419,non-specific,223780,9,238,5.5893e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
19999,Q#772 - >seq7419,non-specific,197320,8,236,4.46097e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20000,Q#772 - >seq7419,non-specific,197321,7,236,1.9624999999999998e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20001,Q#772 - >seq7419,specific,335306,10,229,2.29826e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20002,Q#772 - >seq7419,non-specific,273186,9,237,2.89633e-19,88.49,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20003,Q#772 - >seq7419,non-specific,272954,9,236,2.4926300000000003e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20004,Q#772 - >seq7419,non-specific,197319,8,236,6.65491e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20005,Q#772 - >seq7419,non-specific,197336,7,235,5.49352e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20006,Q#772 - >seq7419,non-specific,238828,516,737,2.47454e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20007,Q#772 - >seq7419,non-specific,197322,9,236,9.73302e-11,64.2606,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20008,Q#772 - >seq7419,non-specific,275209,467,800,4.6439800000000005e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20009,Q#772 - >seq7419,superfamily,275209,467,800,4.6439800000000005e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20010,Q#772 - >seq7419,non-specific,236970,9,238,1.1808699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20011,Q#772 - >seq7419,non-specific,339261,108,232,2.049e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20012,Q#772 - >seq7419,non-specific,197311,7,236,1.5200799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20013,Q#772 - >seq7419,non-specific,197317,139,229,2.3651400000000003e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
20014,Q#772 - >seq7419,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20015,Q#772 - >seq7419,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
20016,Q#772 - >seq7419,non-specific,274009,305,453,0.000968377,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
20017,Q#772 - >seq7419,superfamily,274009,305,453,0.000968377,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
20018,Q#772 - >seq7419,specific,311990,1241,1259,0.00211439,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20019,Q#772 - >seq7419,superfamily,311990,1241,1259,0.00211439,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20020,Q#772 - >seq7419,non-specific,235175,295,464,0.00378654,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
20021,Q#772 - >seq7419,superfamily,235175,295,464,0.00378654,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
20022,Q#772 - >seq7419,non-specific,274008,157,500,0.00415128,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
20023,Q#772 - >seq7419,superfamily,274008,157,500,0.00415128,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
20024,Q#772 - >seq7419,non-specific,239569,525,748,0.008742399999999999,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs5_gmonkey,pars,CompleteHit
20025,Q#772 - >seq7419,non-specific,293702,337,451,0.00906208,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
20026,Q#772 - >seq7419,superfamily,293702,337,451,0.00906208,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
20027,Q#775 - >seq7422,non-specific,335182,157,254,1.2362899999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20028,Q#775 - >seq7422,superfamily,335182,157,254,1.2362899999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20029,Q#775 - >seq7422,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20030,Q#775 - >seq7422,superfamily,340205,257,321,3.589239999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20031,Q#775 - >seq7422,non-specific,340204,112,154,4.74309e-11,57.0324,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20032,Q#775 - >seq7422,superfamily,340204,112,154,4.74309e-11,57.0324,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs5_gmonkey,marg,CompleteHit
20033,Q#775 - >seq7422,non-specific,274009,42,151,0.000279054,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20034,Q#775 - >seq7422,superfamily,274009,42,151,0.000279054,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20035,Q#775 - >seq7422,non-specific,274008,38,164,0.00159604,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20036,Q#775 - >seq7422,superfamily,274008,38,164,0.00159604,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20037,Q#775 - >seq7422,non-specific,235175,54,157,0.00310273,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20038,Q#775 - >seq7422,superfamily,235175,54,157,0.00310273,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20039,Q#775 - >seq7422,non-specific,222878,53,198,0.00335507,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20040,Q#775 - >seq7422,superfamily,222878,53,198,0.00335507,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20041,Q#775 - >seq7422,non-specific,313022,7,154,0.00443402,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
20042,Q#775 - >seq7422,superfamily,313022,7,154,0.00443402,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs5_gmonkey.marg.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
20043,Q#780 - >seq7427,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20044,Q#780 - >seq7427,superfamily,335182,154,251,2.201e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20045,Q#780 - >seq7427,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20046,Q#780 - >seq7427,non-specific,340205,254,318,1.24518e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20047,Q#780 - >seq7427,superfamily,340205,254,318,1.24518e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20048,Q#780 - >seq7427,non-specific,340205,254,318,1.24518e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20049,Q#780 - >seq7427,non-specific,340204,109,151,9.7303e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20050,Q#780 - >seq7427,superfamily,340204,109,151,9.7303e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20051,Q#780 - >seq7427,non-specific,340204,109,151,9.7303e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,marg,CompleteHit
20052,Q#780 - >seq7427,non-specific,274008,38,161,5.12693e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20053,Q#780 - >seq7427,superfamily,274008,38,161,5.12693e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20054,Q#780 - >seq7427,non-specific,274008,38,161,5.12693e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20055,Q#780 - >seq7427,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20056,Q#780 - >seq7427,superfamily,235175,51,154,0.000224292,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20057,Q#780 - >seq7427,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20058,Q#780 - >seq7427,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20059,Q#780 - >seq7427,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20060,Q#780 - >seq7427,non-specific,274008,3,148,0.00495588,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20061,Q#780 - >seq7427,non-specific,274008,3,148,0.00495588,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20062,Q#780 - >seq7427,non-specific,274009,30,202,0.00707424,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20063,Q#780 - >seq7427,superfamily,274009,30,202,0.00707424,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20064,Q#780 - >seq7427,non-specific,274009,30,202,0.00707424,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.marg.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20065,Q#783 - >seq7430,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20066,Q#783 - >seq7430,superfamily,335182,154,251,2.201e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20067,Q#783 - >seq7430,non-specific,335182,154,251,2.201e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20068,Q#783 - >seq7430,non-specific,340205,254,318,1.24518e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20069,Q#783 - >seq7430,superfamily,340205,254,318,1.24518e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20070,Q#783 - >seq7430,non-specific,340205,254,318,1.24518e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20071,Q#783 - >seq7430,non-specific,340204,109,151,9.7303e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20072,Q#783 - >seq7430,superfamily,340204,109,151,9.7303e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20073,Q#783 - >seq7430,non-specific,340204,109,151,9.7303e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs4_gibbon,pars,CompleteHit
20074,Q#783 - >seq7430,non-specific,274008,38,161,5.12693e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20075,Q#783 - >seq7430,superfamily,274008,38,161,5.12693e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20076,Q#783 - >seq7430,non-specific,274008,38,161,5.12693e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20077,Q#783 - >seq7430,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20078,Q#783 - >seq7430,superfamily,235175,51,154,0.000224292,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20079,Q#783 - >seq7430,non-specific,235175,51,154,0.000224292,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20080,Q#783 - >seq7430,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20081,Q#783 - >seq7430,non-specific,235175,52,140,0.000940619,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20082,Q#783 - >seq7430,non-specific,274008,3,148,0.00495588,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20083,Q#783 - >seq7430,non-specific,274008,3,148,0.00495588,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20084,Q#783 - >seq7430,non-specific,274009,30,202,0.00707424,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20085,Q#783 - >seq7430,superfamily,274009,30,202,0.00707424,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20086,Q#783 - >seq7430,non-specific,274009,30,202,0.00707424,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs4_gibbon.pars.frame3,1909131005_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20087,Q#786 - >seq7433,non-specific,335182,157,254,1.2362899999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20088,Q#786 - >seq7433,superfamily,335182,157,254,1.2362899999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20089,Q#786 - >seq7433,non-specific,340205,257,321,3.589239999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20090,Q#786 - >seq7433,superfamily,340205,257,321,3.589239999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20091,Q#786 - >seq7433,non-specific,340204,112,154,4.74309e-11,57.0324,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20092,Q#786 - >seq7433,superfamily,340204,112,154,4.74309e-11,57.0324,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs5_gmonkey,pars,CompleteHit
20093,Q#786 - >seq7433,non-specific,274009,42,151,0.000279054,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20094,Q#786 - >seq7433,superfamily,274009,42,151,0.000279054,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20095,Q#786 - >seq7433,non-specific,274008,38,164,0.00159604,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20096,Q#786 - >seq7433,superfamily,274008,38,164,0.00159604,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20097,Q#786 - >seq7433,non-specific,235175,54,157,0.00310273,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20098,Q#786 - >seq7433,superfamily,235175,54,157,0.00310273,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20099,Q#786 - >seq7433,non-specific,222878,53,198,0.00335507,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20100,Q#786 - >seq7433,superfamily,222878,53,198,0.00335507,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20101,Q#786 - >seq7433,non-specific,313022,7,154,0.00443402,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
20102,Q#786 - >seq7433,superfamily,313022,7,154,0.00443402,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs5_gmonkey.pars.frame3,1909131005_L1PA4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
20103,Q#788 - >seq7435,non-specific,335182,157,254,3.22304e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20104,Q#788 - >seq7435,superfamily,335182,157,254,3.22304e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20105,Q#788 - >seq7435,non-specific,335182,157,254,3.22304e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20106,Q#788 - >seq7435,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20107,Q#788 - >seq7435,superfamily,340205,257,321,3.9483899999999995e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20108,Q#788 - >seq7435,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20109,Q#788 - >seq7435,non-specific,340204,112,154,1.30952e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20110,Q#788 - >seq7435,superfamily,340204,112,154,1.30952e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20111,Q#788 - >seq7435,non-specific,340204,112,154,1.30952e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,marg,CompleteHit
20112,Q#788 - >seq7435,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20113,Q#788 - >seq7435,superfamily,274009,42,151,0.0006791810000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20114,Q#788 - >seq7435,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20115,Q#788 - >seq7435,non-specific,274008,38,164,0.00340261,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20116,Q#788 - >seq7435,superfamily,274008,38,164,0.00340261,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20117,Q#788 - >seq7435,non-specific,274008,38,164,0.00340261,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20118,Q#788 - >seq7435,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20119,Q#788 - >seq7435,superfamily,235175,54,157,0.00501044,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20120,Q#788 - >seq7435,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20121,Q#789 - >seq7436,non-specific,335182,157,254,3.22304e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20122,Q#789 - >seq7436,superfamily,335182,157,254,3.22304e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20123,Q#789 - >seq7436,non-specific,335182,157,254,3.22304e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20124,Q#789 - >seq7436,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20125,Q#789 - >seq7436,superfamily,340205,257,321,3.9483899999999995e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20126,Q#789 - >seq7436,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20127,Q#789 - >seq7436,non-specific,340204,112,154,1.30952e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20128,Q#789 - >seq7436,superfamily,340204,112,154,1.30952e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20129,Q#789 - >seq7436,non-specific,340204,112,154,1.30952e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs5_gmonkey,pars,CompleteHit
20130,Q#789 - >seq7436,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20131,Q#789 - >seq7436,superfamily,274009,42,151,0.0006791810000000001,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20132,Q#789 - >seq7436,non-specific,274009,42,151,0.0006791810000000001,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20133,Q#789 - >seq7436,non-specific,274008,38,164,0.00340261,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20134,Q#789 - >seq7436,superfamily,274008,38,164,0.00340261,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20135,Q#789 - >seq7436,non-specific,274008,38,164,0.00340261,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20136,Q#789 - >seq7436,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20137,Q#789 - >seq7436,superfamily,235175,54,157,0.00501044,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20138,Q#789 - >seq7436,non-specific,235175,54,157,0.00501044,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs5_gmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20139,Q#791 - >seq7438,specific,238827,330,546,1.7866899999999998e-43,157.453,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20140,Q#791 - >seq7438,superfamily,295487,330,546,1.7866899999999998e-43,157.453,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20141,Q#791 - >seq7438,non-specific,333820,331,546,3.52101e-22,94.6665,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20142,Q#791 - >seq7438,superfamily,333820,331,546,3.52101e-22,94.6665,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20143,Q#791 - >seq7438,non-specific,238828,339,514,2.45764e-09,58.3664,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
20144,Q#791 - >seq7438,non-specific,275209,358,578,2.382e-07,54.0008,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
20145,Q#791 - >seq7438,superfamily,275209,358,578,2.382e-07,54.0008,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
20146,Q#791 - >seq7438,non-specific,238185,432,548,0.00196557,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs6_sqmonkey.marg.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20147,Q#795 - >seq7442,specific,238827,287,549,1.1667699999999998e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20148,Q#795 - >seq7442,superfamily,295487,287,549,1.1667699999999998e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20149,Q#795 - >seq7442,specific,333820,293,549,2.2487499999999998e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20150,Q#795 - >seq7442,superfamily,333820,293,549,2.2487499999999998e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20151,Q#795 - >seq7442,non-specific,238828,293,514,1.38913e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20152,Q#795 - >seq7442,non-specific,275209,244,577,1.94757e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20153,Q#795 - >seq7442,superfamily,275209,244,577,1.94757e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20154,Q#795 - >seq7442,non-specific,238185,433,549,0.000104391,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs6_sqmonkey.pars.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA5,ORF2,hs6_sqmonkey,pars,CompleteHit
20155,Q#796 - >seq7443,non-specific,340205,84,139,1.5592299999999998e-16,69.2872,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,CompleteHit
20156,Q#796 - >seq7443,superfamily,340205,84,139,1.5592299999999998e-16,69.2872,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,CompleteHit
20157,Q#799 - >seq7446,non-specific,273422,14,210,0.00778872,39.786,TIGR01061,parC_Gpos,NC,cl36811,"DNA topoisomerase IV, A subunit, Gram-positive; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs6_sqmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA5,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
20158,Q#799 - >seq7446,superfamily,273422,14,210,0.00778872,39.786,cl36811,parC_Gpos superfamily,NC, - ,"DNA topoisomerase IV, A subunit, Gram-positive; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs6_sqmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA5,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
20159,Q#799 - >seq7446,non-specific,339176,36,147,0.00855544,38.7734,pfam14335,DUF4391,N,cl20517,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1PA5.ORF2.hs6_sqmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
20160,Q#799 - >seq7446,superfamily,339176,36,147,0.00855544,38.7734,cl20517,DUF4391 superfamily,N, - ,Domain of unknown function (DUF4391); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.,L1PA5.ORF2.hs6_sqmonkey.pars.frame3,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA5,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
20161,Q#800 - >seq7447,non-specific,274009,98,244,0.000375358,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20162,Q#800 - >seq7447,superfamily,274009,98,244,0.000375358,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20163,Q#800 - >seq7447,non-specific,235175,88,255,0.00105504,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
20164,Q#800 - >seq7447,superfamily,235175,88,255,0.00105504,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
20165,Q#800 - >seq7447,non-specific,274009,98,218,0.00460549,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
20166,Q#800 - >seq7447,non-specific,293702,128,242,0.0054643999999999995,40.1827,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20167,Q#800 - >seq7447,superfamily,293702,128,242,0.0054643999999999995,40.1827,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20168,Q#800 - >seq7447,non-specific,224117,102,219,0.00828871,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20169,Q#800 - >seq7447,superfamily,224117,102,219,0.00828871,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20170,Q#800 - >seq7447,specific,311990,993,1011,0.00912889,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20171,Q#800 - >seq7447,superfamily,311990,993,1011,0.00912889,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA5,ORF2,hs6_sqmonkey,marg,CompleteHit
20172,Q#801 - >seq7448,non-specific,238827,284,330,3.07966e-14,72.709,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20173,Q#801 - >seq7448,superfamily,295487,284,330,3.07966e-14,72.709,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20174,Q#801 - >seq7448,non-specific,333820,290,327,9.47523e-05,44.2054,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20175,Q#801 - >seq7448,superfamily,333820,290,327,9.47523e-05,44.2054,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs6_sqmonkey.marg.frame2,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PA5,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
20176,Q#803 - >seq7450,non-specific,335182,1,80,2.5371e-35,118.559,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,CompleteHit
20177,Q#803 - >seq7450,superfamily,335182,1,80,2.5371e-35,118.559,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,CompleteHit
20178,Q#803 - >seq7450,non-specific,340205,83,102,0.00035296800000000005,36.9304,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
20179,Q#803 - >seq7450,superfamily,340205,83,102,0.00035296800000000005,36.9304,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs6_sqmonkey.marg.frame1,1909131006_L1PA5.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA5,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
20180,Q#805 - >seq7452,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20181,Q#805 - >seq7452,superfamily,335182,154,251,4.06635e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20182,Q#805 - >seq7452,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20183,Q#805 - >seq7452,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20184,Q#805 - >seq7452,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20185,Q#805 - >seq7452,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20186,Q#805 - >seq7452,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20187,Q#805 - >seq7452,superfamily,340204,109,151,1.0835700000000001e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20188,Q#805 - >seq7452,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,pars,CompleteHit
20189,Q#805 - >seq7452,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20190,Q#805 - >seq7452,superfamily,222878,28,195,0.000193827,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20191,Q#805 - >seq7452,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20192,Q#805 - >seq7452,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20193,Q#805 - >seq7452,superfamily,274008,48,161,0.000392775,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20194,Q#805 - >seq7452,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20195,Q#805 - >seq7452,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20196,Q#805 - >seq7452,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20197,Q#805 - >seq7452,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20198,Q#805 - >seq7452,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20199,Q#805 - >seq7452,superfamily,235175,51,154,0.000974057,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20200,Q#805 - >seq7452,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20201,Q#805 - >seq7452,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20202,Q#805 - >seq7452,superfamily,313022,4,151,0.00700167,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20203,Q#805 - >seq7452,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.pars.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20204,Q#807 - >seq7454,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20205,Q#807 - >seq7454,superfamily,335182,154,251,4.06635e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20206,Q#807 - >seq7454,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20207,Q#807 - >seq7454,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20208,Q#807 - >seq7454,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20209,Q#807 - >seq7454,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20210,Q#807 - >seq7454,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20211,Q#807 - >seq7454,superfamily,340204,109,151,1.0835700000000001e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20212,Q#807 - >seq7454,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs4_gibbon,marg,CompleteHit
20213,Q#807 - >seq7454,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20214,Q#807 - >seq7454,superfamily,222878,28,195,0.000193827,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20215,Q#807 - >seq7454,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20216,Q#807 - >seq7454,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20217,Q#807 - >seq7454,superfamily,274008,48,161,0.000392775,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20218,Q#807 - >seq7454,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20219,Q#807 - >seq7454,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20220,Q#807 - >seq7454,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20221,Q#807 - >seq7454,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20222,Q#807 - >seq7454,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20223,Q#807 - >seq7454,superfamily,235175,51,154,0.000974057,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20224,Q#807 - >seq7454,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20225,Q#807 - >seq7454,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20226,Q#807 - >seq7454,superfamily,313022,4,151,0.00700167,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20227,Q#807 - >seq7454,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs4_gibbon.marg.frame3,1909131006_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20228,Q#809 - >seq7456,non-specific,335182,153,250,1.2107e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20229,Q#809 - >seq7456,superfamily,335182,153,250,1.2107e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20230,Q#809 - >seq7456,non-specific,335182,153,250,1.2107e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20231,Q#809 - >seq7456,non-specific,340205,253,317,8.58445e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20232,Q#809 - >seq7456,superfamily,340205,253,317,8.58445e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20233,Q#809 - >seq7456,non-specific,340205,253,317,8.58445e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,pars,CompleteHit
20234,Q#809 - >seq7456,non-specific,340204,108,150,9.49527e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,pars,CompleteHit
20235,Q#809 - >seq7456,superfamily,340204,108,150,9.49527e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,pars,CompleteHit
20236,Q#809 - >seq7456,non-specific,340204,108,150,9.49527e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,pars,CompleteHit
20237,Q#809 - >seq7456,non-specific,274008,35,160,4.2031000000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20238,Q#809 - >seq7456,superfamily,274008,35,160,4.2031000000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20239,Q#809 - >seq7456,non-specific,274008,35,160,4.2031000000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20240,Q#809 - >seq7456,non-specific,235175,50,153,0.000683087,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20241,Q#809 - >seq7456,superfamily,235175,50,153,0.000683087,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20242,Q#809 - >seq7456,non-specific,235175,50,153,0.000683087,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20243,Q#809 - >seq7456,non-specific,235175,42,139,0.00118434,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20244,Q#809 - >seq7456,non-specific,235175,42,139,0.00118434,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20245,Q#809 - >seq7456,non-specific,274008,21,147,0.00199411,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20246,Q#809 - >seq7456,non-specific,274008,21,147,0.00199411,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20247,Q#809 - >seq7456,non-specific,313022,4,150,0.00288149,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,pars,N-TerminusTruncated
20248,Q#809 - >seq7456,superfamily,313022,4,150,0.00288149,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,pars,N-TerminusTruncated
20249,Q#809 - >seq7456,non-specific,313022,4,150,0.00288149,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,pars,N-TerminusTruncated
20250,Q#809 - >seq7456,non-specific,274009,30,201,0.00867175,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20251,Q#809 - >seq7456,superfamily,274009,30,201,0.00867175,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20252,Q#809 - >seq7456,non-specific,274009,30,201,0.00867175,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,pars,BothTerminiTruncated
20253,Q#809 - >seq7456,non-specific,335336,55,119,0.009264,36.2102,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,pars,C-TerminusTruncated
20254,Q#809 - >seq7456,superfamily,355101,55,119,0.009264,36.2102,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,pars,C-TerminusTruncated
20255,Q#809 - >seq7456,non-specific,335336,55,119,0.009264,36.2102,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.pars.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,pars,C-TerminusTruncated
20256,Q#812 - >seq7459,non-specific,335182,153,250,1.2107e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20257,Q#812 - >seq7459,superfamily,335182,153,250,1.2107e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20258,Q#812 - >seq7459,non-specific,335182,153,250,1.2107e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20259,Q#812 - >seq7459,non-specific,340205,253,317,8.58445e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20260,Q#812 - >seq7459,superfamily,340205,253,317,8.58445e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20261,Q#812 - >seq7459,non-specific,340205,253,317,8.58445e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA4,ORF1,hs0_human,marg,CompleteHit
20262,Q#812 - >seq7459,non-specific,340204,108,150,9.49527e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,marg,CompleteHit
20263,Q#812 - >seq7459,superfamily,340204,108,150,9.49527e-12,58.9584,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,marg,CompleteHit
20264,Q#812 - >seq7459,non-specific,340204,108,150,9.49527e-12,58.9584,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA4,ORF1,hs0_human,marg,CompleteHit
20265,Q#812 - >seq7459,non-specific,274008,35,160,4.2031000000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20266,Q#812 - >seq7459,superfamily,274008,35,160,4.2031000000000005e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20267,Q#812 - >seq7459,non-specific,274008,35,160,4.2031000000000005e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20268,Q#812 - >seq7459,non-specific,235175,50,153,0.000683087,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20269,Q#812 - >seq7459,superfamily,235175,50,153,0.000683087,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20270,Q#812 - >seq7459,non-specific,235175,50,153,0.000683087,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20271,Q#812 - >seq7459,non-specific,235175,42,139,0.00118434,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20272,Q#812 - >seq7459,non-specific,235175,42,139,0.00118434,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20273,Q#812 - >seq7459,non-specific,274008,21,147,0.00199411,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20274,Q#812 - >seq7459,non-specific,274008,21,147,0.00199411,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20275,Q#812 - >seq7459,non-specific,313022,4,150,0.00288149,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,marg,N-TerminusTruncated
20276,Q#812 - >seq7459,superfamily,313022,4,150,0.00288149,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,marg,N-TerminusTruncated
20277,Q#812 - >seq7459,non-specific,313022,4,150,0.00288149,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA4,ORF1,hs0_human,marg,N-TerminusTruncated
20278,Q#812 - >seq7459,non-specific,274009,30,201,0.00867175,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20279,Q#812 - >seq7459,superfamily,274009,30,201,0.00867175,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20280,Q#812 - >seq7459,non-specific,274009,30,201,0.00867175,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF1,hs0_human,marg,BothTerminiTruncated
20281,Q#812 - >seq7459,non-specific,335336,55,119,0.009264,36.2102,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,marg,C-TerminusTruncated
20282,Q#812 - >seq7459,superfamily,355101,55,119,0.009264,36.2102,cl23943,PCRF superfamily,C, - ,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,marg,C-TerminusTruncated
20283,Q#812 - >seq7459,non-specific,335336,55,119,0.009264,36.2102,pfam03462,PCRF,C,cl23943,PCRF domain; This domain is found in peptide chain release factors.,L1PA4.ORF1.hs0_human.marg.frame3,1909131006_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA4,ORF1,hs0_human,marg,C-TerminusTruncated
20284,Q#815 - >seq7462,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20285,Q#815 - >seq7462,superfamily,335182,154,251,4.06635e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20286,Q#815 - >seq7462,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20287,Q#815 - >seq7462,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20288,Q#815 - >seq7462,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20289,Q#815 - >seq7462,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20290,Q#815 - >seq7462,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20291,Q#815 - >seq7462,superfamily,340204,109,151,1.0835700000000001e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20292,Q#815 - >seq7462,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,pars,CompleteHit
20293,Q#815 - >seq7462,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20294,Q#815 - >seq7462,superfamily,222878,28,195,0.000193827,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20295,Q#815 - >seq7462,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20296,Q#815 - >seq7462,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20297,Q#815 - >seq7462,superfamily,274008,48,161,0.000392775,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20298,Q#815 - >seq7462,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20299,Q#815 - >seq7462,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20300,Q#815 - >seq7462,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20301,Q#815 - >seq7462,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20302,Q#815 - >seq7462,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20303,Q#815 - >seq7462,superfamily,235175,51,154,0.000974057,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20304,Q#815 - >seq7462,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,pars,BothTerminiTruncated
20305,Q#815 - >seq7462,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,pars,N-TerminusTruncated
20306,Q#815 - >seq7462,superfamily,313022,4,151,0.00700167,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,pars,N-TerminusTruncated
20307,Q#815 - >seq7462,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.pars.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,pars,N-TerminusTruncated
20308,Q#818 - >seq7465,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20309,Q#818 - >seq7465,superfamily,335182,154,251,4.06635e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20310,Q#818 - >seq7465,non-specific,335182,154,251,4.06635e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20311,Q#818 - >seq7465,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20312,Q#818 - >seq7465,superfamily,340205,254,318,1.2429299999999998e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20313,Q#818 - >seq7465,non-specific,340205,254,318,1.2429299999999998e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20314,Q#818 - >seq7465,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20315,Q#818 - >seq7465,superfamily,340204,109,151,1.0835700000000001e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20316,Q#818 - >seq7465,non-specific,340204,109,151,1.0835700000000001e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs3_orang,marg,CompleteHit
20317,Q#818 - >seq7465,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20318,Q#818 - >seq7465,superfamily,222878,28,195,0.000193827,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20319,Q#818 - >seq7465,non-specific,222878,28,195,0.000193827,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20320,Q#818 - >seq7465,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20321,Q#818 - >seq7465,superfamily,274008,48,161,0.000392775,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20322,Q#818 - >seq7465,non-specific,274008,48,161,0.000392775,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20323,Q#818 - >seq7465,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20324,Q#818 - >seq7465,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20325,Q#818 - >seq7465,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20326,Q#818 - >seq7465,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20327,Q#818 - >seq7465,superfamily,235175,51,154,0.000974057,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20328,Q#818 - >seq7465,non-specific,235175,51,154,0.000974057,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs3_orang,marg,BothTerminiTruncated
20329,Q#818 - >seq7465,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,marg,N-TerminusTruncated
20330,Q#818 - >seq7465,superfamily,313022,4,151,0.00700167,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,marg,N-TerminusTruncated
20331,Q#818 - >seq7465,non-specific,313022,4,151,0.00700167,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs3_orang.marg.frame3,1909131006_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs3_orang,marg,N-TerminusTruncated
20332,Q#823 - >seq7470,non-specific,335182,157,254,1.0747899999999998e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20333,Q#823 - >seq7470,superfamily,335182,157,254,1.0747899999999998e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20334,Q#823 - >seq7470,non-specific,340205,257,321,1.5371899999999999e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20335,Q#823 - >seq7470,superfamily,340205,257,321,1.5371899999999999e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20336,Q#823 - >seq7470,non-specific,340204,112,154,1.0035700000000002e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20337,Q#823 - >seq7470,superfamily,340204,112,154,1.0035700000000002e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs2_gorilla,marg,CompleteHit
20338,Q#823 - >seq7470,non-specific,274009,47,151,0.000326506,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20339,Q#823 - >seq7470,superfamily,274009,47,151,0.000326506,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20340,Q#823 - >seq7470,non-specific,274008,47,212,0.00548911,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20341,Q#823 - >seq7470,superfamily,274008,47,212,0.00548911,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20342,Q#823 - >seq7470,non-specific,235600,51,143,0.00719764,37.9848,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA6,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20343,Q#823 - >seq7470,superfamily,235600,51,143,0.00719764,37.9848,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA6.ORF1.hs2_gorilla.marg.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA6,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20344,Q#826 - >seq7473,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20345,Q#826 - >seq7473,superfamily,335182,157,254,1.51695e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20346,Q#826 - >seq7473,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20347,Q#826 - >seq7473,superfamily,340205,257,321,1.8407899999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20348,Q#826 - >seq7473,non-specific,340204,112,154,3.683019999999999e-10,54.336000000000006,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20349,Q#826 - >seq7473,superfamily,340204,112,154,3.683019999999999e-10,54.336000000000006,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs3_orang,pars,CompleteHit
20350,Q#826 - >seq7473,non-specific,274009,47,151,0.000409621,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20351,Q#826 - >seq7473,superfamily,274009,47,151,0.000409621,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20352,Q#826 - >seq7473,non-specific,336322,36,154,0.00241835,39.4226,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20353,Q#826 - >seq7473,superfamily,336322,36,154,0.00241835,39.4226,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20354,Q#826 - >seq7473,non-specific,274008,47,212,0.00259836,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20355,Q#826 - >seq7473,superfamily,274008,47,212,0.00259836,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,pars,BothTerminiTruncated
20356,Q#826 - >seq7473,non-specific,313022,71,154,0.00686198,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA6,ORF1,hs3_orang,pars,N-TerminusTruncated
20357,Q#826 - >seq7473,superfamily,313022,71,154,0.00686198,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs3_orang.pars.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA6,ORF1,hs3_orang,pars,N-TerminusTruncated
20358,Q#829 - >seq7476,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20359,Q#829 - >seq7476,superfamily,335182,157,254,1.51695e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20360,Q#829 - >seq7476,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20361,Q#829 - >seq7476,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20362,Q#829 - >seq7476,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20363,Q#829 - >seq7476,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20364,Q#829 - >seq7476,non-specific,340204,112,154,1.23434e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20365,Q#829 - >seq7476,superfamily,340204,112,154,1.23434e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20366,Q#829 - >seq7476,non-specific,340204,112,154,1.23434e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,pars,CompleteHit
20367,Q#829 - >seq7476,non-specific,274009,47,151,0.000190067,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20368,Q#829 - >seq7476,superfamily,274009,47,151,0.000190067,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20369,Q#829 - >seq7476,non-specific,274009,47,151,0.000190067,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20370,Q#829 - >seq7476,non-specific,313022,4,154,0.00556453,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20371,Q#829 - >seq7476,superfamily,313022,4,154,0.00556453,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20372,Q#829 - >seq7476,non-specific,313022,4,154,0.00556453,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,pars,N-TerminusTruncated
20373,Q#829 - >seq7476,non-specific,274008,47,212,0.00825831,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20374,Q#829 - >seq7476,superfamily,274008,47,212,0.00825831,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20375,Q#829 - >seq7476,non-specific,274008,47,212,0.00825831,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.pars.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,pars,BothTerminiTruncated
20376,Q#834 - >seq7481,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20377,Q#834 - >seq7481,superfamily,335182,157,254,1.51695e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20378,Q#834 - >seq7481,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20379,Q#834 - >seq7481,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20380,Q#834 - >seq7481,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20381,Q#834 - >seq7481,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20382,Q#834 - >seq7481,non-specific,340204,112,154,1.23434e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20383,Q#834 - >seq7481,superfamily,340204,112,154,1.23434e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20384,Q#834 - >seq7481,non-specific,340204,112,154,1.23434e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs4_gibbon,marg,CompleteHit
20385,Q#834 - >seq7481,non-specific,274009,47,151,0.000190067,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20386,Q#834 - >seq7481,superfamily,274009,47,151,0.000190067,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20387,Q#834 - >seq7481,non-specific,274009,47,151,0.000190067,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20388,Q#834 - >seq7481,non-specific,313022,4,154,0.00556453,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20389,Q#834 - >seq7481,superfamily,313022,4,154,0.00556453,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20390,Q#834 - >seq7481,non-specific,313022,4,154,0.00556453,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA6,ORF1,hs4_gibbon,marg,N-TerminusTruncated
20391,Q#834 - >seq7481,non-specific,274008,47,212,0.00825831,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20392,Q#834 - >seq7481,superfamily,274008,47,212,0.00825831,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20393,Q#834 - >seq7481,non-specific,274008,47,212,0.00825831,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs4_gibbon.marg.frame3,1909131010_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs4_gibbon,marg,BothTerminiTruncated
20394,Q#836 - >seq7483,non-specific,335182,157,254,1.51695e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20395,Q#836 - >seq7483,superfamily,335182,157,254,1.51695e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20396,Q#836 - >seq7483,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20397,Q#836 - >seq7483,superfamily,340205,257,321,1.8407899999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20398,Q#836 - >seq7483,non-specific,340204,112,154,3.683019999999999e-10,54.336000000000006,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20399,Q#836 - >seq7483,superfamily,340204,112,154,3.683019999999999e-10,54.336000000000006,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs3_orang,marg,CompleteHit
20400,Q#836 - >seq7483,non-specific,274009,47,151,0.000409621,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20401,Q#836 - >seq7483,superfamily,274009,47,151,0.000409621,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20402,Q#836 - >seq7483,non-specific,336322,36,154,0.00241835,39.4226,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20403,Q#836 - >seq7483,superfamily,336322,36,154,0.00241835,39.4226,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20404,Q#836 - >seq7483,non-specific,274008,47,212,0.00259836,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20405,Q#836 - >seq7483,superfamily,274008,47,212,0.00259836,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs3_orang,marg,BothTerminiTruncated
20406,Q#836 - >seq7483,non-specific,313022,71,154,0.00686198,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA6,ORF1,hs3_orang,marg,N-TerminusTruncated
20407,Q#836 - >seq7483,superfamily,313022,71,154,0.00686198,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA6.ORF1.hs3_orang.marg.frame3,1909131010_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA6,ORF1,hs3_orang,marg,N-TerminusTruncated
20408,Q#842 - >seq7489,non-specific,335182,153,250,2.8353900000000004e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,pars,CompleteHit
20409,Q#842 - >seq7489,superfamily,335182,153,250,2.8353900000000004e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,pars,CompleteHit
20410,Q#842 - >seq7489,non-specific,340205,253,317,1.08386e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,pars,CompleteHit
20411,Q#842 - >seq7489,superfamily,340205,253,317,1.08386e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,pars,CompleteHit
20412,Q#842 - >seq7489,non-specific,340204,108,150,8.94712e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs0_human,pars,CompleteHit
20413,Q#842 - >seq7489,superfamily,340204,108,150,8.94712e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs0_human,pars,CompleteHit
20414,Q#842 - >seq7489,non-specific,222878,28,194,0.000153331,43.0793,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20415,Q#842 - >seq7489,superfamily,222878,28,194,0.000153331,43.0793,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20416,Q#842 - >seq7489,non-specific,274008,35,160,0.00024589,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20417,Q#842 - >seq7489,superfamily,274008,35,160,0.00024589,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20418,Q#842 - >seq7489,non-specific,274009,50,147,0.000485394,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20419,Q#842 - >seq7489,superfamily,274009,50,147,0.000485394,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20420,Q#842 - >seq7489,non-specific,235175,50,153,0.000943763,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20421,Q#842 - >seq7489,superfamily,235175,50,153,0.000943763,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20422,Q#842 - >seq7489,non-specific,313022,4,150,0.00491177,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs0_human,pars,N-TerminusTruncated
20423,Q#842 - >seq7489,superfamily,313022,4,150,0.00491177,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs0_human,pars,N-TerminusTruncated
20424,Q#842 - >seq7489,non-specific,274008,42,208,0.00680223,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20425,Q#842 - >seq7489,non-specific,235175,42,139,0.00683771,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.pars.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,pars,BothTerminiTruncated
20426,Q#844 - >seq7491,non-specific,335182,157,254,1.0747899999999998e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20427,Q#844 - >seq7491,superfamily,335182,157,254,1.0747899999999998e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20428,Q#844 - >seq7491,non-specific,340205,257,321,1.5371899999999999e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20429,Q#844 - >seq7491,superfamily,340205,257,321,1.5371899999999999e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20430,Q#844 - >seq7491,non-specific,340204,112,154,1.0035700000000002e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20431,Q#844 - >seq7491,superfamily,340204,112,154,1.0035700000000002e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs2_gorilla,pars,CompleteHit
20432,Q#844 - >seq7491,non-specific,274009,47,151,0.000326506,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20433,Q#844 - >seq7491,superfamily,274009,47,151,0.000326506,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20434,Q#844 - >seq7491,non-specific,274008,47,212,0.00548911,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20435,Q#844 - >seq7491,superfamily,274008,47,212,0.00548911,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20436,Q#844 - >seq7491,non-specific,235600,51,143,0.00719764,37.9848,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA6,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20437,Q#844 - >seq7491,superfamily,235600,51,143,0.00719764,37.9848,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA6.ORF1.hs2_gorilla.pars.frame3,1909131010_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA6,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20438,Q#845 - >seq7492,non-specific,335182,153,250,2.8353900000000004e-48,157.465,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,marg,CompleteHit
20439,Q#845 - >seq7492,superfamily,335182,153,250,2.8353900000000004e-48,157.465,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,marg,CompleteHit
20440,Q#845 - >seq7492,non-specific,340205,253,317,1.08386e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,marg,CompleteHit
20441,Q#845 - >seq7492,superfamily,340205,253,317,1.08386e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs0_human,marg,CompleteHit
20442,Q#845 - >seq7492,non-specific,340204,108,150,8.94712e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs0_human,marg,CompleteHit
20443,Q#845 - >seq7492,superfamily,340204,108,150,8.94712e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs0_human,marg,CompleteHit
20444,Q#845 - >seq7492,non-specific,222878,28,194,0.000153331,43.0793,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20445,Q#845 - >seq7492,superfamily,222878,28,194,0.000153331,43.0793,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20446,Q#845 - >seq7492,non-specific,274008,35,160,0.00024589,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20447,Q#845 - >seq7492,superfamily,274008,35,160,0.00024589,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20448,Q#845 - >seq7492,non-specific,274009,50,147,0.000485394,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20449,Q#845 - >seq7492,superfamily,274009,50,147,0.000485394,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20450,Q#845 - >seq7492,non-specific,235175,50,153,0.000943763,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20451,Q#845 - >seq7492,superfamily,235175,50,153,0.000943763,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20452,Q#845 - >seq7492,non-specific,313022,4,150,0.00491177,38.291,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs0_human,marg,N-TerminusTruncated
20453,Q#845 - >seq7492,superfamily,313022,4,150,0.00491177,38.291,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs0_human,marg,N-TerminusTruncated
20454,Q#845 - >seq7492,non-specific,274008,42,208,0.00680223,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20455,Q#845 - >seq7492,non-specific,235175,42,139,0.00683771,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs0_human.marg.frame3,1909131010_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs0_human,marg,BothTerminiTruncated
20456,Q#847 - >seq7494,specific,340205,239,303,8.292819999999999e-36,123.6,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame2,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA6,ORF1,hs1_chimp,pars,CompleteHit
20457,Q#847 - >seq7494,superfamily,340205,239,303,8.292819999999999e-36,123.6,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame2,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA6,ORF1,hs1_chimp,pars,CompleteHit
20458,Q#847 - >seq7494,non-specific,335182,194,236,7.385189999999999e-18,77.3431,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame2,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA6,ORF1,hs1_chimp,pars,N-TerminusTruncated
20459,Q#847 - >seq7494,superfamily,335182,194,236,7.385189999999999e-18,77.3431,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame2,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PA6,ORF1,hs1_chimp,pars,N-TerminusTruncated
20460,Q#848 - >seq7495,non-specific,335182,156,211,3.38061e-23,91.5954,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,pars,C-TerminusTruncated
20461,Q#848 - >seq7495,superfamily,335182,156,211,3.38061e-23,91.5954,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,pars,C-TerminusTruncated
20462,Q#848 - >seq7495,non-specific,340204,113,153,2.94052e-11,57.4176,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs1_chimp,pars,CompleteHit
20463,Q#848 - >seq7495,superfamily,340204,113,153,2.94052e-11,57.4176,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs1_chimp,pars,CompleteHit
20464,Q#848 - >seq7495,non-specific,336322,36,153,0.00374756,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs1_chimp,pars,BothTerminiTruncated
20465,Q#848 - >seq7495,superfamily,336322,36,153,0.00374756,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF1,hs1_chimp,pars,BothTerminiTruncated
20466,Q#848 - >seq7495,non-specific,225293,109,195,0.00397872,36.9229,COG2445,YutE,C,cl01031,"Uncharacterized conserved protein YutE, UPF0331/DUF86 family  [Function unknown]; Uncharacterized conserved protein [Function unknown].",L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA6,ORF1,hs1_chimp,pars,C-TerminusTruncated
20467,Q#848 - >seq7495,superfamily,321310,109,195,0.00397872,36.9229,cl01031,DUF86 superfamily,C, - ,Protein of unknown function DUF86; The function of members of this family is unknown.,L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA6,ORF1,hs1_chimp,pars,C-TerminusTruncated
20468,Q#848 - >seq7495,non-specific,274009,47,150,0.00533698,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs1_chimp,pars,BothTerminiTruncated
20469,Q#848 - >seq7495,superfamily,274009,47,150,0.00533698,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs1_chimp.pars.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs1_chimp,pars,BothTerminiTruncated
20470,Q#850 - >seq7497,non-specific,335182,156,253,5.849679999999999e-49,159.005,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20471,Q#850 - >seq7497,superfamily,335182,156,253,5.849679999999999e-49,159.005,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20472,Q#850 - >seq7497,non-specific,340205,256,320,1.4280299999999998e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20473,Q#850 - >seq7497,superfamily,340205,256,320,1.4280299999999998e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20474,Q#850 - >seq7497,non-specific,340204,113,153,1.7703999999999996e-10,55.4916,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20475,Q#850 - >seq7497,superfamily,340204,113,153,1.7703999999999996e-10,55.4916,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs1_chimp.marg.frame3,1909131010_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs1_chimp,marg,CompleteHit
20476,Q#854 - >seq7501,non-specific,335182,157,254,5.88041e-49,159.005,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20477,Q#854 - >seq7501,superfamily,335182,157,254,5.88041e-49,159.005,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20478,Q#854 - >seq7501,non-specific,335182,157,254,5.88041e-49,159.005,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20479,Q#854 - >seq7501,non-specific,340205,257,321,1.67327e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20480,Q#854 - >seq7501,superfamily,340205,257,321,1.67327e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20481,Q#854 - >seq7501,non-specific,340205,257,321,1.67327e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,marg,CompleteHit
20482,Q#854 - >seq7501,non-specific,340204,112,154,6.89989e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,marg,CompleteHit
20483,Q#854 - >seq7501,superfamily,340204,112,154,6.89989e-11,56.6472,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,marg,CompleteHit
20484,Q#854 - >seq7501,non-specific,340204,112,154,6.89989e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,marg,CompleteHit
20485,Q#854 - >seq7501,non-specific,274009,47,151,0.000144993,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20486,Q#854 - >seq7501,superfamily,274009,47,151,0.000144993,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20487,Q#854 - >seq7501,non-specific,274009,47,151,0.000144993,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20488,Q#854 - >seq7501,non-specific,274008,47,212,0.00367965,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20489,Q#854 - >seq7501,superfamily,274008,47,212,0.00367965,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20490,Q#854 - >seq7501,non-specific,274008,47,212,0.00367965,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20491,Q#854 - >seq7501,non-specific,235175,54,157,0.00971159,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20492,Q#854 - >seq7501,superfamily,235175,54,157,0.00971159,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20493,Q#854 - >seq7501,non-specific,235175,54,157,0.00971159,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20494,Q#854 - >seq7501,non-specific,274008,49,164,0.00974044,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20495,Q#854 - >seq7501,non-specific,274008,49,164,0.00974044,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.marg.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,marg,BothTerminiTruncated
20496,Q#857 - >seq7504,non-specific,335182,157,254,5.88041e-49,159.005,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20497,Q#857 - >seq7504,superfamily,335182,157,254,5.88041e-49,159.005,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20498,Q#857 - >seq7504,non-specific,335182,157,254,5.88041e-49,159.005,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20499,Q#857 - >seq7504,non-specific,340205,257,321,1.67327e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20500,Q#857 - >seq7504,superfamily,340205,257,321,1.67327e-33,118.208,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20501,Q#857 - >seq7504,non-specific,340205,257,321,1.67327e-33,118.208,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs0_human,pars,CompleteHit
20502,Q#857 - >seq7504,non-specific,340204,112,154,6.89989e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,pars,CompleteHit
20503,Q#857 - >seq7504,superfamily,340204,112,154,6.89989e-11,56.6472,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,pars,CompleteHit
20504,Q#857 - >seq7504,non-specific,340204,112,154,6.89989e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs0_human,pars,CompleteHit
20505,Q#857 - >seq7504,non-specific,274009,47,151,0.000144993,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20506,Q#857 - >seq7504,superfamily,274009,47,151,0.000144993,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20507,Q#857 - >seq7504,non-specific,274009,47,151,0.000144993,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20508,Q#857 - >seq7504,non-specific,274008,47,212,0.00367965,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20509,Q#857 - >seq7504,superfamily,274008,47,212,0.00367965,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20510,Q#857 - >seq7504,non-specific,274008,47,212,0.00367965,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20511,Q#857 - >seq7504,non-specific,235175,54,157,0.00971159,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20512,Q#857 - >seq7504,superfamily,235175,54,157,0.00971159,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20513,Q#857 - >seq7504,non-specific,235175,54,157,0.00971159,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20514,Q#857 - >seq7504,non-specific,274008,49,164,0.00974044,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20515,Q#857 - >seq7504,non-specific,274008,49,164,0.00974044,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs0_human.pars.frame3,1909131012_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs0_human,pars,BothTerminiTruncated
20516,Q#861 - >seq7508,non-specific,335182,157,254,1.0864299999999999e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20517,Q#861 - >seq7508,superfamily,335182,157,254,1.0864299999999999e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20518,Q#861 - >seq7508,non-specific,335182,157,254,1.0864299999999999e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20519,Q#861 - >seq7508,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20520,Q#861 - >seq7508,superfamily,340205,257,321,1.8407899999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20521,Q#861 - >seq7508,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20522,Q#861 - >seq7508,non-specific,340204,112,154,5.83483e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20523,Q#861 - >seq7508,superfamily,340204,112,154,5.83483e-11,56.6472,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20524,Q#861 - >seq7508,non-specific,340204,112,154,5.83483e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,pars,CompleteHit
20525,Q#861 - >seq7508,non-specific,274009,47,151,0.000580562,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20526,Q#861 - >seq7508,superfamily,274009,47,151,0.000580562,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20527,Q#861 - >seq7508,non-specific,274009,47,151,0.000580562,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20528,Q#861 - >seq7508,non-specific,274008,47,212,0.00700149,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20529,Q#861 - >seq7508,superfamily,274008,47,212,0.00700149,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20530,Q#861 - >seq7508,non-specific,274008,47,212,0.00700149,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.pars.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
20531,Q#864 - >seq7511,non-specific,335182,157,254,1.0864299999999999e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20532,Q#864 - >seq7511,superfamily,335182,157,254,1.0864299999999999e-48,158.62,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20533,Q#864 - >seq7511,non-specific,335182,157,254,1.0864299999999999e-48,158.62,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20534,Q#864 - >seq7511,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20535,Q#864 - >seq7511,superfamily,340205,257,321,1.8407899999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20536,Q#864 - >seq7511,non-specific,340205,257,321,1.8407899999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20537,Q#864 - >seq7511,non-specific,340204,112,154,5.83483e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20538,Q#864 - >seq7511,superfamily,340204,112,154,5.83483e-11,56.6472,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20539,Q#864 - >seq7511,non-specific,340204,112,154,5.83483e-11,56.6472,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA6,ORF1,hs5_gmonkey,marg,CompleteHit
20540,Q#864 - >seq7511,non-specific,274009,47,151,0.000580562,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20541,Q#864 - >seq7511,superfamily,274009,47,151,0.000580562,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20542,Q#864 - >seq7511,non-specific,274009,47,151,0.000580562,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20543,Q#864 - >seq7511,non-specific,274008,47,212,0.00700149,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20544,Q#864 - >seq7511,superfamily,274008,47,212,0.00700149,38.1139,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20545,Q#864 - >seq7511,non-specific,274008,47,212,0.00700149,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF1.hs5_gmonkey.marg.frame3,1909131012_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
20546,Q#866 - >seq7513,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20547,Q#866 - >seq7513,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20548,Q#866 - >seq7513,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20549,Q#866 - >seq7513,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20550,Q#866 - >seq7513,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20551,Q#866 - >seq7513,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20552,Q#866 - >seq7513,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20553,Q#866 - >seq7513,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20554,Q#866 - >seq7513,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20555,Q#866 - >seq7513,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20556,Q#866 - >seq7513,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20557,Q#866 - >seq7513,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20558,Q#866 - >seq7513,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20559,Q#866 - >seq7513,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20560,Q#866 - >seq7513,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,marg,CompleteHit
20561,Q#866 - >seq7513,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20562,Q#866 - >seq7513,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20563,Q#866 - >seq7513,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20564,Q#866 - >seq7513,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20565,Q#866 - >seq7513,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20566,Q#866 - >seq7513,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20567,Q#866 - >seq7513,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20568,Q#866 - >seq7513,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20569,Q#866 - >seq7513,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20570,Q#866 - >seq7513,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20571,Q#866 - >seq7513,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20572,Q#866 - >seq7513,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20573,Q#866 - >seq7513,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20574,Q#866 - >seq7513,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20575,Q#866 - >seq7513,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20576,Q#866 - >seq7513,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20577,Q#866 - >seq7513,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20578,Q#866 - >seq7513,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20579,Q#866 - >seq7513,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20580,Q#866 - >seq7513,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20581,Q#866 - >seq7513,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20582,Q#866 - >seq7513,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20583,Q#866 - >seq7513,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20584,Q#866 - >seq7513,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20585,Q#866 - >seq7513,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20586,Q#866 - >seq7513,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20587,Q#866 - >seq7513,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20588,Q#866 - >seq7513,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20589,Q#866 - >seq7513,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20590,Q#866 - >seq7513,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20591,Q#866 - >seq7513,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20592,Q#866 - >seq7513,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20593,Q#866 - >seq7513,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20594,Q#866 - >seq7513,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20595,Q#866 - >seq7513,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20596,Q#866 - >seq7513,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20597,Q#866 - >seq7513,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20598,Q#866 - >seq7513,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20599,Q#866 - >seq7513,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20600,Q#866 - >seq7513,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20601,Q#866 - >seq7513,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20602,Q#866 - >seq7513,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20603,Q#866 - >seq7513,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20604,Q#866 - >seq7513,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20605,Q#866 - >seq7513,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20606,Q#866 - >seq7513,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20607,Q#866 - >seq7513,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20608,Q#866 - >seq7513,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20609,Q#866 - >seq7513,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20610,Q#866 - >seq7513,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20611,Q#866 - >seq7513,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20612,Q#866 - >seq7513,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20613,Q#866 - >seq7513,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20614,Q#866 - >seq7513,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20615,Q#866 - >seq7513,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20616,Q#866 - >seq7513,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20617,Q#866 - >seq7513,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20618,Q#866 - >seq7513,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20619,Q#866 - >seq7513,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20620,Q#866 - >seq7513,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20621,Q#866 - >seq7513,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20622,Q#866 - >seq7513,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20623,Q#866 - >seq7513,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20624,Q#866 - >seq7513,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20625,Q#866 - >seq7513,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20626,Q#866 - >seq7513,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20627,Q#866 - >seq7513,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20628,Q#866 - >seq7513,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20629,Q#866 - >seq7513,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20630,Q#866 - >seq7513,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20631,Q#866 - >seq7513,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20632,Q#866 - >seq7513,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20633,Q#866 - >seq7513,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20634,Q#866 - >seq7513,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20635,Q#866 - >seq7513,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20636,Q#866 - >seq7513,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,N-TerminusTruncated
20637,Q#866 - >seq7513,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20638,Q#866 - >seq7513,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20639,Q#866 - >seq7513,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20640,Q#866 - >seq7513,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20641,Q#866 - >seq7513,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20642,Q#866 - >seq7513,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20643,Q#866 - >seq7513,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20644,Q#866 - >seq7513,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20645,Q#866 - >seq7513,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20646,Q#866 - >seq7513,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20647,Q#866 - >seq7513,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20648,Q#866 - >seq7513,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20649,Q#866 - >seq7513,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20650,Q#866 - >seq7513,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20651,Q#866 - >seq7513,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20652,Q#866 - >seq7513,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20653,Q#866 - >seq7513,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20654,Q#866 - >seq7513,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20655,Q#866 - >seq7513,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20656,Q#866 - >seq7513,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20657,Q#866 - >seq7513,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20658,Q#866 - >seq7513,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20659,Q#866 - >seq7513,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,marg,C-TerminusTruncated
20660,Q#866 - >seq7513,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20661,Q#866 - >seq7513,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20662,Q#866 - >seq7513,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20663,Q#866 - >seq7513,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20664,Q#866 - >seq7513,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.marg.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,marg,BothTerminiTruncated
20665,Q#869 - >seq7516,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20666,Q#869 - >seq7516,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20667,Q#869 - >seq7516,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20668,Q#869 - >seq7516,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20669,Q#869 - >seq7516,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20670,Q#869 - >seq7516,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20671,Q#869 - >seq7516,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20672,Q#869 - >seq7516,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20673,Q#869 - >seq7516,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20674,Q#869 - >seq7516,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20675,Q#869 - >seq7516,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20676,Q#869 - >seq7516,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20677,Q#869 - >seq7516,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20678,Q#869 - >seq7516,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20679,Q#869 - >seq7516,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs3_orang,pars,CompleteHit
20680,Q#869 - >seq7516,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20681,Q#869 - >seq7516,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20682,Q#869 - >seq7516,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20683,Q#869 - >seq7516,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20684,Q#869 - >seq7516,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20685,Q#869 - >seq7516,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20686,Q#869 - >seq7516,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20687,Q#869 - >seq7516,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20688,Q#869 - >seq7516,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20689,Q#869 - >seq7516,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20690,Q#869 - >seq7516,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20691,Q#869 - >seq7516,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20692,Q#869 - >seq7516,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20693,Q#869 - >seq7516,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20694,Q#869 - >seq7516,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20695,Q#869 - >seq7516,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20696,Q#869 - >seq7516,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20697,Q#869 - >seq7516,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20698,Q#869 - >seq7516,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20699,Q#869 - >seq7516,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20700,Q#869 - >seq7516,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20701,Q#869 - >seq7516,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20702,Q#869 - >seq7516,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20703,Q#869 - >seq7516,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20704,Q#869 - >seq7516,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20705,Q#869 - >seq7516,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20706,Q#869 - >seq7516,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20707,Q#869 - >seq7516,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20708,Q#869 - >seq7516,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20709,Q#869 - >seq7516,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20710,Q#869 - >seq7516,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20711,Q#869 - >seq7516,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20712,Q#869 - >seq7516,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20713,Q#869 - >seq7516,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20714,Q#869 - >seq7516,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20715,Q#869 - >seq7516,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20716,Q#869 - >seq7516,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20717,Q#869 - >seq7516,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20718,Q#869 - >seq7516,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20719,Q#869 - >seq7516,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20720,Q#869 - >seq7516,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20721,Q#869 - >seq7516,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20722,Q#869 - >seq7516,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20723,Q#869 - >seq7516,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20724,Q#869 - >seq7516,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20725,Q#869 - >seq7516,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20726,Q#869 - >seq7516,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20727,Q#869 - >seq7516,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20728,Q#869 - >seq7516,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20729,Q#869 - >seq7516,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20730,Q#869 - >seq7516,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20731,Q#869 - >seq7516,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20732,Q#869 - >seq7516,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20733,Q#869 - >seq7516,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20734,Q#869 - >seq7516,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20735,Q#869 - >seq7516,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20736,Q#869 - >seq7516,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20737,Q#869 - >seq7516,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20738,Q#869 - >seq7516,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20739,Q#869 - >seq7516,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20740,Q#869 - >seq7516,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20741,Q#869 - >seq7516,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20742,Q#869 - >seq7516,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20743,Q#869 - >seq7516,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20744,Q#869 - >seq7516,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20745,Q#869 - >seq7516,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20746,Q#869 - >seq7516,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20747,Q#869 - >seq7516,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20748,Q#869 - >seq7516,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20749,Q#869 - >seq7516,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20750,Q#869 - >seq7516,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20751,Q#869 - >seq7516,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20752,Q#869 - >seq7516,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20753,Q#869 - >seq7516,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20754,Q#869 - >seq7516,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20755,Q#869 - >seq7516,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,N-TerminusTruncated
20756,Q#869 - >seq7516,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20757,Q#869 - >seq7516,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20758,Q#869 - >seq7516,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20759,Q#869 - >seq7516,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20760,Q#869 - >seq7516,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20761,Q#869 - >seq7516,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20762,Q#869 - >seq7516,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20763,Q#869 - >seq7516,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20764,Q#869 - >seq7516,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20765,Q#869 - >seq7516,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20766,Q#869 - >seq7516,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20767,Q#869 - >seq7516,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20768,Q#869 - >seq7516,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20769,Q#869 - >seq7516,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20770,Q#869 - >seq7516,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20771,Q#869 - >seq7516,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20772,Q#869 - >seq7516,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20773,Q#869 - >seq7516,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20774,Q#869 - >seq7516,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20775,Q#869 - >seq7516,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20776,Q#869 - >seq7516,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20777,Q#869 - >seq7516,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20778,Q#869 - >seq7516,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs3_orang,pars,C-TerminusTruncated
20779,Q#869 - >seq7516,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20780,Q#869 - >seq7516,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20781,Q#869 - >seq7516,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20782,Q#869 - >seq7516,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20783,Q#869 - >seq7516,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs3_orang.pars.frame3,1909131013_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs3_orang,pars,BothTerminiTruncated
20784,Q#871 - >seq7518,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20785,Q#871 - >seq7518,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20786,Q#871 - >seq7518,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20787,Q#871 - >seq7518,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20788,Q#871 - >seq7518,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20789,Q#871 - >seq7518,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20790,Q#871 - >seq7518,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20791,Q#871 - >seq7518,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20792,Q#871 - >seq7518,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20793,Q#871 - >seq7518,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20794,Q#871 - >seq7518,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20795,Q#871 - >seq7518,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20796,Q#871 - >seq7518,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20797,Q#871 - >seq7518,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20798,Q#871 - >seq7518,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,marg,CompleteHit
20799,Q#871 - >seq7518,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20800,Q#871 - >seq7518,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20801,Q#871 - >seq7518,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20802,Q#871 - >seq7518,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20803,Q#871 - >seq7518,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20804,Q#871 - >seq7518,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20805,Q#871 - >seq7518,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20806,Q#871 - >seq7518,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20807,Q#871 - >seq7518,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20808,Q#871 - >seq7518,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20809,Q#871 - >seq7518,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20810,Q#871 - >seq7518,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20811,Q#871 - >seq7518,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20812,Q#871 - >seq7518,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20813,Q#871 - >seq7518,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20814,Q#871 - >seq7518,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20815,Q#871 - >seq7518,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20816,Q#871 - >seq7518,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20817,Q#871 - >seq7518,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20818,Q#871 - >seq7518,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20819,Q#871 - >seq7518,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20820,Q#871 - >seq7518,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20821,Q#871 - >seq7518,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20822,Q#871 - >seq7518,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20823,Q#871 - >seq7518,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20824,Q#871 - >seq7518,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20825,Q#871 - >seq7518,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20826,Q#871 - >seq7518,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20827,Q#871 - >seq7518,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20828,Q#871 - >seq7518,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20829,Q#871 - >seq7518,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20830,Q#871 - >seq7518,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20831,Q#871 - >seq7518,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20832,Q#871 - >seq7518,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20833,Q#871 - >seq7518,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20834,Q#871 - >seq7518,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20835,Q#871 - >seq7518,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20836,Q#871 - >seq7518,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20837,Q#871 - >seq7518,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20838,Q#871 - >seq7518,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20839,Q#871 - >seq7518,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20840,Q#871 - >seq7518,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20841,Q#871 - >seq7518,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20842,Q#871 - >seq7518,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20843,Q#871 - >seq7518,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20844,Q#871 - >seq7518,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20845,Q#871 - >seq7518,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20846,Q#871 - >seq7518,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20847,Q#871 - >seq7518,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20848,Q#871 - >seq7518,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20849,Q#871 - >seq7518,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20850,Q#871 - >seq7518,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20851,Q#871 - >seq7518,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20852,Q#871 - >seq7518,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20853,Q#871 - >seq7518,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20854,Q#871 - >seq7518,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20855,Q#871 - >seq7518,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20856,Q#871 - >seq7518,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20857,Q#871 - >seq7518,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20858,Q#871 - >seq7518,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20859,Q#871 - >seq7518,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20860,Q#871 - >seq7518,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20861,Q#871 - >seq7518,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20862,Q#871 - >seq7518,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20863,Q#871 - >seq7518,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20864,Q#871 - >seq7518,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20865,Q#871 - >seq7518,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20866,Q#871 - >seq7518,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20867,Q#871 - >seq7518,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20868,Q#871 - >seq7518,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20869,Q#871 - >seq7518,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20870,Q#871 - >seq7518,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20871,Q#871 - >seq7518,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20872,Q#871 - >seq7518,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20873,Q#871 - >seq7518,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20874,Q#871 - >seq7518,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,N-TerminusTruncated
20875,Q#871 - >seq7518,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20876,Q#871 - >seq7518,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20877,Q#871 - >seq7518,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20878,Q#871 - >seq7518,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20879,Q#871 - >seq7518,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20880,Q#871 - >seq7518,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20881,Q#871 - >seq7518,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20882,Q#871 - >seq7518,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20883,Q#871 - >seq7518,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20884,Q#871 - >seq7518,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20885,Q#871 - >seq7518,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20886,Q#871 - >seq7518,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20887,Q#871 - >seq7518,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20888,Q#871 - >seq7518,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20889,Q#871 - >seq7518,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20890,Q#871 - >seq7518,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20891,Q#871 - >seq7518,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20892,Q#871 - >seq7518,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20893,Q#871 - >seq7518,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20894,Q#871 - >seq7518,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20895,Q#871 - >seq7518,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20896,Q#871 - >seq7518,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20897,Q#871 - >seq7518,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,marg,C-TerminusTruncated
20898,Q#871 - >seq7518,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20899,Q#871 - >seq7518,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20900,Q#871 - >seq7518,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20901,Q#871 - >seq7518,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20902,Q#871 - >seq7518,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.marg.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,marg,BothTerminiTruncated
20903,Q#874 - >seq7521,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20904,Q#874 - >seq7521,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20905,Q#874 - >seq7521,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20906,Q#874 - >seq7521,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20907,Q#874 - >seq7521,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20908,Q#874 - >seq7521,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20909,Q#874 - >seq7521,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20910,Q#874 - >seq7521,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20911,Q#874 - >seq7521,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20912,Q#874 - >seq7521,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20913,Q#874 - >seq7521,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20914,Q#874 - >seq7521,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20915,Q#874 - >seq7521,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20916,Q#874 - >seq7521,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20917,Q#874 - >seq7521,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs2_gorilla,pars,CompleteHit
20918,Q#874 - >seq7521,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20919,Q#874 - >seq7521,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20920,Q#874 - >seq7521,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20921,Q#874 - >seq7521,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20922,Q#874 - >seq7521,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20923,Q#874 - >seq7521,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20924,Q#874 - >seq7521,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20925,Q#874 - >seq7521,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20926,Q#874 - >seq7521,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20927,Q#874 - >seq7521,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20928,Q#874 - >seq7521,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20929,Q#874 - >seq7521,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20930,Q#874 - >seq7521,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20931,Q#874 - >seq7521,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20932,Q#874 - >seq7521,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20933,Q#874 - >seq7521,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20934,Q#874 - >seq7521,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20935,Q#874 - >seq7521,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20936,Q#874 - >seq7521,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20937,Q#874 - >seq7521,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20938,Q#874 - >seq7521,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20939,Q#874 - >seq7521,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20940,Q#874 - >seq7521,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20941,Q#874 - >seq7521,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20942,Q#874 - >seq7521,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20943,Q#874 - >seq7521,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20944,Q#874 - >seq7521,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20945,Q#874 - >seq7521,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20946,Q#874 - >seq7521,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20947,Q#874 - >seq7521,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20948,Q#874 - >seq7521,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20949,Q#874 - >seq7521,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20950,Q#874 - >seq7521,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20951,Q#874 - >seq7521,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20952,Q#874 - >seq7521,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20953,Q#874 - >seq7521,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20954,Q#874 - >seq7521,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20955,Q#874 - >seq7521,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20956,Q#874 - >seq7521,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20957,Q#874 - >seq7521,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20958,Q#874 - >seq7521,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20959,Q#874 - >seq7521,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20960,Q#874 - >seq7521,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20961,Q#874 - >seq7521,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20962,Q#874 - >seq7521,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20963,Q#874 - >seq7521,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20964,Q#874 - >seq7521,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20965,Q#874 - >seq7521,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20966,Q#874 - >seq7521,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20967,Q#874 - >seq7521,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20968,Q#874 - >seq7521,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20969,Q#874 - >seq7521,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20970,Q#874 - >seq7521,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20971,Q#874 - >seq7521,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20972,Q#874 - >seq7521,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20973,Q#874 - >seq7521,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20974,Q#874 - >seq7521,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20975,Q#874 - >seq7521,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20976,Q#874 - >seq7521,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20977,Q#874 - >seq7521,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20978,Q#874 - >seq7521,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20979,Q#874 - >seq7521,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20980,Q#874 - >seq7521,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20981,Q#874 - >seq7521,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20982,Q#874 - >seq7521,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20983,Q#874 - >seq7521,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20984,Q#874 - >seq7521,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20985,Q#874 - >seq7521,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20986,Q#874 - >seq7521,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20987,Q#874 - >seq7521,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20988,Q#874 - >seq7521,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20989,Q#874 - >seq7521,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20990,Q#874 - >seq7521,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20991,Q#874 - >seq7521,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20992,Q#874 - >seq7521,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20993,Q#874 - >seq7521,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,N-TerminusTruncated
20994,Q#874 - >seq7521,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20995,Q#874 - >seq7521,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20996,Q#874 - >seq7521,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20997,Q#874 - >seq7521,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
20998,Q#874 - >seq7521,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
20999,Q#874 - >seq7521,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21000,Q#874 - >seq7521,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21001,Q#874 - >seq7521,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21002,Q#874 - >seq7521,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21003,Q#874 - >seq7521,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21004,Q#874 - >seq7521,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21005,Q#874 - >seq7521,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21006,Q#874 - >seq7521,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21007,Q#874 - >seq7521,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21008,Q#874 - >seq7521,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21009,Q#874 - >seq7521,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21010,Q#874 - >seq7521,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21011,Q#874 - >seq7521,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21012,Q#874 - >seq7521,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21013,Q#874 - >seq7521,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21014,Q#874 - >seq7521,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21015,Q#874 - >seq7521,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21016,Q#874 - >seq7521,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21017,Q#874 - >seq7521,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21018,Q#874 - >seq7521,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21019,Q#874 - >seq7521,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21020,Q#874 - >seq7521,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21021,Q#874 - >seq7521,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs2_gorilla.pars.frame3,1909131013_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21022,Q#877 - >seq7524,non-specific,335182,157,254,4.218319999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21023,Q#877 - >seq7524,superfamily,335182,157,254,4.218319999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21024,Q#877 - >seq7524,non-specific,335182,157,254,4.218319999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21025,Q#877 - >seq7524,non-specific,340205,257,321,4.67782e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21026,Q#877 - >seq7524,superfamily,340205,257,321,4.67782e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21027,Q#877 - >seq7524,non-specific,340205,257,321,4.67782e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21028,Q#877 - >seq7524,non-specific,340204,112,154,1.9145900000000003e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21029,Q#877 - >seq7524,superfamily,340204,112,154,1.9145900000000003e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21030,Q#877 - >seq7524,non-specific,340204,112,154,1.9145900000000003e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,marg,CompleteHit
21031,Q#877 - >seq7524,non-specific,222878,67,151,0.000202324,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21032,Q#877 - >seq7524,superfamily,222878,67,151,0.000202324,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21033,Q#877 - >seq7524,non-specific,222878,67,151,0.000202324,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21034,Q#877 - >seq7524,non-specific,337766,52,141,0.00045549800000000004,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21035,Q#877 - >seq7524,superfamily,337766,52,141,0.00045549800000000004,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21036,Q#877 - >seq7524,non-specific,337766,52,141,0.00045549800000000004,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21037,Q#877 - >seq7524,non-specific,274765,48,128,0.000534241,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21038,Q#877 - >seq7524,superfamily,274765,48,128,0.000534241,41.5514,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21039,Q#877 - >seq7524,non-specific,274765,48,128,0.000534241,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21040,Q#877 - >seq7524,non-specific,335555,66,133,0.000731062,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21041,Q#877 - >seq7524,superfamily,354396,66,133,0.000731062,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21042,Q#877 - >seq7524,non-specific,335555,66,133,0.000731062,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21043,Q#877 - >seq7524,non-specific,274008,47,259,0.0008162239999999999,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21044,Q#877 - >seq7524,superfamily,274008,47,259,0.0008162239999999999,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21045,Q#877 - >seq7524,non-specific,274008,47,259,0.0008162239999999999,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21046,Q#877 - >seq7524,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21047,Q#877 - >seq7524,superfamily,235175,55,143,0.000875918,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21048,Q#877 - >seq7524,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21049,Q#877 - >seq7524,non-specific,224117,66,151,0.000885681,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21050,Q#877 - >seq7524,superfamily,224117,66,151,0.000885681,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21051,Q#877 - >seq7524,non-specific,224117,66,151,0.000885681,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21052,Q#877 - >seq7524,non-specific,335556,66,150,0.00135738,39.0533,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21053,Q#877 - >seq7524,superfamily,335556,66,150,0.00135738,39.0533,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21054,Q#877 - >seq7524,non-specific,335556,66,150,0.00135738,39.0533,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21055,Q#877 - >seq7524,non-specific,336322,36,134,0.00158747,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21056,Q#877 - >seq7524,superfamily,336322,36,134,0.00158747,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21057,Q#877 - >seq7524,non-specific,336322,36,134,0.00158747,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21058,Q#877 - >seq7524,non-specific,179385,61,146,0.0018858,40.0234,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21059,Q#877 - >seq7524,superfamily,179385,61,146,0.0018858,40.0234,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21060,Q#877 - >seq7524,non-specific,179385,61,146,0.0018858,40.0234,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21061,Q#877 - >seq7524,non-specific,274009,50,211,0.00193146,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21062,Q#877 - >seq7524,superfamily,274009,50,211,0.00193146,40.0511,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21063,Q#877 - >seq7524,non-specific,274009,50,211,0.00193146,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21064,Q#877 - >seq7524,non-specific,224117,55,151,0.00193926,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21065,Q#877 - >seq7524,non-specific,224117,55,151,0.00193926,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21066,Q#877 - >seq7524,non-specific,222878,53,198,0.00205383,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21067,Q#877 - >seq7524,non-specific,222878,53,198,0.00205383,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21068,Q#877 - >seq7524,non-specific,224117,55,151,0.00234847,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21069,Q#877 - >seq7524,non-specific,224117,55,151,0.00234847,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21070,Q#877 - >seq7524,non-specific,224117,50,151,0.002369,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21071,Q#877 - >seq7524,non-specific,224117,50,151,0.002369,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21072,Q#877 - >seq7524,non-specific,224117,56,150,0.00256197,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21073,Q#877 - >seq7524,non-specific,224117,56,150,0.00256197,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21074,Q#877 - >seq7524,non-specific,224117,71,239,0.0026526999999999996,39.3124,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21075,Q#877 - >seq7524,superfamily,224117,71,239,0.0026526999999999996,39.3124,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21076,Q#877 - >seq7524,non-specific,224117,71,239,0.0026526999999999996,39.3124,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21077,Q#877 - >seq7524,non-specific,274008,56,212,0.00283454,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21078,Q#877 - >seq7524,superfamily,274008,56,212,0.00283454,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21079,Q#877 - >seq7524,non-specific,274008,56,212,0.00283454,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21080,Q#877 - >seq7524,non-specific,224117,55,204,0.00329716,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21081,Q#877 - >seq7524,non-specific,224117,55,204,0.00329716,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21082,Q#877 - >seq7524,non-specific,273690,75,197,0.00351376,38.8661,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21083,Q#877 - >seq7524,superfamily,355611,75,197,0.00351376,38.8661,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21084,Q#877 - >seq7524,non-specific,273690,75,197,0.00351376,38.8661,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21085,Q#877 - >seq7524,non-specific,235461,59,130,0.00351776,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21086,Q#877 - >seq7524,superfamily,235461,59,130,0.00351776,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21087,Q#877 - >seq7524,non-specific,235461,59,130,0.00351776,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21088,Q#877 - >seq7524,non-specific,197874,57,163,0.00521046,38.0749,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21089,Q#877 - >seq7524,superfamily,197874,57,163,0.00521046,38.0749,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21090,Q#877 - >seq7524,non-specific,197874,57,163,0.00521046,38.0749,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21091,Q#877 - >seq7524,non-specific,337715,71,138,0.00667337,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21092,Q#877 - >seq7524,superfamily,337715,71,138,0.00667337,37.9785,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21093,Q#877 - >seq7524,non-specific,337715,71,138,0.00667337,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21094,Q#877 - >seq7524,non-specific,336322,35,168,0.00735827,37.8818,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21095,Q#877 - >seq7524,non-specific,336322,35,168,0.00735827,37.8818,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21096,Q#877 - >seq7524,non-specific,274008,41,164,0.007770999999999999,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21097,Q#877 - >seq7524,non-specific,274008,41,164,0.007770999999999999,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21098,Q#877 - >seq7524,non-specific,223266,67,141,0.00781623,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21099,Q#877 - >seq7524,superfamily,223266,67,141,0.00781623,38.0218,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21100,Q#877 - >seq7524,non-specific,223266,67,141,0.00781623,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21101,Q#877 - >seq7524,non-specific,274008,51,150,0.00908649,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21102,Q#877 - >seq7524,non-specific,274008,51,150,0.00908649,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,marg,BothTerminiTruncated
21103,Q#877 - >seq7524,non-specific,337663,69,149,0.00948136,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21104,Q#877 - >seq7524,superfamily,337663,69,149,0.00948136,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21105,Q#877 - >seq7524,non-specific,337663,69,149,0.00948136,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,marg,C-TerminusTruncated
21106,Q#877 - >seq7524,non-specific,313022,71,154,0.00972982,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21107,Q#877 - >seq7524,superfamily,313022,71,154,0.00972982,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21108,Q#877 - >seq7524,non-specific,313022,71,154,0.00972982,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.marg.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,marg,N-TerminusTruncated
21109,Q#880 - >seq7527,non-specific,335182,157,254,4.218319999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21110,Q#880 - >seq7527,superfamily,335182,157,254,4.218319999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21111,Q#880 - >seq7527,non-specific,335182,157,254,4.218319999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21112,Q#880 - >seq7527,non-specific,340205,257,321,4.67782e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21113,Q#880 - >seq7527,superfamily,340205,257,321,4.67782e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21114,Q#880 - >seq7527,non-specific,340205,257,321,4.67782e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21115,Q#880 - >seq7527,non-specific,340204,112,154,1.9145900000000003e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21116,Q#880 - >seq7527,superfamily,340204,112,154,1.9145900000000003e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21117,Q#880 - >seq7527,non-specific,340204,112,154,1.9145900000000003e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs1_chimp,pars,CompleteHit
21118,Q#880 - >seq7527,non-specific,222878,67,151,0.000202324,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21119,Q#880 - >seq7527,superfamily,222878,67,151,0.000202324,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21120,Q#880 - >seq7527,non-specific,222878,67,151,0.000202324,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21121,Q#880 - >seq7527,non-specific,337766,52,141,0.00045549800000000004,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21122,Q#880 - >seq7527,superfamily,337766,52,141,0.00045549800000000004,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21123,Q#880 - >seq7527,non-specific,337766,52,141,0.00045549800000000004,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21124,Q#880 - >seq7527,non-specific,274765,48,128,0.000534241,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21125,Q#880 - >seq7527,superfamily,274765,48,128,0.000534241,41.5514,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21126,Q#880 - >seq7527,non-specific,274765,48,128,0.000534241,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21127,Q#880 - >seq7527,non-specific,335555,66,133,0.000731062,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21128,Q#880 - >seq7527,superfamily,354396,66,133,0.000731062,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21129,Q#880 - >seq7527,non-specific,335555,66,133,0.000731062,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21130,Q#880 - >seq7527,non-specific,274008,47,259,0.0008162239999999999,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21131,Q#880 - >seq7527,superfamily,274008,47,259,0.0008162239999999999,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21132,Q#880 - >seq7527,non-specific,274008,47,259,0.0008162239999999999,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21133,Q#880 - >seq7527,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21134,Q#880 - >seq7527,superfamily,235175,55,143,0.000875918,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21135,Q#880 - >seq7527,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21136,Q#880 - >seq7527,non-specific,224117,66,151,0.000885681,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21137,Q#880 - >seq7527,superfamily,224117,66,151,0.000885681,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21138,Q#880 - >seq7527,non-specific,224117,66,151,0.000885681,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21139,Q#880 - >seq7527,non-specific,335556,66,150,0.00135738,39.0533,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21140,Q#880 - >seq7527,superfamily,335556,66,150,0.00135738,39.0533,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21141,Q#880 - >seq7527,non-specific,335556,66,150,0.00135738,39.0533,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21142,Q#880 - >seq7527,non-specific,336322,36,134,0.00158747,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21143,Q#880 - >seq7527,superfamily,336322,36,134,0.00158747,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21144,Q#880 - >seq7527,non-specific,336322,36,134,0.00158747,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21145,Q#880 - >seq7527,non-specific,179385,61,146,0.0018858,40.0234,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21146,Q#880 - >seq7527,superfamily,179385,61,146,0.0018858,40.0234,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21147,Q#880 - >seq7527,non-specific,179385,61,146,0.0018858,40.0234,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21148,Q#880 - >seq7527,non-specific,274009,50,211,0.00193146,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21149,Q#880 - >seq7527,superfamily,274009,50,211,0.00193146,40.0511,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21150,Q#880 - >seq7527,non-specific,274009,50,211,0.00193146,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21151,Q#880 - >seq7527,non-specific,224117,55,151,0.00193926,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21152,Q#880 - >seq7527,non-specific,224117,55,151,0.00193926,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21153,Q#880 - >seq7527,non-specific,222878,53,198,0.00205383,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21154,Q#880 - >seq7527,non-specific,222878,53,198,0.00205383,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21155,Q#880 - >seq7527,non-specific,224117,55,151,0.00234847,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21156,Q#880 - >seq7527,non-specific,224117,55,151,0.00234847,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21157,Q#880 - >seq7527,non-specific,224117,50,151,0.002369,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21158,Q#880 - >seq7527,non-specific,224117,50,151,0.002369,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21159,Q#880 - >seq7527,non-specific,224117,56,150,0.00256197,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21160,Q#880 - >seq7527,non-specific,224117,56,150,0.00256197,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21161,Q#880 - >seq7527,non-specific,224117,71,239,0.0026526999999999996,39.3124,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21162,Q#880 - >seq7527,superfamily,224117,71,239,0.0026526999999999996,39.3124,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21163,Q#880 - >seq7527,non-specific,224117,71,239,0.0026526999999999996,39.3124,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21164,Q#880 - >seq7527,non-specific,274008,56,212,0.00283454,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21165,Q#880 - >seq7527,superfamily,274008,56,212,0.00283454,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21166,Q#880 - >seq7527,non-specific,274008,56,212,0.00283454,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21167,Q#880 - >seq7527,non-specific,224117,55,204,0.00329716,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21168,Q#880 - >seq7527,non-specific,224117,55,204,0.00329716,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21169,Q#880 - >seq7527,non-specific,273690,75,197,0.00351376,38.8661,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21170,Q#880 - >seq7527,superfamily,355611,75,197,0.00351376,38.8661,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21171,Q#880 - >seq7527,non-specific,273690,75,197,0.00351376,38.8661,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21172,Q#880 - >seq7527,non-specific,235461,59,130,0.00351776,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21173,Q#880 - >seq7527,superfamily,235461,59,130,0.00351776,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21174,Q#880 - >seq7527,non-specific,235461,59,130,0.00351776,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21175,Q#880 - >seq7527,non-specific,197874,57,163,0.00521046,38.0749,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21176,Q#880 - >seq7527,superfamily,197874,57,163,0.00521046,38.0749,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21177,Q#880 - >seq7527,non-specific,197874,57,163,0.00521046,38.0749,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21178,Q#880 - >seq7527,non-specific,337715,71,138,0.00667337,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21179,Q#880 - >seq7527,superfamily,337715,71,138,0.00667337,37.9785,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21180,Q#880 - >seq7527,non-specific,337715,71,138,0.00667337,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21181,Q#880 - >seq7527,non-specific,336322,35,168,0.00735827,37.8818,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21182,Q#880 - >seq7527,non-specific,336322,35,168,0.00735827,37.8818,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21183,Q#880 - >seq7527,non-specific,274008,41,164,0.007770999999999999,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21184,Q#880 - >seq7527,non-specific,274008,41,164,0.007770999999999999,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21185,Q#880 - >seq7527,non-specific,223266,67,141,0.00781623,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21186,Q#880 - >seq7527,superfamily,223266,67,141,0.00781623,38.0218,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21187,Q#880 - >seq7527,non-specific,223266,67,141,0.00781623,38.0218,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21188,Q#880 - >seq7527,non-specific,274008,51,150,0.00908649,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21189,Q#880 - >seq7527,non-specific,274008,51,150,0.00908649,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs1_chimp,pars,BothTerminiTruncated
21190,Q#880 - >seq7527,non-specific,337663,69,149,0.00948136,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21191,Q#880 - >seq7527,superfamily,337663,69,149,0.00948136,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21192,Q#880 - >seq7527,non-specific,337663,69,149,0.00948136,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs1_chimp,pars,C-TerminusTruncated
21193,Q#880 - >seq7527,non-specific,313022,71,154,0.00972982,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21194,Q#880 - >seq7527,superfamily,313022,71,154,0.00972982,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21195,Q#880 - >seq7527,non-specific,313022,71,154,0.00972982,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs1_chimp.pars.frame3,1909131013_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs1_chimp,pars,N-TerminusTruncated
21196,Q#883 - >seq7530,non-specific,335182,146,243,7.144609999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21197,Q#883 - >seq7530,superfamily,335182,146,243,7.144609999999999e-47,153.613,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21198,Q#883 - >seq7530,non-specific,340205,246,310,5.398779999999999e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21199,Q#883 - >seq7530,superfamily,340205,246,310,5.398779999999999e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21200,Q#883 - >seq7530,non-specific,340204,101,143,2.64404e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21201,Q#883 - >seq7530,superfamily,340204,101,143,2.64404e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs3_orang,pars,CompleteHit
21202,Q#883 - >seq7530,non-specific,224117,55,172,0.00135896,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21203,Q#883 - >seq7530,superfamily,224117,55,172,0.00135896,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21204,Q#883 - >seq7530,non-specific,179877,25,185,0.00389859,38.6634,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21205,Q#883 - >seq7530,superfamily,179877,25,185,0.00389859,38.6634,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21206,Q#883 - >seq7530,non-specific,235461,37,164,0.00461298,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21207,Q#883 - >seq7530,superfamily,235461,37,164,0.00461298,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21208,Q#883 - >seq7530,non-specific,334565,62,139,0.00499722,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21209,Q#883 - >seq7530,superfamily,334565,62,139,0.00499722,38.2396,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21210,Q#883 - >seq7530,non-specific,235175,24,146,0.00665341,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21211,Q#883 - >seq7530,superfamily,235175,24,146,0.00665341,38.1212,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21212,Q#883 - >seq7530,non-specific,274009,56,137,0.00678775,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21213,Q#883 - >seq7530,superfamily,274009,56,137,0.00678775,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,pars,BothTerminiTruncated
21214,Q#883 - >seq7530,non-specific,223250,36,165,0.00869997,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21215,Q#883 - >seq7530,superfamily,223250,36,165,0.00869997,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,pars,C-TerminusTruncated
21216,Q#883 - >seq7530,non-specific,197874,44,152,0.00882356,37.3045,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,pars,N-TerminusTruncated
21217,Q#883 - >seq7530,superfamily,197874,44,152,0.00882356,37.3045,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA8A.ORF1.hs3_orang.pars.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,pars,N-TerminusTruncated
21218,Q#886 - >seq7533,non-specific,335182,157,254,1.1690899999999997e-45,150.531,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21219,Q#886 - >seq7533,superfamily,335182,157,254,1.1690899999999997e-45,150.531,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21220,Q#886 - >seq7533,non-specific,340205,257,321,7.102039999999999e-32,113.97,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21221,Q#886 - >seq7533,superfamily,340205,257,321,7.102039999999999e-32,113.97,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21222,Q#886 - >seq7533,non-specific,340204,112,154,6.427809999999999e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21223,Q#886 - >seq7533,superfamily,340204,112,154,6.427809999999999e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs2_gorilla,marg,CompleteHit
21224,Q#886 - >seq7533,non-specific,274008,39,206,0.00222168,39.6547,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,N-TerminusTruncated
21225,Q#886 - >seq7533,superfamily,274008,39,206,0.00222168,39.6547,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,N-TerminusTruncated
21226,Q#886 - >seq7533,non-specific,224117,66,183,0.00310239,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21227,Q#886 - >seq7533,superfamily,224117,66,183,0.00310239,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21228,Q#886 - >seq7533,non-specific,274009,67,148,0.00477306,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21229,Q#886 - >seq7533,superfamily,274009,67,148,0.00477306,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21230,Q#886 - >seq7533,non-specific,235175,41,157,0.00645019,38.1212,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,C-TerminusTruncated
21231,Q#886 - >seq7533,superfamily,235175,41,157,0.00645019,38.1212,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,marg,C-TerminusTruncated
21232,Q#886 - >seq7533,non-specific,235461,67,175,0.00887029,37.355,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs2_gorilla,marg,C-TerminusTruncated
21233,Q#886 - >seq7533,superfamily,235461,67,175,0.00887029,37.355,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs2_gorilla.marg.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs2_gorilla,marg,C-TerminusTruncated
21234,Q#888 - >seq7535,non-specific,254188,73,158,0.00287518,38.94,pfam07404,TEBP_beta,N,cl06441,"Telomere-binding protein beta subunit (TEBP beta); This family consists of several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.",L1PA8A.ORF1.hs1_chimp.marg.frame2,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21235,Q#888 - >seq7535,superfamily,254188,73,158,0.00287518,38.94,cl06441,TEBP_beta superfamily,N, - ,"Telomere-binding protein beta subunit (TEBP beta); This family consists of several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.",L1PA8A.ORF1.hs1_chimp.marg.frame2,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21236,Q#889 - >seq7536,non-specific,335182,147,244,1.4459699999999998e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21237,Q#889 - >seq7536,superfamily,335182,147,244,1.4459699999999998e-46,152.842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21238,Q#889 - >seq7536,non-specific,340205,247,311,4.80018e-32,113.97,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21239,Q#889 - >seq7536,superfamily,340205,247,311,4.80018e-32,113.97,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21240,Q#889 - >seq7536,non-specific,340204,102,144,3.2921399999999997e-07,46.2468,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21241,Q#889 - >seq7536,superfamily,340204,102,144,3.2921399999999997e-07,46.2468,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs2_gorilla,pars,CompleteHit
21242,Q#889 - >seq7536,non-specific,274008,29,196,0.00144772,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,N-TerminusTruncated
21243,Q#889 - >seq7536,superfamily,274008,29,196,0.00144772,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,N-TerminusTruncated
21244,Q#889 - >seq7536,non-specific,224117,56,173,0.00209513,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21245,Q#889 - >seq7536,superfamily,224117,56,173,0.00209513,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21246,Q#889 - >seq7536,non-specific,274009,57,138,0.0037090000000000005,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21247,Q#889 - >seq7536,superfamily,274009,57,138,0.0037090000000000005,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21248,Q#889 - >seq7536,non-specific,235175,31,147,0.00459608,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21249,Q#889 - >seq7536,superfamily,235175,31,147,0.00459608,38.5064,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21250,Q#889 - >seq7536,non-specific,235175,24,147,0.00755692,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21251,Q#889 - >seq7536,non-specific,235461,57,165,0.00780193,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21252,Q#889 - >seq7536,superfamily,235461,57,165,0.00780193,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs2_gorilla,pars,C-TerminusTruncated
21253,Q#889 - >seq7536,non-specific,222878,43,188,0.00843866,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21254,Q#889 - >seq7536,superfamily,222878,43,188,0.00843866,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8A.ORF1.hs2_gorilla.pars.frame3,1909131014_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21255,Q#892 - >seq7539,non-specific,335182,147,244,4.873759999999999e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21256,Q#892 - >seq7539,superfamily,335182,147,244,4.873759999999999e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21257,Q#892 - >seq7539,non-specific,340205,247,311,4.90592e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21258,Q#892 - >seq7539,superfamily,340205,247,311,4.90592e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21259,Q#892 - >seq7539,non-specific,340204,102,144,4.00649e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21260,Q#892 - >seq7539,superfamily,340204,102,144,4.00649e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs1_chimp,marg,CompleteHit
21261,Q#892 - >seq7539,non-specific,224117,44,194,0.00049641,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21262,Q#892 - >seq7539,superfamily,224117,44,194,0.00049641,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21263,Q#892 - >seq7539,non-specific,274008,29,196,0.00186433,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21264,Q#892 - >seq7539,superfamily,274008,29,196,0.00186433,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21265,Q#892 - >seq7539,non-specific,224117,56,173,0.001887,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,BothTerminiTruncated
21266,Q#892 - >seq7539,non-specific,235175,31,147,0.00253851,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,C-TerminusTruncated
21267,Q#892 - >seq7539,superfamily,235175,31,147,0.00253851,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,C-TerminusTruncated
21268,Q#892 - >seq7539,non-specific,235175,24,147,0.00321342,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,BothTerminiTruncated
21269,Q#892 - >seq7539,non-specific,337766,42,120,0.00754069,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21270,Q#892 - >seq7539,superfamily,337766,42,120,0.00754069,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8A,ORF1,hs1_chimp,marg,N-TerminusTruncated
21271,Q#892 - >seq7539,non-specific,179385,49,136,0.00930705,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,BothTerminiTruncated
21272,Q#892 - >seq7539,superfamily,179385,49,136,0.00930705,37.7122,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.marg.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,marg,BothTerminiTruncated
21273,Q#899 - >seq7546,non-specific,335182,157,254,5.94078e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21274,Q#899 - >seq7546,superfamily,335182,157,254,5.94078e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21275,Q#899 - >seq7546,non-specific,340205,257,321,9.922959999999998e-33,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21276,Q#899 - >seq7546,superfamily,340205,257,321,9.922959999999998e-33,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21277,Q#899 - >seq7546,non-specific,340204,112,154,1.61094e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21278,Q#899 - >seq7546,superfamily,340204,112,154,1.61094e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs4_gibbon,pars,CompleteHit
21279,Q#899 - >seq7546,non-specific,224117,66,183,0.00341389,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21280,Q#899 - >seq7546,superfamily,224117,66,183,0.00341389,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21281,Q#899 - >seq7546,non-specific,274008,39,206,0.00377691,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21282,Q#899 - >seq7546,superfamily,274008,39,206,0.00377691,38.8843,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21283,Q#899 - >seq7546,non-specific,179385,59,146,0.00416873,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21284,Q#899 - >seq7546,superfamily,179385,59,146,0.00416873,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21285,Q#899 - >seq7546,non-specific,235175,41,157,0.00467315,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21286,Q#899 - >seq7546,superfamily,235175,41,157,0.00467315,38.5064,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21287,Q#899 - >seq7546,non-specific,235175,35,157,0.00561118,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21288,Q#899 - >seq7546,non-specific,235461,67,175,0.00646059,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21289,Q#899 - >seq7546,superfamily,235461,67,175,0.00646059,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21290,Q#902 - >seq7549,non-specific,335182,157,254,5.94078e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21291,Q#902 - >seq7549,superfamily,335182,157,254,5.94078e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21292,Q#902 - >seq7549,non-specific,340205,257,321,9.922959999999998e-33,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21293,Q#902 - >seq7549,superfamily,340205,257,321,9.922959999999998e-33,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21294,Q#902 - >seq7549,non-specific,340204,112,154,1.61094e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21295,Q#902 - >seq7549,superfamily,340204,112,154,1.61094e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs4_gibbon,marg,CompleteHit
21296,Q#902 - >seq7549,non-specific,224117,66,183,0.00341389,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21297,Q#902 - >seq7549,superfamily,224117,66,183,0.00341389,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21298,Q#902 - >seq7549,non-specific,274008,39,206,0.00377691,38.8843,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21299,Q#902 - >seq7549,superfamily,274008,39,206,0.00377691,38.8843,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21300,Q#902 - >seq7549,non-specific,179385,59,146,0.00416873,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21301,Q#902 - >seq7549,superfamily,179385,59,146,0.00416873,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21302,Q#902 - >seq7549,non-specific,235175,41,157,0.00467315,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21303,Q#902 - >seq7549,superfamily,235175,41,157,0.00467315,38.5064,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21304,Q#902 - >seq7549,non-specific,235175,35,157,0.00561118,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21305,Q#902 - >seq7549,non-specific,235461,67,175,0.00646059,37.7402,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21306,Q#902 - >seq7549,superfamily,235461,67,175,0.00646059,37.7402,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21307,Q#905 - >seq7552,non-specific,335182,147,244,1.0245600000000001e-46,153.227,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21308,Q#905 - >seq7552,superfamily,335182,147,244,1.0245600000000001e-46,153.227,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21309,Q#905 - >seq7552,non-specific,340205,247,311,3.92543e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21310,Q#905 - >seq7552,superfamily,340205,247,311,3.92543e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21311,Q#905 - >seq7552,non-specific,340204,102,144,6.386350000000001e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21312,Q#905 - >seq7552,superfamily,340204,102,144,6.386350000000001e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs5_gmonkey,pars,CompleteHit
21313,Q#905 - >seq7552,non-specific,274008,29,196,0.00186433,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21314,Q#905 - >seq7552,superfamily,274008,29,196,0.00186433,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21315,Q#905 - >seq7552,non-specific,224117,56,173,0.00200576,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21316,Q#905 - >seq7552,superfamily,224117,56,173,0.00200576,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21317,Q#905 - >seq7552,non-specific,235175,31,147,0.00249456,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21318,Q#905 - >seq7552,superfamily,235175,31,147,0.00249456,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21319,Q#905 - >seq7552,non-specific,179385,49,136,0.00251392,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21320,Q#905 - >seq7552,superfamily,179385,49,136,0.00251392,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21321,Q#905 - >seq7552,non-specific,235175,25,147,0.00313035,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21322,Q#905 - >seq7552,non-specific,235461,57,165,0.00548279,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21323,Q#905 - >seq7552,superfamily,235461,57,165,0.00548279,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21324,Q#905 - >seq7552,non-specific,179877,26,186,0.00693031,37.893,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21325,Q#905 - >seq7552,superfamily,179877,26,186,0.00693031,37.893,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21326,Q#905 - >seq7552,non-specific,274009,57,138,0.00812117,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21327,Q#905 - >seq7552,superfamily,274009,57,138,0.00812117,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21328,Q#907 - >seq7554,non-specific,335182,157,254,8.11312e-46,150.916,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21329,Q#907 - >seq7554,superfamily,335182,157,254,8.11312e-46,150.916,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21330,Q#907 - >seq7554,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21331,Q#907 - >seq7554,superfamily,340205,257,321,6.16117e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21332,Q#907 - >seq7554,non-specific,340204,112,154,1.32384e-07,47.4024,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21333,Q#907 - >seq7554,superfamily,340204,112,154,1.32384e-07,47.4024,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs5_gmonkey,marg,CompleteHit
21334,Q#907 - >seq7554,non-specific,224117,66,183,0.00299629,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21335,Q#907 - >seq7554,superfamily,224117,66,183,0.00299629,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21336,Q#907 - >seq7554,non-specific,274008,39,206,0.00303882,39.2695,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21337,Q#907 - >seq7554,superfamily,274008,39,206,0.00303882,39.2695,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21338,Q#907 - >seq7554,non-specific,179385,59,146,0.00338201,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21339,Q#907 - >seq7554,superfamily,179385,59,146,0.00338201,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21340,Q#907 - >seq7554,non-specific,235175,41,157,0.00375847,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21341,Q#907 - >seq7554,superfamily,235175,41,157,0.00375847,38.8916,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21342,Q#907 - >seq7554,non-specific,235175,35,157,0.00467315,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21343,Q#907 - >seq7554,non-specific,235461,67,175,0.00607432,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21344,Q#907 - >seq7554,superfamily,235461,67,175,0.00607432,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21345,Q#908 - >seq7555,non-specific,335182,156,253,3.49299e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21346,Q#908 - >seq7555,superfamily,335182,156,253,3.49299e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21347,Q#908 - >seq7555,non-specific,340205,256,320,8.12196e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21348,Q#908 - >seq7555,superfamily,340205,256,320,8.12196e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21349,Q#908 - >seq7555,non-specific,340204,111,153,4.16095e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21350,Q#908 - >seq7555,superfamily,340204,111,153,4.16095e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs3_orang,marg,CompleteHit
21351,Q#908 - >seq7555,non-specific,224117,65,182,0.00155182,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21352,Q#908 - >seq7555,superfamily,224117,65,182,0.00155182,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21353,Q#908 - >seq7555,non-specific,334565,72,149,0.0044973,38.6248,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21354,Q#908 - >seq7555,superfamily,334565,72,149,0.0044973,38.6248,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21355,Q#908 - >seq7555,non-specific,179877,35,195,0.00472125,38.6634,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21356,Q#908 - >seq7555,superfamily,179877,35,195,0.00472125,38.6634,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21357,Q#908 - >seq7555,non-specific,235461,47,174,0.00476528,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21358,Q#908 - >seq7555,superfamily,235461,47,174,0.00476528,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21359,Q#908 - >seq7555,non-specific,274009,66,147,0.00746326,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21360,Q#908 - >seq7555,superfamily,274009,66,147,0.00746326,38.1251,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21361,Q#908 - >seq7555,non-specific,235175,34,156,0.00819049,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21362,Q#908 - >seq7555,superfamily,235175,34,156,0.00819049,37.736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs3_orang,marg,BothTerminiTruncated
21363,Q#908 - >seq7555,non-specific,223250,46,175,0.00913685,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21364,Q#908 - >seq7555,superfamily,223250,46,175,0.00913685,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PA8A.ORF1.hs3_orang.marg.frame3,1909131014_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs3_orang,marg,C-TerminusTruncated
21365,Q#911 - >seq7558,non-specific,254188,73,158,0.00287518,38.94,pfam07404,TEBP_beta,N,cl06441,"Telomere-binding protein beta subunit (TEBP beta); This family consists of several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.",L1PA8A.ORF1.hs1_chimp.pars.frame2,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21366,Q#911 - >seq7558,superfamily,254188,73,158,0.00287518,38.94,cl06441,TEBP_beta superfamily,N, - ,"Telomere-binding protein beta subunit (TEBP beta); This family consists of several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.",L1PA8A.ORF1.hs1_chimp.pars.frame2,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21367,Q#913 - >seq7560,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21368,Q#913 - >seq7560,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21369,Q#913 - >seq7560,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21370,Q#913 - >seq7560,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21371,Q#913 - >seq7560,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21372,Q#913 - >seq7560,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21373,Q#913 - >seq7560,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21374,Q#913 - >seq7560,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21375,Q#913 - >seq7560,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,pars,CompleteHit
21376,Q#913 - >seq7560,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21377,Q#913 - >seq7560,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21378,Q#913 - >seq7560,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21379,Q#913 - >seq7560,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21380,Q#913 - >seq7560,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21381,Q#913 - >seq7560,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21382,Q#913 - >seq7560,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21383,Q#913 - >seq7560,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21384,Q#913 - >seq7560,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21385,Q#913 - >seq7560,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21386,Q#913 - >seq7560,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21387,Q#913 - >seq7560,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21388,Q#913 - >seq7560,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21389,Q#913 - >seq7560,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21390,Q#913 - >seq7560,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21391,Q#913 - >seq7560,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21392,Q#913 - >seq7560,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21393,Q#913 - >seq7560,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21394,Q#913 - >seq7560,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21395,Q#913 - >seq7560,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21396,Q#913 - >seq7560,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21397,Q#913 - >seq7560,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21398,Q#913 - >seq7560,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21399,Q#913 - >seq7560,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21400,Q#913 - >seq7560,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21401,Q#913 - >seq7560,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21402,Q#913 - >seq7560,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21403,Q#913 - >seq7560,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21404,Q#913 - >seq7560,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21405,Q#913 - >seq7560,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21406,Q#913 - >seq7560,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21407,Q#913 - >seq7560,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21408,Q#913 - >seq7560,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21409,Q#913 - >seq7560,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21410,Q#913 - >seq7560,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21411,Q#913 - >seq7560,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21412,Q#913 - >seq7560,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21413,Q#913 - >seq7560,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21414,Q#913 - >seq7560,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21415,Q#913 - >seq7560,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21416,Q#913 - >seq7560,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21417,Q#913 - >seq7560,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21418,Q#913 - >seq7560,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21419,Q#913 - >seq7560,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,N-TerminusTruncated
21420,Q#913 - >seq7560,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21421,Q#913 - >seq7560,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21422,Q#913 - >seq7560,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21423,Q#913 - >seq7560,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21424,Q#913 - >seq7560,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21425,Q#913 - >seq7560,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21426,Q#913 - >seq7560,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21427,Q#913 - >seq7560,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21428,Q#913 - >seq7560,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21429,Q#913 - >seq7560,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21430,Q#913 - >seq7560,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21431,Q#913 - >seq7560,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21432,Q#913 - >seq7560,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,pars,C-TerminusTruncated
21433,Q#913 - >seq7560,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21434,Q#913 - >seq7560,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21435,Q#913 - >seq7560,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.pars.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,pars,BothTerminiTruncated
21436,Q#916 - >seq7563,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21437,Q#916 - >seq7563,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21438,Q#916 - >seq7563,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21439,Q#916 - >seq7563,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21440,Q#916 - >seq7563,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21441,Q#916 - >seq7563,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21442,Q#916 - >seq7563,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21443,Q#916 - >seq7563,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21444,Q#916 - >seq7563,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs4_gibbon,marg,CompleteHit
21445,Q#916 - >seq7563,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21446,Q#916 - >seq7563,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21447,Q#916 - >seq7563,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21448,Q#916 - >seq7563,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21449,Q#916 - >seq7563,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21450,Q#916 - >seq7563,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21451,Q#916 - >seq7563,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21452,Q#916 - >seq7563,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21453,Q#916 - >seq7563,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21454,Q#916 - >seq7563,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21455,Q#916 - >seq7563,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21456,Q#916 - >seq7563,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21457,Q#916 - >seq7563,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21458,Q#916 - >seq7563,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21459,Q#916 - >seq7563,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21460,Q#916 - >seq7563,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21461,Q#916 - >seq7563,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21462,Q#916 - >seq7563,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21463,Q#916 - >seq7563,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21464,Q#916 - >seq7563,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21465,Q#916 - >seq7563,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21466,Q#916 - >seq7563,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21467,Q#916 - >seq7563,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21468,Q#916 - >seq7563,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21469,Q#916 - >seq7563,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21470,Q#916 - >seq7563,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21471,Q#916 - >seq7563,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21472,Q#916 - >seq7563,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21473,Q#916 - >seq7563,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21474,Q#916 - >seq7563,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21475,Q#916 - >seq7563,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21476,Q#916 - >seq7563,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21477,Q#916 - >seq7563,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21478,Q#916 - >seq7563,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21479,Q#916 - >seq7563,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21480,Q#916 - >seq7563,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21481,Q#916 - >seq7563,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21482,Q#916 - >seq7563,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21483,Q#916 - >seq7563,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21484,Q#916 - >seq7563,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21485,Q#916 - >seq7563,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21486,Q#916 - >seq7563,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21487,Q#916 - >seq7563,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21488,Q#916 - >seq7563,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,N-TerminusTruncated
21489,Q#916 - >seq7563,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21490,Q#916 - >seq7563,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21491,Q#916 - >seq7563,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21492,Q#916 - >seq7563,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21493,Q#916 - >seq7563,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21494,Q#916 - >seq7563,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21495,Q#916 - >seq7563,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21496,Q#916 - >seq7563,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21497,Q#916 - >seq7563,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21498,Q#916 - >seq7563,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21499,Q#916 - >seq7563,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21500,Q#916 - >seq7563,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21501,Q#916 - >seq7563,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs4_gibbon,marg,C-TerminusTruncated
21502,Q#916 - >seq7563,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21503,Q#916 - >seq7563,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21504,Q#916 - >seq7563,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs4_gibbon.marg.frame3,1909131014_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs4_gibbon,marg,BothTerminiTruncated
21505,Q#919 - >seq7566,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21506,Q#919 - >seq7566,superfamily,335182,157,254,2.5720400000000002e-47,155.153,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21507,Q#919 - >seq7566,non-specific,340205,257,321,7.37672e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21508,Q#919 - >seq7566,superfamily,340205,257,321,7.37672e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21509,Q#919 - >seq7566,non-specific,340204,112,154,9.53484e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21510,Q#919 - >seq7566,superfamily,340204,112,154,9.53484e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs5_gmonkey,pars,CompleteHit
21511,Q#919 - >seq7566,non-specific,337766,52,133,0.000435709,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21512,Q#919 - >seq7566,superfamily,337766,52,133,0.000435709,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21513,Q#919 - >seq7566,non-specific,179385,61,146,0.0005754509999999999,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21514,Q#919 - >seq7566,superfamily,179385,61,146,0.0005754509999999999,41.5642,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21515,Q#919 - >seq7566,non-specific,224117,66,151,0.000681945,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21516,Q#919 - >seq7566,superfamily,224117,66,151,0.000681945,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21517,Q#919 - >seq7566,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21518,Q#919 - >seq7566,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21519,Q#919 - >seq7566,non-specific,222878,67,151,0.0007894919999999999,40.7681,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21520,Q#919 - >seq7566,superfamily,222878,67,151,0.0007894919999999999,40.7681,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21521,Q#919 - >seq7566,non-specific,335555,66,133,0.000849247,40.7068,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21522,Q#919 - >seq7566,superfamily,354396,66,133,0.000849247,40.7068,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21523,Q#919 - >seq7566,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21524,Q#919 - >seq7566,superfamily,235175,55,143,0.000875918,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21525,Q#919 - >seq7566,non-specific,335556,66,150,0.000989145,39.4385,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21526,Q#919 - >seq7566,superfamily,335556,66,150,0.000989145,39.4385,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21527,Q#919 - >seq7566,non-specific,336322,36,134,0.00167326,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21528,Q#919 - >seq7566,superfamily,336322,36,134,0.00167326,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21529,Q#919 - >seq7566,non-specific,274008,56,212,0.00168162,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21530,Q#919 - >seq7566,superfamily,274008,56,212,0.00168162,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21531,Q#919 - >seq7566,non-specific,274008,47,259,0.0024662,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21532,Q#919 - >seq7566,non-specific,313022,71,154,0.00301875,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21533,Q#919 - >seq7566,superfamily,313022,71,154,0.00301875,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21534,Q#919 - >seq7566,non-specific,336322,34,168,0.00306416,39.0374,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21535,Q#919 - >seq7566,non-specific,224117,71,239,0.00375663,38.9272,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21536,Q#919 - >seq7566,superfamily,224117,71,239,0.00375663,38.9272,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21537,Q#919 - >seq7566,non-specific,235461,59,130,0.00509318,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21538,Q#919 - >seq7566,superfamily,235461,59,130,0.00509318,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21539,Q#919 - >seq7566,non-specific,224117,66,157,0.00565292,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21540,Q#919 - >seq7566,non-specific,224117,50,151,0.0074655,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21541,Q#919 - >seq7566,non-specific,274009,50,156,0.00790206,38.1251,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21542,Q#919 - >seq7566,superfamily,274009,50,156,0.00790206,38.1251,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
21543,Q#919 - >seq7566,non-specific,273690,75,197,0.00798766,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21544,Q#919 - >seq7566,superfamily,355611,75,197,0.00798766,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21545,Q#919 - >seq7566,non-specific,222878,53,198,0.00894571,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21546,Q#919 - >seq7566,non-specific,235600,37,131,0.00935409,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21547,Q#919 - >seq7566,superfamily,235600,37,131,0.00935409,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
21548,Q#919 - >seq7566,non-specific,224117,55,151,0.00968861,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
21549,Q#921 - >seq7568,non-specific,335182,147,244,4.873759999999999e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21550,Q#921 - >seq7568,superfamily,335182,147,244,4.873759999999999e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21551,Q#921 - >seq7568,non-specific,340205,247,311,4.90592e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21552,Q#921 - >seq7568,superfamily,340205,247,311,4.90592e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21553,Q#921 - >seq7568,non-specific,340204,102,144,4.00649e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21554,Q#921 - >seq7568,superfamily,340204,102,144,4.00649e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs1_chimp,pars,CompleteHit
21555,Q#921 - >seq7568,non-specific,224117,44,194,0.00049641,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21556,Q#921 - >seq7568,superfamily,224117,44,194,0.00049641,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21557,Q#921 - >seq7568,non-specific,274008,29,196,0.00186433,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21558,Q#921 - >seq7568,superfamily,274008,29,196,0.00186433,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21559,Q#921 - >seq7568,non-specific,224117,56,173,0.001887,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,BothTerminiTruncated
21560,Q#921 - >seq7568,non-specific,235175,31,147,0.00253851,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,C-TerminusTruncated
21561,Q#921 - >seq7568,superfamily,235175,31,147,0.00253851,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,C-TerminusTruncated
21562,Q#921 - >seq7568,non-specific,235175,24,147,0.00321342,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,BothTerminiTruncated
21563,Q#921 - >seq7568,non-specific,337766,42,120,0.00754069,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21564,Q#921 - >seq7568,superfamily,337766,42,120,0.00754069,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8A,ORF1,hs1_chimp,pars,N-TerminusTruncated
21565,Q#921 - >seq7568,non-specific,179385,49,136,0.00930705,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,BothTerminiTruncated
21566,Q#921 - >seq7568,superfamily,179385,49,136,0.00930705,37.7122,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs1_chimp.pars.frame3,1909131014_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs1_chimp,pars,BothTerminiTruncated
21567,Q#922 - >seq7569,non-specific,335182,157,254,2.5720400000000002e-47,155.153,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21568,Q#922 - >seq7569,superfamily,335182,157,254,2.5720400000000002e-47,155.153,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21569,Q#922 - >seq7569,non-specific,340205,257,321,7.37672e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21570,Q#922 - >seq7569,superfamily,340205,257,321,7.37672e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21571,Q#922 - >seq7569,non-specific,340204,112,154,9.53484e-09,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21572,Q#922 - >seq7569,superfamily,340204,112,154,9.53484e-09,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs5_gmonkey,marg,CompleteHit
21573,Q#922 - >seq7569,non-specific,337766,52,133,0.000435709,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21574,Q#922 - >seq7569,superfamily,337766,52,133,0.000435709,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21575,Q#922 - >seq7569,non-specific,179385,61,146,0.0005754509999999999,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21576,Q#922 - >seq7569,superfamily,179385,61,146,0.0005754509999999999,41.5642,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21577,Q#922 - >seq7569,non-specific,224117,66,151,0.000681945,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21578,Q#922 - >seq7569,superfamily,224117,66,151,0.000681945,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21579,Q#922 - >seq7569,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21580,Q#922 - >seq7569,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21581,Q#922 - >seq7569,non-specific,222878,67,151,0.0007894919999999999,40.7681,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21582,Q#922 - >seq7569,superfamily,222878,67,151,0.0007894919999999999,40.7681,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21583,Q#922 - >seq7569,non-specific,335555,66,133,0.000849247,40.7068,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21584,Q#922 - >seq7569,superfamily,354396,66,133,0.000849247,40.7068,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21585,Q#922 - >seq7569,non-specific,235175,55,143,0.000875918,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21586,Q#922 - >seq7569,superfamily,235175,55,143,0.000875918,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21587,Q#922 - >seq7569,non-specific,335556,66,150,0.000989145,39.4385,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21588,Q#922 - >seq7569,superfamily,335556,66,150,0.000989145,39.4385,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21589,Q#922 - >seq7569,non-specific,336322,36,134,0.00167326,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21590,Q#922 - >seq7569,superfamily,336322,36,134,0.00167326,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21591,Q#922 - >seq7569,non-specific,274008,56,212,0.00168162,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21592,Q#922 - >seq7569,superfamily,274008,56,212,0.00168162,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21593,Q#922 - >seq7569,non-specific,274008,47,259,0.0024662,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21594,Q#922 - >seq7569,non-specific,313022,71,154,0.00301875,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21595,Q#922 - >seq7569,superfamily,313022,71,154,0.00301875,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21596,Q#922 - >seq7569,non-specific,336322,34,168,0.00306416,39.0374,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21597,Q#922 - >seq7569,non-specific,224117,71,239,0.00375663,38.9272,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21598,Q#922 - >seq7569,superfamily,224117,71,239,0.00375663,38.9272,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21599,Q#922 - >seq7569,non-specific,235461,59,130,0.00509318,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21600,Q#922 - >seq7569,superfamily,235461,59,130,0.00509318,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21601,Q#922 - >seq7569,non-specific,224117,66,157,0.00565292,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21602,Q#922 - >seq7569,non-specific,224117,50,151,0.0074655,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21603,Q#922 - >seq7569,non-specific,274009,50,156,0.00790206,38.1251,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21604,Q#922 - >seq7569,superfamily,274009,50,156,0.00790206,38.1251,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
21605,Q#922 - >seq7569,non-specific,273690,75,197,0.00798766,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21606,Q#922 - >seq7569,superfamily,355611,75,197,0.00798766,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21607,Q#922 - >seq7569,non-specific,222878,53,198,0.00894571,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21608,Q#922 - >seq7569,non-specific,235600,37,131,0.00935409,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21609,Q#922 - >seq7569,superfamily,235600,37,131,0.00935409,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
21610,Q#922 - >seq7569,non-specific,224117,55,151,0.00968861,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs5_gmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
21611,Q#925 - >seq7572,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21612,Q#925 - >seq7572,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21613,Q#925 - >seq7572,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21614,Q#925 - >seq7572,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21615,Q#925 - >seq7572,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21616,Q#925 - >seq7572,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21617,Q#925 - >seq7572,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21618,Q#925 - >seq7572,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21619,Q#925 - >seq7572,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,pars,CompleteHit
21620,Q#925 - >seq7572,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21621,Q#925 - >seq7572,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21622,Q#925 - >seq7572,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21623,Q#925 - >seq7572,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21624,Q#925 - >seq7572,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21625,Q#925 - >seq7572,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21626,Q#925 - >seq7572,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21627,Q#925 - >seq7572,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21628,Q#925 - >seq7572,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21629,Q#925 - >seq7572,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21630,Q#925 - >seq7572,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21631,Q#925 - >seq7572,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21632,Q#925 - >seq7572,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21633,Q#925 - >seq7572,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21634,Q#925 - >seq7572,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21635,Q#925 - >seq7572,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21636,Q#925 - >seq7572,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21637,Q#925 - >seq7572,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21638,Q#925 - >seq7572,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21639,Q#925 - >seq7572,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21640,Q#925 - >seq7572,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21641,Q#925 - >seq7572,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21642,Q#925 - >seq7572,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21643,Q#925 - >seq7572,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21644,Q#925 - >seq7572,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21645,Q#925 - >seq7572,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21646,Q#925 - >seq7572,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21647,Q#925 - >seq7572,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21648,Q#925 - >seq7572,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21649,Q#925 - >seq7572,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21650,Q#925 - >seq7572,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21651,Q#925 - >seq7572,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21652,Q#925 - >seq7572,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21653,Q#925 - >seq7572,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21654,Q#925 - >seq7572,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21655,Q#925 - >seq7572,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21656,Q#925 - >seq7572,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21657,Q#925 - >seq7572,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21658,Q#925 - >seq7572,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21659,Q#925 - >seq7572,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21660,Q#925 - >seq7572,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21661,Q#925 - >seq7572,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21662,Q#925 - >seq7572,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21663,Q#925 - >seq7572,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
21664,Q#925 - >seq7572,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21665,Q#925 - >seq7572,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21666,Q#925 - >seq7572,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21667,Q#925 - >seq7572,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21668,Q#925 - >seq7572,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21669,Q#925 - >seq7572,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21670,Q#925 - >seq7572,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21671,Q#925 - >seq7572,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21672,Q#925 - >seq7572,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21673,Q#925 - >seq7572,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21674,Q#925 - >seq7572,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21675,Q#925 - >seq7572,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21676,Q#925 - >seq7572,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
21677,Q#925 - >seq7572,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21678,Q#925 - >seq7572,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21679,Q#925 - >seq7572,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.pars.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
21680,Q#928 - >seq7575,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21681,Q#928 - >seq7575,superfamily,335182,157,254,5.52025e-47,153.998,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21682,Q#928 - >seq7575,non-specific,335182,157,254,5.52025e-47,153.998,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21683,Q#928 - >seq7575,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21684,Q#928 - >seq7575,superfamily,340205,257,321,1.09151e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21685,Q#928 - >seq7575,non-specific,340205,257,321,1.09151e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21686,Q#928 - >seq7575,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21687,Q#928 - >seq7575,superfamily,340204,112,154,3.1115700000000002e-09,52.0248,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21688,Q#928 - >seq7575,non-specific,340204,112,154,3.1115700000000002e-09,52.0248,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs6_sqmonkey,marg,CompleteHit
21689,Q#928 - >seq7575,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21690,Q#928 - >seq7575,superfamily,337766,52,141,0.00020286799999999998,42.5999,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21691,Q#928 - >seq7575,non-specific,337766,52,141,0.00020286799999999998,42.5999,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21692,Q#928 - >seq7575,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21693,Q#928 - >seq7575,superfamily,224117,55,151,0.0006701610000000001,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21694,Q#928 - >seq7575,non-specific,224117,55,151,0.0006701610000000001,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21695,Q#928 - >seq7575,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21696,Q#928 - >seq7575,superfamily,222878,67,151,0.000692102,41.1533,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21697,Q#928 - >seq7575,non-specific,222878,67,151,0.000692102,41.1533,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21698,Q#928 - >seq7575,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21699,Q#928 - >seq7575,superfamily,235175,55,143,0.000704164,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21700,Q#928 - >seq7575,non-specific,235175,55,143,0.000704164,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21701,Q#928 - >seq7575,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21702,Q#928 - >seq7575,superfamily,274765,48,128,0.0007665889999999999,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21703,Q#928 - >seq7575,non-specific,274765,48,128,0.0007665889999999999,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21704,Q#928 - >seq7575,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21705,Q#928 - >seq7575,non-specific,224117,66,151,0.00083328,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21706,Q#928 - >seq7575,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21707,Q#928 - >seq7575,superfamily,274008,56,212,0.00098008,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21708,Q#928 - >seq7575,non-specific,274008,56,212,0.00098008,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21709,Q#928 - >seq7575,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21710,Q#928 - >seq7575,superfamily,335556,66,150,0.00150365,38.6681,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21711,Q#928 - >seq7575,non-specific,335556,66,150,0.00150365,38.6681,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21712,Q#928 - >seq7575,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21713,Q#928 - >seq7575,superfamily,336322,36,134,0.00150608,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21714,Q#928 - >seq7575,non-specific,336322,36,134,0.00150608,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21715,Q#928 - >seq7575,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21716,Q#928 - >seq7575,non-specific,224117,50,151,0.0019058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21717,Q#928 - >seq7575,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21718,Q#928 - >seq7575,superfamily,224117,71,239,0.00234847,39.6976,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21719,Q#928 - >seq7575,non-specific,224117,71,239,0.00234847,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21720,Q#928 - >seq7575,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21721,Q#928 - >seq7575,superfamily,274008,47,259,0.00264397,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21722,Q#928 - >seq7575,non-specific,274008,47,259,0.00264397,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21723,Q#928 - >seq7575,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21724,Q#928 - >seq7575,superfamily,179385,61,146,0.00296754,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21725,Q#928 - >seq7575,non-specific,179385,61,146,0.00296754,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21726,Q#928 - >seq7575,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21727,Q#928 - >seq7575,non-specific,336322,35,168,0.00361934,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21728,Q#928 - >seq7575,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21729,Q#928 - >seq7575,superfamily,354396,66,141,0.00400026,38.7808,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21730,Q#928 - >seq7575,non-specific,335555,66,141,0.00400026,38.7808,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21731,Q#928 - >seq7575,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21732,Q#928 - >seq7575,non-specific,224117,56,150,0.00439316,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
21733,Q#928 - >seq7575,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21734,Q#928 - >seq7575,non-specific,224117,55,151,0.00470962,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21735,Q#928 - >seq7575,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21736,Q#928 - >seq7575,superfamily,235461,59,130,0.00532252,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21737,Q#928 - >seq7575,non-specific,235461,59,130,0.00532252,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21738,Q#928 - >seq7575,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21739,Q#928 - >seq7575,non-specific,224117,55,151,0.00632917,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21740,Q#928 - >seq7575,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21741,Q#928 - >seq7575,superfamily,337663,69,149,0.0067117999999999995,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21742,Q#928 - >seq7575,non-specific,337663,69,149,0.0067117999999999995,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21743,Q#928 - >seq7575,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21744,Q#928 - >seq7575,superfamily,235600,37,131,0.0088765,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21745,Q#928 - >seq7575,non-specific,235600,37,131,0.0088765,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA7,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
21746,Q#928 - >seq7575,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21747,Q#928 - >seq7575,superfamily,274009,50,150,0.00908064,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21748,Q#928 - >seq7575,non-specific,274009,50,150,0.00908064,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs6_sqmonkey.marg.frame3,1909131014_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
21749,Q#931 - >seq7578,non-specific,335182,147,244,9.897030000000001e-48,155.924,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,pars,CompleteHit
21750,Q#931 - >seq7578,superfamily,335182,147,244,9.897030000000001e-48,155.924,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,pars,CompleteHit
21751,Q#931 - >seq7578,non-specific,340205,247,311,2.9468999999999998e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,pars,CompleteHit
21752,Q#931 - >seq7578,superfamily,340205,247,311,2.9468999999999998e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,pars,CompleteHit
21753,Q#931 - >seq7578,non-specific,340204,102,144,1.2136799999999999e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs0_human,pars,CompleteHit
21754,Q#931 - >seq7578,superfamily,340204,102,144,1.2136799999999999e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA7,ORF1,hs0_human,pars,CompleteHit
21755,Q#931 - >seq7578,non-specific,222878,57,141,0.00017209099999999998,43.0793,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21756,Q#931 - >seq7578,superfamily,222878,57,141,0.00017209099999999998,43.0793,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21757,Q#931 - >seq7578,non-specific,337766,42,131,0.00036843900000000003,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21758,Q#931 - >seq7578,superfamily,337766,42,131,0.00036843900000000003,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21759,Q#931 - >seq7578,non-specific,274765,38,118,0.0005064059999999999,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21760,Q#931 - >seq7578,superfamily,274765,38,118,0.0005064059999999999,41.5514,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21761,Q#931 - >seq7578,non-specific,235175,45,133,0.000660659,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21762,Q#931 - >seq7578,superfamily,235175,45,133,0.000660659,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21763,Q#931 - >seq7578,non-specific,335555,56,123,0.000687352,41.092,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21764,Q#931 - >seq7578,superfamily,354396,56,123,0.000687352,41.092,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21765,Q#931 - >seq7578,non-specific,224117,56,141,0.000691793,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21766,Q#931 - >seq7578,superfamily,224117,56,141,0.000691793,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21767,Q#931 - >seq7578,non-specific,335556,56,140,0.00096601,39.4385,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21768,Q#931 - >seq7578,superfamily,335556,56,140,0.00096601,39.4385,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21769,Q#931 - >seq7578,non-specific,224117,45,141,0.00109874,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21770,Q#931 - >seq7578,non-specific,336322,24,158,0.00126339,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21771,Q#931 - >seq7578,superfamily,336322,24,158,0.00126339,40.193000000000005,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21772,Q#931 - >seq7578,non-specific,274008,37,249,0.00136197,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21773,Q#931 - >seq7578,superfamily,274008,37,249,0.00136197,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21774,Q#931 - >seq7578,non-specific,336322,26,124,0.00142879,40.193000000000005,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21775,Q#931 - >seq7578,non-specific,224117,45,141,0.00153064,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21776,Q#931 - >seq7578,non-specific,274009,40,140,0.00172237,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21777,Q#931 - >seq7578,superfamily,274009,40,140,0.00172237,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21778,Q#931 - >seq7578,non-specific,179385,51,136,0.00172671,40.0234,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21779,Q#931 - >seq7578,superfamily,179385,51,136,0.00172671,40.0234,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21780,Q#931 - >seq7578,non-specific,274008,46,202,0.0017692999999999997,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21781,Q#931 - >seq7578,superfamily,274008,46,202,0.0017692999999999997,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21782,Q#931 - >seq7578,non-specific,224117,40,141,0.00187062,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21783,Q#931 - >seq7578,non-specific,222878,43,188,0.00194983,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21784,Q#931 - >seq7578,non-specific,224117,45,141,0.00195397,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21785,Q#931 - >seq7578,non-specific,224117,46,140,0.00200576,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21786,Q#931 - >seq7578,non-specific,235461,49,120,0.00334506,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21787,Q#931 - >seq7578,superfamily,235461,49,120,0.00334506,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21788,Q#931 - >seq7578,non-specific,224117,45,194,0.00341336,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21789,Q#931 - >seq7578,non-specific,273690,65,147,0.00368593,38.4809,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21790,Q#931 - >seq7578,superfamily,355611,65,147,0.00368593,38.4809,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21791,Q#931 - >seq7578,non-specific,224117,61,229,0.00399289,38.9272,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21792,Q#931 - >seq7578,superfamily,224117,61,229,0.00399289,38.9272,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21793,Q#931 - >seq7578,non-specific,197874,47,146,0.00492433,38.0749,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21794,Q#931 - >seq7578,superfamily,197874,47,146,0.00492433,38.0749,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21795,Q#931 - >seq7578,non-specific,337715,61,128,0.00635018,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21796,Q#931 - >seq7578,superfamily,337715,61,128,0.00635018,37.9785,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21797,Q#931 - >seq7578,non-specific,274008,41,140,0.00732031,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21798,Q#931 - >seq7578,non-specific,313022,61,144,0.00784175,37.9058,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21799,Q#931 - >seq7578,superfamily,313022,61,144,0.00784175,37.9058,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA7,ORF1,hs0_human,pars,N-TerminusTruncated
21800,Q#931 - >seq7578,non-specific,223266,57,131,0.00789851,37.6366,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21801,Q#931 - >seq7578,superfamily,223266,57,131,0.00789851,37.6366,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,pars,BothTerminiTruncated
21802,Q#931 - >seq7578,non-specific,337663,59,139,0.00888291,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21803,Q#931 - >seq7578,superfamily,337663,59,139,0.00888291,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs0_human.pars.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF1,hs0_human,pars,C-TerminusTruncated
21804,Q#934 - >seq7581,non-specific,335182,157,254,7.957239999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,marg,CompleteHit
21805,Q#934 - >seq7581,superfamily,335182,157,254,7.957239999999999e-47,153.613,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,marg,CompleteHit
21806,Q#934 - >seq7581,non-specific,340205,257,321,6.16117e-33,116.667,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,marg,CompleteHit
21807,Q#934 - >seq7581,superfamily,340205,257,321,6.16117e-33,116.667,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA7,ORF1,hs0_human,marg,CompleteHit
21808,Q#934 - >seq7581,non-specific,340204,112,154,2.78027e-08,49.3284,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs0_human,marg,CompleteHit
21809,Q#934 - >seq7581,superfamily,340204,112,154,2.78027e-08,49.3284,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA7,ORF1,hs0_human,marg,CompleteHit
21810,Q#934 - >seq7581,non-specific,222878,67,151,0.000218983,42.6941,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21811,Q#934 - >seq7581,superfamily,222878,67,151,0.000218983,42.6941,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21812,Q#934 - >seq7581,non-specific,337766,52,141,0.00048043300000000005,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21813,Q#934 - >seq7581,superfamily,337766,52,141,0.00048043300000000005,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21814,Q#934 - >seq7581,non-specific,274765,48,128,0.000534241,41.5514,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21815,Q#934 - >seq7581,superfamily,274765,48,128,0.000534241,41.5514,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21816,Q#934 - >seq7581,non-specific,335555,66,133,0.000805501,40.7068,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21817,Q#934 - >seq7581,superfamily,354396,66,133,0.000805501,40.7068,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21818,Q#934 - >seq7581,non-specific,235175,55,143,0.00102494,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21819,Q#934 - >seq7581,superfamily,235175,55,143,0.00102494,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21820,Q#934 - >seq7581,non-specific,224117,66,151,0.00110117,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21821,Q#934 - >seq7581,superfamily,224117,66,151,0.00110117,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21822,Q#934 - >seq7581,non-specific,335556,66,150,0.00135738,39.0533,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21823,Q#934 - >seq7581,superfamily,335556,66,150,0.00135738,39.0533,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21824,Q#934 - >seq7581,non-specific,224117,55,151,0.00188928,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21825,Q#934 - >seq7581,non-specific,336322,34,168,0.00189186,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21826,Q#934 - >seq7581,superfamily,336322,34,168,0.00189186,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21827,Q#934 - >seq7581,non-specific,336322,36,134,0.00192534,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21828,Q#934 - >seq7581,non-specific,274008,47,259,0.00207227,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21829,Q#934 - >seq7581,superfamily,274008,47,259,0.00207227,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21830,Q#934 - >seq7581,non-specific,179385,61,146,0.00242839,39.6382,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21831,Q#934 - >seq7581,superfamily,179385,61,146,0.00242839,39.6382,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21832,Q#934 - >seq7581,non-specific,224117,55,151,0.00245291,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21833,Q#934 - >seq7581,non-specific,274008,56,212,0.00248775,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21834,Q#934 - >seq7581,superfamily,274008,56,212,0.00248775,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21835,Q#934 - >seq7581,non-specific,274009,50,150,0.00264205,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21836,Q#934 - >seq7581,superfamily,274009,50,150,0.00264205,39.6659,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21837,Q#934 - >seq7581,non-specific,222878,53,198,0.00276684,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21838,Q#934 - >seq7581,non-specific,224117,50,151,0.00291911,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21839,Q#934 - >seq7581,non-specific,224117,55,151,0.00302247,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21840,Q#934 - >seq7581,non-specific,224117,56,150,0.00315683,39.3124,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21841,Q#934 - >seq7581,non-specific,235461,59,130,0.00358031,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21842,Q#934 - >seq7581,superfamily,235461,59,130,0.00358031,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21843,Q#934 - >seq7581,non-specific,273690,75,157,0.00442097,38.4809,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21844,Q#934 - >seq7581,superfamily,355611,75,157,0.00442097,38.4809,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21845,Q#934 - >seq7581,non-specific,224117,55,204,0.00575205,38.542,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21846,Q#934 - >seq7581,non-specific,224117,71,239,0.00632917,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21847,Q#934 - >seq7581,superfamily,224117,71,239,0.00632917,38.1568,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21848,Q#934 - >seq7581,non-specific,197874,57,156,0.00692763,37.6897,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21849,Q#934 - >seq7581,superfamily,197874,57,156,0.00692763,37.6897,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21850,Q#934 - >seq7581,non-specific,337715,71,138,0.00709637,37.9785,pfam10359,Fmp27_WPPW,NC,cl26543,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21851,Q#934 - >seq7581,superfamily,337715,71,138,0.00709637,37.9785,cl26543,Fmp27_WPPW superfamily,NC, - ,RNA pol II promoter Fmp27 protein domain; Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305.,L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21852,Q#934 - >seq7581,non-specific,223266,67,141,0.00922356,37.6366,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21853,Q#934 - >seq7581,superfamily,223266,67,141,0.00922356,37.6366,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF1,hs0_human,marg,BothTerminiTruncated
21854,Q#934 - >seq7581,non-specific,313022,71,154,0.00972982,37.5206,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21855,Q#934 - >seq7581,superfamily,313022,71,154,0.00972982,37.5206,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA7,ORF1,hs0_human,marg,N-TerminusTruncated
21856,Q#934 - >seq7581,non-specific,337663,69,149,0.00982324,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21857,Q#934 - >seq7581,superfamily,337663,69,149,0.00982324,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA7.ORF1.hs0_human.marg.frame3,1909131014_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF1,hs0_human,marg,C-TerminusTruncated
21858,Q#938 - >seq7585,non-specific,335182,157,254,5.52082e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21859,Q#938 - >seq7585,superfamily,335182,157,254,5.52082e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21860,Q#938 - >seq7585,non-specific,335182,157,254,5.52082e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21861,Q#938 - >seq7585,non-specific,340205,257,321,1.20451e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21862,Q#938 - >seq7585,superfamily,340205,257,321,1.20451e-33,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21863,Q#938 - >seq7585,non-specific,340205,257,321,1.20451e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21864,Q#938 - >seq7585,non-specific,340204,112,154,6.66003e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21865,Q#938 - >seq7585,superfamily,340204,112,154,6.66003e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21866,Q#938 - >seq7585,non-specific,340204,112,154,6.66003e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,marg,CompleteHit
21867,Q#938 - >seq7585,non-specific,224117,66,151,0.00269927,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21868,Q#938 - >seq7585,superfamily,224117,66,151,0.00269927,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21869,Q#938 - >seq7585,non-specific,224117,66,151,0.00269927,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21870,Q#938 - >seq7585,non-specific,222878,53,198,0.00369448,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21871,Q#938 - >seq7585,superfamily,222878,53,198,0.00369448,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21872,Q#938 - >seq7585,non-specific,222878,53,198,0.00369448,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.marg.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,marg,BothTerminiTruncated
21873,Q#942 - >seq7589,non-specific,335182,157,254,5.52082e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21874,Q#942 - >seq7589,superfamily,335182,157,254,5.52082e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21875,Q#942 - >seq7589,non-specific,335182,157,254,5.52082e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21876,Q#942 - >seq7589,non-specific,340205,257,321,1.20451e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21877,Q#942 - >seq7589,superfamily,340205,257,321,1.20451e-33,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21878,Q#942 - >seq7589,non-specific,340205,257,321,1.20451e-33,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21879,Q#942 - >seq7589,non-specific,340204,112,154,6.66003e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21880,Q#942 - >seq7589,superfamily,340204,112,154,6.66003e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21881,Q#942 - >seq7589,non-specific,340204,112,154,6.66003e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs2_gorilla,pars,CompleteHit
21882,Q#942 - >seq7589,non-specific,224117,66,151,0.00269927,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21883,Q#942 - >seq7589,superfamily,224117,66,151,0.00269927,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21884,Q#942 - >seq7589,non-specific,224117,66,151,0.00269927,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21885,Q#942 - >seq7589,non-specific,222878,53,198,0.00369448,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21886,Q#942 - >seq7589,superfamily,222878,53,198,0.00369448,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21887,Q#942 - >seq7589,non-specific,222878,53,198,0.00369448,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs2_gorilla.pars.frame3,1909131017_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs2_gorilla,pars,BothTerminiTruncated
21888,Q#945 - >seq7592,non-specific,335182,147,244,2.4503999999999998e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21889,Q#945 - >seq7592,superfamily,335182,147,244,2.4503999999999998e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21890,Q#945 - >seq7592,non-specific,335182,147,244,2.4503999999999998e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21891,Q#945 - >seq7592,non-specific,340205,247,311,1.33041e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21892,Q#945 - >seq7592,superfamily,340205,247,311,1.33041e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21893,Q#945 - >seq7592,non-specific,340205,247,311,1.33041e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21894,Q#945 - >seq7592,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21895,Q#945 - >seq7592,superfamily,340204,102,144,8.91821e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21896,Q#945 - >seq7592,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,pars,CompleteHit
21897,Q#945 - >seq7592,non-specific,224117,56,173,0.00226614,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21898,Q#945 - >seq7592,superfamily,224117,56,173,0.00226614,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21899,Q#945 - >seq7592,non-specific,224117,56,173,0.00226614,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21900,Q#945 - >seq7592,non-specific,274008,29,196,0.00246422,39.6547,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,N-TerminusTruncated
21901,Q#945 - >seq7592,superfamily,274008,29,196,0.00246422,39.6547,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,N-TerminusTruncated
21902,Q#945 - >seq7592,non-specific,274008,29,196,0.00246422,39.6547,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,N-TerminusTruncated
21903,Q#945 - >seq7592,non-specific,179385,49,136,0.00291624,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21904,Q#945 - >seq7592,superfamily,179385,49,136,0.00291624,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21905,Q#945 - >seq7592,non-specific,179385,49,136,0.00291624,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21906,Q#945 - >seq7592,non-specific,235175,31,147,0.00304942,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,C-TerminusTruncated
21907,Q#945 - >seq7592,superfamily,235175,31,147,0.00304942,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,C-TerminusTruncated
21908,Q#945 - >seq7592,non-specific,235175,31,147,0.00304942,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,C-TerminusTruncated
21909,Q#945 - >seq7592,non-specific,235175,25,147,0.00389379,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21910,Q#945 - >seq7592,non-specific,235175,25,147,0.00389379,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21911,Q#945 - >seq7592,non-specific,224117,44,194,0.00859115,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21912,Q#945 - >seq7592,superfamily,224117,44,194,0.00859115,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21913,Q#945 - >seq7592,non-specific,224117,44,194,0.00859115,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21914,Q#945 - >seq7592,non-specific,274009,57,138,0.00941612,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21915,Q#945 - >seq7592,superfamily,274009,57,138,0.00941612,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21916,Q#945 - >seq7592,non-specific,274009,57,138,0.00941612,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.pars.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,pars,BothTerminiTruncated
21917,Q#948 - >seq7595,non-specific,335182,147,244,2.4503999999999998e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21918,Q#948 - >seq7595,superfamily,335182,147,244,2.4503999999999998e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21919,Q#948 - >seq7595,non-specific,335182,147,244,2.4503999999999998e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21920,Q#948 - >seq7595,non-specific,340205,247,311,1.33041e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21921,Q#948 - >seq7595,superfamily,340205,247,311,1.33041e-32,115.51100000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21922,Q#948 - >seq7595,non-specific,340205,247,311,1.33041e-32,115.51100000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21923,Q#948 - >seq7595,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21924,Q#948 - >seq7595,superfamily,340204,102,144,8.91821e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21925,Q#948 - >seq7595,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs0_human,marg,CompleteHit
21926,Q#948 - >seq7595,non-specific,224117,56,173,0.00226614,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21927,Q#948 - >seq7595,superfamily,224117,56,173,0.00226614,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21928,Q#948 - >seq7595,non-specific,224117,56,173,0.00226614,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21929,Q#948 - >seq7595,non-specific,274008,29,196,0.00246422,39.6547,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,N-TerminusTruncated
21930,Q#948 - >seq7595,superfamily,274008,29,196,0.00246422,39.6547,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,N-TerminusTruncated
21931,Q#948 - >seq7595,non-specific,274008,29,196,0.00246422,39.6547,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,N-TerminusTruncated
21932,Q#948 - >seq7595,non-specific,179385,49,136,0.00291624,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21933,Q#948 - >seq7595,superfamily,179385,49,136,0.00291624,39.253,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21934,Q#948 - >seq7595,non-specific,179385,49,136,0.00291624,39.253,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21935,Q#948 - >seq7595,non-specific,235175,31,147,0.00304942,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,C-TerminusTruncated
21936,Q#948 - >seq7595,superfamily,235175,31,147,0.00304942,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,C-TerminusTruncated
21937,Q#948 - >seq7595,non-specific,235175,31,147,0.00304942,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,C-TerminusTruncated
21938,Q#948 - >seq7595,non-specific,235175,25,147,0.00389379,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21939,Q#948 - >seq7595,non-specific,235175,25,147,0.00389379,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21940,Q#948 - >seq7595,non-specific,224117,44,194,0.00859115,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21941,Q#948 - >seq7595,superfamily,224117,44,194,0.00859115,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21942,Q#948 - >seq7595,non-specific,224117,44,194,0.00859115,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21943,Q#948 - >seq7595,non-specific,274009,57,138,0.00941612,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21944,Q#948 - >seq7595,superfamily,274009,57,138,0.00941612,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21945,Q#948 - >seq7595,non-specific,274009,57,138,0.00941612,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs0_human.marg.frame3,1909131017_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs0_human,marg,BothTerminiTruncated
21946,Q#950 - >seq7597,non-specific,335182,156,252,2.83768e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21947,Q#950 - >seq7597,superfamily,335182,156,252,2.83768e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21948,Q#950 - >seq7597,non-specific,335182,156,252,2.83768e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21949,Q#950 - >seq7597,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21950,Q#950 - >seq7597,superfamily,340205,255,318,8.44937e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21951,Q#950 - >seq7597,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21952,Q#950 - >seq7597,non-specific,235175,49,156,8.64268e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21953,Q#950 - >seq7597,superfamily,235175,49,156,8.64268e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21954,Q#950 - >seq7597,non-specific,235175,49,156,8.64268e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21955,Q#950 - >seq7597,non-specific,340204,111,153,1.7881199999999997e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21956,Q#950 - >seq7597,superfamily,340204,111,153,1.7881199999999997e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21957,Q#950 - >seq7597,non-specific,340204,111,153,1.7881199999999997e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,marg,CompleteHit
21958,Q#950 - >seq7597,non-specific,237177,42,149,2.1665e-05,45.5394,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21959,Q#950 - >seq7597,superfamily,237177,42,149,2.1665e-05,45.5394,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21960,Q#950 - >seq7597,non-specific,237177,42,149,2.1665e-05,45.5394,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21961,Q#950 - >seq7597,non-specific,274009,33,150,4.61679e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21962,Q#950 - >seq7597,superfamily,274009,33,150,4.61679e-05,45.0587,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21963,Q#950 - >seq7597,non-specific,274009,33,150,4.61679e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21964,Q#950 - >seq7597,non-specific,274008,41,202,0.00021993700000000002,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21965,Q#950 - >seq7597,superfamily,274008,41,202,0.00021993700000000002,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21966,Q#950 - >seq7597,non-specific,274008,41,202,0.00021993700000000002,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21967,Q#950 - >seq7597,non-specific,223250,47,159,0.00100252,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21968,Q#950 - >seq7597,superfamily,223250,47,159,0.00100252,40.2741,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21969,Q#950 - >seq7597,non-specific,223250,47,159,0.00100252,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21970,Q#950 - >seq7597,non-specific,336159,60,145,0.00137988,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21971,Q#950 - >seq7597,superfamily,336159,60,145,0.00137988,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21972,Q#950 - >seq7597,non-specific,336159,60,145,0.00137988,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21973,Q#950 - >seq7597,non-specific,274009,60,162,0.00180622,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21974,Q#950 - >seq7597,non-specific,274009,60,162,0.00180622,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21975,Q#950 - >seq7597,non-specific,224117,28,161,0.00181365,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21976,Q#950 - >seq7597,superfamily,224117,28,161,0.00181365,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21977,Q#950 - >seq7597,non-specific,224117,28,161,0.00181365,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21978,Q#950 - >seq7597,non-specific,310273,60,148,0.00470208,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21979,Q#950 - >seq7597,superfamily,310273,60,148,0.00470208,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21980,Q#950 - >seq7597,non-specific,310273,60,148,0.00470208,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21981,Q#950 - >seq7597,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21982,Q#950 - >seq7597,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21983,Q#950 - >seq7597,non-specific,226400,79,149,0.00639069,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21984,Q#950 - >seq7597,superfamily,226400,79,149,0.00639069,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21985,Q#950 - >seq7597,non-specific,226400,79,149,0.00639069,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,C-TerminusTruncated
21986,Q#950 - >seq7597,non-specific,274091,65,149,0.00697873,38.0606,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21987,Q#950 - >seq7597,superfamily,274091,65,149,0.00697873,38.0606,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21988,Q#950 - >seq7597,non-specific,274091,65,149,0.00697873,38.0606,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21989,Q#950 - >seq7597,non-specific,275056,60,151,0.00722442,36.9097,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21990,Q#950 - >seq7597,superfamily,275056,60,151,0.00722442,36.9097,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21991,Q#950 - >seq7597,non-specific,275056,60,151,0.00722442,36.9097,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs3_orang,marg,N-TerminusTruncated
21992,Q#950 - >seq7597,non-specific,227512,50,143,0.00880235,37.6542,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21993,Q#950 - >seq7597,superfamily,227512,50,143,0.00880235,37.6542,cl34933,HEC1 superfamily,NC, - ,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21994,Q#950 - >seq7597,non-specific,227512,50,143,0.00880235,37.6542,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21995,Q#950 - >seq7597,non-specific,224117,24,149,0.00933908,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21996,Q#950 - >seq7597,non-specific,224117,24,149,0.00933908,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21997,Q#950 - >seq7597,non-specific,224117,46,149,0.00950316,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21998,Q#950 - >seq7597,non-specific,224117,46,149,0.00950316,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.marg.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,marg,BothTerminiTruncated
21999,Q#953 - >seq7600,non-specific,335182,156,252,2.83768e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22000,Q#953 - >seq7600,superfamily,335182,156,252,2.83768e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22001,Q#953 - >seq7600,non-specific,335182,156,252,2.83768e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22002,Q#953 - >seq7600,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22003,Q#953 - >seq7600,superfamily,340205,255,318,8.44937e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22004,Q#953 - >seq7600,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22005,Q#953 - >seq7600,non-specific,235175,49,156,8.64268e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22006,Q#953 - >seq7600,superfamily,235175,49,156,8.64268e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22007,Q#953 - >seq7600,non-specific,235175,49,156,8.64268e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22008,Q#953 - >seq7600,non-specific,340204,111,153,1.7881199999999997e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22009,Q#953 - >seq7600,superfamily,340204,111,153,1.7881199999999997e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22010,Q#953 - >seq7600,non-specific,340204,111,153,1.7881199999999997e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs3_orang,pars,CompleteHit
22011,Q#953 - >seq7600,non-specific,237177,42,149,2.1665e-05,45.5394,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22012,Q#953 - >seq7600,superfamily,237177,42,149,2.1665e-05,45.5394,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22013,Q#953 - >seq7600,non-specific,237177,42,149,2.1665e-05,45.5394,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22014,Q#953 - >seq7600,non-specific,274009,33,150,4.61679e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22015,Q#953 - >seq7600,superfamily,274009,33,150,4.61679e-05,45.0587,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22016,Q#953 - >seq7600,non-specific,274009,33,150,4.61679e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22017,Q#953 - >seq7600,non-specific,274008,41,202,0.00021993700000000002,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22018,Q#953 - >seq7600,superfamily,274008,41,202,0.00021993700000000002,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22019,Q#953 - >seq7600,non-specific,274008,41,202,0.00021993700000000002,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22020,Q#953 - >seq7600,non-specific,223250,47,159,0.00100252,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22021,Q#953 - >seq7600,superfamily,223250,47,159,0.00100252,40.2741,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22022,Q#953 - >seq7600,non-specific,223250,47,159,0.00100252,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22023,Q#953 - >seq7600,non-specific,336159,60,145,0.00137988,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22024,Q#953 - >seq7600,superfamily,336159,60,145,0.00137988,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22025,Q#953 - >seq7600,non-specific,336159,60,145,0.00137988,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22026,Q#953 - >seq7600,non-specific,274009,60,162,0.00180622,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22027,Q#953 - >seq7600,non-specific,274009,60,162,0.00180622,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22028,Q#953 - >seq7600,non-specific,224117,28,161,0.00181365,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22029,Q#953 - >seq7600,superfamily,224117,28,161,0.00181365,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22030,Q#953 - >seq7600,non-specific,224117,28,161,0.00181365,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22031,Q#953 - >seq7600,non-specific,310273,60,148,0.00470208,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22032,Q#953 - >seq7600,superfamily,310273,60,148,0.00470208,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22033,Q#953 - >seq7600,non-specific,310273,60,148,0.00470208,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22034,Q#953 - >seq7600,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22035,Q#953 - >seq7600,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22036,Q#953 - >seq7600,non-specific,226400,79,149,0.00639069,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22037,Q#953 - >seq7600,superfamily,226400,79,149,0.00639069,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22038,Q#953 - >seq7600,non-specific,226400,79,149,0.00639069,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,C-TerminusTruncated
22039,Q#953 - >seq7600,non-specific,274091,65,149,0.00697873,38.0606,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22040,Q#953 - >seq7600,superfamily,274091,65,149,0.00697873,38.0606,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22041,Q#953 - >seq7600,non-specific,274091,65,149,0.00697873,38.0606,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22042,Q#953 - >seq7600,non-specific,275056,60,151,0.00722442,36.9097,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22043,Q#953 - >seq7600,superfamily,275056,60,151,0.00722442,36.9097,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22044,Q#953 - >seq7600,non-specific,275056,60,151,0.00722442,36.9097,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs3_orang,pars,N-TerminusTruncated
22045,Q#953 - >seq7600,non-specific,227512,50,143,0.00880235,37.6542,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22046,Q#953 - >seq7600,superfamily,227512,50,143,0.00880235,37.6542,cl34933,HEC1 superfamily,NC, - ,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22047,Q#953 - >seq7600,non-specific,227512,50,143,0.00880235,37.6542,COG5185,HEC1,NC,cl34933,"Protein involved in chromosome segregation, interacts with SMC proteins  [Cell cycle control, cell division, chromosome partitioning]; Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22048,Q#953 - >seq7600,non-specific,224117,24,149,0.00933908,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22049,Q#953 - >seq7600,non-specific,224117,24,149,0.00933908,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22050,Q#953 - >seq7600,non-specific,224117,46,149,0.00950316,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22051,Q#953 - >seq7600,non-specific,224117,46,149,0.00950316,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs3_orang.pars.frame3,1909131019_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs3_orang,pars,BothTerminiTruncated
22052,Q#955 - >seq7602,non-specific,335182,156,252,2.2008099999999997e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22053,Q#955 - >seq7602,superfamily,335182,156,252,2.2008099999999997e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22054,Q#955 - >seq7602,non-specific,340205,255,318,1.5592299999999998e-24,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22055,Q#955 - >seq7602,superfamily,340205,255,318,1.5592299999999998e-24,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22056,Q#955 - >seq7602,non-specific,340204,111,153,2.20597e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22057,Q#955 - >seq7602,superfamily,340204,111,153,2.20597e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs2_gorilla,marg,CompleteHit
22058,Q#955 - >seq7602,non-specific,237177,42,149,5.196e-06,47.4654,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22059,Q#955 - >seq7602,superfamily,237177,42,149,5.196e-06,47.4654,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22060,Q#955 - >seq7602,non-specific,235175,49,156,6.633630000000001e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22061,Q#955 - >seq7602,superfamily,235175,49,156,6.633630000000001e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22062,Q#955 - >seq7602,non-specific,274008,41,202,0.00024861,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22063,Q#955 - >seq7602,superfamily,274008,41,202,0.00024861,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22064,Q#955 - >seq7602,non-specific,274009,33,150,0.00043106300000000003,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22065,Q#955 - >seq7602,superfamily,274009,33,150,0.00043106300000000003,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22066,Q#955 - >seq7602,non-specific,188306,43,150,0.00052122,41.4498,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22067,Q#955 - >seq7602,superfamily,188306,43,150,0.00052122,41.4498,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22068,Q#955 - >seq7602,non-specific,224117,28,161,0.0008863580000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22069,Q#955 - >seq7602,superfamily,224117,28,161,0.0008863580000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22070,Q#955 - >seq7602,non-specific,274008,45,150,0.0011682,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22071,Q#955 - >seq7602,non-specific,336159,60,145,0.00132071,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22072,Q#955 - >seq7602,superfamily,336159,60,145,0.00132071,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22073,Q#955 - >seq7602,non-specific,310273,60,150,0.00158627,40.1138,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22074,Q#955 - >seq7602,superfamily,310273,60,150,0.00158627,40.1138,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22075,Q#955 - >seq7602,non-specific,223250,47,159,0.00160162,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22076,Q#955 - >seq7602,superfamily,223250,47,159,0.00160162,39.8889,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
22077,Q#955 - >seq7602,non-specific,274091,65,150,0.00171454,39.9866,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22078,Q#955 - >seq7602,superfamily,274091,65,150,0.00171454,39.9866,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22079,Q#955 - >seq7602,non-specific,275056,53,152,0.00238679,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22080,Q#955 - >seq7602,superfamily,275056,53,152,0.00238679,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
22081,Q#955 - >seq7602,non-specific,274008,60,145,0.00284507,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22082,Q#955 - >seq7602,non-specific,224117,46,149,0.00316975,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22083,Q#955 - >seq7602,non-specific,224117,33,149,0.00494442,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22084,Q#955 - >seq7602,non-specific,274386,11,147,0.00617729,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22085,Q#955 - >seq7602,superfamily,274386,11,147,0.00617729,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22086,Q#955 - >seq7602,non-specific,224117,49,150,0.00757752,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22087,Q#955 - >seq7602,non-specific,274009,33,150,0.009140700000000002,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.marg.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
22088,Q#956 - >seq7603,non-specific,178500,184,211,0.0029465,37.7037,PLN02912,PLN02912,NC,cl31950,"oxidoreductase, 2OG-Fe(II) oxygenase family protein",L1PB1.ORF1.hs4_gibbon.pars.frame2,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22089,Q#956 - >seq7603,superfamily,178500,184,211,0.0029465,37.7037,cl31950,PLN02912 superfamily,NC, - ,"oxidoreductase, 2OG-Fe(II) oxygenase family protein",L1PB1.ORF1.hs4_gibbon.pars.frame2,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22090,Q#959 - >seq7606,non-specific,335182,156,252,2.2008099999999997e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22091,Q#959 - >seq7606,superfamily,335182,156,252,2.2008099999999997e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22092,Q#959 - >seq7606,non-specific,340205,255,318,1.5592299999999998e-24,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22093,Q#959 - >seq7606,superfamily,340205,255,318,1.5592299999999998e-24,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22094,Q#959 - >seq7606,non-specific,340204,111,153,2.20597e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22095,Q#959 - >seq7606,superfamily,340204,111,153,2.20597e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs2_gorilla,pars,CompleteHit
22096,Q#959 - >seq7606,non-specific,237177,42,149,5.196e-06,47.4654,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22097,Q#959 - >seq7606,superfamily,237177,42,149,5.196e-06,47.4654,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22098,Q#959 - >seq7606,non-specific,235175,49,156,6.633630000000001e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22099,Q#959 - >seq7606,superfamily,235175,49,156,6.633630000000001e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22100,Q#959 - >seq7606,non-specific,274008,41,202,0.00024861,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22101,Q#959 - >seq7606,superfamily,274008,41,202,0.00024861,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22102,Q#959 - >seq7606,non-specific,274009,33,150,0.00043106300000000003,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22103,Q#959 - >seq7606,superfamily,274009,33,150,0.00043106300000000003,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22104,Q#959 - >seq7606,non-specific,188306,43,150,0.00052122,41.4498,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22105,Q#959 - >seq7606,superfamily,188306,43,150,0.00052122,41.4498,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22106,Q#959 - >seq7606,non-specific,224117,28,161,0.0008863580000000001,40.8532,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22107,Q#959 - >seq7606,superfamily,224117,28,161,0.0008863580000000001,40.8532,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22108,Q#959 - >seq7606,non-specific,274008,45,150,0.0011682,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22109,Q#959 - >seq7606,non-specific,336159,60,145,0.00132071,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22110,Q#959 - >seq7606,superfamily,336159,60,145,0.00132071,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22111,Q#959 - >seq7606,non-specific,310273,60,150,0.00158627,40.1138,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22112,Q#959 - >seq7606,superfamily,310273,60,150,0.00158627,40.1138,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22113,Q#959 - >seq7606,non-specific,223250,47,159,0.00160162,39.8889,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22114,Q#959 - >seq7606,superfamily,223250,47,159,0.00160162,39.8889,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
22115,Q#959 - >seq7606,non-specific,274091,65,150,0.00171454,39.9866,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22116,Q#959 - >seq7606,superfamily,274091,65,150,0.00171454,39.9866,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22117,Q#959 - >seq7606,non-specific,275056,53,152,0.00238679,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22118,Q#959 - >seq7606,superfamily,275056,53,152,0.00238679,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,N-TerminusTruncated
22119,Q#959 - >seq7606,non-specific,274008,60,145,0.00284507,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22120,Q#959 - >seq7606,non-specific,224117,46,149,0.00316975,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22121,Q#959 - >seq7606,non-specific,224117,33,149,0.00494442,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22122,Q#959 - >seq7606,non-specific,274386,11,147,0.00617729,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22123,Q#959 - >seq7606,superfamily,274386,11,147,0.00617729,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22124,Q#959 - >seq7606,non-specific,224117,49,150,0.00757752,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22125,Q#959 - >seq7606,non-specific,274009,33,150,0.009140700000000002,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs2_gorilla.pars.frame3,1909131019_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs2_gorilla,pars,BothTerminiTruncated
22126,Q#961 - >seq7608,non-specific,335182,155,251,5.04042e-35,122.79700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22127,Q#961 - >seq7608,superfamily,335182,155,251,5.04042e-35,122.79700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22128,Q#961 - >seq7608,non-specific,340205,254,317,4.35608e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22129,Q#961 - >seq7608,superfamily,340205,254,317,4.35608e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22130,Q#961 - >seq7608,non-specific,340204,111,153,3.5934899999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22131,Q#961 - >seq7608,superfamily,340204,111,153,3.5934899999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs1_chimp,marg,CompleteHit
22132,Q#961 - >seq7608,non-specific,237177,42,149,7.83825e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22133,Q#961 - >seq7608,superfamily,237177,42,149,7.83825e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22134,Q#961 - >seq7608,non-specific,235175,49,155,0.000234304,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22135,Q#961 - >seq7608,superfamily,235175,49,155,0.000234304,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22136,Q#961 - >seq7608,non-specific,274008,41,201,0.00144492,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22137,Q#961 - >seq7608,superfamily,274008,41,201,0.00144492,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22138,Q#961 - >seq7608,non-specific,275056,60,152,0.00173523,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22139,Q#961 - >seq7608,superfamily,275056,60,152,0.00173523,38.8357,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22140,Q#961 - >seq7608,non-specific,224117,28,155,0.00190043,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22141,Q#961 - >seq7608,superfamily,224117,28,155,0.00190043,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22142,Q#961 - >seq7608,non-specific,129694,80,146,0.00269878,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22143,Q#961 - >seq7608,superfamily,129694,80,146,0.00269878,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22144,Q#961 - >seq7608,non-specific,274008,45,150,0.0027804,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22145,Q#961 - >seq7608,non-specific,336159,60,145,0.00279047,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22146,Q#961 - >seq7608,superfamily,336159,60,145,0.00279047,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22147,Q#961 - >seq7608,non-specific,235175,60,144,0.00323876,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22148,Q#961 - >seq7608,non-specific,235461,47,169,0.00325872,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22149,Q#961 - >seq7608,superfamily,235461,47,169,0.00325872,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22150,Q#961 - >seq7608,non-specific,274386,27,147,0.00447743,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22151,Q#961 - >seq7608,superfamily,274386,27,147,0.00447743,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22152,Q#961 - >seq7608,non-specific,337663,79,147,0.00635275,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22153,Q#961 - >seq7608,superfamily,337663,79,147,0.00635275,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22154,Q#961 - >seq7608,non-specific,223250,47,150,0.00714659,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22155,Q#961 - >seq7608,superfamily,223250,47,150,0.00714659,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22156,Q#961 - >seq7608,non-specific,274008,60,145,0.00764315,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22157,Q#961 - >seq7608,non-specific,223671,70,161,0.00779412,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22158,Q#961 - >seq7608,superfamily,320984,70,161,0.00779412,37.3045,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22159,Q#961 - >seq7608,non-specific,188306,43,150,0.0078663,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22160,Q#961 - >seq7608,superfamily,188306,43,150,0.0078663,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22161,Q#961 - >seq7608,non-specific,310273,60,148,0.00826284,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22162,Q#961 - >seq7608,superfamily,310273,60,148,0.00826284,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22163,Q#961 - >seq7608,non-specific,313406,73,235,0.00840059,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22164,Q#961 - >seq7608,superfamily,313406,73,235,0.00840059,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,marg,N-TerminusTruncated
22165,Q#961 - >seq7608,non-specific,224117,49,201,0.00844089,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22166,Q#961 - >seq7608,non-specific,235600,70,185,0.00851994,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22167,Q#961 - >seq7608,superfamily,235600,70,185,0.00851994,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22168,Q#961 - >seq7608,non-specific,112704,2,148,0.00870723,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22169,Q#961 - >seq7608,superfamily,112704,2,148,0.00870723,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,marg,C-TerminusTruncated
22170,Q#961 - >seq7608,non-specific,274009,33,150,0.00933295,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22171,Q#961 - >seq7608,superfamily,274009,33,150,0.00933295,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.marg.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,marg,BothTerminiTruncated
22172,Q#963 - >seq7610,non-specific,335182,56,152,1.5083399999999998e-31,110.855,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22173,Q#963 - >seq7610,superfamily,335182,56,152,1.5083399999999998e-31,110.855,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22174,Q#963 - >seq7610,non-specific,340205,155,218,9.346130000000001e-26,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22175,Q#963 - >seq7610,superfamily,340205,155,218,9.346130000000001e-26,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22176,Q#963 - >seq7610,non-specific,340204,11,53,2.30139e-07,45.8616,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22177,Q#963 - >seq7610,superfamily,340204,11,53,2.30139e-07,45.8616,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs4_gibbon,pars,CompleteHit
22178,Q#964 - >seq7611,non-specific,335182,156,252,1.01209e-29,108.929,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22179,Q#964 - >seq7611,superfamily,335182,156,252,1.01209e-29,108.929,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22180,Q#964 - >seq7611,non-specific,340205,255,318,2.22364e-24,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22181,Q#964 - >seq7611,superfamily,340205,255,318,2.22364e-24,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22182,Q#964 - >seq7611,non-specific,340204,111,153,2.36297e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22183,Q#964 - >seq7611,superfamily,340204,111,153,2.36297e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs4_gibbon,marg,CompleteHit
22184,Q#964 - >seq7611,non-specific,237177,42,149,5.15007e-06,47.4654,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22185,Q#964 - >seq7611,superfamily,237177,42,149,5.15007e-06,47.4654,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22186,Q#964 - >seq7611,non-specific,235175,49,156,6.6924000000000005e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22187,Q#964 - >seq7611,superfamily,235175,49,156,6.6924000000000005e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22188,Q#964 - >seq7611,non-specific,274009,33,150,0.00043866900000000004,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22189,Q#964 - >seq7611,superfamily,274009,33,150,0.00043866900000000004,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22190,Q#964 - >seq7611,non-specific,188306,43,150,0.000525835,41.4498,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22191,Q#964 - >seq7611,superfamily,188306,43,150,0.000525835,41.4498,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22192,Q#964 - >seq7611,non-specific,224117,28,163,0.000647137,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22193,Q#964 - >seq7611,superfamily,224117,28,163,0.000647137,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22194,Q#964 - >seq7611,non-specific,274008,41,202,0.000697734,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22195,Q#964 - >seq7611,superfamily,274008,41,202,0.000697734,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22196,Q#964 - >seq7611,non-specific,223250,47,165,0.000710045,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22197,Q#964 - >seq7611,superfamily,223250,47,165,0.000710045,40.6593,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22198,Q#964 - >seq7611,non-specific,274008,45,150,0.00124184,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22199,Q#964 - >seq7611,non-specific,336159,60,145,0.00137988,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22200,Q#964 - >seq7611,superfamily,336159,60,145,0.00137988,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22201,Q#964 - >seq7611,non-specific,310273,60,165,0.00153159,40.1138,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22202,Q#964 - >seq7611,superfamily,310273,60,165,0.00153159,40.1138,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22203,Q#964 - >seq7611,non-specific,237177,44,150,0.00165397,39.7614,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22204,Q#964 - >seq7611,non-specific,274091,65,150,0.00182324,39.6014,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22205,Q#964 - >seq7611,superfamily,274091,65,150,0.00182324,39.6014,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22206,Q#964 - >seq7611,non-specific,275056,60,152,0.00254629,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22207,Q#964 - >seq7611,superfamily,275056,60,152,0.00254629,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
22208,Q#964 - >seq7611,non-specific,274008,60,145,0.00294607,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22209,Q#964 - >seq7611,non-specific,224117,46,149,0.00342853,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22210,Q#964 - >seq7611,non-specific,224117,24,149,0.00490151,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22211,Q#964 - >seq7611,non-specific,224117,33,149,0.00534784,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22212,Q#964 - >seq7611,non-specific,274386,11,147,0.00645489,37.7234,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22213,Q#964 - >seq7611,superfamily,274386,11,147,0.00645489,37.7234,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22214,Q#964 - >seq7611,non-specific,224117,49,150,0.00812435,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22215,Q#968 - >seq7615,non-specific,335182,154,250,3.6566699999999996e-35,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22216,Q#968 - >seq7615,superfamily,335182,154,250,3.6566699999999996e-35,123.182,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22217,Q#968 - >seq7615,non-specific,335182,154,250,3.6566699999999996e-35,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22218,Q#968 - >seq7615,non-specific,340205,253,316,7.93625e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22219,Q#968 - >seq7615,superfamily,340205,253,316,7.93625e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22220,Q#968 - >seq7615,non-specific,340205,253,316,7.93625e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22221,Q#968 - >seq7615,non-specific,340204,110,152,3.37711e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22222,Q#968 - >seq7615,superfamily,340204,110,152,3.37711e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22223,Q#968 - >seq7615,non-specific,340204,110,152,3.37711e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,pars,CompleteHit
22224,Q#968 - >seq7615,non-specific,237177,41,148,7.8595e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22225,Q#968 - >seq7615,superfamily,237177,41,148,7.8595e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22226,Q#968 - >seq7615,non-specific,237177,41,148,7.8595e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22227,Q#968 - >seq7615,non-specific,235175,48,154,0.000220945,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22228,Q#968 - >seq7615,superfamily,235175,48,154,0.000220945,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22229,Q#968 - >seq7615,non-specific,235175,48,154,0.000220945,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22230,Q#968 - >seq7615,non-specific,274008,40,200,0.00143668,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22231,Q#968 - >seq7615,superfamily,274008,40,200,0.00143668,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22232,Q#968 - >seq7615,non-specific,274008,40,200,0.00143668,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22233,Q#968 - >seq7615,non-specific,275056,59,151,0.00171155,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22234,Q#968 - >seq7615,superfamily,275056,59,151,0.00171155,38.8357,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22235,Q#968 - >seq7615,non-specific,275056,59,151,0.00171155,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22236,Q#968 - >seq7615,non-specific,224117,27,154,0.0018733,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22237,Q#968 - >seq7615,superfamily,224117,27,154,0.0018733,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22238,Q#968 - >seq7615,non-specific,224117,27,154,0.0018733,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22239,Q#968 - >seq7615,non-specific,129694,79,145,0.00256938,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22240,Q#968 - >seq7615,superfamily,129694,79,145,0.00256938,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22241,Q#968 - >seq7615,non-specific,129694,79,145,0.00256938,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22242,Q#968 - >seq7615,non-specific,274008,44,149,0.00276493,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22243,Q#968 - >seq7615,non-specific,274008,44,149,0.00276493,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22244,Q#968 - >seq7615,non-specific,336159,59,144,0.00279963,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22245,Q#968 - >seq7615,superfamily,336159,59,144,0.00279963,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22246,Q#968 - >seq7615,non-specific,336159,59,144,0.00279963,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22247,Q#968 - >seq7615,non-specific,235175,59,143,0.00284999,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22248,Q#968 - >seq7615,non-specific,235175,59,143,0.00284999,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22249,Q#968 - >seq7615,non-specific,235461,46,168,0.00327022,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22250,Q#968 - >seq7615,superfamily,235461,46,168,0.00327022,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22251,Q#968 - >seq7615,non-specific,235461,46,168,0.00327022,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22252,Q#968 - >seq7615,non-specific,274386,26,146,0.00418777,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22253,Q#968 - >seq7615,superfamily,274386,26,146,0.00418777,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22254,Q#968 - >seq7615,non-specific,274386,26,146,0.00418777,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22255,Q#968 - >seq7615,non-specific,337663,78,146,0.00620956,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22256,Q#968 - >seq7615,superfamily,337663,78,146,0.00620956,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22257,Q#968 - >seq7615,non-specific,337663,78,146,0.00620956,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22258,Q#968 - >seq7615,non-specific,223250,46,149,0.00692407,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22259,Q#968 - >seq7615,superfamily,223250,46,149,0.00692407,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22260,Q#968 - >seq7615,non-specific,223250,46,149,0.00692407,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22261,Q#968 - >seq7615,non-specific,223671,69,160,0.00709491,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22262,Q#968 - >seq7615,superfamily,320984,69,160,0.00709491,37.3045,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22263,Q#968 - >seq7615,non-specific,223671,69,160,0.00709491,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22264,Q#968 - >seq7615,non-specific,274008,59,144,0.00773578,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22265,Q#968 - >seq7615,non-specific,274008,59,144,0.00773578,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22266,Q#968 - >seq7615,non-specific,188306,42,149,0.00782534,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22267,Q#968 - >seq7615,superfamily,188306,42,149,0.00782534,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22268,Q#968 - >seq7615,non-specific,188306,42,149,0.00782534,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22269,Q#968 - >seq7615,non-specific,313406,72,234,0.00806898,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22270,Q#968 - >seq7615,superfamily,313406,72,234,0.00806898,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22271,Q#968 - >seq7615,non-specific,313406,72,234,0.00806898,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PB1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22272,Q#968 - >seq7615,non-specific,310273,59,147,0.00807685,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22273,Q#968 - >seq7615,superfamily,310273,59,147,0.00807685,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22274,Q#968 - >seq7615,non-specific,310273,59,147,0.00807685,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22275,Q#968 - >seq7615,non-specific,112704,1,147,0.00813329,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22276,Q#968 - >seq7615,superfamily,112704,1,147,0.00813329,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22277,Q#968 - >seq7615,non-specific,112704,1,147,0.00813329,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22278,Q#968 - >seq7615,non-specific,224117,48,200,0.00832299,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22279,Q#968 - >seq7615,non-specific,224117,48,200,0.00832299,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22280,Q#968 - >seq7615,non-specific,235600,69,184,0.00847513,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22281,Q#968 - >seq7615,superfamily,235600,69,184,0.00847513,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22282,Q#968 - >seq7615,non-specific,235600,69,184,0.00847513,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22283,Q#968 - >seq7615,non-specific,274009,32,149,0.00928326,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22284,Q#968 - >seq7615,superfamily,274009,32,149,0.00928326,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22285,Q#968 - >seq7615,non-specific,274009,32,149,0.00928326,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22286,Q#971 - >seq7618,non-specific,335182,154,250,3.6566699999999996e-35,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22287,Q#971 - >seq7618,superfamily,335182,154,250,3.6566699999999996e-35,123.182,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22288,Q#971 - >seq7618,non-specific,335182,154,250,3.6566699999999996e-35,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22289,Q#971 - >seq7618,non-specific,340205,253,316,7.93625e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22290,Q#971 - >seq7618,superfamily,340205,253,316,7.93625e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22291,Q#971 - >seq7618,non-specific,340205,253,316,7.93625e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22292,Q#971 - >seq7618,non-specific,340204,110,152,3.37711e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22293,Q#971 - >seq7618,superfamily,340204,110,152,3.37711e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22294,Q#971 - >seq7618,non-specific,340204,110,152,3.37711e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs5_gmonkey,marg,CompleteHit
22295,Q#971 - >seq7618,non-specific,237177,41,148,7.8595e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22296,Q#971 - >seq7618,superfamily,237177,41,148,7.8595e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22297,Q#971 - >seq7618,non-specific,237177,41,148,7.8595e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22298,Q#971 - >seq7618,non-specific,235175,48,154,0.000220945,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22299,Q#971 - >seq7618,superfamily,235175,48,154,0.000220945,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22300,Q#971 - >seq7618,non-specific,235175,48,154,0.000220945,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22301,Q#971 - >seq7618,non-specific,274008,40,200,0.00143668,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22302,Q#971 - >seq7618,superfamily,274008,40,200,0.00143668,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22303,Q#971 - >seq7618,non-specific,274008,40,200,0.00143668,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22304,Q#971 - >seq7618,non-specific,275056,59,151,0.00171155,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22305,Q#971 - >seq7618,superfamily,275056,59,151,0.00171155,38.8357,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22306,Q#971 - >seq7618,non-specific,275056,59,151,0.00171155,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22307,Q#971 - >seq7618,non-specific,224117,27,154,0.0018733,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22308,Q#971 - >seq7618,superfamily,224117,27,154,0.0018733,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22309,Q#971 - >seq7618,non-specific,224117,27,154,0.0018733,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22310,Q#971 - >seq7618,non-specific,129694,79,145,0.00256938,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22311,Q#971 - >seq7618,superfamily,129694,79,145,0.00256938,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22312,Q#971 - >seq7618,non-specific,129694,79,145,0.00256938,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22313,Q#971 - >seq7618,non-specific,274008,44,149,0.00276493,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22314,Q#971 - >seq7618,non-specific,274008,44,149,0.00276493,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22315,Q#971 - >seq7618,non-specific,336159,59,144,0.00279963,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22316,Q#971 - >seq7618,superfamily,336159,59,144,0.00279963,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22317,Q#971 - >seq7618,non-specific,336159,59,144,0.00279963,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22318,Q#971 - >seq7618,non-specific,235175,59,143,0.00284999,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22319,Q#971 - >seq7618,non-specific,235175,59,143,0.00284999,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22320,Q#971 - >seq7618,non-specific,235461,46,168,0.00327022,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22321,Q#971 - >seq7618,superfamily,235461,46,168,0.00327022,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22322,Q#971 - >seq7618,non-specific,235461,46,168,0.00327022,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22323,Q#971 - >seq7618,non-specific,274386,26,146,0.00418777,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22324,Q#971 - >seq7618,superfamily,274386,26,146,0.00418777,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22325,Q#971 - >seq7618,non-specific,274386,26,146,0.00418777,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22326,Q#971 - >seq7618,non-specific,337663,78,146,0.00620956,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22327,Q#971 - >seq7618,superfamily,337663,78,146,0.00620956,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22328,Q#971 - >seq7618,non-specific,337663,78,146,0.00620956,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22329,Q#971 - >seq7618,non-specific,223250,46,149,0.00692407,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22330,Q#971 - >seq7618,superfamily,223250,46,149,0.00692407,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22331,Q#971 - >seq7618,non-specific,223250,46,149,0.00692407,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22332,Q#971 - >seq7618,non-specific,223671,69,160,0.00709491,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22333,Q#971 - >seq7618,superfamily,320984,69,160,0.00709491,37.3045,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22334,Q#971 - >seq7618,non-specific,223671,69,160,0.00709491,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22335,Q#971 - >seq7618,non-specific,274008,59,144,0.00773578,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22336,Q#971 - >seq7618,non-specific,274008,59,144,0.00773578,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22337,Q#971 - >seq7618,non-specific,188306,42,149,0.00782534,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22338,Q#971 - >seq7618,superfamily,188306,42,149,0.00782534,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22339,Q#971 - >seq7618,non-specific,188306,42,149,0.00782534,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22340,Q#971 - >seq7618,non-specific,313406,72,234,0.00806898,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22341,Q#971 - >seq7618,superfamily,313406,72,234,0.00806898,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22342,Q#971 - >seq7618,non-specific,313406,72,234,0.00806898,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PB1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22343,Q#971 - >seq7618,non-specific,310273,59,147,0.00807685,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22344,Q#971 - >seq7618,superfamily,310273,59,147,0.00807685,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22345,Q#971 - >seq7618,non-specific,310273,59,147,0.00807685,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22346,Q#971 - >seq7618,non-specific,112704,1,147,0.00813329,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22347,Q#971 - >seq7618,superfamily,112704,1,147,0.00813329,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22348,Q#971 - >seq7618,non-specific,112704,1,147,0.00813329,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22349,Q#971 - >seq7618,non-specific,224117,48,200,0.00832299,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22350,Q#971 - >seq7618,non-specific,224117,48,200,0.00832299,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22351,Q#971 - >seq7618,non-specific,235600,69,184,0.00847513,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22352,Q#971 - >seq7618,superfamily,235600,69,184,0.00847513,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22353,Q#971 - >seq7618,non-specific,235600,69,184,0.00847513,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22354,Q#971 - >seq7618,non-specific,274009,32,149,0.00928326,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22355,Q#971 - >seq7618,superfamily,274009,32,149,0.00928326,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22356,Q#971 - >seq7618,non-specific,274009,32,149,0.00928326,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22357,Q#974 - >seq7621,non-specific,335182,145,240,3.3667499999999997e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs0_human,pars,CompleteHit
22358,Q#974 - >seq7621,superfamily,335182,145,240,3.3667499999999997e-31,112.396,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs0_human,pars,CompleteHit
22359,Q#974 - >seq7621,non-specific,340205,243,306,9.018849999999999e-28,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs0_human,pars,CompleteHit
22360,Q#974 - >seq7621,superfamily,340205,243,306,9.018849999999999e-28,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs0_human,pars,CompleteHit
22361,Q#974 - >seq7621,non-specific,340204,99,141,4.152e-06,42.78,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs0_human,pars,CompleteHit
22362,Q#974 - >seq7621,superfamily,340204,99,141,4.152e-06,42.78,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs0_human,pars,CompleteHit
22363,Q#974 - >seq7621,non-specific,314569,81,130,0.00690535,37.396,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs0_human,pars,BothTerminiTruncated
22364,Q#974 - >seq7621,superfamily,327698,81,130,0.00690535,37.396,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs0_human.pars.frame3,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs0_human,pars,BothTerminiTruncated
22365,Q#975 - >seq7622,non-specific,335182,152,247,4.3925699999999995e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB2,ORF1,hs0_human,marg,CompleteHit
22366,Q#975 - >seq7622,superfamily,335182,152,247,4.3925699999999995e-31,112.396,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB2,ORF1,hs0_human,marg,CompleteHit
22367,Q#975 - >seq7622,non-specific,340205,250,313,1.2077e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB2,ORF1,hs0_human,marg,CompleteHit
22368,Q#975 - >seq7622,superfamily,340205,250,313,1.2077e-27,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB2,ORF1,hs0_human,marg,CompleteHit
22369,Q#975 - >seq7622,non-specific,340204,106,148,2.4432e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PB2,ORF1,hs0_human,marg,CompleteHit
22370,Q#975 - >seq7622,superfamily,340204,106,148,2.4432e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PB2,ORF1,hs0_human,marg,CompleteHit
22371,Q#975 - >seq7622,non-specific,235175,35,238,0.000138048,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22372,Q#975 - >seq7622,superfamily,235175,35,238,0.000138048,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22373,Q#975 - >seq7622,non-specific,188306,40,145,0.000160095,42.9906,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22374,Q#975 - >seq7622,superfamily,188306,40,145,0.000160095,42.9906,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22375,Q#975 - >seq7622,non-specific,274009,29,150,0.000182853,43.1327,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,N-TerminusTruncated
22376,Q#975 - >seq7622,superfamily,274009,29,150,0.000182853,43.1327,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,N-TerminusTruncated
22377,Q#975 - >seq7622,non-specific,235943,33,127,0.000512638,41.3418,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22378,Q#975 - >seq7622,superfamily,235943,33,127,0.000512638,41.3418,cl35548,PRK07133 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22379,Q#975 - >seq7622,non-specific,274008,25,144,0.00100096,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22380,Q#975 - >seq7622,superfamily,274008,25,144,0.00100096,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22381,Q#975 - >seq7622,non-specific,224117,29,145,0.00121752,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22382,Q#975 - >seq7622,superfamily,224117,29,145,0.00121752,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22383,Q#975 - >seq7622,non-specific,235175,30,135,0.00152796,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22384,Q#975 - >seq7622,superfamily,235175,30,135,0.00152796,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22385,Q#975 - >seq7622,non-specific,237177,39,145,0.00160467,39.7614,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22386,Q#975 - >seq7622,superfamily,237177,39,145,0.00160467,39.7614,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22387,Q#975 - >seq7622,non-specific,274009,30,145,0.00187718,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22388,Q#975 - >seq7622,non-specific,335623,38,138,0.00680968,37.539,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22389,Q#975 - >seq7622,superfamily,335623,38,138,0.00680968,37.539,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22390,Q#975 - >seq7622,non-specific,335555,31,121,0.00773331,37.6252,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PB2,ORF1,hs0_human,marg,N-TerminusTruncated
22391,Q#975 - >seq7622,superfamily,354396,31,121,0.00773331,37.6252,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1PB2,ORF1,hs0_human,marg,N-TerminusTruncated
22392,Q#975 - >seq7622,non-specific,235175,39,150,0.00784419,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,C-TerminusTruncated
22393,Q#975 - >seq7622,non-specific,274008,42,145,0.00927964,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22394,Q#975 - >seq7622,non-specific,314569,88,137,0.00953367,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22395,Q#975 - >seq7622,superfamily,327698,88,137,0.00953367,37.0108,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs0_human.marg.frame1,1909131019_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF1,hs0_human,marg,BothTerminiTruncated
22396,Q#985 - >seq7632,non-specific,335182,156,253,8.165369999999999e-46,150.916,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22397,Q#985 - >seq7632,superfamily,335182,156,253,8.165369999999999e-46,150.916,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22398,Q#985 - >seq7632,non-specific,340205,256,320,3.40654e-33,117.43700000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22399,Q#985 - >seq7632,superfamily,340205,256,320,3.40654e-33,117.43700000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22400,Q#985 - >seq7632,non-specific,340204,111,153,1.3141e-08,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22401,Q#985 - >seq7632,superfamily,340204,111,153,1.3141e-08,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs3_orang,pars,CompleteHit
22402,Q#985 - >seq7632,non-specific,179877,33,167,0.00022475,42.5154,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs3_orang,pars,BothTerminiTruncated
22403,Q#985 - >seq7632,superfamily,179877,33,167,0.00022475,42.5154,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs3_orang,pars,BothTerminiTruncated
22404,Q#985 - >seq7632,non-specific,224117,65,150,0.0037375,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs3_orang,pars,BothTerminiTruncated
22405,Q#985 - >seq7632,superfamily,224117,65,150,0.0037375,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs3_orang,pars,BothTerminiTruncated
22406,Q#985 - >seq7632,non-specific,309330,57,156,0.00654973,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs3_orang,pars,N-TerminusTruncated
22407,Q#985 - >seq7632,superfamily,309330,57,156,0.00654973,37.0643,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs3_orang.pars.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8,ORF1,hs3_orang,pars,N-TerminusTruncated
22408,Q#988 - >seq7635,non-specific,335182,157,254,9.229719999999998e-46,150.916,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22409,Q#988 - >seq7635,superfamily,335182,157,254,9.229719999999998e-46,150.916,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22410,Q#988 - >seq7635,non-specific,340205,257,321,3.744639999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22411,Q#988 - >seq7635,superfamily,340205,257,321,3.744639999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22412,Q#988 - >seq7635,non-specific,340204,112,154,1.0014700000000001e-08,50.483999999999995,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22413,Q#988 - >seq7635,superfamily,340204,112,154,1.0014700000000001e-08,50.483999999999995,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs3_orang,marg,CompleteHit
22414,Q#988 - >seq7635,non-specific,179877,34,168,0.000198068,42.9006,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs3_orang,marg,BothTerminiTruncated
22415,Q#988 - >seq7635,superfamily,179877,34,168,0.000198068,42.9006,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs3_orang,marg,BothTerminiTruncated
22416,Q#988 - >seq7635,non-specific,224117,66,151,0.00324029,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs3_orang,marg,BothTerminiTruncated
22417,Q#988 - >seq7635,superfamily,224117,66,151,0.00324029,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs3_orang,marg,BothTerminiTruncated
22418,Q#988 - >seq7635,non-specific,309330,58,157,0.00556613,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs3_orang,marg,N-TerminusTruncated
22419,Q#988 - >seq7635,superfamily,309330,58,157,0.00556613,37.0643,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs3_orang.marg.frame3,1909131019_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA8,ORF1,hs3_orang,marg,N-TerminusTruncated
22420,Q#991 - >seq7638,non-specific,335182,157,254,6.135429999999999e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22421,Q#991 - >seq7638,superfamily,335182,157,254,6.135429999999999e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22422,Q#991 - >seq7638,non-specific,335182,157,254,6.135429999999999e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22423,Q#991 - >seq7638,non-specific,340205,257,321,7.07072e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22424,Q#991 - >seq7638,superfamily,340205,257,321,7.07072e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22425,Q#991 - >seq7638,non-specific,340205,257,321,7.07072e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22426,Q#991 - >seq7638,non-specific,340204,112,154,7.20403e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22427,Q#991 - >seq7638,superfamily,340204,112,154,7.20403e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22428,Q#991 - >seq7638,non-specific,340204,112,154,7.20403e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,pars,CompleteHit
22429,Q#991 - >seq7638,non-specific,274765,16,128,0.000727138,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22430,Q#991 - >seq7638,superfamily,274765,16,128,0.000727138,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22431,Q#991 - >seq7638,non-specific,274765,16,128,0.000727138,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22432,Q#991 - >seq7638,non-specific,224117,66,198,0.00253978,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22433,Q#991 - >seq7638,superfamily,224117,66,198,0.00253978,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22434,Q#991 - >seq7638,non-specific,224117,66,198,0.00253978,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22435,Q#991 - >seq7638,non-specific,337663,73,149,0.00394352,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22436,Q#991 - >seq7638,superfamily,337663,73,149,0.00394352,38.5599,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22437,Q#991 - >seq7638,non-specific,337663,73,149,0.00394352,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22438,Q#991 - >seq7638,non-specific,235461,67,130,0.00419575,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22439,Q#991 - >seq7638,superfamily,235461,67,130,0.00419575,38.5106,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22440,Q#991 - >seq7638,non-specific,235461,67,130,0.00419575,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22441,Q#991 - >seq7638,non-specific,334565,67,148,0.00592372,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22442,Q#991 - >seq7638,superfamily,334565,67,148,0.00592372,38.2396,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22443,Q#991 - >seq7638,non-specific,334565,67,148,0.00592372,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22444,Q#991 - >seq7638,non-specific,224117,71,241,0.00678489,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22445,Q#991 - >seq7638,non-specific,224117,71,241,0.00678489,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,pars,C-TerminusTruncated
22446,Q#991 - >seq7638,non-specific,222878,67,151,0.00694032,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22447,Q#991 - >seq7638,superfamily,222878,67,151,0.00694032,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22448,Q#991 - >seq7638,non-specific,222878,67,151,0.00694032,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22449,Q#991 - >seq7638,non-specific,179877,35,168,0.0085299,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22450,Q#991 - >seq7638,superfamily,179877,35,168,0.0085299,37.5078,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22451,Q#991 - >seq7638,non-specific,179877,35,168,0.0085299,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.pars.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,pars,BothTerminiTruncated
22452,Q#993 - >seq7640,non-specific,335182,157,254,6.135429999999999e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22453,Q#993 - >seq7640,superfamily,335182,157,254,6.135429999999999e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22454,Q#993 - >seq7640,non-specific,335182,157,254,6.135429999999999e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22455,Q#993 - >seq7640,non-specific,340205,257,321,7.07072e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22456,Q#993 - >seq7640,superfamily,340205,257,321,7.07072e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22457,Q#993 - >seq7640,non-specific,340205,257,321,7.07072e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22458,Q#993 - >seq7640,non-specific,340204,112,154,7.20403e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22459,Q#993 - >seq7640,superfamily,340204,112,154,7.20403e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22460,Q#993 - >seq7640,non-specific,340204,112,154,7.20403e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs4_gibbon,marg,CompleteHit
22461,Q#993 - >seq7640,non-specific,274765,16,128,0.000727138,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22462,Q#993 - >seq7640,superfamily,274765,16,128,0.000727138,40.781,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22463,Q#993 - >seq7640,non-specific,274765,16,128,0.000727138,40.781,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22464,Q#993 - >seq7640,non-specific,224117,66,198,0.00253978,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22465,Q#993 - >seq7640,superfamily,224117,66,198,0.00253978,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22466,Q#993 - >seq7640,non-specific,224117,66,198,0.00253978,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22467,Q#993 - >seq7640,non-specific,337663,73,149,0.00394352,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22468,Q#993 - >seq7640,superfamily,337663,73,149,0.00394352,38.5599,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22469,Q#993 - >seq7640,non-specific,337663,73,149,0.00394352,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22470,Q#993 - >seq7640,non-specific,235461,67,130,0.00419575,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22471,Q#993 - >seq7640,superfamily,235461,67,130,0.00419575,38.5106,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22472,Q#993 - >seq7640,non-specific,235461,67,130,0.00419575,38.5106,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22473,Q#993 - >seq7640,non-specific,334565,67,148,0.00592372,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22474,Q#993 - >seq7640,superfamily,334565,67,148,0.00592372,38.2396,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22475,Q#993 - >seq7640,non-specific,334565,67,148,0.00592372,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22476,Q#993 - >seq7640,non-specific,224117,71,241,0.00678489,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22477,Q#993 - >seq7640,non-specific,224117,71,241,0.00678489,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs4_gibbon,marg,C-TerminusTruncated
22478,Q#993 - >seq7640,non-specific,222878,67,151,0.00694032,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22479,Q#993 - >seq7640,superfamily,222878,67,151,0.00694032,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22480,Q#993 - >seq7640,non-specific,222878,67,151,0.00694032,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22481,Q#993 - >seq7640,non-specific,179877,35,168,0.0085299,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22482,Q#993 - >seq7640,superfamily,179877,35,168,0.0085299,37.5078,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22483,Q#993 - >seq7640,non-specific,179877,35,168,0.0085299,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8.ORF1.hs4_gibbon.marg.frame3,1909131019_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs4_gibbon,marg,BothTerminiTruncated
22484,Q#996 - >seq7643,non-specific,335182,157,254,7.540669999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22485,Q#996 - >seq7643,superfamily,335182,157,254,7.540669999999999e-47,153.613,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22486,Q#996 - >seq7643,non-specific,335182,157,254,7.540669999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22487,Q#996 - >seq7643,non-specific,340205,257,321,2.29978e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22488,Q#996 - >seq7643,superfamily,340205,257,321,2.29978e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22489,Q#996 - >seq7643,non-specific,340205,257,321,2.29978e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22490,Q#996 - >seq7643,non-specific,340204,112,154,1.21108e-09,53.1804,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22491,Q#996 - >seq7643,superfamily,340204,112,154,1.21108e-09,53.1804,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22492,Q#996 - >seq7643,non-specific,340204,112,154,1.21108e-09,53.1804,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,pars,CompleteHit
22493,Q#996 - >seq7643,non-specific,337766,52,141,0.000221735,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22494,Q#996 - >seq7643,superfamily,337766,52,141,0.000221735,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22495,Q#996 - >seq7643,non-specific,337766,52,141,0.000221735,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22496,Q#996 - >seq7643,non-specific,235175,55,143,0.00107065,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22497,Q#996 - >seq7643,superfamily,235175,55,143,0.00107065,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22498,Q#996 - >seq7643,non-specific,235175,55,143,0.00107065,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22499,Q#996 - >seq7643,non-specific,224117,66,151,0.00123318,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22500,Q#996 - >seq7643,superfamily,224117,66,151,0.00123318,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22501,Q#996 - >seq7643,non-specific,224117,66,151,0.00123318,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22502,Q#996 - >seq7643,non-specific,224117,50,151,0.0023897,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22503,Q#996 - >seq7643,non-specific,224117,50,151,0.0023897,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22504,Q#996 - >seq7643,non-specific,336322,34,168,0.0038483000000000002,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22505,Q#996 - >seq7643,superfamily,336322,34,168,0.0038483000000000002,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22506,Q#996 - >seq7643,non-specific,336322,34,168,0.0038483000000000002,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22507,Q#996 - >seq7643,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22508,Q#996 - >seq7643,superfamily,274765,48,128,0.0039715,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22509,Q#996 - >seq7643,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22510,Q#996 - >seq7643,non-specific,335556,66,150,0.00417848,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22511,Q#996 - >seq7643,superfamily,335556,66,150,0.00417848,37.5125,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22512,Q#996 - >seq7643,non-specific,335556,66,150,0.00417848,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22513,Q#996 - >seq7643,non-specific,222878,67,151,0.00425031,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22514,Q#996 - >seq7643,superfamily,222878,67,151,0.00425031,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22515,Q#996 - >seq7643,non-specific,222878,67,151,0.00425031,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22516,Q#996 - >seq7643,non-specific,335555,66,133,0.0046454999999999995,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22517,Q#996 - >seq7643,superfamily,354396,66,133,0.0046454999999999995,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22518,Q#996 - >seq7643,non-specific,335555,66,133,0.0046454999999999995,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22519,Q#996 - >seq7643,non-specific,235175,69,151,0.0049239,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22520,Q#996 - >seq7643,non-specific,235175,69,151,0.0049239,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22521,Q#996 - >seq7643,non-specific,337663,73,149,0.00542597,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22522,Q#996 - >seq7643,superfamily,337663,73,149,0.00542597,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22523,Q#996 - >seq7643,non-specific,337663,73,149,0.00542597,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22524,Q#996 - >seq7643,non-specific,224117,71,241,0.00595556,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22525,Q#996 - >seq7643,superfamily,224117,71,241,0.00595556,38.542,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22526,Q#996 - >seq7643,non-specific,224117,71,241,0.00595556,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22527,Q#996 - >seq7643,non-specific,273690,75,197,0.00737771,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22528,Q#996 - >seq7643,superfamily,355611,75,197,0.00737771,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22529,Q#996 - >seq7643,non-specific,273690,75,197,0.00737771,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22530,Q#996 - >seq7643,non-specific,275316,52,151,0.00753827,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22531,Q#996 - >seq7643,superfamily,275316,52,151,0.00753827,38.0776,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22532,Q#996 - >seq7643,non-specific,275316,52,151,0.00753827,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22533,Q#996 - >seq7643,non-specific,274008,56,163,0.00833038,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22534,Q#996 - >seq7643,superfamily,274008,56,163,0.00833038,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22535,Q#996 - >seq7643,non-specific,274008,56,163,0.00833038,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22536,Q#996 - >seq7643,non-specific,274008,66,150,0.00855036,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22537,Q#996 - >seq7643,non-specific,274008,66,150,0.00855036,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
22538,Q#996 - >seq7643,non-specific,235600,37,131,0.00943615,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22539,Q#996 - >seq7643,superfamily,235600,37,131,0.00943615,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22540,Q#996 - >seq7643,non-specific,235600,37,131,0.00943615,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
22541,Q#996 - >seq7643,non-specific,335555,69,141,0.00972215,37.24,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22542,Q#996 - >seq7643,non-specific,335555,69,141,0.00972215,37.24,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22543,Q#996 - >seq7643,non-specific,224117,56,150,0.00985841,37.7716,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22544,Q#996 - >seq7643,non-specific,224117,56,150,0.00985841,37.7716,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
22545,Q#999 - >seq7646,non-specific,335182,157,254,7.540669999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22546,Q#999 - >seq7646,superfamily,335182,157,254,7.540669999999999e-47,153.613,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22547,Q#999 - >seq7646,non-specific,335182,157,254,7.540669999999999e-47,153.613,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22548,Q#999 - >seq7646,non-specific,340205,257,321,2.29978e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22549,Q#999 - >seq7646,superfamily,340205,257,321,2.29978e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22550,Q#999 - >seq7646,non-specific,340205,257,321,2.29978e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22551,Q#999 - >seq7646,non-specific,340204,112,154,1.21108e-09,53.1804,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22552,Q#999 - >seq7646,superfamily,340204,112,154,1.21108e-09,53.1804,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22553,Q#999 - >seq7646,non-specific,340204,112,154,1.21108e-09,53.1804,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs5_gmonkey,marg,CompleteHit
22554,Q#999 - >seq7646,non-specific,337766,52,141,0.000221735,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22555,Q#999 - >seq7646,superfamily,337766,52,141,0.000221735,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22556,Q#999 - >seq7646,non-specific,337766,52,141,0.000221735,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22557,Q#999 - >seq7646,non-specific,235175,55,143,0.00107065,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22558,Q#999 - >seq7646,superfamily,235175,55,143,0.00107065,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22559,Q#999 - >seq7646,non-specific,235175,55,143,0.00107065,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22560,Q#999 - >seq7646,non-specific,224117,66,151,0.00123318,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22561,Q#999 - >seq7646,superfamily,224117,66,151,0.00123318,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22562,Q#999 - >seq7646,non-specific,224117,66,151,0.00123318,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22563,Q#999 - >seq7646,non-specific,224117,50,151,0.0023897,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22564,Q#999 - >seq7646,non-specific,224117,50,151,0.0023897,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22565,Q#999 - >seq7646,non-specific,336322,34,168,0.0038483000000000002,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22566,Q#999 - >seq7646,superfamily,336322,34,168,0.0038483000000000002,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22567,Q#999 - >seq7646,non-specific,336322,34,168,0.0038483000000000002,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22568,Q#999 - >seq7646,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22569,Q#999 - >seq7646,superfamily,274765,48,128,0.0039715,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22570,Q#999 - >seq7646,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22571,Q#999 - >seq7646,non-specific,335556,66,150,0.00417848,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22572,Q#999 - >seq7646,superfamily,335556,66,150,0.00417848,37.5125,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22573,Q#999 - >seq7646,non-specific,335556,66,150,0.00417848,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22574,Q#999 - >seq7646,non-specific,222878,67,151,0.00425031,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22575,Q#999 - >seq7646,superfamily,222878,67,151,0.00425031,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22576,Q#999 - >seq7646,non-specific,222878,67,151,0.00425031,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22577,Q#999 - >seq7646,non-specific,335555,66,133,0.0046454999999999995,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22578,Q#999 - >seq7646,superfamily,354396,66,133,0.0046454999999999995,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22579,Q#999 - >seq7646,non-specific,335555,66,133,0.0046454999999999995,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22580,Q#999 - >seq7646,non-specific,235175,69,151,0.0049239,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22581,Q#999 - >seq7646,non-specific,235175,69,151,0.0049239,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22582,Q#999 - >seq7646,non-specific,337663,73,149,0.00542597,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22583,Q#999 - >seq7646,superfamily,337663,73,149,0.00542597,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22584,Q#999 - >seq7646,non-specific,337663,73,149,0.00542597,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22585,Q#999 - >seq7646,non-specific,224117,71,241,0.00595556,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22586,Q#999 - >seq7646,superfamily,224117,71,241,0.00595556,38.542,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22587,Q#999 - >seq7646,non-specific,224117,71,241,0.00595556,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22588,Q#999 - >seq7646,non-specific,273690,75,197,0.00737771,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22589,Q#999 - >seq7646,superfamily,355611,75,197,0.00737771,37.7105,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22590,Q#999 - >seq7646,non-specific,273690,75,197,0.00737771,37.7105,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22591,Q#999 - >seq7646,non-specific,275316,52,151,0.00753827,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22592,Q#999 - >seq7646,superfamily,275316,52,151,0.00753827,38.0776,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22593,Q#999 - >seq7646,non-specific,275316,52,151,0.00753827,38.0776,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22594,Q#999 - >seq7646,non-specific,274008,56,163,0.00833038,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22595,Q#999 - >seq7646,superfamily,274008,56,163,0.00833038,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22596,Q#999 - >seq7646,non-specific,274008,56,163,0.00833038,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22597,Q#999 - >seq7646,non-specific,274008,66,150,0.00855036,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22598,Q#999 - >seq7646,non-specific,274008,66,150,0.00855036,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
22599,Q#999 - >seq7646,non-specific,235600,37,131,0.00943615,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22600,Q#999 - >seq7646,superfamily,235600,37,131,0.00943615,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22601,Q#999 - >seq7646,non-specific,235600,37,131,0.00943615,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
22602,Q#999 - >seq7646,non-specific,335555,69,141,0.00972215,37.24,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22603,Q#999 - >seq7646,non-specific,335555,69,141,0.00972215,37.24,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22604,Q#999 - >seq7646,non-specific,224117,56,150,0.00985841,37.7716,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22605,Q#999 - >seq7646,non-specific,224117,56,150,0.00985841,37.7716,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs5_gmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
22606,Q#1002 - >seq7649,non-specific,335182,155,251,5.04042e-35,122.79700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22607,Q#1002 - >seq7649,superfamily,335182,155,251,5.04042e-35,122.79700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22608,Q#1002 - >seq7649,non-specific,340205,254,317,4.35608e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22609,Q#1002 - >seq7649,superfamily,340205,254,317,4.35608e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22610,Q#1002 - >seq7649,non-specific,340204,111,153,3.5934899999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22611,Q#1002 - >seq7649,superfamily,340204,111,153,3.5934899999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs1_chimp,pars,CompleteHit
22612,Q#1002 - >seq7649,non-specific,237177,42,149,7.83825e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22613,Q#1002 - >seq7649,superfamily,237177,42,149,7.83825e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22614,Q#1002 - >seq7649,non-specific,235175,49,155,0.000234304,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22615,Q#1002 - >seq7649,superfamily,235175,49,155,0.000234304,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22616,Q#1002 - >seq7649,non-specific,274008,41,201,0.00144492,40.0399,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22617,Q#1002 - >seq7649,superfamily,274008,41,201,0.00144492,40.0399,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22618,Q#1002 - >seq7649,non-specific,275056,60,152,0.00173523,38.8357,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22619,Q#1002 - >seq7649,superfamily,275056,60,152,0.00173523,38.8357,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22620,Q#1002 - >seq7649,non-specific,224117,28,155,0.00190043,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22621,Q#1002 - >seq7649,superfamily,224117,28,155,0.00190043,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22622,Q#1002 - >seq7649,non-specific,129694,80,146,0.00269878,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22623,Q#1002 - >seq7649,superfamily,129694,80,146,0.00269878,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22624,Q#1002 - >seq7649,non-specific,274008,45,150,0.0027804,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22625,Q#1002 - >seq7649,non-specific,336159,60,145,0.00279047,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22626,Q#1002 - >seq7649,superfamily,336159,60,145,0.00279047,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22627,Q#1002 - >seq7649,non-specific,235175,60,144,0.00323876,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22628,Q#1002 - >seq7649,non-specific,235461,47,169,0.00325872,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22629,Q#1002 - >seq7649,superfamily,235461,47,169,0.00325872,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22630,Q#1002 - >seq7649,non-specific,274386,27,147,0.00447743,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22631,Q#1002 - >seq7649,superfamily,274386,27,147,0.00447743,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22632,Q#1002 - >seq7649,non-specific,337663,79,147,0.00635275,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22633,Q#1002 - >seq7649,superfamily,337663,79,147,0.00635275,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22634,Q#1002 - >seq7649,non-specific,223250,47,150,0.00714659,37.5777,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22635,Q#1002 - >seq7649,superfamily,223250,47,150,0.00714659,37.5777,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22636,Q#1002 - >seq7649,non-specific,274008,60,145,0.00764315,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22637,Q#1002 - >seq7649,non-specific,223671,70,161,0.00779412,37.3045,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22638,Q#1002 - >seq7649,superfamily,320984,70,161,0.00779412,37.3045,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22639,Q#1002 - >seq7649,non-specific,188306,43,150,0.0078663,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22640,Q#1002 - >seq7649,superfamily,188306,43,150,0.0078663,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22641,Q#1002 - >seq7649,non-specific,310273,60,148,0.00826284,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22642,Q#1002 - >seq7649,superfamily,310273,60,148,0.00826284,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22643,Q#1002 - >seq7649,non-specific,313406,73,235,0.00840059,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22644,Q#1002 - >seq7649,superfamily,313406,73,235,0.00840059,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs1_chimp,pars,N-TerminusTruncated
22645,Q#1002 - >seq7649,non-specific,224117,49,201,0.00844089,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22646,Q#1002 - >seq7649,non-specific,235600,70,185,0.00851994,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22647,Q#1002 - >seq7649,superfamily,235600,70,185,0.00851994,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22648,Q#1002 - >seq7649,non-specific,112704,2,148,0.00870723,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22649,Q#1002 - >seq7649,superfamily,112704,2,148,0.00870723,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs1_chimp,pars,C-TerminusTruncated
22650,Q#1002 - >seq7649,non-specific,274009,33,150,0.00933295,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22651,Q#1002 - >seq7649,superfamily,274009,33,150,0.00933295,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs1_chimp.pars.frame3,1909131019_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs1_chimp,pars,BothTerminiTruncated
22652,Q#1005 - >seq7652,non-specific,335182,157,254,1.9011399999999997e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22653,Q#1005 - >seq7652,superfamily,335182,157,254,1.9011399999999997e-46,152.842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22654,Q#1005 - >seq7652,non-specific,335182,157,254,1.9011399999999997e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22655,Q#1005 - >seq7652,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22656,Q#1005 - >seq7652,superfamily,340205,257,321,3.9483899999999995e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22657,Q#1005 - >seq7652,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,pars,CompleteHit
22658,Q#1005 - >seq7652,non-specific,340204,112,154,6.128779999999999e-09,50.8692,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,pars,CompleteHit
22659,Q#1005 - >seq7652,superfamily,340204,112,154,6.128779999999999e-09,50.8692,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,pars,CompleteHit
22660,Q#1005 - >seq7652,non-specific,340204,112,154,6.128779999999999e-09,50.8692,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,pars,CompleteHit
22661,Q#1005 - >seq7652,non-specific,337766,52,141,0.000229764,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22662,Q#1005 - >seq7652,superfamily,337766,52,141,0.000229764,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22663,Q#1005 - >seq7652,non-specific,337766,52,141,0.000229764,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22664,Q#1005 - >seq7652,non-specific,222878,67,151,0.00131325,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22665,Q#1005 - >seq7652,superfamily,222878,67,151,0.00131325,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22666,Q#1005 - >seq7652,non-specific,222878,67,151,0.00131325,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22667,Q#1005 - >seq7652,non-specific,224117,50,151,0.00141753,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22668,Q#1005 - >seq7652,superfamily,224117,50,151,0.00141753,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22669,Q#1005 - >seq7652,non-specific,224117,50,151,0.00141753,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22670,Q#1005 - >seq7652,non-specific,235175,55,143,0.00172999,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22671,Q#1005 - >seq7652,superfamily,235175,55,143,0.00172999,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22672,Q#1005 - >seq7652,non-specific,235175,55,143,0.00172999,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22673,Q#1005 - >seq7652,non-specific,274765,48,128,0.00276978,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22674,Q#1005 - >seq7652,superfamily,274765,48,128,0.00276978,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22675,Q#1005 - >seq7652,non-specific,274765,48,128,0.00276978,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22676,Q#1005 - >seq7652,non-specific,224117,66,151,0.00294461,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22677,Q#1005 - >seq7652,non-specific,224117,66,151,0.00294461,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22678,Q#1005 - >seq7652,non-specific,224117,56,150,0.00406246,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22679,Q#1005 - >seq7652,non-specific,224117,56,150,0.00406246,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22680,Q#1005 - >seq7652,non-specific,335555,66,133,0.00481184,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22681,Q#1005 - >seq7652,superfamily,354396,66,133,0.00481184,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22682,Q#1005 - >seq7652,non-specific,335555,66,133,0.00481184,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs0_human,pars,N-TerminusTruncated
22683,Q#1005 - >seq7652,non-specific,337663,73,149,0.00505457,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22684,Q#1005 - >seq7652,superfamily,337663,73,149,0.00505457,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22685,Q#1005 - >seq7652,non-specific,337663,73,149,0.00505457,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22686,Q#1005 - >seq7652,non-specific,273690,75,197,0.00513712,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22687,Q#1005 - >seq7652,superfamily,355611,75,197,0.00513712,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22688,Q#1005 - >seq7652,non-specific,273690,75,197,0.00513712,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22689,Q#1005 - >seq7652,non-specific,274008,66,150,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22690,Q#1005 - >seq7652,superfamily,274008,66,150,0.00516506,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22691,Q#1005 - >seq7652,non-specific,274008,66,150,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22692,Q#1005 - >seq7652,non-specific,335556,66,150,0.00616893,37.1273,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22693,Q#1005 - >seq7652,superfamily,335556,66,150,0.00616893,37.1273,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22694,Q#1005 - >seq7652,non-specific,335556,66,150,0.00616893,37.1273,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22695,Q#1005 - >seq7652,non-specific,224117,55,151,0.00772955,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22696,Q#1005 - >seq7652,non-specific,224117,55,151,0.00772955,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22697,Q#1005 - >seq7652,non-specific,224117,71,241,0.00786506,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22698,Q#1005 - >seq7652,superfamily,224117,71,241,0.00786506,38.1568,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22699,Q#1005 - >seq7652,non-specific,224117,71,241,0.00786506,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22700,Q#1005 - >seq7652,non-specific,235175,69,151,0.00890194,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22701,Q#1005 - >seq7652,non-specific,235175,69,151,0.00890194,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,pars,BothTerminiTruncated
22702,Q#1005 - >seq7652,non-specific,334565,67,148,0.00956942,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22703,Q#1005 - >seq7652,superfamily,334565,67,148,0.00956942,37.4692,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22704,Q#1005 - >seq7652,non-specific,334565,67,148,0.00956942,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.pars.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,pars,C-TerminusTruncated
22705,Q#1007 - >seq7654,non-specific,335182,157,254,1.9011399999999997e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22706,Q#1007 - >seq7654,superfamily,335182,157,254,1.9011399999999997e-46,152.842,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22707,Q#1007 - >seq7654,non-specific,335182,157,254,1.9011399999999997e-46,152.842,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22708,Q#1007 - >seq7654,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22709,Q#1007 - >seq7654,superfamily,340205,257,321,3.9483899999999995e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22710,Q#1007 - >seq7654,non-specific,340205,257,321,3.9483899999999995e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs0_human,marg,CompleteHit
22711,Q#1007 - >seq7654,non-specific,340204,112,154,6.128779999999999e-09,50.8692,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,marg,CompleteHit
22712,Q#1007 - >seq7654,superfamily,340204,112,154,6.128779999999999e-09,50.8692,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,marg,CompleteHit
22713,Q#1007 - >seq7654,non-specific,340204,112,154,6.128779999999999e-09,50.8692,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs0_human,marg,CompleteHit
22714,Q#1007 - >seq7654,non-specific,337766,52,141,0.000229764,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22715,Q#1007 - >seq7654,superfamily,337766,52,141,0.000229764,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22716,Q#1007 - >seq7654,non-specific,337766,52,141,0.000229764,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22717,Q#1007 - >seq7654,non-specific,222878,67,151,0.00131325,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22718,Q#1007 - >seq7654,superfamily,222878,67,151,0.00131325,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22719,Q#1007 - >seq7654,non-specific,222878,67,151,0.00131325,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22720,Q#1007 - >seq7654,non-specific,224117,50,151,0.00141753,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22721,Q#1007 - >seq7654,superfamily,224117,50,151,0.00141753,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22722,Q#1007 - >seq7654,non-specific,224117,50,151,0.00141753,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22723,Q#1007 - >seq7654,non-specific,235175,55,143,0.00172999,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22724,Q#1007 - >seq7654,superfamily,235175,55,143,0.00172999,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22725,Q#1007 - >seq7654,non-specific,235175,55,143,0.00172999,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22726,Q#1007 - >seq7654,non-specific,274765,48,128,0.00276978,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22727,Q#1007 - >seq7654,superfamily,274765,48,128,0.00276978,39.2402,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22728,Q#1007 - >seq7654,non-specific,274765,48,128,0.00276978,39.2402,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22729,Q#1007 - >seq7654,non-specific,224117,66,151,0.00294461,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22730,Q#1007 - >seq7654,non-specific,224117,66,151,0.00294461,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22731,Q#1007 - >seq7654,non-specific,224117,56,150,0.00406246,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22732,Q#1007 - >seq7654,non-specific,224117,56,150,0.00406246,38.9272,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22733,Q#1007 - >seq7654,non-specific,335555,66,133,0.00481184,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22734,Q#1007 - >seq7654,superfamily,354396,66,133,0.00481184,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22735,Q#1007 - >seq7654,non-specific,335555,66,133,0.00481184,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs0_human,marg,N-TerminusTruncated
22736,Q#1007 - >seq7654,non-specific,337663,73,149,0.00505457,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22737,Q#1007 - >seq7654,superfamily,337663,73,149,0.00505457,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22738,Q#1007 - >seq7654,non-specific,337663,73,149,0.00505457,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22739,Q#1007 - >seq7654,non-specific,273690,75,197,0.00513712,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22740,Q#1007 - >seq7654,superfamily,355611,75,197,0.00513712,38.0957,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22741,Q#1007 - >seq7654,non-specific,273690,75,197,0.00513712,38.0957,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22742,Q#1007 - >seq7654,non-specific,274008,66,150,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22743,Q#1007 - >seq7654,superfamily,274008,66,150,0.00516506,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22744,Q#1007 - >seq7654,non-specific,274008,66,150,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22745,Q#1007 - >seq7654,non-specific,335556,66,150,0.00616893,37.1273,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22746,Q#1007 - >seq7654,superfamily,335556,66,150,0.00616893,37.1273,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22747,Q#1007 - >seq7654,non-specific,335556,66,150,0.00616893,37.1273,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22748,Q#1007 - >seq7654,non-specific,224117,55,151,0.00772955,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22749,Q#1007 - >seq7654,non-specific,224117,55,151,0.00772955,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22750,Q#1007 - >seq7654,non-specific,224117,71,241,0.00786506,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22751,Q#1007 - >seq7654,superfamily,224117,71,241,0.00786506,38.1568,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22752,Q#1007 - >seq7654,non-specific,224117,71,241,0.00786506,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22753,Q#1007 - >seq7654,non-specific,235175,69,151,0.00890194,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22754,Q#1007 - >seq7654,non-specific,235175,69,151,0.00890194,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs0_human,marg,BothTerminiTruncated
22755,Q#1007 - >seq7654,non-specific,334565,67,148,0.00956942,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22756,Q#1007 - >seq7654,superfamily,334565,67,148,0.00956942,37.4692,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22757,Q#1007 - >seq7654,non-specific,334565,67,148,0.00956942,37.4692,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PA8.ORF1.hs0_human.marg.frame3,1909131019_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PA8,ORF1,hs0_human,marg,C-TerminusTruncated
22758,Q#1008 - >seq7655,non-specific,335182,157,254,2.0497299999999995e-46,152.457,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22759,Q#1008 - >seq7655,superfamily,335182,157,254,2.0497299999999995e-46,152.457,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22760,Q#1008 - >seq7655,non-specific,335182,157,254,2.0497299999999995e-46,152.457,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22761,Q#1008 - >seq7655,non-specific,340205,257,321,3.824849999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22762,Q#1008 - >seq7655,superfamily,340205,257,321,3.824849999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22763,Q#1008 - >seq7655,non-specific,340205,257,321,3.824849999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22764,Q#1008 - >seq7655,non-specific,340204,112,154,1.62655e-09,52.7952,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22765,Q#1008 - >seq7655,superfamily,340204,112,154,1.62655e-09,52.7952,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22766,Q#1008 - >seq7655,non-specific,340204,112,154,1.62655e-09,52.7952,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,marg,CompleteHit
22767,Q#1008 - >seq7655,non-specific,337766,52,141,0.000244519,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22768,Q#1008 - >seq7655,superfamily,337766,52,141,0.000244519,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22769,Q#1008 - >seq7655,non-specific,337766,52,141,0.000244519,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22770,Q#1008 - >seq7655,non-specific,235175,55,143,0.00124186,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22771,Q#1008 - >seq7655,superfamily,235175,55,143,0.00124186,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22772,Q#1008 - >seq7655,non-specific,235175,55,143,0.00124186,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22773,Q#1008 - >seq7655,non-specific,224117,66,151,0.0015874,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22774,Q#1008 - >seq7655,superfamily,224117,66,151,0.0015874,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22775,Q#1008 - >seq7655,non-specific,224117,66,151,0.0015874,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22776,Q#1008 - >seq7655,non-specific,224117,50,151,0.00302247,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22777,Q#1008 - >seq7655,non-specific,224117,50,151,0.00302247,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22778,Q#1008 - >seq7655,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22779,Q#1008 - >seq7655,superfamily,274765,48,128,0.0039715,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22780,Q#1008 - >seq7655,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22781,Q#1008 - >seq7655,non-specific,335556,66,150,0.00425675,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22782,Q#1008 - >seq7655,superfamily,335556,66,150,0.00425675,37.5125,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22783,Q#1008 - >seq7655,non-specific,335556,66,150,0.00425675,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22784,Q#1008 - >seq7655,non-specific,222878,67,151,0.00451905,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22785,Q#1008 - >seq7655,superfamily,222878,67,151,0.00451905,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22786,Q#1008 - >seq7655,non-specific,222878,67,151,0.00451905,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22787,Q#1008 - >seq7655,non-specific,336322,34,168,0.00458535,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22788,Q#1008 - >seq7655,superfamily,336322,34,168,0.00458535,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22789,Q#1008 - >seq7655,non-specific,336322,34,168,0.00458535,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22790,Q#1008 - >seq7655,non-specific,335555,66,133,0.00498414,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22791,Q#1008 - >seq7655,superfamily,354396,66,133,0.00498414,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22792,Q#1008 - >seq7655,non-specific,335555,66,133,0.00498414,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22793,Q#1008 - >seq7655,non-specific,274008,1,163,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22794,Q#1008 - >seq7655,superfamily,274008,1,163,0.00516506,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22795,Q#1008 - >seq7655,non-specific,274008,1,163,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22796,Q#1008 - >seq7655,non-specific,337663,73,149,0.00557216,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22797,Q#1008 - >seq7655,superfamily,337663,73,149,0.00557216,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22798,Q#1008 - >seq7655,non-specific,337663,73,149,0.00557216,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22799,Q#1008 - >seq7655,non-specific,235175,69,151,0.00633882,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22800,Q#1008 - >seq7655,non-specific,235175,69,151,0.00633882,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22801,Q#1008 - >seq7655,non-specific,224117,71,241,0.00766268,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22802,Q#1008 - >seq7655,superfamily,224117,71,241,0.00766268,38.1568,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22803,Q#1008 - >seq7655,non-specific,224117,71,241,0.00766268,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22804,Q#1008 - >seq7655,non-specific,275316,52,151,0.00897458,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22805,Q#1008 - >seq7655,superfamily,275316,52,151,0.00897458,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22806,Q#1008 - >seq7655,non-specific,275316,52,151,0.00897458,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22807,Q#1008 - >seq7655,non-specific,273690,75,197,0.00969916,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22808,Q#1008 - >seq7655,superfamily,355611,75,197,0.00969916,37.3253,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22809,Q#1008 - >seq7655,non-specific,273690,75,197,0.00969916,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs6_sqmonkey.marg.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22810,Q#1011 - >seq7658,non-specific,335182,157,254,2.0497299999999995e-46,152.457,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22811,Q#1011 - >seq7658,superfamily,335182,157,254,2.0497299999999995e-46,152.457,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22812,Q#1011 - >seq7658,non-specific,335182,157,254,2.0497299999999995e-46,152.457,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22813,Q#1011 - >seq7658,non-specific,340205,257,321,3.824849999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22814,Q#1011 - >seq7658,superfamily,340205,257,321,3.824849999999999e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22815,Q#1011 - >seq7658,non-specific,340205,257,321,3.824849999999999e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22816,Q#1011 - >seq7658,non-specific,340204,112,154,1.62655e-09,52.7952,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22817,Q#1011 - >seq7658,superfamily,340204,112,154,1.62655e-09,52.7952,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22818,Q#1011 - >seq7658,non-specific,340204,112,154,1.62655e-09,52.7952,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs6_sqmonkey,pars,CompleteHit
22819,Q#1011 - >seq7658,non-specific,337766,52,141,0.000244519,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22820,Q#1011 - >seq7658,superfamily,337766,52,141,0.000244519,42.2147,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22821,Q#1011 - >seq7658,non-specific,337766,52,141,0.000244519,42.2147,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22822,Q#1011 - >seq7658,non-specific,235175,55,143,0.00124186,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22823,Q#1011 - >seq7658,superfamily,235175,55,143,0.00124186,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22824,Q#1011 - >seq7658,non-specific,235175,55,143,0.00124186,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22825,Q#1011 - >seq7658,non-specific,224117,66,151,0.0015874,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22826,Q#1011 - >seq7658,superfamily,224117,66,151,0.0015874,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22827,Q#1011 - >seq7658,non-specific,224117,66,151,0.0015874,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22828,Q#1011 - >seq7658,non-specific,224117,50,151,0.00302247,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22829,Q#1011 - >seq7658,non-specific,224117,50,151,0.00302247,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22830,Q#1011 - >seq7658,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22831,Q#1011 - >seq7658,superfamily,274765,48,128,0.0039715,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22832,Q#1011 - >seq7658,non-specific,274765,48,128,0.0039715,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22833,Q#1011 - >seq7658,non-specific,335556,66,150,0.00425675,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22834,Q#1011 - >seq7658,superfamily,335556,66,150,0.00425675,37.5125,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22835,Q#1011 - >seq7658,non-specific,335556,66,150,0.00425675,37.5125,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22836,Q#1011 - >seq7658,non-specific,222878,67,151,0.00451905,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22837,Q#1011 - >seq7658,superfamily,222878,67,151,0.00451905,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22838,Q#1011 - >seq7658,non-specific,222878,67,151,0.00451905,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22839,Q#1011 - >seq7658,non-specific,336322,34,168,0.00458535,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22840,Q#1011 - >seq7658,superfamily,336322,34,168,0.00458535,38.6522,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22841,Q#1011 - >seq7658,non-specific,336322,34,168,0.00458535,38.6522,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22842,Q#1011 - >seq7658,non-specific,335555,66,133,0.00498414,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22843,Q#1011 - >seq7658,superfamily,354396,66,133,0.00498414,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22844,Q#1011 - >seq7658,non-specific,335555,66,133,0.00498414,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22845,Q#1011 - >seq7658,non-specific,274008,1,163,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22846,Q#1011 - >seq7658,superfamily,274008,1,163,0.00516506,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22847,Q#1011 - >seq7658,non-specific,274008,1,163,0.00516506,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22848,Q#1011 - >seq7658,non-specific,337663,73,149,0.00557216,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22849,Q#1011 - >seq7658,superfamily,337663,73,149,0.00557216,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22850,Q#1011 - >seq7658,non-specific,337663,73,149,0.00557216,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22851,Q#1011 - >seq7658,non-specific,235175,69,151,0.00633882,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22852,Q#1011 - >seq7658,non-specific,235175,69,151,0.00633882,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22853,Q#1011 - >seq7658,non-specific,224117,71,241,0.00766268,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22854,Q#1011 - >seq7658,superfamily,224117,71,241,0.00766268,38.1568,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22855,Q#1011 - >seq7658,non-specific,224117,71,241,0.00766268,38.1568,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22856,Q#1011 - >seq7658,non-specific,275316,52,151,0.00897458,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22857,Q#1011 - >seq7658,superfamily,275316,52,151,0.00897458,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22858,Q#1011 - >seq7658,non-specific,275316,52,151,0.00897458,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA8,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22859,Q#1011 - >seq7658,non-specific,273690,75,197,0.00969916,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22860,Q#1011 - >seq7658,superfamily,355611,75,197,0.00969916,37.3253,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22861,Q#1011 - >seq7658,non-specific,273690,75,197,0.00969916,37.3253,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA8.ORF1.hs6_sqmonkey.pars.frame3,1909131019_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA8,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22862,Q#1015 - >seq7662,non-specific,335182,157,252,1.5652600000000002e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22863,Q#1015 - >seq7662,superfamily,335182,157,252,1.5652600000000002e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22864,Q#1015 - >seq7662,non-specific,340205,255,318,3.4467699999999996e-29,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22865,Q#1015 - >seq7662,superfamily,340205,255,318,3.4467699999999996e-29,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22866,Q#1015 - >seq7662,non-specific,340204,111,153,1.34713e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22867,Q#1015 - >seq7662,superfamily,340204,111,153,1.34713e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs6_sqmonkey,marg,CompleteHit
22868,Q#1015 - >seq7662,non-specific,235175,42,184,2.9379899999999996e-05,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22869,Q#1015 - >seq7662,superfamily,235175,42,184,2.9379899999999996e-05,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22870,Q#1015 - >seq7662,non-specific,274008,33,149,4.78249e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22871,Q#1015 - >seq7662,superfamily,274008,33,149,4.78249e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22872,Q#1015 - >seq7662,non-specific,237177,42,149,0.000204096,42.843,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22873,Q#1015 - >seq7662,superfamily,237177,42,149,0.000204096,42.843,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22874,Q#1015 - >seq7662,non-specific,224117,32,150,0.000228027,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22875,Q#1015 - >seq7662,superfamily,224117,32,150,0.000228027,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22876,Q#1015 - >seq7662,non-specific,197874,49,162,0.000317162,41.5417,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22877,Q#1015 - >seq7662,superfamily,197874,49,162,0.000317162,41.5417,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22878,Q#1015 - >seq7662,non-specific,274009,40,240,0.0007388010000000001,41.2067,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22879,Q#1015 - >seq7662,superfamily,274009,40,240,0.0007388010000000001,41.2067,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22880,Q#1015 - >seq7662,non-specific,336852,50,125,0.00206076,37.1792,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22881,Q#1015 - >seq7662,superfamily,336852,50,125,0.00206076,37.1792,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
22882,Q#1015 - >seq7662,non-specific,222878,54,150,0.00269817,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22883,Q#1015 - >seq7662,superfamily,222878,54,150,0.00269817,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22884,Q#1015 - >seq7662,non-specific,235461,45,122,0.00285363,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22885,Q#1015 - >seq7662,superfamily,235461,45,122,0.00285363,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22886,Q#1015 - >seq7662,non-specific,235175,38,243,0.00597126,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22887,Q#1015 - >seq7662,non-specific,112704,2,121,0.00813324,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22888,Q#1015 - >seq7662,superfamily,112704,2,121,0.00813324,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22889,Q#1015 - >seq7662,non-specific,129694,50,146,0.00815826,37.7189,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22890,Q#1015 - >seq7662,superfamily,129694,50,146,0.00815826,37.7189,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22891,Q#1015 - >seq7662,non-specific,337033,42,128,0.00903798,37.5585,pfam08385,DHC_N1,NC,cl20356,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22892,Q#1015 - >seq7662,superfamily,337033,42,128,0.00903798,37.5585,cl20356,DHC_N1 superfamily,NC, - ,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
22893,Q#1015 - >seq7662,non-specific,188306,43,150,0.00970492,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22894,Q#1015 - >seq7662,superfamily,188306,43,150,0.00970492,37.2126,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB3.ORF1.hs6_sqmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
22895,Q#1020 - >seq7667,non-specific,335182,67,162,6.874229999999999e-37,125.10799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,marg,CompleteHit
22896,Q#1020 - >seq7667,superfamily,335182,67,162,6.874229999999999e-37,125.10799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,marg,CompleteHit
22897,Q#1020 - >seq7667,non-specific,340205,165,228,2.0003799999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,marg,CompleteHit
22898,Q#1020 - >seq7667,superfamily,340205,165,228,2.0003799999999996e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,marg,CompleteHit
22899,Q#1020 - >seq7667,non-specific,340204,21,63,1.1332200000000001e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs0_human,marg,CompleteHit
22900,Q#1020 - >seq7667,superfamily,340204,21,63,1.1332200000000001e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs0_human,marg,CompleteHit
22901,Q#1020 - >seq7667,non-specific,334565,22,145,0.00373878,37.8544,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB3,ORF1,hs0_human,marg,C-TerminusTruncated
22902,Q#1020 - >seq7667,superfamily,334565,22,145,0.00373878,37.8544,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs0_human.marg.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB3,ORF1,hs0_human,marg,C-TerminusTruncated
22903,Q#1024 - >seq7671,non-specific,335182,206,299,7.879529999999999e-29,107.389,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs1_chimp.marg.frame2,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs1_chimp,marg,CompleteHit
22904,Q#1024 - >seq7671,superfamily,335182,206,299,7.879529999999999e-29,107.389,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs1_chimp.marg.frame2,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs1_chimp,marg,CompleteHit
22905,Q#1024 - >seq7671,non-specific,340205,302,365,1.3295099999999997e-23,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs1_chimp.marg.frame2,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs1_chimp,marg,CompleteHit
22906,Q#1024 - >seq7671,superfamily,340205,302,365,1.3295099999999997e-23,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs1_chimp.marg.frame2,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs1_chimp,marg,CompleteHit
22907,Q#1027 - >seq7674,non-specific,335182,86,179,2.94931e-29,105.848,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs1_chimp.pars.frame1,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs1_chimp,pars,CompleteHit
22908,Q#1027 - >seq7674,superfamily,335182,86,179,2.94931e-29,105.848,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs1_chimp.pars.frame1,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs1_chimp,pars,CompleteHit
22909,Q#1027 - >seq7674,non-specific,340205,182,245,5.4286e-24,91.2436,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs1_chimp.pars.frame1,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs1_chimp,pars,CompleteHit
22910,Q#1027 - >seq7674,superfamily,340205,182,245,5.4286e-24,91.2436,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs1_chimp.pars.frame1,1909131022_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs1_chimp,pars,CompleteHit
22911,Q#1029 - >seq7676,non-specific,335182,67,162,6.874229999999999e-37,125.10799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,pars,CompleteHit
22912,Q#1029 - >seq7676,superfamily,335182,67,162,6.874229999999999e-37,125.10799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,pars,CompleteHit
22913,Q#1029 - >seq7676,non-specific,340205,165,228,2.0003799999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,pars,CompleteHit
22914,Q#1029 - >seq7676,superfamily,340205,165,228,2.0003799999999996e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs0_human,pars,CompleteHit
22915,Q#1029 - >seq7676,non-specific,340204,21,63,1.1332200000000001e-08,49.7136,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs0_human,pars,CompleteHit
22916,Q#1029 - >seq7676,superfamily,340204,21,63,1.1332200000000001e-08,49.7136,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs0_human,pars,CompleteHit
22917,Q#1029 - >seq7676,non-specific,334565,22,145,0.00373878,37.8544,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs0_human,pars,C-TerminusTruncated
22918,Q#1029 - >seq7676,superfamily,334565,22,145,0.00373878,37.8544,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs0_human.pars.frame3,1909131022_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs0_human,pars,C-TerminusTruncated
22919,Q#1033 - >seq7680,non-specific,335182,67,162,1.0481100000000001e-36,124.723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22920,Q#1033 - >seq7680,superfamily,335182,67,162,1.0481100000000001e-36,124.723,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22921,Q#1033 - >seq7680,non-specific,335182,67,162,1.0481100000000001e-36,124.723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22922,Q#1033 - >seq7680,non-specific,340205,165,228,2.5078599999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22923,Q#1033 - >seq7680,superfamily,340205,165,228,2.5078599999999996e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22924,Q#1033 - >seq7680,non-specific,340205,165,228,2.5078599999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22925,Q#1033 - >seq7680,non-specific,340204,21,63,3.4695300000000004e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22926,Q#1033 - >seq7680,superfamily,340204,21,63,3.4695300000000004e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22927,Q#1033 - >seq7680,non-specific,340204,21,63,3.4695300000000004e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.pars.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,pars,CompleteHit
22928,Q#1036 - >seq7683,non-specific,335182,67,162,1.0481100000000001e-36,124.723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22929,Q#1036 - >seq7683,superfamily,335182,67,162,1.0481100000000001e-36,124.723,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22930,Q#1036 - >seq7683,non-specific,335182,67,162,1.0481100000000001e-36,124.723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22931,Q#1036 - >seq7683,non-specific,340205,165,228,2.5078599999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22932,Q#1036 - >seq7683,superfamily,340205,165,228,2.5078599999999996e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22933,Q#1036 - >seq7683,non-specific,340205,165,228,2.5078599999999996e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22934,Q#1036 - >seq7683,non-specific,340204,21,63,3.4695300000000004e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22935,Q#1036 - >seq7683,superfamily,340204,21,63,3.4695300000000004e-08,48.1728,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22936,Q#1036 - >seq7683,non-specific,340204,21,63,3.4695300000000004e-08,48.1728,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs4_gibbon.marg.frame3,1909131022_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs4_gibbon,marg,CompleteHit
22937,Q#1038 - >seq7685,non-specific,335182,157,252,2.43159e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs5_gmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,pars,CompleteHit
22938,Q#1038 - >seq7685,superfamily,335182,157,252,2.43159e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs5_gmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,pars,CompleteHit
22939,Q#1038 - >seq7685,non-specific,340205,255,318,1.1265299999999999e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs5_gmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,pars,CompleteHit
22940,Q#1038 - >seq7685,superfamily,340205,255,318,1.1265299999999999e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs5_gmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,pars,CompleteHit
22941,Q#1039 - >seq7686,non-specific,335182,157,252,1.5652600000000002e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22942,Q#1039 - >seq7686,superfamily,335182,157,252,1.5652600000000002e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22943,Q#1039 - >seq7686,non-specific,340205,255,318,3.4467699999999996e-29,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22944,Q#1039 - >seq7686,superfamily,340205,255,318,3.4467699999999996e-29,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22945,Q#1039 - >seq7686,non-specific,340204,111,153,1.34713e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22946,Q#1039 - >seq7686,superfamily,340204,111,153,1.34713e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs6_sqmonkey,pars,CompleteHit
22947,Q#1039 - >seq7686,non-specific,235175,42,184,2.9379899999999996e-05,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22948,Q#1039 - >seq7686,superfamily,235175,42,184,2.9379899999999996e-05,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22949,Q#1039 - >seq7686,non-specific,274008,33,149,4.78249e-05,45.0475,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22950,Q#1039 - >seq7686,superfamily,274008,33,149,4.78249e-05,45.0475,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22951,Q#1039 - >seq7686,non-specific,237177,42,149,0.000204096,42.843,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22952,Q#1039 - >seq7686,superfamily,237177,42,149,0.000204096,42.843,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22953,Q#1039 - >seq7686,non-specific,224117,32,150,0.000228027,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22954,Q#1039 - >seq7686,superfamily,224117,32,150,0.000228027,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22955,Q#1039 - >seq7686,non-specific,197874,49,162,0.000317162,41.5417,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22956,Q#1039 - >seq7686,superfamily,197874,49,162,0.000317162,41.5417,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22957,Q#1039 - >seq7686,non-specific,274009,40,240,0.0007388010000000001,41.2067,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22958,Q#1039 - >seq7686,superfamily,274009,40,240,0.0007388010000000001,41.2067,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22959,Q#1039 - >seq7686,non-specific,336852,50,125,0.00206076,37.1792,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22960,Q#1039 - >seq7686,superfamily,336852,50,125,0.00206076,37.1792,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
22961,Q#1039 - >seq7686,non-specific,222878,54,150,0.00269817,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22962,Q#1039 - >seq7686,superfamily,222878,54,150,0.00269817,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22963,Q#1039 - >seq7686,non-specific,235461,45,122,0.00285363,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22964,Q#1039 - >seq7686,superfamily,235461,45,122,0.00285363,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22965,Q#1039 - >seq7686,non-specific,235175,38,243,0.00597126,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22966,Q#1039 - >seq7686,non-specific,112704,2,121,0.00813324,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22967,Q#1039 - >seq7686,superfamily,112704,2,121,0.00813324,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22968,Q#1039 - >seq7686,non-specific,129694,50,146,0.00815826,37.7189,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22969,Q#1039 - >seq7686,superfamily,129694,50,146,0.00815826,37.7189,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22970,Q#1039 - >seq7686,non-specific,337033,42,128,0.00903798,37.5585,pfam08385,DHC_N1,NC,cl20356,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22971,Q#1039 - >seq7686,superfamily,337033,42,128,0.00903798,37.5585,cl20356,DHC_N1 superfamily,NC, - ,"Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
22972,Q#1039 - >seq7686,non-specific,188306,43,150,0.00970492,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22973,Q#1039 - >seq7686,superfamily,188306,43,150,0.00970492,37.2126,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB3.ORF1.hs6_sqmonkey.pars.frame3,1909131022_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
22974,Q#1042 - >seq7689,non-specific,335182,157,252,2.43159e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs5_gmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,marg,CompleteHit
22975,Q#1042 - >seq7689,superfamily,335182,157,252,2.43159e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs5_gmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,marg,CompleteHit
22976,Q#1042 - >seq7689,non-specific,340205,255,318,1.1265299999999999e-29,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs5_gmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,marg,CompleteHit
22977,Q#1042 - >seq7689,superfamily,340205,255,318,1.1265299999999999e-29,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs5_gmonkey.marg.frame3,1909131022_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs5_gmonkey,marg,CompleteHit
22978,Q#1047 - >seq7694,non-specific,335182,200,294,3.9015899999999997e-29,108.15899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs2_gorilla.marg.frame2,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs2_gorilla,marg,CompleteHit
22979,Q#1047 - >seq7694,superfamily,335182,200,294,3.9015899999999997e-29,108.15899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs2_gorilla.marg.frame2,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs2_gorilla,marg,CompleteHit
22980,Q#1047 - >seq7694,non-specific,340205,297,359,2.1437e-20,83.5396,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs2_gorilla.marg.frame2,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs2_gorilla,marg,CompleteHit
22981,Q#1047 - >seq7694,superfamily,340205,297,359,2.1437e-20,83.5396,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs2_gorilla.marg.frame2,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs2_gorilla,marg,CompleteHit
22982,Q#1050 - >seq7697,non-specific,335182,52,146,2.4505599999999997e-33,115.09299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs2_gorilla.pars.frame3,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs2_gorilla,pars,CompleteHit
22983,Q#1050 - >seq7697,superfamily,335182,52,146,2.4505599999999997e-33,115.09299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs2_gorilla.pars.frame3,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs2_gorilla,pars,CompleteHit
22984,Q#1050 - >seq7697,non-specific,340205,149,211,2.4035700000000003e-22,85.8508,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs2_gorilla.pars.frame3,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs2_gorilla,pars,CompleteHit
22985,Q#1050 - >seq7697,superfamily,340205,149,211,2.4035700000000003e-22,85.8508,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs2_gorilla.pars.frame3,1909131023_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs2_gorilla,pars,CompleteHit
22986,Q#1052 - >seq7699,non-specific,335182,157,252,7.5145e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,marg,CompleteHit
22987,Q#1052 - >seq7699,superfamily,335182,157,252,7.5145e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,marg,CompleteHit
22988,Q#1052 - >seq7699,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,marg,CompleteHit
22989,Q#1052 - >seq7699,superfamily,340205,255,318,7.4266099999999995e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,marg,CompleteHit
22990,Q#1052 - >seq7699,non-specific,340204,111,153,1.96071e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs0_human,marg,CompleteHit
22991,Q#1052 - >seq7699,superfamily,340204,111,153,1.96071e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs0_human,marg,CompleteHit
22992,Q#1052 - >seq7699,non-specific,224117,41,150,5.4297e-05,44.7052,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
22993,Q#1052 - >seq7699,superfamily,224117,41,150,5.4297e-05,44.7052,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
22994,Q#1052 - >seq7699,non-specific,274008,28,149,9.40324e-05,43.8919,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
22995,Q#1052 - >seq7699,superfamily,274008,28,149,9.40324e-05,43.8919,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
22996,Q#1052 - >seq7699,non-specific,274009,32,155,0.00025059,42.7475,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,N-TerminusTruncated
22997,Q#1052 - >seq7699,superfamily,274009,32,155,0.00025059,42.7475,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,N-TerminusTruncated
22998,Q#1052 - >seq7699,non-specific,235175,42,155,0.00025285,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
22999,Q#1052 - >seq7699,superfamily,235175,42,155,0.00025285,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23000,Q#1052 - >seq7699,non-specific,224117,29,150,0.000335878,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23001,Q#1052 - >seq7699,non-specific,274009,33,150,0.000513443,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23002,Q#1052 - >seq7699,non-specific,237177,44,149,0.000627694,40.917,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23003,Q#1052 - >seq7699,superfamily,237177,44,149,0.000627694,40.917,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23004,Q#1052 - >seq7699,non-specific,224117,33,149,0.00123522,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23005,Q#1052 - >seq7699,non-specific,274009,33,150,0.00130768,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23006,Q#1052 - >seq7699,non-specific,337663,62,147,0.00131287,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23007,Q#1052 - >seq7699,superfamily,337663,62,147,0.00131287,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23008,Q#1052 - >seq7699,non-specific,224117,43,149,0.00163331,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23009,Q#1052 - >seq7699,non-specific,274008,45,150,0.00217098,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23010,Q#1052 - >seq7699,non-specific,226400,82,149,0.0040025,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23011,Q#1052 - >seq7699,superfamily,226400,82,149,0.0040025,38.161,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23012,Q#1052 - >seq7699,non-specific,223250,48,150,0.00458074,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23013,Q#1052 - >seq7699,superfamily,223250,48,150,0.00458074,38.3481,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23014,Q#1052 - >seq7699,non-specific,235461,49,165,0.00504942,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23015,Q#1052 - >seq7699,superfamily,235461,49,165,0.00504942,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23016,Q#1052 - >seq7699,non-specific,274008,32,144,0.00561556,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23017,Q#1052 - >seq7699,non-specific,226447,50,125,0.00637262,35.5258,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,N-TerminusTruncated
23018,Q#1052 - >seq7699,superfamily,352825,50,125,0.00637262,35.5258,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,marg,N-TerminusTruncated
23019,Q#1052 - >seq7699,non-specific,112704,2,148,0.00828307,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23020,Q#1052 - >seq7699,superfamily,112704,2,148,0.00828307,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs0_human,marg,C-TerminusTruncated
23021,Q#1052 - >seq7699,non-specific,240419,48,138,0.00986288,37.5036,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23022,Q#1052 - >seq7699,superfamily,240419,48,138,0.00986288,37.5036,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs0_human.marg.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,marg,BothTerminiTruncated
23023,Q#1054 - >seq7701,non-specific,335182,155,251,2.46351e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23024,Q#1054 - >seq7701,superfamily,335182,155,251,2.46351e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23025,Q#1054 - >seq7701,non-specific,335182,155,251,2.46351e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23026,Q#1054 - >seq7701,non-specific,340205,254,317,1.05095e-25,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23027,Q#1054 - >seq7701,superfamily,340205,254,317,1.05095e-25,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23028,Q#1054 - >seq7701,non-specific,340205,254,317,1.05095e-25,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23029,Q#1054 - >seq7701,non-specific,340204,111,153,3.2366700000000003e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23030,Q#1054 - >seq7701,superfamily,340204,111,153,3.2366700000000003e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23031,Q#1054 - >seq7701,non-specific,340204,111,153,3.2366700000000003e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,marg,CompleteHit
23032,Q#1054 - >seq7701,non-specific,274008,53,149,0.000190996,43.1215,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23033,Q#1054 - >seq7701,superfamily,274008,53,149,0.000190996,43.1215,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23034,Q#1054 - >seq7701,non-specific,274008,53,149,0.000190996,43.1215,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23035,Q#1054 - >seq7701,non-specific,237177,44,149,0.00048627800000000004,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23036,Q#1054 - >seq7701,superfamily,237177,44,149,0.00048627800000000004,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23037,Q#1054 - >seq7701,non-specific,237177,44,149,0.00048627800000000004,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23038,Q#1054 - >seq7701,non-specific,274009,33,150,0.00123043,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23039,Q#1054 - >seq7701,superfamily,274009,33,150,0.00123043,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23040,Q#1054 - >seq7701,non-specific,274009,33,150,0.00123043,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23041,Q#1054 - >seq7701,non-specific,274009,32,153,0.00165594,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23042,Q#1054 - >seq7701,non-specific,274009,32,153,0.00165594,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23043,Q#1054 - >seq7701,non-specific,224117,29,150,0.00212333,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23044,Q#1054 - >seq7701,superfamily,224117,29,150,0.00212333,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23045,Q#1054 - >seq7701,non-specific,224117,29,150,0.00212333,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23046,Q#1054 - >seq7701,non-specific,274009,33,150,0.00218976,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23047,Q#1054 - >seq7701,non-specific,274009,33,150,0.00218976,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23048,Q#1054 - >seq7701,non-specific,235505,51,150,0.00224099,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23049,Q#1054 - >seq7701,superfamily,235505,51,150,0.00224099,39.4686,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23050,Q#1054 - >seq7701,non-specific,235505,51,150,0.00224099,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23051,Q#1054 - >seq7701,non-specific,274008,41,149,0.00234974,39.6547,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23052,Q#1054 - >seq7701,non-specific,274008,41,149,0.00234974,39.6547,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23053,Q#1054 - >seq7701,non-specific,337663,62,147,0.00238749,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23054,Q#1054 - >seq7701,superfamily,337663,62,147,0.00238749,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23055,Q#1054 - >seq7701,non-specific,337663,62,147,0.00238749,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23056,Q#1054 - >seq7701,non-specific,224117,41,150,0.0024416,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23057,Q#1054 - >seq7701,non-specific,224117,41,150,0.0024416,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23058,Q#1054 - >seq7701,non-specific,235175,42,155,0.00271296,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23059,Q#1054 - >seq7701,superfamily,235175,42,155,0.00271296,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23060,Q#1054 - >seq7701,non-specific,235175,42,155,0.00271296,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23061,Q#1054 - >seq7701,non-specific,226447,50,125,0.00453265,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23062,Q#1054 - >seq7701,superfamily,352825,50,125,0.00453265,35.911,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23063,Q#1054 - >seq7701,non-specific,226447,50,125,0.00453265,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23064,Q#1054 - >seq7701,non-specific,224117,33,149,0.00512539,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23065,Q#1054 - >seq7701,non-specific,224117,33,149,0.00512539,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23066,Q#1054 - >seq7701,non-specific,274008,45,150,0.00973485,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23067,Q#1054 - >seq7701,non-specific,274008,45,150,0.00973485,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23068,Q#1057 - >seq7704,non-specific,335182,155,251,2.46351e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23069,Q#1057 - >seq7704,superfamily,335182,155,251,2.46351e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23070,Q#1057 - >seq7704,non-specific,335182,155,251,2.46351e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23071,Q#1057 - >seq7704,non-specific,340205,254,317,1.05095e-25,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23072,Q#1057 - >seq7704,superfamily,340205,254,317,1.05095e-25,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23073,Q#1057 - >seq7704,non-specific,340205,254,317,1.05095e-25,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23074,Q#1057 - >seq7704,non-specific,340204,111,153,3.2366700000000003e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23075,Q#1057 - >seq7704,superfamily,340204,111,153,3.2366700000000003e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23076,Q#1057 - >seq7704,non-specific,340204,111,153,3.2366700000000003e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs2_gorilla,pars,CompleteHit
23077,Q#1057 - >seq7704,non-specific,274008,53,149,0.000190996,43.1215,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23078,Q#1057 - >seq7704,superfamily,274008,53,149,0.000190996,43.1215,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23079,Q#1057 - >seq7704,non-specific,274008,53,149,0.000190996,43.1215,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23080,Q#1057 - >seq7704,non-specific,237177,44,149,0.00048627800000000004,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23081,Q#1057 - >seq7704,superfamily,237177,44,149,0.00048627800000000004,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23082,Q#1057 - >seq7704,non-specific,237177,44,149,0.00048627800000000004,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23083,Q#1057 - >seq7704,non-specific,274009,33,150,0.00123043,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23084,Q#1057 - >seq7704,superfamily,274009,33,150,0.00123043,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23085,Q#1057 - >seq7704,non-specific,274009,33,150,0.00123043,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23086,Q#1057 - >seq7704,non-specific,274009,32,153,0.00165594,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,N-TerminusTruncated
23087,Q#1057 - >seq7704,non-specific,274009,32,153,0.00165594,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,N-TerminusTruncated
23088,Q#1057 - >seq7704,non-specific,224117,29,150,0.00212333,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23089,Q#1057 - >seq7704,superfamily,224117,29,150,0.00212333,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23090,Q#1057 - >seq7704,non-specific,224117,29,150,0.00212333,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23091,Q#1057 - >seq7704,non-specific,274009,33,150,0.00218976,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23092,Q#1057 - >seq7704,non-specific,274009,33,150,0.00218976,39.6659,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23093,Q#1057 - >seq7704,non-specific,235505,51,150,0.00224099,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23094,Q#1057 - >seq7704,superfamily,235505,51,150,0.00224099,39.4686,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23095,Q#1057 - >seq7704,non-specific,235505,51,150,0.00224099,39.4686,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23096,Q#1057 - >seq7704,non-specific,274008,41,149,0.00234974,39.6547,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23097,Q#1057 - >seq7704,non-specific,274008,41,149,0.00234974,39.6547,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23098,Q#1057 - >seq7704,non-specific,337663,62,147,0.00238749,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23099,Q#1057 - >seq7704,superfamily,337663,62,147,0.00238749,38.9451,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23100,Q#1057 - >seq7704,non-specific,337663,62,147,0.00238749,38.9451,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23101,Q#1057 - >seq7704,non-specific,224117,41,150,0.0024416,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23102,Q#1057 - >seq7704,non-specific,224117,41,150,0.0024416,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23103,Q#1057 - >seq7704,non-specific,235175,42,155,0.00271296,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23104,Q#1057 - >seq7704,superfamily,235175,42,155,0.00271296,39.2768,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23105,Q#1057 - >seq7704,non-specific,235175,42,155,0.00271296,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23106,Q#1057 - >seq7704,non-specific,226447,50,125,0.00453265,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,N-TerminusTruncated
23107,Q#1057 - >seq7704,superfamily,352825,50,125,0.00453265,35.911,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs2_gorilla,pars,N-TerminusTruncated
23108,Q#1057 - >seq7704,non-specific,226447,50,125,0.00453265,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs2_gorilla,pars,N-TerminusTruncated
23109,Q#1057 - >seq7704,non-specific,224117,33,149,0.00512539,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23110,Q#1057 - >seq7704,non-specific,224117,33,149,0.00512539,38.542,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23111,Q#1057 - >seq7704,non-specific,274008,45,150,0.00973485,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23112,Q#1057 - >seq7704,non-specific,274008,45,150,0.00973485,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs2_gorilla,pars,BothTerminiTruncated
23113,Q#1058 - >seq7705,non-specific,335182,156,252,2.5796299999999995e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23114,Q#1058 - >seq7705,superfamily,335182,156,252,2.5796299999999995e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23115,Q#1058 - >seq7705,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23116,Q#1058 - >seq7705,superfamily,340205,255,318,8.44937e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23117,Q#1058 - >seq7705,non-specific,340204,111,153,3.02065e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23118,Q#1058 - >seq7705,superfamily,340204,111,153,3.02065e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs3_orang,marg,CompleteHit
23119,Q#1058 - >seq7705,non-specific,274009,60,203,1.5128800000000002e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23120,Q#1058 - >seq7705,superfamily,274009,60,203,1.5128800000000002e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23121,Q#1058 - >seq7705,non-specific,235175,49,156,6.37332e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23122,Q#1058 - >seq7705,superfamily,235175,49,156,6.37332e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23123,Q#1058 - >seq7705,non-specific,237177,41,149,6.785649999999999e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23124,Q#1058 - >seq7705,superfamily,237177,41,149,6.785649999999999e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23125,Q#1058 - >seq7705,non-specific,274008,53,202,0.000115033,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23126,Q#1058 - >seq7705,superfamily,274008,53,202,0.000115033,43.8919,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23127,Q#1058 - >seq7705,non-specific,224117,28,177,0.000497856,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23128,Q#1058 - >seq7705,superfamily,224117,28,177,0.000497856,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23129,Q#1058 - >seq7705,non-specific,223250,47,170,0.00119643,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23130,Q#1058 - >seq7705,superfamily,223250,47,170,0.00119643,40.2741,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23131,Q#1058 - >seq7705,non-specific,129694,80,146,0.00248722,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23132,Q#1058 - >seq7705,superfamily,129694,80,146,0.00248722,39.6449,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23133,Q#1058 - >seq7705,non-specific,275056,64,152,0.00292478,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23134,Q#1058 - >seq7705,superfamily,275056,64,152,0.00292478,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23135,Q#1058 - >seq7705,non-specific,235461,47,170,0.00330505,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23136,Q#1058 - >seq7705,superfamily,235461,47,170,0.00330505,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23137,Q#1058 - >seq7705,non-specific,112704,2,148,0.00378936,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23138,Q#1058 - >seq7705,superfamily,112704,2,148,0.00378936,38.0707,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23139,Q#1058 - >seq7705,non-specific,336159,60,145,0.00401735,38.5045,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23140,Q#1058 - >seq7705,superfamily,336159,60,145,0.00401735,38.5045,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs3_orang,marg,N-TerminusTruncated
23141,Q#1058 - >seq7705,non-specific,310273,65,194,0.00466108,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23142,Q#1058 - >seq7705,superfamily,310273,65,194,0.00466108,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23143,Q#1058 - >seq7705,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23144,Q#1058 - >seq7705,superfamily,337663,79,183,0.00497954,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23145,Q#1058 - >seq7705,non-specific,226400,79,149,0.00505781,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23146,Q#1058 - >seq7705,superfamily,226400,79,149,0.00505781,37.7758,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,C-TerminusTruncated
23147,Q#1058 - >seq7705,non-specific,235175,41,144,0.00549965,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23148,Q#1058 - >seq7705,non-specific,222878,57,150,0.00646662,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23149,Q#1058 - >seq7705,superfamily,222878,57,150,0.00646662,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23150,Q#1058 - >seq7705,non-specific,274008,45,150,0.00662651,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23151,Q#1058 - >seq7705,non-specific,274386,27,147,0.00704802,37.7234,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23152,Q#1058 - >seq7705,superfamily,274386,27,147,0.00704802,37.7234,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,marg,BothTerminiTruncated
23153,Q#1060 - >seq7707,non-specific,335182,155,251,3.93287e-30,110.085,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23154,Q#1060 - >seq7707,superfamily,335182,155,251,3.93287e-30,110.085,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23155,Q#1060 - >seq7707,non-specific,340205,254,317,6.040149999999999e-25,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23156,Q#1060 - >seq7707,superfamily,340205,254,317,6.040149999999999e-25,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23157,Q#1060 - >seq7707,non-specific,340204,111,153,2.6300000000000002e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23158,Q#1060 - >seq7707,superfamily,340204,111,153,2.6300000000000002e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs1_chimp,marg,CompleteHit
23159,Q#1060 - >seq7707,non-specific,274008,28,149,0.000461363,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23160,Q#1060 - >seq7707,superfamily,274008,28,149,0.000461363,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23161,Q#1060 - >seq7707,non-specific,224117,41,150,0.00058093,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23162,Q#1060 - >seq7707,superfamily,224117,41,150,0.00058093,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23163,Q#1060 - >seq7707,non-specific,237177,44,149,0.0007588089999999999,40.917,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs1_chimp,marg,C-TerminusTruncated
23164,Q#1060 - >seq7707,superfamily,237177,44,149,0.0007588089999999999,40.917,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs1_chimp,marg,C-TerminusTruncated
23165,Q#1060 - >seq7707,non-specific,224117,33,149,0.00187062,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23166,Q#1060 - >seq7707,non-specific,274008,41,149,0.00334306,39.2695,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,C-TerminusTruncated
23167,Q#1060 - >seq7707,non-specific,274009,32,153,0.00358197,38.8955,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,N-TerminusTruncated
23168,Q#1060 - >seq7707,superfamily,274009,32,153,0.00358197,38.8955,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,marg,N-TerminusTruncated
23169,Q#1060 - >seq7707,non-specific,240419,48,138,0.0045335,38.6592,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23170,Q#1060 - >seq7707,superfamily,240419,48,138,0.0045335,38.6592,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,marg,BothTerminiTruncated
23171,Q#1060 - >seq7707,non-specific,313406,38,146,0.00783154,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa,ORF1,hs1_chimp,marg,N-TerminusTruncated
23172,Q#1060 - >seq7707,superfamily,313406,38,146,0.00783154,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs1_chimp.marg.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,marg,N-TerminusTruncated
23173,Q#1063 - >seq7710,non-specific,335182,155,251,2.2836799999999997e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23174,Q#1063 - >seq7710,superfamily,335182,155,251,2.2836799999999997e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23175,Q#1063 - >seq7710,non-specific,340205,254,317,5.338649999999999e-25,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23176,Q#1063 - >seq7710,superfamily,340205,254,317,5.338649999999999e-25,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23177,Q#1063 - >seq7710,non-specific,340204,111,153,3.44393e-05,40.4688,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23178,Q#1063 - >seq7710,superfamily,340204,111,153,3.44393e-05,40.4688,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs1_chimp,pars,CompleteHit
23179,Q#1063 - >seq7710,non-specific,274008,28,149,0.000562387,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23180,Q#1063 - >seq7710,superfamily,274008,28,149,0.000562387,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23181,Q#1063 - >seq7710,non-specific,224117,41,150,0.00076626,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23182,Q#1063 - >seq7710,superfamily,224117,41,150,0.00076626,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23183,Q#1063 - >seq7710,non-specific,237177,44,149,0.0010874,40.5318,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs1_chimp,pars,C-TerminusTruncated
23184,Q#1063 - >seq7710,superfamily,237177,44,149,0.0010874,40.5318,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs1_chimp,pars,C-TerminusTruncated
23185,Q#1063 - >seq7710,non-specific,224117,33,149,0.00267086,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23186,Q#1063 - >seq7710,non-specific,274008,41,149,0.00397555,38.8843,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,C-TerminusTruncated
23187,Q#1063 - >seq7710,non-specific,274009,32,153,0.00502741,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,N-TerminusTruncated
23188,Q#1063 - >seq7710,superfamily,274009,32,153,0.00502741,38.5103,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs1_chimp,pars,N-TerminusTruncated
23189,Q#1063 - >seq7710,non-specific,240419,48,138,0.0053413,38.6592,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23190,Q#1063 - >seq7710,superfamily,240419,48,138,0.0053413,38.6592,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,pars,BothTerminiTruncated
23191,Q#1063 - >seq7710,non-specific,313406,38,146,0.007563500000000001,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PBa,ORF1,hs1_chimp,pars,N-TerminusTruncated
23192,Q#1063 - >seq7710,superfamily,313406,38,146,0.007563500000000001,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs1_chimp.pars.frame3,1909131024_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs1_chimp,pars,N-TerminusTruncated
23193,Q#1066 - >seq7713,non-specific,335182,155,251,3.10314e-30,110.085,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23194,Q#1066 - >seq7713,superfamily,335182,155,251,3.10314e-30,110.085,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23195,Q#1066 - >seq7713,non-specific,340205,254,317,1.1105799999999998e-25,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23196,Q#1066 - >seq7713,superfamily,340205,254,317,1.1105799999999998e-25,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23197,Q#1066 - >seq7713,non-specific,340204,111,153,6.542819999999999e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23198,Q#1066 - >seq7713,superfamily,340204,111,153,6.542819999999999e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs3_orang,pars,CompleteHit
23199,Q#1066 - >seq7713,non-specific,274008,28,149,0.00031025,42.3511,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23200,Q#1066 - >seq7713,superfamily,274008,28,149,0.00031025,42.3511,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23201,Q#1066 - >seq7713,non-specific,237177,44,150,0.000586791,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs3_orang,pars,C-TerminusTruncated
23202,Q#1066 - >seq7713,superfamily,237177,44,150,0.000586791,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs3_orang,pars,C-TerminusTruncated
23203,Q#1066 - >seq7713,non-specific,224117,41,150,0.00175685,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23204,Q#1066 - >seq7713,superfamily,224117,41,150,0.00175685,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23205,Q#1066 - >seq7713,non-specific,274009,32,153,0.00237472,39.6659,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,N-TerminusTruncated
23206,Q#1066 - >seq7713,superfamily,274009,32,153,0.00237472,39.6659,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,N-TerminusTruncated
23207,Q#1066 - >seq7713,non-specific,224117,33,149,0.00242645,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23208,Q#1066 - >seq7713,non-specific,224117,29,150,0.00420347,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23209,Q#1066 - >seq7713,non-specific,240419,48,159,0.00477076,38.6592,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23210,Q#1066 - >seq7713,superfamily,240419,48,159,0.00477076,38.6592,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23211,Q#1066 - >seq7713,non-specific,235175,42,155,0.00492595,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,C-TerminusTruncated
23212,Q#1066 - >seq7713,superfamily,235175,42,155,0.00492595,38.5064,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,C-TerminusTruncated
23213,Q#1066 - >seq7713,non-specific,274008,41,149,0.00719097,38.1139,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,pars,C-TerminusTruncated
23214,Q#1066 - >seq7713,non-specific,235505,51,150,0.0099919,37.1574,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23215,Q#1066 - >seq7713,superfamily,235505,51,150,0.0099919,37.1574,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,pars,BothTerminiTruncated
23216,Q#1069 - >seq7716,non-specific,335182,155,251,1.99035e-30,110.855,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23217,Q#1069 - >seq7716,superfamily,335182,155,251,1.99035e-30,110.855,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23218,Q#1069 - >seq7716,non-specific,340205,254,317,3.9418000000000007e-25,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23219,Q#1069 - >seq7716,superfamily,340205,254,317,3.9418000000000007e-25,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23220,Q#1069 - >seq7716,non-specific,340204,111,153,7.218260000000001e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23221,Q#1069 - >seq7716,superfamily,340204,111,153,7.218260000000001e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs5_gmonkey,pars,CompleteHit
23222,Q#1069 - >seq7716,non-specific,274008,53,149,0.000463965,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23223,Q#1069 - >seq7716,superfamily,274008,53,149,0.000463965,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23224,Q#1069 - >seq7716,non-specific,224117,41,150,0.000544895,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23225,Q#1069 - >seq7716,superfamily,224117,41,150,0.000544895,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23226,Q#1069 - >seq7716,non-specific,237177,44,149,0.00125197,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23227,Q#1069 - >seq7716,superfamily,237177,44,149,0.00125197,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23228,Q#1069 - >seq7716,non-specific,274009,33,150,0.00170442,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23229,Q#1069 - >seq7716,superfamily,274009,33,150,0.00170442,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23230,Q#1069 - >seq7716,non-specific,224117,33,149,0.00269426,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23231,Q#1069 - >seq7716,non-specific,274009,32,153,0.00273047,39.2807,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
23232,Q#1069 - >seq7716,non-specific,235175,42,155,0.00326718,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23233,Q#1069 - >seq7716,superfamily,235175,42,155,0.00326718,38.8916,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23234,Q#1069 - >seq7716,non-specific,226447,50,125,0.00410392,36.2962,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
23235,Q#1069 - >seq7716,superfamily,352825,50,125,0.00410392,36.2962,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
23236,Q#1069 - >seq7716,non-specific,274008,41,149,0.00614716,38.1139,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23237,Q#1069 - >seq7716,non-specific,274008,32,144,0.00700545,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
23238,Q#1070 - >seq7717,non-specific,335182,155,251,3.10314e-30,110.085,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23239,Q#1070 - >seq7717,superfamily,335182,155,251,3.10314e-30,110.085,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23240,Q#1070 - >seq7717,non-specific,340205,254,317,1.1105799999999998e-25,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23241,Q#1070 - >seq7717,superfamily,340205,254,317,1.1105799999999998e-25,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23242,Q#1070 - >seq7717,non-specific,340204,111,153,6.542819999999999e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23243,Q#1070 - >seq7717,superfamily,340204,111,153,6.542819999999999e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs3_orang,marg,CompleteHit
23244,Q#1070 - >seq7717,non-specific,274008,28,149,0.00031025,42.3511,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23245,Q#1070 - >seq7717,superfamily,274008,28,149,0.00031025,42.3511,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23246,Q#1070 - >seq7717,non-specific,237177,44,150,0.000586791,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs3_orang,marg,C-TerminusTruncated
23247,Q#1070 - >seq7717,superfamily,237177,44,150,0.000586791,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs3_orang,marg,C-TerminusTruncated
23248,Q#1070 - >seq7717,non-specific,224117,41,150,0.00175685,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23249,Q#1070 - >seq7717,superfamily,224117,41,150,0.00175685,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23250,Q#1070 - >seq7717,non-specific,274009,32,153,0.00237472,39.6659,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,N-TerminusTruncated
23251,Q#1070 - >seq7717,superfamily,274009,32,153,0.00237472,39.6659,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,N-TerminusTruncated
23252,Q#1070 - >seq7717,non-specific,224117,33,149,0.00242645,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23253,Q#1070 - >seq7717,non-specific,224117,29,150,0.00420347,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23254,Q#1070 - >seq7717,non-specific,240419,48,159,0.00477076,38.6592,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23255,Q#1070 - >seq7717,superfamily,240419,48,159,0.00477076,38.6592,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23256,Q#1070 - >seq7717,non-specific,235175,42,155,0.00492595,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,C-TerminusTruncated
23257,Q#1070 - >seq7717,superfamily,235175,42,155,0.00492595,38.5064,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,C-TerminusTruncated
23258,Q#1070 - >seq7717,non-specific,274008,41,149,0.00719097,38.1139,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs3_orang,marg,C-TerminusTruncated
23259,Q#1070 - >seq7717,non-specific,235505,51,150,0.0099919,37.1574,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23260,Q#1070 - >seq7717,superfamily,235505,51,150,0.0099919,37.1574,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PBa.ORF1.hs3_orang.marg.frame3,1909131024_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs3_orang,marg,BothTerminiTruncated
23261,Q#1074 - >seq7721,non-specific,335182,157,252,7.5145e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,pars,CompleteHit
23262,Q#1074 - >seq7721,superfamily,335182,157,252,7.5145e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,pars,CompleteHit
23263,Q#1074 - >seq7721,non-specific,340205,255,318,7.4266099999999995e-25,95.0956,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,pars,CompleteHit
23264,Q#1074 - >seq7721,superfamily,340205,255,318,7.4266099999999995e-25,95.0956,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs0_human,pars,CompleteHit
23265,Q#1074 - >seq7721,non-specific,340204,111,153,1.96071e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs0_human,pars,CompleteHit
23266,Q#1074 - >seq7721,superfamily,340204,111,153,1.96071e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs0_human,pars,CompleteHit
23267,Q#1074 - >seq7721,non-specific,224117,41,150,5.4297e-05,44.7052,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23268,Q#1074 - >seq7721,superfamily,224117,41,150,5.4297e-05,44.7052,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23269,Q#1074 - >seq7721,non-specific,274008,28,149,9.40324e-05,43.8919,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23270,Q#1074 - >seq7721,superfamily,274008,28,149,9.40324e-05,43.8919,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23271,Q#1074 - >seq7721,non-specific,274009,32,155,0.00025059,42.7475,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,N-TerminusTruncated
23272,Q#1074 - >seq7721,superfamily,274009,32,155,0.00025059,42.7475,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,N-TerminusTruncated
23273,Q#1074 - >seq7721,non-specific,235175,42,155,0.00025285,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23274,Q#1074 - >seq7721,superfamily,235175,42,155,0.00025285,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23275,Q#1074 - >seq7721,non-specific,224117,29,150,0.000335878,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23276,Q#1074 - >seq7721,non-specific,274009,33,150,0.000513443,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23277,Q#1074 - >seq7721,non-specific,237177,44,149,0.000627694,40.917,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23278,Q#1074 - >seq7721,superfamily,237177,44,149,0.000627694,40.917,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23279,Q#1074 - >seq7721,non-specific,224117,33,149,0.00123522,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23280,Q#1074 - >seq7721,non-specific,274009,33,150,0.00130768,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23281,Q#1074 - >seq7721,non-specific,337663,62,147,0.00131287,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23282,Q#1074 - >seq7721,superfamily,337663,62,147,0.00131287,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23283,Q#1074 - >seq7721,non-specific,224117,43,149,0.00163331,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23284,Q#1074 - >seq7721,non-specific,274008,45,150,0.00217098,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23285,Q#1074 - >seq7721,non-specific,226400,82,149,0.0040025,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23286,Q#1074 - >seq7721,superfamily,226400,82,149,0.0040025,38.161,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23287,Q#1074 - >seq7721,non-specific,223250,48,150,0.00458074,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23288,Q#1074 - >seq7721,superfamily,223250,48,150,0.00458074,38.3481,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23289,Q#1074 - >seq7721,non-specific,235461,49,165,0.00504942,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23290,Q#1074 - >seq7721,superfamily,235461,49,165,0.00504942,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23291,Q#1074 - >seq7721,non-specific,274008,32,144,0.00561556,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23292,Q#1074 - >seq7721,non-specific,226447,50,125,0.00637262,35.5258,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,N-TerminusTruncated
23293,Q#1074 - >seq7721,superfamily,352825,50,125,0.00637262,35.5258,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,pars,N-TerminusTruncated
23294,Q#1074 - >seq7721,non-specific,112704,2,148,0.00828307,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23295,Q#1074 - >seq7721,superfamily,112704,2,148,0.00828307,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs0_human,pars,C-TerminusTruncated
23296,Q#1074 - >seq7721,non-specific,240419,48,138,0.00986288,37.5036,PTZ00440,PTZ00440,NC,cl36566,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23297,Q#1074 - >seq7721,superfamily,240419,48,138,0.00986288,37.5036,cl36566,PTZ00440 superfamily,NC, - ,reticulocyte binding protein 2-like protein; Provisional,L1PBa.ORF1.hs0_human.pars.frame3,1909131024_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs0_human,pars,BothTerminiTruncated
23298,Q#1077 - >seq7724,non-specific,335182,155,251,1.99035e-30,110.855,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23299,Q#1077 - >seq7724,superfamily,335182,155,251,1.99035e-30,110.855,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23300,Q#1077 - >seq7724,non-specific,340205,254,317,3.9418000000000007e-25,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23301,Q#1077 - >seq7724,superfamily,340205,254,317,3.9418000000000007e-25,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23302,Q#1077 - >seq7724,non-specific,340204,111,153,7.218260000000001e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23303,Q#1077 - >seq7724,superfamily,340204,111,153,7.218260000000001e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs5_gmonkey,marg,CompleteHit
23304,Q#1077 - >seq7724,non-specific,274008,53,149,0.000463965,41.9659,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23305,Q#1077 - >seq7724,superfamily,274008,53,149,0.000463965,41.9659,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23306,Q#1077 - >seq7724,non-specific,224117,41,150,0.000544895,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23307,Q#1077 - >seq7724,superfamily,224117,41,150,0.000544895,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23308,Q#1077 - >seq7724,non-specific,237177,44,149,0.00125197,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23309,Q#1077 - >seq7724,superfamily,237177,44,149,0.00125197,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23310,Q#1077 - >seq7724,non-specific,274009,33,150,0.00170442,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23311,Q#1077 - >seq7724,superfamily,274009,33,150,0.00170442,40.0511,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23312,Q#1077 - >seq7724,non-specific,224117,33,149,0.00269426,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23313,Q#1077 - >seq7724,non-specific,274009,32,153,0.00273047,39.2807,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
23314,Q#1077 - >seq7724,non-specific,235175,42,155,0.00326718,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23315,Q#1077 - >seq7724,superfamily,235175,42,155,0.00326718,38.8916,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23316,Q#1077 - >seq7724,non-specific,226447,50,125,0.00410392,36.2962,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
23317,Q#1077 - >seq7724,superfamily,352825,50,125,0.00410392,36.2962,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
23318,Q#1077 - >seq7724,non-specific,274008,41,149,0.00614716,38.1139,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23319,Q#1077 - >seq7724,non-specific,274008,32,144,0.00700545,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
23320,Q#1082 - >seq7729,non-specific,335182,155,251,7.408849999999999e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23321,Q#1082 - >seq7729,superfamily,335182,155,251,7.408849999999999e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23322,Q#1082 - >seq7729,non-specific,340205,254,317,4.60393e-25,95.4808,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23323,Q#1082 - >seq7729,superfamily,340205,254,317,4.60393e-25,95.4808,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23324,Q#1082 - >seq7729,non-specific,340204,111,153,6.0236400000000005e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23325,Q#1082 - >seq7729,superfamily,340204,111,153,6.0236400000000005e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs4_gibbon,marg,CompleteHit
23326,Q#1082 - >seq7729,non-specific,274009,33,150,0.00018408,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23327,Q#1082 - >seq7729,superfamily,274009,33,150,0.00018408,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23328,Q#1082 - >seq7729,non-specific,274008,28,149,0.00021946099999999998,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23329,Q#1082 - >seq7729,superfamily,274008,28,149,0.00021946099999999998,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23330,Q#1082 - >seq7729,non-specific,224117,41,150,0.00035927800000000004,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23331,Q#1082 - >seq7729,superfamily,224117,41,150,0.00035927800000000004,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23332,Q#1082 - >seq7729,non-specific,274009,32,145,0.00114305,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23333,Q#1082 - >seq7729,non-specific,224117,33,149,0.00150417,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,C-TerminusTruncated
23334,Q#1082 - >seq7729,non-specific,235175,34,155,0.00240892,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23335,Q#1082 - >seq7729,superfamily,235175,34,155,0.00240892,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23336,Q#1082 - >seq7729,non-specific,226447,50,125,0.0024749000000000004,36.6814,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23337,Q#1082 - >seq7729,superfamily,352825,50,125,0.0024749000000000004,36.6814,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23338,Q#1082 - >seq7729,non-specific,274008,41,149,0.00250755,39.6547,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,C-TerminusTruncated
23339,Q#1082 - >seq7729,non-specific,274008,45,150,0.00314525,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23340,Q#1082 - >seq7729,non-specific,235175,43,155,0.00321342,39.2768,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,C-TerminusTruncated
23341,Q#1082 - >seq7729,non-specific,224117,33,149,0.00417064,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23342,Q#1082 - >seq7729,non-specific,274009,33,150,0.00465176,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23343,Q#1082 - >seq7729,non-specific,237177,36,150,0.00604482,38.2206,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,marg,C-TerminusTruncated
23344,Q#1082 - >seq7729,superfamily,237177,36,150,0.00604482,38.2206,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,marg,C-TerminusTruncated
23345,Q#1082 - >seq7729,non-specific,274008,60,140,0.00625863,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,marg,BothTerminiTruncated
23346,Q#1082 - >seq7729,non-specific,313406,38,143,0.00730263,37.7094,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23347,Q#1082 - >seq7729,superfamily,313406,38,143,0.00730263,37.7094,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23348,Q#1082 - >seq7729,non-specific,337766,42,131,0.0077438,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23349,Q#1082 - >seq7729,superfamily,337766,42,131,0.0077438,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PBa.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PBa,ORF1,hs4_gibbon,marg,N-TerminusTruncated
23350,Q#1085 - >seq7732,non-specific,335182,155,251,4.67023e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23351,Q#1085 - >seq7732,superfamily,335182,155,251,4.67023e-31,112.396,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23352,Q#1085 - >seq7732,non-specific,340205,254,317,3.51328e-25,95.866,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23353,Q#1085 - >seq7732,superfamily,340205,254,317,3.51328e-25,95.866,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23354,Q#1085 - >seq7732,non-specific,340204,111,153,7.732160000000001e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23355,Q#1085 - >seq7732,superfamily,340204,111,153,7.732160000000001e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs4_gibbon,pars,CompleteHit
23356,Q#1085 - >seq7732,non-specific,274009,33,150,0.000251263,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23357,Q#1085 - >seq7732,superfamily,274009,33,150,0.000251263,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23358,Q#1085 - >seq7732,non-specific,274008,28,149,0.000260429,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23359,Q#1085 - >seq7732,superfamily,274008,28,149,0.000260429,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23360,Q#1085 - >seq7732,non-specific,224117,41,150,0.000517044,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23361,Q#1085 - >seq7732,superfamily,224117,41,150,0.000517044,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23362,Q#1085 - >seq7732,non-specific,274009,32,145,0.00146933,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23363,Q#1085 - >seq7732,non-specific,224117,33,149,0.00216624,39.6976,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,C-TerminusTruncated
23364,Q#1085 - >seq7732,non-specific,274008,41,149,0.00316906,39.2695,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,C-TerminusTruncated
23365,Q#1085 - >seq7732,non-specific,235175,34,155,0.00341309,38.8916,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23366,Q#1085 - >seq7732,superfamily,235175,34,155,0.00341309,38.8916,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23367,Q#1085 - >seq7732,non-specific,274008,45,150,0.00351868,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23368,Q#1085 - >seq7732,non-specific,226447,50,125,0.0035828,36.2962,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23369,Q#1085 - >seq7732,superfamily,352825,50,125,0.0035828,36.2962,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23370,Q#1085 - >seq7732,non-specific,235175,43,155,0.00459351,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,C-TerminusTruncated
23371,Q#1085 - >seq7732,non-specific,274009,33,150,0.00567988,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23372,Q#1085 - >seq7732,non-specific,224117,33,149,0.00590538,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23373,Q#1085 - >seq7732,non-specific,313406,38,143,0.00692993,38.0946,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23374,Q#1085 - >seq7732,superfamily,313406,38,143,0.00692993,38.0946,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23375,Q#1085 - >seq7732,non-specific,237177,36,150,0.00720863,37.8354,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,pars,C-TerminusTruncated
23376,Q#1085 - >seq7732,superfamily,237177,36,150,0.00720863,37.8354,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs4_gibbon,pars,C-TerminusTruncated
23377,Q#1085 - >seq7732,non-specific,274008,60,140,0.00731737,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs4_gibbon,pars,BothTerminiTruncated
23378,Q#1085 - >seq7732,non-specific,337766,42,131,0.00789565,37.5923,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23379,Q#1085 - >seq7732,superfamily,337766,42,131,0.00789565,37.5923,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PBa.ORF1.hs4_gibbon.pars.frame3,1909131024_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PBa,ORF1,hs4_gibbon,pars,N-TerminusTruncated
23380,Q#1090 - >seq7737,non-specific,335182,18,113,2.6990799999999997e-33,114.322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs6_sqmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,marg,CompleteHit
23381,Q#1090 - >seq7737,superfamily,335182,18,113,2.6990799999999997e-33,114.322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs6_sqmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,marg,CompleteHit
23382,Q#1090 - >seq7737,non-specific,340205,116,179,5.42341e-28,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs6_sqmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,marg,CompleteHit
23383,Q#1090 - >seq7737,superfamily,340205,116,179,5.42341e-28,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs6_sqmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,marg,CompleteHit
23384,Q#1092 - >seq7739,non-specific,340205,237,296,8.90187e-22,86.236,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame1,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,CompleteHit
23385,Q#1092 - >seq7739,superfamily,340205,237,296,8.90187e-22,86.236,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame1,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,CompleteHit
23386,Q#1093 - >seq7740,non-specific,335182,54,117,6.804930000000001e-16,70.0243,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23387,Q#1093 - >seq7740,superfamily,335182,54,117,6.804930000000001e-16,70.0243,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame3,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
23388,Q#1094 - >seq7741,non-specific,335182,111,143,2.3009e-06,44.2159,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
23389,Q#1094 - >seq7741,superfamily,335182,111,143,2.3009e-06,44.2159,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
23390,Q#1095 - >seq7742,non-specific,340205,150,209,3.7779200000000005e-23,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame1,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,CompleteHit
23391,Q#1095 - >seq7742,superfamily,340205,150,209,3.7779200000000005e-23,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs5_gmonkey.pars.frame1,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs5_gmonkey,pars,CompleteHit
23392,Q#1096 - >seq7743,non-specific,335182,151,246,2.09083e-31,113.167,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs4_gibbon,marg,CompleteHit
23393,Q#1096 - >seq7743,superfamily,335182,151,246,2.09083e-31,113.167,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs4_gibbon,marg,CompleteHit
23394,Q#1096 - >seq7743,non-specific,340205,249,312,2.81256e-27,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs4_gibbon,marg,CompleteHit
23395,Q#1096 - >seq7743,superfamily,340205,249,312,2.81256e-27,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs4_gibbon.marg.frame3,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs4_gibbon,marg,CompleteHit
23396,Q#1099 - >seq7746,non-specific,335182,205,237,8.86608e-06,43.4455,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
23397,Q#1099 - >seq7746,superfamily,335182,205,237,8.86608e-06,43.4455,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame2,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
23398,Q#1101 - >seq7748,non-specific,335182,99,194,1.41487e-32,114.70700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs4_gibbon.pars.frame1,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs4_gibbon,pars,CompleteHit
23399,Q#1101 - >seq7748,superfamily,335182,99,194,1.41487e-32,114.70700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs4_gibbon.pars.frame1,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs4_gibbon,pars,CompleteHit
23400,Q#1101 - >seq7748,non-specific,340205,197,260,3.17729e-27,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs4_gibbon.pars.frame1,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs4_gibbon,pars,CompleteHit
23401,Q#1101 - >seq7748,superfamily,340205,197,260,3.17729e-27,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs4_gibbon.pars.frame1,1909131024_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PB4,ORF1,hs4_gibbon,pars,CompleteHit
23402,Q#1102 - >seq7749,non-specific,335182,155,250,9.12771e-32,114.322,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs3_orang.marg.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,marg,CompleteHit
23403,Q#1102 - >seq7749,superfamily,335182,155,250,9.12771e-32,114.322,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs3_orang.marg.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,marg,CompleteHit
23404,Q#1102 - >seq7749,non-specific,340205,253,316,1.7738900000000001e-28,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs3_orang.marg.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,marg,CompleteHit
23405,Q#1102 - >seq7749,superfamily,340205,253,316,1.7738900000000001e-28,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs3_orang.marg.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,marg,CompleteHit
23406,Q#1105 - >seq7752,non-specific,335182,44,139,2.1028400000000002e-34,118.17399999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs3_orang.pars.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,pars,CompleteHit
23407,Q#1105 - >seq7752,superfamily,335182,44,139,2.1028400000000002e-34,118.17399999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs3_orang.pars.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,pars,CompleteHit
23408,Q#1105 - >seq7752,non-specific,340205,142,205,7.48431e-30,105.49600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs3_orang.pars.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,pars,CompleteHit
23409,Q#1105 - >seq7752,superfamily,340205,142,205,7.48431e-30,105.49600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs3_orang.pars.frame3,1909131024_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs3_orang,pars,CompleteHit
23410,Q#1107 - >seq7754,non-specific,335182,156,252,2.5796299999999995e-35,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23411,Q#1107 - >seq7754,superfamily,335182,156,252,2.5796299999999995e-35,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23412,Q#1107 - >seq7754,non-specific,340205,255,318,8.44937e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23413,Q#1107 - >seq7754,superfamily,340205,255,318,8.44937e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23414,Q#1107 - >seq7754,non-specific,340204,111,153,3.02065e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23415,Q#1107 - >seq7754,superfamily,340204,111,153,3.02065e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs3_orang,pars,CompleteHit
23416,Q#1107 - >seq7754,non-specific,274009,60,203,1.5128800000000002e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23417,Q#1107 - >seq7754,superfamily,274009,60,203,1.5128800000000002e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23418,Q#1107 - >seq7754,non-specific,235175,49,156,6.37332e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23419,Q#1107 - >seq7754,superfamily,235175,49,156,6.37332e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23420,Q#1107 - >seq7754,non-specific,237177,41,149,6.785649999999999e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23421,Q#1107 - >seq7754,superfamily,237177,41,149,6.785649999999999e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23422,Q#1107 - >seq7754,non-specific,274008,53,202,0.000115033,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23423,Q#1107 - >seq7754,superfamily,274008,53,202,0.000115033,43.8919,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23424,Q#1107 - >seq7754,non-specific,224117,28,177,0.000497856,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23425,Q#1107 - >seq7754,superfamily,224117,28,177,0.000497856,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23426,Q#1107 - >seq7754,non-specific,223250,47,170,0.00119643,40.2741,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23427,Q#1107 - >seq7754,superfamily,223250,47,170,0.00119643,40.2741,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23428,Q#1107 - >seq7754,non-specific,129694,80,146,0.00248722,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23429,Q#1107 - >seq7754,superfamily,129694,80,146,0.00248722,39.6449,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23430,Q#1107 - >seq7754,non-specific,275056,64,152,0.00292478,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23431,Q#1107 - >seq7754,superfamily,275056,64,152,0.00292478,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23432,Q#1107 - >seq7754,non-specific,235461,47,170,0.00330505,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23433,Q#1107 - >seq7754,superfamily,235461,47,170,0.00330505,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23434,Q#1107 - >seq7754,non-specific,112704,2,148,0.00378936,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23435,Q#1107 - >seq7754,superfamily,112704,2,148,0.00378936,38.0707,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23436,Q#1107 - >seq7754,non-specific,336159,60,145,0.00401735,38.5045,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23437,Q#1107 - >seq7754,superfamily,336159,60,145,0.00401735,38.5045,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs3_orang,pars,N-TerminusTruncated
23438,Q#1107 - >seq7754,non-specific,310273,65,194,0.00466108,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23439,Q#1107 - >seq7754,superfamily,310273,65,194,0.00466108,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23440,Q#1107 - >seq7754,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23441,Q#1107 - >seq7754,superfamily,337663,79,183,0.00497954,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23442,Q#1107 - >seq7754,non-specific,226400,79,149,0.00505781,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23443,Q#1107 - >seq7754,superfamily,226400,79,149,0.00505781,37.7758,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,C-TerminusTruncated
23444,Q#1107 - >seq7754,non-specific,235175,41,144,0.00549965,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23445,Q#1107 - >seq7754,non-specific,222878,57,150,0.00646662,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23446,Q#1107 - >seq7754,superfamily,222878,57,150,0.00646662,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23447,Q#1107 - >seq7754,non-specific,274008,45,150,0.00662651,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23448,Q#1107 - >seq7754,non-specific,274386,27,147,0.00704802,37.7234,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23449,Q#1107 - >seq7754,superfamily,274386,27,147,0.00704802,37.7234,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs3_orang.pars.frame3,1909131024_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs3_orang,pars,BothTerminiTruncated
23450,Q#1109 - >seq7756,non-specific,335182,152,215,4.921509999999999e-16,72.3355,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23451,Q#1109 - >seq7756,superfamily,335182,152,215,4.921509999999999e-16,72.3355,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs5_gmonkey.marg.frame3,1909131024_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
23452,Q#1111 - >seq7758,non-specific,335182,18,113,3.90025e-33,113.552,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs6_sqmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,pars,CompleteHit
23453,Q#1111 - >seq7758,superfamily,335182,18,113,3.90025e-33,113.552,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs6_sqmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,pars,CompleteHit
23454,Q#1111 - >seq7758,non-specific,340205,116,179,4.83931e-28,99.7179,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs6_sqmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,pars,CompleteHit
23455,Q#1111 - >seq7758,superfamily,340205,116,179,4.83931e-28,99.7179,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs6_sqmonkey.pars.frame2,1909131024_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB4,ORF1,hs6_sqmonkey,pars,CompleteHit
23456,Q#1113 - >seq7760,non-specific,335182,155,251,4.51659e-34,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23457,Q#1113 - >seq7760,superfamily,335182,155,251,4.51659e-34,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23458,Q#1113 - >seq7760,non-specific,340205,254,317,9.82784e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23459,Q#1113 - >seq7760,superfamily,340205,254,317,9.82784e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23460,Q#1113 - >seq7760,non-specific,340204,111,153,3.5934899999999997e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23461,Q#1113 - >seq7760,superfamily,340204,111,153,3.5934899999999997e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs2_gorilla,marg,CompleteHit
23462,Q#1113 - >seq7760,non-specific,237177,41,149,6.74415e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23463,Q#1113 - >seq7760,superfamily,237177,41,149,6.74415e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23464,Q#1113 - >seq7760,non-specific,235175,49,155,0.000207226,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23465,Q#1113 - >seq7760,superfamily,235175,49,155,0.000207226,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23466,Q#1113 - >seq7760,non-specific,235461,47,169,0.00100553,40.4366,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23467,Q#1113 - >seq7760,superfamily,235461,47,169,0.00100553,40.4366,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23468,Q#1113 - >seq7760,non-specific,274008,53,149,0.00145759,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23469,Q#1113 - >seq7760,superfamily,274008,53,149,0.00145759,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23470,Q#1113 - >seq7760,non-specific,129694,80,146,0.00284366,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23471,Q#1113 - >seq7760,superfamily,129694,80,146,0.00284366,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23472,Q#1113 - >seq7760,non-specific,275056,64,152,0.00288503,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23473,Q#1113 - >seq7760,superfamily,275056,64,152,0.00288503,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23474,Q#1113 - >seq7760,non-specific,223250,47,167,0.00325826,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23475,Q#1113 - >seq7760,superfamily,223250,47,167,0.00325826,38.7333,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23476,Q#1113 - >seq7760,non-specific,224117,28,155,0.00409495,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23477,Q#1113 - >seq7760,superfamily,224117,28,155,0.00409495,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23478,Q#1113 - >seq7760,non-specific,112704,2,148,0.00444321,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23479,Q#1113 - >seq7760,superfamily,112704,2,148,0.00444321,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23480,Q#1113 - >seq7760,non-specific,336159,60,145,0.00447739,38.5045,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23481,Q#1113 - >seq7760,superfamily,336159,60,145,0.00447739,38.5045,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23482,Q#1113 - >seq7760,non-specific,223671,70,162,0.00512904,38.0749,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23483,Q#1113 - >seq7760,superfamily,320984,70,162,0.00512904,38.0749,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23484,Q#1113 - >seq7760,non-specific,235175,41,144,0.00623568,38.1212,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23485,Q#1113 - >seq7760,non-specific,274008,45,150,0.00676551,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23486,Q#1113 - >seq7760,non-specific,313406,73,235,0.00705225,38.0946,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23487,Q#1113 - >seq7760,superfamily,313406,73,235,0.00705225,38.0946,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs2_gorilla,marg,N-TerminusTruncated
23488,Q#1113 - >seq7760,non-specific,274386,27,147,0.00726252,37.7234,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23489,Q#1113 - >seq7760,superfamily,274386,27,147,0.00726252,37.7234,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23490,Q#1113 - >seq7760,non-specific,222878,57,150,0.00746757,37.6865,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23491,Q#1113 - >seq7760,superfamily,222878,57,150,0.00746757,37.6865,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs2_gorilla,marg,BothTerminiTruncated
23492,Q#1113 - >seq7760,non-specific,337663,79,147,0.00758676,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23493,Q#1113 - >seq7760,superfamily,337663,79,147,0.00758676,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs2_gorilla.marg.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,marg,C-TerminusTruncated
23494,Q#1118 - >seq7765,non-specific,335182,147,243,9.343119999999999e-35,122.02600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23495,Q#1118 - >seq7765,superfamily,335182,147,243,9.343119999999999e-35,122.02600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23496,Q#1118 - >seq7765,non-specific,340205,246,309,5.87501e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23497,Q#1118 - >seq7765,superfamily,340205,246,309,5.87501e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23498,Q#1118 - >seq7765,non-specific,340204,103,145,9.295489999999999e-07,44.706,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23499,Q#1118 - >seq7765,superfamily,340204,103,145,9.295489999999999e-07,44.706,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PBa1,ORF1,hs2_gorilla,pars,CompleteHit
23500,Q#1118 - >seq7765,non-specific,129694,13,138,0.0009526939999999999,40.8005,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_DNARepair,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23501,Q#1118 - >seq7765,superfamily,129694,13,138,0.0009526939999999999,40.8005,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_DNARepair,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23502,Q#1118 - >seq7765,non-specific,237177,74,141,0.0027159000000000003,38.991,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23503,Q#1118 - >seq7765,superfamily,237177,74,141,0.0027159000000000003,38.991,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23504,Q#1118 - >seq7765,non-specific,227278,74,141,0.00698591,37.7793,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23505,Q#1118 - >seq7765,superfamily,227278,74,141,0.00698591,37.7793,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs2_gorilla.pars.frame1,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23506,Q#1119 - >seq7766,non-specific,335182,63,158,1.39519e-32,113.552,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs0_human.marg.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,marg,CompleteHit
23507,Q#1119 - >seq7766,superfamily,335182,63,158,1.39519e-32,113.552,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs0_human.marg.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,marg,CompleteHit
23508,Q#1119 - >seq7766,non-specific,340205,161,224,1.9793099999999997e-26,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs0_human.marg.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,marg,CompleteHit
23509,Q#1119 - >seq7766,superfamily,340205,161,224,1.9793099999999997e-26,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs0_human.marg.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,marg,CompleteHit
23510,Q#1120 - >seq7767,non-specific,112704,1,89,0.00255065,38.4559,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23511,Q#1120 - >seq7767,superfamily,112704,1,89,0.00255065,38.4559,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs2_gorilla.pars.frame3,1909131024_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23512,Q#1122 - >seq7769,non-specific,335182,62,157,1.3561099999999998e-32,113.552,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs0_human.pars.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,pars,CompleteHit
23513,Q#1122 - >seq7769,superfamily,335182,62,157,1.3561099999999998e-32,113.552,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB4.ORF1.hs0_human.pars.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,pars,CompleteHit
23514,Q#1122 - >seq7769,non-specific,340205,160,223,1.92945e-26,97.0216,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs0_human.pars.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,pars,CompleteHit
23515,Q#1122 - >seq7769,superfamily,340205,160,223,1.92945e-26,97.0216,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB4.ORF1.hs0_human.pars.frame3,1909131024_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB4,ORF1,hs0_human,pars,CompleteHit
23516,Q#1131 - >seq7778,non-specific,335182,30,125,5.5455899999999995e-34,116.24799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs5_gmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,pars,CompleteHit
23517,Q#1131 - >seq7778,superfamily,335182,30,125,5.5455899999999995e-34,116.24799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs5_gmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,pars,CompleteHit
23518,Q#1131 - >seq7778,non-specific,340205,128,191,1.7747299999999997e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs5_gmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,pars,CompleteHit
23519,Q#1131 - >seq7778,superfamily,340205,128,191,1.7747299999999997e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs5_gmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,pars,CompleteHit
23520,Q#1134 - >seq7781,specific,197310,12,236,2.6695099999999995e-52,181.01,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23521,Q#1134 - >seq7781,superfamily,351117,12,236,2.6695099999999995e-52,181.01,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23522,Q#1134 - >seq7781,non-specific,197306,9,236,5.10439e-22,95.626,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23523,Q#1134 - >seq7781,non-specific,197307,9,236,4.35175e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23524,Q#1134 - >seq7781,non-specific,197320,13,206,2.68763e-14,73.3181,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23525,Q#1134 - >seq7781,non-specific,197319,13,236,3.14189e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23526,Q#1134 - >seq7781,non-specific,223780,13,237,7.198560000000001e-12,66.0827,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23527,Q#1134 - >seq7781,non-specific,197321,13,236,1.22149e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23528,Q#1134 - >seq7781,specific,335306,12,229,8.766469999999999e-10,59.181000000000004,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23529,Q#1134 - >seq7781,non-specific,273186,13,237,2.19834e-09,58.4444,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23530,Q#1134 - >seq7781,non-specific,272954,13,236,2.46004e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23531,Q#1134 - >seq7781,non-specific,197311,39,146,3.43112e-05,45.3605,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs4_gibbon,marg,C-TerminusTruncated
23532,Q#1134 - >seq7781,non-specific,339261,108,232,0.00138655,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23533,Q#1135 - >seq7782,non-specific,238827,491,694,1.2344799999999999e-06,49.9822,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs4_gibbon.marg.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23534,Q#1135 - >seq7782,superfamily,295487,491,694,1.2344799999999999e-06,49.9822,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs4_gibbon.marg.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs4_gibbon,marg,CompleteHit
23535,Q#1138 - >seq7785,specific,197310,31,235,4.65818e-46,162.136,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23536,Q#1138 - >seq7785,superfamily,351117,31,235,4.65818e-46,162.136,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23537,Q#1138 - >seq7785,non-specific,197306,34,235,7.606069999999999e-18,82.9144,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23538,Q#1138 - >seq7785,non-specific,197320,31,205,1.37545e-12,67.5402,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23539,Q#1138 - >seq7785,non-specific,197307,31,235,5.45855e-11,63.0757,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23540,Q#1138 - >seq7785,specific,335306,39,228,4.4427e-09,56.8698,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23541,Q#1138 - >seq7785,non-specific,223780,60,236,6.3832e-09,56.8379,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs4_gibbon,pars,N-TerminusTruncated
23542,Q#1138 - >seq7785,non-specific,197319,31,235,1.05139e-08,56.1309,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23543,Q#1138 - >seq7785,non-specific,197321,31,235,4.7281699999999996e-08,54.0952,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23544,Q#1138 - >seq7785,non-specific,238827,485,536,6.09843e-07,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs4_gibbon,pars,C-TerminusTruncated
23545,Q#1138 - >seq7785,superfamily,295487,485,536,6.09843e-07,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs4_gibbon,pars,C-TerminusTruncated
23546,Q#1138 - >seq7785,non-specific,272954,105,235,7.98685e-07,50.4593,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,N-TerminusTruncated
23547,Q#1138 - >seq7785,non-specific,273186,105,236,1.10835e-06,49.97,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,N-TerminusTruncated
23548,Q#1138 - >seq7785,non-specific,197311,38,145,2.58581e-05,45.3605,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs4_gibbon,pars,C-TerminusTruncated
23549,Q#1138 - >seq7785,non-specific,339261,107,231,0.00473863,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs4_gibbon.pars.frame2,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PBb,ORF2,hs4_gibbon,pars,CompleteHit
23550,Q#1140 - >seq7787,non-specific,335182,65,160,1.17572e-36,124.337,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23551,Q#1140 - >seq7787,superfamily,335182,65,160,1.17572e-36,124.337,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23552,Q#1140 - >seq7787,non-specific,340205,163,226,1.16356e-31,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23553,Q#1140 - >seq7787,superfamily,340205,163,226,1.16356e-31,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23554,Q#1140 - >seq7787,non-specific,340204,20,61,3.11175e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23555,Q#1140 - >seq7787,superfamily,340204,20,61,3.11175e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs4_gibbon.marg.frame3,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs4_gibbon,marg,CompleteHit
23556,Q#1143 - >seq7790,non-specific,335182,62,157,1.7885799999999998e-33,116.24799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs5_gmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,marg,CompleteHit
23557,Q#1143 - >seq7790,superfamily,335182,62,157,1.7885799999999998e-33,116.24799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs5_gmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,marg,CompleteHit
23558,Q#1143 - >seq7790,non-specific,340205,160,223,1.22826e-31,110.50399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs5_gmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,marg,CompleteHit
23559,Q#1143 - >seq7790,superfamily,340205,160,223,1.22826e-31,110.50399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs5_gmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs5_gmonkey,marg,CompleteHit
23560,Q#1145 - >seq7792,non-specific,197310,95,204,5.86254e-19,81.2437,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23561,Q#1145 - >seq7792,superfamily,351117,95,204,5.86254e-19,81.2437,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23562,Q#1145 - >seq7792,non-specific,197320,96,195,4.64173e-06,45.5838,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23563,Q#1145 - >seq7792,non-specific,197306,90,200,1.06823e-05,44.3945,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23564,Q#1145 - >seq7792,non-specific,197307,90,197,0.00014754,41.1193,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23565,Q#1145 - >seq7792,non-specific,339261,97,135,0.00226863,36.5463,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PBb,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
23566,Q#1145 - >seq7792,non-specific,272954,87,196,0.00341306,36.9773,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23567,Q#1145 - >seq7792,non-specific,335306,101,199,0.00524912,36.4542,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23568,Q#1145 - >seq7792,non-specific,197319,96,183,0.00964648,35.7154,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs5_gmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBb,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
23569,Q#1149 - >seq7796,non-specific,197310,14,145,1.42409e-25,104.741,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23570,Q#1149 - >seq7796,superfamily,351117,14,145,1.42409e-25,104.741,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23571,Q#1149 - >seq7796,non-specific,197306,9,160,1.30011e-12,67.5065,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23572,Q#1149 - >seq7796,non-specific,223780,14,166,7.227230000000001e-10,59.5343,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23573,Q#1149 - >seq7796,non-specific,197320,14,145,5.037789999999999e-09,56.7546,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23574,Q#1149 - >seq7796,non-specific,197307,9,165,8.74734e-09,56.1421,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23575,Q#1149 - >seq7796,non-specific,197321,14,123,2.5638e-06,48.7024,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23576,Q#1149 - >seq7796,non-specific,197319,14,123,0.000140436,43.4193,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23577,Q#1149 - >seq7796,non-specific,197336,14,90,0.00014101,43.3699,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23578,Q#1149 - >seq7796,non-specific,273186,14,123,0.000515309,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23579,Q#1149 - >seq7796,non-specific,272954,14,123,0.000687268,41.2145,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23580,Q#1149 - >seq7796,specific,335306,14,124,0.00482887,38.3802,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
23581,Q#1150 - >seq7797,non-specific,197310,139,215,1.81083e-09,58.1317,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs6_sqmonkey.marg.frame2,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
23582,Q#1150 - >seq7797,superfamily,351117,139,215,1.81083e-09,58.1317,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.marg.frame2,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
23583,Q#1152 - >seq7799,non-specific,197310,14,77,6.99997e-11,60.8281,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23584,Q#1152 - >seq7799,superfamily,351117,14,77,6.99997e-11,60.8281,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23585,Q#1152 - >seq7799,non-specific,197321,14,86,1.99939e-07,51.0136,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23586,Q#1152 - >seq7799,non-specific,223780,14,78,1.5919499999999999e-06,48.3635,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23587,Q#1152 - >seq7799,non-specific,197306,9,112,8.58153e-06,45.9353,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23588,Q#1152 - >seq7799,non-specific,197336,14,78,2.31082e-05,44.9107,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23589,Q#1152 - >seq7799,non-specific,197320,14,78,4.5839899999999995e-05,43.6578,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23590,Q#1152 - >seq7799,non-specific,197307,9,78,4.7238900000000006e-05,43.8157,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23591,Q#1152 - >seq7799,non-specific,273186,14,81,0.000651846,40.34,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23592,Q#1152 - >seq7799,specific,335306,14,78,0.00177805,38.7654,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23593,Q#1152 - >seq7799,non-specific,197319,14,87,0.00430219,37.6413,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
23594,Q#1153 - >seq7800,non-specific,197310,86,133,1.06613e-05,45.8053,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs6_sqmonkey.pars.frame2,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
23595,Q#1153 - >seq7800,superfamily,351117,86,133,1.06613e-05,45.8053,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.pars.frame2,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
23596,Q#1154 - >seq7801,non-specific,197310,133,208,1.4279200000000001e-08,54.2797,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs6_sqmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
23597,Q#1154 - >seq7801,superfamily,351117,133,208,1.4279200000000001e-08,54.2797,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs6_sqmonkey.pars.frame1,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
23598,Q#1155 - >seq7802,non-specific,335182,156,251,4.73613e-33,117.789,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23599,Q#1155 - >seq7802,superfamily,335182,156,251,4.73613e-33,117.789,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23600,Q#1155 - >seq7802,non-specific,340205,254,317,9.476460000000001e-26,97.4068,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23601,Q#1155 - >seq7802,superfamily,340205,254,317,9.476460000000001e-26,97.4068,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23602,Q#1155 - >seq7802,non-specific,340204,110,152,6.2263800000000005e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23603,Q#1155 - >seq7802,superfamily,340204,110,152,6.2263800000000005e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs6_sqmonkey,marg,CompleteHit
23604,Q#1155 - >seq7802,non-specific,235175,48,183,0.000133731,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23605,Q#1155 - >seq7802,superfamily,235175,48,183,0.000133731,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23606,Q#1155 - >seq7802,non-specific,235175,42,178,0.00126996,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23607,Q#1155 - >seq7802,superfamily,235175,42,178,0.00126996,40.4324,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23608,Q#1155 - >seq7802,non-specific,222878,52,149,0.00175135,39.6125,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23609,Q#1155 - >seq7802,superfamily,222878,52,149,0.00175135,39.6125,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23610,Q#1155 - >seq7802,non-specific,274008,33,148,0.00227315,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23611,Q#1155 - >seq7802,superfamily,274008,33,148,0.00227315,39.6547,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23612,Q#1155 - >seq7802,non-specific,224117,32,154,0.00242444,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23613,Q#1155 - >seq7802,superfamily,224117,32,154,0.00242444,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBb,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
23614,Q#1155 - >seq7802,non-specific,237177,42,148,0.00432222,38.6058,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23615,Q#1155 - >seq7802,superfamily,237177,42,148,0.00432222,38.6058,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23616,Q#1155 - >seq7802,non-specific,336997,34,148,0.00442283,37.981,pfam08317,Spc7,N,cl38261,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
23617,Q#1155 - >seq7802,superfamily,336997,34,148,0.00442283,37.981,cl38261,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
23618,Q#1155 - >seq7802,non-specific,311007,41,149,0.00916166,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23619,Q#1155 - >seq7802,superfamily,311007,41,149,0.00916166,37.3841,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PBb.ORF1.hs6_sqmonkey.marg.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
23620,Q#1157 - >seq7804,non-specific,340204,25,67,0.000151304,35.4612,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs6_sqmonkey,pars,CompleteHit
23621,Q#1157 - >seq7804,superfamily,340204,25,67,0.000151304,35.4612,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs6_sqmonkey,pars,CompleteHit
23622,Q#1157 - >seq7804,non-specific,227013,7,66,0.00926118,32.7162,COG4667,YjjU,N,cl34803,"Predicted phospholipase, patatin/cPLA2 family [Lipid transport and metabolism]; Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only].",L1PBb.ORF1.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
23623,Q#1157 - >seq7804,superfamily,227013,7,66,0.00926118,32.7162,cl34803,YjjU superfamily,N, - ,"Predicted phospholipase, patatin/cPLA2 family [Lipid transport and metabolism]; Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only].",L1PBb.ORF1.hs6_sqmonkey.pars.frame3,1909131027_L1PBb.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
23624,Q#1162 - >seq7809,specific,238827,534,804,1.7277400000000001e-34,131.645,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs5_gmonkey,marg,CompleteHit
23625,Q#1162 - >seq7809,superfamily,295487,534,804,1.7277400000000001e-34,131.645,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs5_gmonkey,marg,CompleteHit
23626,Q#1162 - >seq7809,non-specific,197310,18,232,2.0848e-21,94.3405,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBb,ORF2,hs5_gmonkey,marg,CompleteHit
23627,Q#1162 - >seq7809,superfamily,351117,18,232,2.0848e-21,94.3405,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs5_gmonkey,marg,CompleteHit
23628,Q#1162 - >seq7809,non-specific,333820,540,639,8.98435e-14,70.7842,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
23629,Q#1162 - >seq7809,superfamily,333820,540,639,8.98435e-14,70.7842,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
23630,Q#1162 - >seq7809,non-specific,197306,15,234,2.33875e-06,50.1725,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PBb,ORF2,hs5_gmonkey,marg,CompleteHit
23631,Q#1162 - >seq7809,non-specific,197320,76,220,2.6814799999999995e-06,49.821000000000005,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PBb,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
23632,Q#1162 - >seq7809,non-specific,197307,113,232,0.000533963,43.0453,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PBb,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
23633,Q#1162 - >seq7809,non-specific,197319,119,232,0.00571023,39.5673,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs5_gmonkey.marg.frame1,1909131027_L1PBb.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBb,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
23634,Q#1164 - >seq7811,non-specific,335182,20,115,1.0450499999999999e-37,125.493,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs4_gibbon.pars.frame1,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs4_gibbon,pars,CompleteHit
23635,Q#1164 - >seq7811,superfamily,335182,20,115,1.0450499999999999e-37,125.493,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs4_gibbon.pars.frame1,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs4_gibbon,pars,CompleteHit
23636,Q#1164 - >seq7811,non-specific,340205,118,181,1.64265e-32,111.274,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs4_gibbon.pars.frame1,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs4_gibbon,pars,CompleteHit
23637,Q#1164 - >seq7811,superfamily,340205,118,181,1.64265e-32,111.274,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs4_gibbon.pars.frame1,1909131027_L1PBb.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs4_gibbon,pars,CompleteHit
23638,Q#1166 - >seq7813,non-specific,197310,146,216,4.89383e-09,56.9761,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs3_orang.marg.frame2,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs3_orang,marg,N-TerminusTruncated
23639,Q#1166 - >seq7813,superfamily,351117,146,216,4.89383e-09,56.9761,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs3_orang.marg.frame2,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs3_orang,marg,N-TerminusTruncated
23640,Q#1167 - >seq7814,non-specific,340204,21,55,0.00750757,33.15,pfam17489,Tnp_22_trimer,C,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs2_gorilla.pars.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23641,Q#1167 - >seq7814,superfamily,340204,21,55,0.00750757,33.15,cl38761,Tnp_22_trimer superfamily,C, - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs2_gorilla.pars.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23642,Q#1167 - >seq7814,non-specific,334349,10,64,0.0090729,35.2706,pfam01025,GrpE,C,cl03075,GrpE; GrpE.  ,L1PBb.ORF1.hs2_gorilla.pars.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23643,Q#1167 - >seq7814,superfamily,351939,10,64,0.0090729,35.2706,cl03075,GrpE superfamily,C, - ,"nucleotide exchange factor GrpE; GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. In bacteria, the DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis. GrpE participates actively in response to heat shock by preventing aggregation of stress-denatured proteins; unfolded proteins initially bind to DnaJ, the J-domain ATPase-activating protein (Hsp40 family), whereupon DnaK hydrolyzes its bound ATP, resulting in a stable complex. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent.  Over-expression of Hsp70 molecular chaperones is important in suppressing toxicity of aberrantly folded proteins that occur in Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis, as well as several polyQ-diseases  such as Huntington's disease and ataxias.",L1PBb.ORF1.hs2_gorilla.pars.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23644,Q#1168 - >seq7815,non-specific,335182,69,158,2.5049999999999998e-33,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs2_gorilla,pars,CompleteHit
23645,Q#1168 - >seq7815,superfamily,335182,69,158,2.5049999999999998e-33,115.478,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs2_gorilla,pars,CompleteHit
23646,Q#1168 - >seq7815,non-specific,340205,161,224,3.73737e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs2_gorilla,pars,CompleteHit
23647,Q#1168 - >seq7815,superfamily,340205,161,224,3.73737e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBb,ORF1,hs2_gorilla,pars,CompleteHit
23648,Q#1169 - >seq7816,specific,238827,505,743,1.8015e-38,143.201,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,CompleteHit
23649,Q#1169 - >seq7816,superfamily,295487,505,743,1.8015e-38,143.201,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,CompleteHit
23650,Q#1169 - >seq7816,non-specific,197310,12,85,1.14696e-16,80.4733,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23651,Q#1169 - >seq7816,superfamily,351117,12,85,1.14696e-16,80.4733,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23652,Q#1169 - >seq7816,non-specific,333820,497,673,8.22046e-15,73.8658,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23653,Q#1169 - >seq7816,superfamily,333820,497,673,8.22046e-15,73.8658,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23654,Q#1169 - >seq7816,non-specific,238828,543,685,1.17394e-11,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23655,Q#1169 - >seq7816,non-specific,197306,9,81,4.45899e-07,52.0985,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23656,Q#1169 - >seq7816,non-specific,197321,7,80,1.1839600000000001e-05,47.931999999999995,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23657,Q#1169 - >seq7816,non-specific,223780,13,80,4.05367e-05,46.4375,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23658,Q#1169 - >seq7816,non-specific,275209,548,632,5.51876e-05,46.681999999999995,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23659,Q#1169 - >seq7816,superfamily,275209,548,632,5.51876e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23660,Q#1169 - >seq7816,specific,335306,12,77,0.000120586,44.5434,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23661,Q#1169 - >seq7816,non-specific,197307,9,80,0.000198867,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23662,Q#1169 - >seq7816,non-specific,197320,13,76,0.00101472,42.117,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23663,Q#1169 - >seq7816,non-specific,273186,13,43,0.00839729,39.1844,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23664,Q#1170 - >seq7817,non-specific,197310,74,230,8.599769999999999e-27,110.134,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23665,Q#1170 - >seq7817,superfamily,351117,74,230,8.599769999999999e-27,110.134,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23666,Q#1170 - >seq7817,non-specific,197306,73,230,4.5160699999999997e-13,70.2029,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23667,Q#1170 - >seq7817,non-specific,197320,100,200,2.3846e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23668,Q#1170 - >seq7817,non-specific,223780,87,199,2.0218900000000002e-06,50.2895,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23669,Q#1170 - >seq7817,non-specific,197307,87,202,2.6732200000000002e-06,49.9789,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23670,Q#1170 - >seq7817,non-specific,272954,84,201,3.66083e-05,46.6073,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23671,Q#1170 - >seq7817,non-specific,223496,293,495,7.110930000000001e-05,47.0623,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23672,Q#1170 - >seq7817,superfamily,223496,293,495,7.110930000000001e-05,47.0623,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23673,Q#1170 - >seq7817,non-specific,235175,284,482,0.000282829,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23674,Q#1170 - >seq7817,superfamily,235175,284,482,0.000282829,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PBb,ORF2,hs1_chimp,marg,BothTerminiTruncated
23675,Q#1170 - >seq7817,non-specific,197319,100,188,0.00031473,43.8045,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23676,Q#1170 - >seq7817,non-specific,197321,100,188,0.000326815,43.6948,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23677,Q#1170 - >seq7817,non-specific,273186,100,202,0.0008026489999999999,42.266000000000005,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23678,Q#1170 - >seq7817,non-specific,339261,102,142,0.00229576,38.8575,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1PBb,ORF2,hs1_chimp,marg,C-TerminusTruncated
23679,Q#1170 - >seq7817,non-specific,335306,106,204,0.00766086,39.1506,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs1_chimp.marg.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,marg,N-TerminusTruncated
23680,Q#1174 - >seq7821,specific,197310,36,233,5.110130000000001e-41,150.194,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23681,Q#1174 - >seq7821,superfamily,351117,36,233,5.110130000000001e-41,150.194,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23682,Q#1174 - >seq7821,specific,238827,526,755,9.905409999999998e-35,131.645,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23683,Q#1174 - >seq7821,superfamily,295487,526,755,9.905409999999998e-35,131.645,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23684,Q#1174 - >seq7821,non-specific,197306,36,233,7.5608000000000005e-16,77.5216,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23685,Q#1174 - >seq7821,non-specific,333820,525,686,2.03957e-12,66.1618,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,C-TerminusTruncated
23686,Q#1174 - >seq7821,superfamily,333820,525,686,2.03957e-12,66.1618,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,C-TerminusTruncated
23687,Q#1174 - >seq7821,non-specific,197320,54,203,2.3259000000000002e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23688,Q#1174 - >seq7821,non-specific,238828,564,700,1.32102e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,N-TerminusTruncated
23689,Q#1174 - >seq7821,non-specific,223780,50,202,3.34253e-07,52.2155,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23690,Q#1174 - >seq7821,non-specific,197307,50,205,3.6755899999999996e-07,51.9049,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23691,Q#1174 - >seq7821,specific,335306,36,207,2.20946e-06,49.1658,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs1_chimp,pars,CompleteHit
23692,Q#1174 - >seq7821,non-specific,275209,569,653,3.89691e-05,46.2968,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,BothTerminiTruncated
23693,Q#1174 - >seq7821,superfamily,275209,569,653,3.89691e-05,46.2968,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs1_chimp,pars,BothTerminiTruncated
23694,Q#1174 - >seq7821,non-specific,272954,103,204,4.4931999999999996e-05,45.4517,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,N-TerminusTruncated
23695,Q#1174 - >seq7821,non-specific,197321,103,191,0.000373577,42.5392,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,N-TerminusTruncated
23696,Q#1174 - >seq7821,non-specific,197319,103,191,0.00039740099999999997,42.6489,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,N-TerminusTruncated
23697,Q#1174 - >seq7821,non-specific,273186,103,205,0.0006761889999999999,41.8808,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,N-TerminusTruncated
23698,Q#1174 - >seq7821,non-specific,197311,36,143,0.000713682,41.5085,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs1_chimp,pars,C-TerminusTruncated
23699,Q#1174 - >seq7821,non-specific,339261,105,145,0.00178673,38.8575,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs1_chimp.pars.frame2,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PBb,ORF2,hs1_chimp,pars,C-TerminusTruncated
23700,Q#1175 - >seq7822,non-specific,335182,67,162,3.87782e-36,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23701,Q#1175 - >seq7822,superfamily,335182,67,162,3.87782e-36,123.182,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23702,Q#1175 - >seq7822,non-specific,335182,67,162,3.87782e-36,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23703,Q#1175 - >seq7822,non-specific,340205,165,228,1.46385e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23704,Q#1175 - >seq7822,superfamily,340205,165,228,1.46385e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23705,Q#1175 - >seq7822,non-specific,340205,165,228,1.46385e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23706,Q#1175 - >seq7822,non-specific,340204,21,63,8.12021e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23707,Q#1175 - >seq7822,superfamily,340204,21,63,8.12021e-09,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23708,Q#1175 - >seq7822,non-specific,340204,21,63,8.12021e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,marg,CompleteHit
23709,Q#1175 - >seq7822,non-specific,334565,22,145,0.00332738,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,marg,C-TerminusTruncated
23710,Q#1175 - >seq7822,superfamily,334565,22,145,0.00332738,38.2396,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,marg,C-TerminusTruncated
23711,Q#1175 - >seq7822,non-specific,334565,22,145,0.00332738,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.marg.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,marg,C-TerminusTruncated
23712,Q#1178 - >seq7825,non-specific,335182,67,162,3.87782e-36,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23713,Q#1178 - >seq7825,superfamily,335182,67,162,3.87782e-36,123.182,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23714,Q#1178 - >seq7825,non-specific,335182,67,162,3.87782e-36,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23715,Q#1178 - >seq7825,non-specific,340205,165,228,1.46385e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23716,Q#1178 - >seq7825,superfamily,340205,165,228,1.46385e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23717,Q#1178 - >seq7825,non-specific,340205,165,228,1.46385e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23718,Q#1178 - >seq7825,non-specific,340204,21,63,8.12021e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23719,Q#1178 - >seq7825,superfamily,340204,21,63,8.12021e-09,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23720,Q#1178 - >seq7825,non-specific,340204,21,63,8.12021e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs1_chimp,pars,CompleteHit
23721,Q#1178 - >seq7825,non-specific,334565,22,145,0.00332738,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,pars,C-TerminusTruncated
23722,Q#1178 - >seq7825,superfamily,334565,22,145,0.00332738,38.2396,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,pars,C-TerminusTruncated
23723,Q#1178 - >seq7825,non-specific,334565,22,145,0.00332738,38.2396,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PBb.ORF1.hs1_chimp.pars.frame3,1909131027_L1PBb.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PBb,ORF1,hs1_chimp,pars,C-TerminusTruncated
23724,Q#1182 - >seq7829,non-specific,335182,68,157,2.0585599999999998e-32,113.552,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs2_gorilla.marg.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23725,Q#1182 - >seq7829,superfamily,335182,68,157,2.0585599999999998e-32,113.552,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs2_gorilla.marg.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23726,Q#1182 - >seq7829,non-specific,340205,160,223,1.47338e-31,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs2_gorilla.marg.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23727,Q#1182 - >seq7829,superfamily,340205,160,223,1.47338e-31,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs2_gorilla.marg.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,Transposase22,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23728,Q#1184 - >seq7831,specific,238827,472,708,2.93724e-44,158.22299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23729,Q#1184 - >seq7831,superfamily,295487,472,708,2.93724e-44,158.22299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23730,Q#1184 - >seq7831,non-specific,333820,472,689,2.4843000000000003e-22,94.6665,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23731,Q#1184 - >seq7831,superfamily,333820,472,689,2.4843000000000003e-22,94.6665,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23732,Q#1184 - >seq7831,non-specific,238828,532,661,3.10154e-07,51.818000000000005,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs2_gorilla.pars.frame1,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs2_gorilla,pars,N-TerminusTruncated
23733,Q#1185 - >seq7832,non-specific,238827,499,559,3.33385e-08,54.2194,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23734,Q#1185 - >seq7832,superfamily,295487,499,559,3.33385e-08,54.2194,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23735,Q#1185 - >seq7832,non-specific,335609,401,479,3.17131e-05,44.4614,pfam04079,SMC_ScpB,N,cl00612,"Segregation and condensation complex subunit ScpB; This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerizes and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBb,ORF2,hs3_orang,marg,N-TerminusTruncated
23736,Q#1185 - >seq7832,superfamily,351177,401,479,3.17131e-05,44.4614,cl00612,SMC_ScpB superfamily,N, - ,"Segregation and condensation complex subunit ScpB; This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerizes and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBb,ORF2,hs3_orang,marg,N-TerminusTruncated
23737,Q#1185 - >seq7832,non-specific,333820,505,579,0.0006331619999999999,41.1238,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23738,Q#1185 - >seq7832,superfamily,333820,505,579,0.0006331619999999999,41.1238,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs3_orang.marg.frame1,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23739,Q#1186 - >seq7833,specific,197310,12,221,2.39042e-38,141.335,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23740,Q#1186 - >seq7833,superfamily,351117,12,221,2.39042e-38,141.335,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23741,Q#1186 - >seq7833,non-specific,197306,9,220,1.82939e-16,79.0624,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23742,Q#1186 - >seq7833,non-specific,197320,13,201,4.1104200000000003e-10,60.6066,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23743,Q#1186 - >seq7833,non-specific,197307,9,218,1.4745399999999999e-08,55.7569,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23744,Q#1186 - >seq7833,non-specific,223780,13,200,1.86564e-08,55.6823,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23745,Q#1186 - >seq7833,non-specific,273186,13,220,1.18821e-06,49.97,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23746,Q#1186 - >seq7833,non-specific,197321,7,189,1.2390700000000001e-06,49.858000000000004,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23747,Q#1186 - >seq7833,non-specific,272954,13,223,2.45238e-05,45.8369,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs3_orang,pars,CompleteHit
23748,Q#1186 - >seq7833,non-specific,340095,310,475,4.6553599999999994e-05,46.3592,pfam17380,DUF5401,N,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF2,hs3_orang,pars,N-TerminusTruncated
23749,Q#1186 - >seq7833,superfamily,340095,310,475,4.6553599999999994e-05,46.3592,cl38662,DUF5401 superfamily,N, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1PBb.ORF2.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBb,ORF2,hs3_orang,pars,N-TerminusTruncated
23750,Q#1188 - >seq7835,non-specific,197310,12,154,3.19056e-17,81.2437,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23751,Q#1188 - >seq7835,superfamily,351117,12,154,3.19056e-17,81.2437,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23752,Q#1188 - >seq7835,non-specific,197306,9,159,0.000264206,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs3_orang,marg,C-TerminusTruncated
23753,Q#1189 - >seq7836,non-specific,340204,21,63,8.18604e-07,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23754,Q#1189 - >seq7836,superfamily,340204,21,63,8.18604e-07,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs2_gorilla,marg,CompleteHit
23755,Q#1192 - >seq7839,non-specific,335182,67,162,5.7174999999999994e-36,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23756,Q#1192 - >seq7839,superfamily,335182,67,162,5.7174999999999994e-36,122.411,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23757,Q#1192 - >seq7839,non-specific,340205,165,228,1.6147599999999998e-30,107.42200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23758,Q#1192 - >seq7839,superfamily,340205,165,228,1.6147599999999998e-30,107.42200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23759,Q#1192 - >seq7839,non-specific,340204,21,63,1.1521499999999999e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23760,Q#1192 - >seq7839,superfamily,340204,21,63,1.1521499999999999e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs3_orang.pars.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs3_orang,pars,CompleteHit
23761,Q#1193 - >seq7840,non-specific,335182,67,162,2.8650199999999998e-36,123.56700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23762,Q#1193 - >seq7840,superfamily,335182,67,162,2.8650199999999998e-36,123.56700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23763,Q#1193 - >seq7840,non-specific,340205,165,228,1.31441e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23764,Q#1193 - >seq7840,superfamily,340205,165,228,1.31441e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23765,Q#1193 - >seq7840,non-specific,340204,21,63,6.80642e-08,47.4024,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23766,Q#1193 - >seq7840,superfamily,340204,21,63,6.80642e-08,47.4024,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs3_orang.marg.frame3,1909131027_L1PBb.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs3_orang,marg,CompleteHit
23767,Q#1195 - >seq7842,specific,197310,12,236,7.158879999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23768,Q#1195 - >seq7842,superfamily,351117,12,236,7.158879999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23769,Q#1195 - >seq7842,specific,238827,506,762,7.417349999999999e-51,178.639,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23770,Q#1195 - >seq7842,superfamily,295487,506,762,7.417349999999999e-51,178.639,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23771,Q#1195 - >seq7842,non-specific,197306,9,236,6.71553e-29,116.042,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23772,Q#1195 - >seq7842,non-specific,333820,513,741,2.0399200000000002e-25,104.29700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23773,Q#1195 - >seq7842,superfamily,333820,513,741,2.0399200000000002e-25,104.29700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23774,Q#1195 - >seq7842,non-specific,197307,9,236,1.9550599999999996e-18,86.1877,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23775,Q#1195 - >seq7842,non-specific,197320,13,206,9.19483e-18,84.1037,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23776,Q#1195 - >seq7842,non-specific,223780,13,237,3.0102099999999996e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23777,Q#1195 - >seq7842,specific,335306,12,229,2.7971400000000003e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23778,Q#1195 - >seq7842,non-specific,197321,7,236,3.2944199999999997e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23779,Q#1195 - >seq7842,non-specific,197319,13,236,9.46222e-16,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23780,Q#1195 - >seq7842,non-specific,273186,13,237,1.5501600000000001e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23781,Q#1195 - >seq7842,non-specific,272954,13,236,1.64162e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23782,Q#1195 - >seq7842,non-specific,238828,573,715,4.70253e-07,51.818000000000005,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23783,Q#1195 - >seq7842,non-specific,197336,9,194,4.0003699999999994e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,CompleteHit
23784,Q#1195 - >seq7842,non-specific,197311,7,146,6.21346e-06,48.0569,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23785,Q#1195 - >seq7842,non-specific,339261,108,148,0.00210273,39.2427,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBb,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23786,Q#1195 - >seq7842,non-specific,236970,13,194,0.00751618,39.4922,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBb.ORF2.hs2_gorilla.marg.frame3,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23787,Q#1199 - >seq7846,specific,197310,24,234,2.06425e-51,178.699,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23788,Q#1199 - >seq7846,superfamily,351117,24,234,2.06425e-51,178.699,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23789,Q#1199 - >seq7846,non-specific,197306,25,234,8.806760000000001e-24,100.634,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23790,Q#1199 - >seq7846,non-specific,197307,22,234,4.70206e-14,72.3205,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23791,Q#1199 - >seq7846,non-specific,197320,24,204,2.60236e-13,70.2366,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23792,Q#1199 - >seq7846,specific,335306,24,227,4.27588e-12,66.1146,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23793,Q#1199 - >seq7846,non-specific,223780,29,235,1.2036e-11,65.3123,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23794,Q#1199 - >seq7846,non-specific,197321,29,234,5.32999e-11,63.34,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23795,Q#1199 - >seq7846,non-specific,197319,29,234,6.20784e-11,63.0645,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23796,Q#1199 - >seq7846,non-specific,272954,24,234,6.7443699999999995e-09,57.0077,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23797,Q#1199 - >seq7846,non-specific,273186,29,235,1.5155699999999999e-07,53.0516,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,CompleteHit
23798,Q#1199 - >seq7846,non-specific,197311,33,144,1.05475e-06,49.5977,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PBb,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23799,Q#1199 - >seq7846,non-specific,339261,106,146,0.00163153,38.8575,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PBb,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23800,Q#1199 - >seq7846,non-specific,236970,24,192,0.00186641,40.6478,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBb.ORF2.hs2_gorilla.pars.frame2,1909131027_L1PBb.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PBb,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23801,Q#1201 - >seq7848,non-specific,238827,547,736,8.795389999999999e-24,100.443,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,N-TerminusTruncated
23802,Q#1201 - >seq7848,superfamily,295487,547,736,8.795389999999999e-24,100.443,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,N-TerminusTruncated
23803,Q#1201 - >seq7848,non-specific,333820,546,689,9.81254e-15,73.0954,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,N-TerminusTruncated
23804,Q#1201 - >seq7848,superfamily,333820,546,689,9.81254e-15,73.0954,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,N-TerminusTruncated
23805,Q#1201 - >seq7848,non-specific,238828,549,685,2.37186e-09,58.3664,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,N-TerminusTruncated
23806,Q#1201 - >seq7848,non-specific,275209,550,632,8.54472e-05,45.5264,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,BothTerminiTruncated
23807,Q#1201 - >seq7848,superfamily,275209,550,632,8.54472e-05,45.5264,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,BothTerminiTruncated
23808,Q#1201 - >seq7848,non-specific,238185,617,706,0.00867578,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.marg.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBb,ORF2,hs0_human,marg,CompleteHit
23809,Q#1203 - >seq7850,specific,238827,487,735,5.16496e-40,147.438,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23810,Q#1203 - >seq7850,superfamily,295487,487,735,5.16496e-40,147.438,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23811,Q#1203 - >seq7850,non-specific,333820,506,702,4.3553199999999995e-20,88.8885,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23812,Q#1203 - >seq7850,superfamily,333820,506,702,4.3553199999999995e-20,88.8885,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23813,Q#1203 - >seq7850,non-specific,238828,532,675,8.32567e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,N-TerminusTruncated
23814,Q#1203 - >seq7850,non-specific,275209,537,675,6.37348e-06,49.3784,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,BothTerminiTruncated
23815,Q#1203 - >seq7850,superfamily,275209,537,675,6.37348e-06,49.3784,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,BothTerminiTruncated
23816,Q#1203 - >seq7850,non-specific,238185,606,721,0.00835536,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs1_chimp.marg.frame2,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23817,Q#1204 - >seq7851,specific,197310,10,240,1.18602e-46,167.143,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23818,Q#1204 - >seq7851,superfamily,351117,10,240,1.18602e-46,167.143,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23819,Q#1204 - >seq7851,non-specific,197306,10,240,5.0156700000000004e-26,107.95200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23820,Q#1204 - >seq7851,non-specific,197320,9,233,4.9431999999999995e-15,76.0145,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23821,Q#1204 - >seq7851,non-specific,197307,10,240,9.52992e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23822,Q#1204 - >seq7851,non-specific,223780,10,241,4.895680000000001e-13,70.3199,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23823,Q#1204 - >seq7851,non-specific,197321,8,240,2.35574e-11,65.266,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23824,Q#1204 - >seq7851,non-specific,238827,522,575,3.03473e-11,64.2346,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs1_chimp,marg,C-TerminusTruncated
23825,Q#1204 - >seq7851,superfamily,295487,522,575,3.03473e-11,64.2346,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs1_chimp,marg,C-TerminusTruncated
23826,Q#1204 - >seq7851,non-specific,197319,9,240,1.48743e-10,62.6793,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23827,Q#1204 - >seq7851,specific,335306,11,233,2.8494799999999997e-10,61.4922,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23828,Q#1204 - >seq7851,non-specific,273186,10,241,1.0366199999999999e-09,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23829,Q#1204 - >seq7851,non-specific,272954,10,240,1.0512299999999998e-08,57.3929,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23830,Q#1204 - >seq7851,non-specific,333820,528,575,2.51018e-06,49.213,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs1_chimp,marg,C-TerminusTruncated
23831,Q#1204 - >seq7851,superfamily,333820,528,575,2.51018e-06,49.213,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs1_chimp,marg,C-TerminusTruncated
23832,Q#1204 - >seq7851,non-specific,339261,112,236,0.000430484,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PB,ORF2,hs1_chimp,marg,CompleteHit
23833,Q#1204 - >seq7851,non-specific,197311,74,240,0.00134997,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs1_chimp,marg,N-TerminusTruncated
23834,Q#1204 - >seq7851,non-specific,235175,295,481,0.00152036,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs1_chimp,marg,BothTerminiTruncated
23835,Q#1204 - >seq7851,superfamily,235175,295,481,0.00152036,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs1_chimp,marg,BothTerminiTruncated
23836,Q#1204 - >seq7851,non-specific,236970,70,193,0.00178734,41.4182,PRK11756,PRK11756,NC,cl00490,exonuclease III; Provisional,L1PB.ORF2.hs1_chimp.marg.frame1,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs1_chimp,marg,BothTerminiTruncated
23837,Q#1205 - >seq7852,specific,238827,325,586,1.9678499999999995e-66,222.166,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23838,Q#1205 - >seq7852,superfamily,295487,325,586,1.9678499999999995e-66,222.166,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23839,Q#1205 - >seq7852,specific,333820,331,563,1.69376e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23840,Q#1205 - >seq7852,superfamily,333820,331,563,1.69376e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23841,Q#1205 - >seq7852,non-specific,238828,331,551,1.52682e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23842,Q#1205 - >seq7852,non-specific,197310,1,53,2.21571e-09,58.9021,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs1_chimp,pars,N-TerminusTruncated
23843,Q#1205 - >seq7852,superfamily,351117,1,53,2.21571e-09,58.9021,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs1_chimp,pars,N-TerminusTruncated
23844,Q#1205 - >seq7852,non-specific,275209,281,551,3.41129e-09,59.3936,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,C-TerminusTruncated
23845,Q#1205 - >seq7852,superfamily,275209,281,551,3.41129e-09,59.3936,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,C-TerminusTruncated
23846,Q#1205 - >seq7852,non-specific,238185,470,584,4.5355900000000004e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23847,Q#1205 - >seq7852,non-specific,239569,355,552,0.00021841299999999998,43.3303,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs1_chimp,pars,CompleteHit
23848,Q#1205 - >seq7852,non-specific,235175,123,267,0.00100991,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs1_chimp,pars,BothTerminiTruncated
23849,Q#1205 - >seq7852,superfamily,235175,123,267,0.00100991,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs1_chimp,pars,BothTerminiTruncated
23850,Q#1205 - >seq7852,non-specific,334125,29,227,0.00205975,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB,ORF2,hs1_chimp,pars,N-TerminusTruncated
23851,Q#1205 - >seq7852,superfamily,334125,29,227,0.00205975,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB,ORF2,hs1_chimp,pars,N-TerminusTruncated
23852,Q#1205 - >seq7852,non-specific,274009,111,227,0.00540475,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs1_chimp,pars,BothTerminiTruncated
23853,Q#1205 - >seq7852,superfamily,274009,111,227,0.00540475,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs1_chimp,pars,BothTerminiTruncated
23854,Q#1205 - >seq7852,non-specific,274009,124,275,0.00832547,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs1_chimp.pars.frame3,1909131028_L1PB.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs1_chimp,pars,C-TerminusTruncated
23855,Q#1208 - >seq7855,specific,197310,9,236,2.4757399999999996e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23856,Q#1208 - >seq7855,superfamily,351117,9,236,2.4757399999999996e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23857,Q#1208 - >seq7855,non-specific,197306,9,236,1.51509e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23858,Q#1208 - >seq7855,non-specific,238827,508,589,7.84672e-23,97.74700000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23859,Q#1208 - >seq7855,superfamily,295487,508,589,7.84672e-23,97.74700000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23860,Q#1208 - >seq7855,non-specific,197307,9,236,9.08116e-22,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23861,Q#1208 - >seq7855,non-specific,223780,9,237,6.3756200000000005e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23862,Q#1208 - >seq7855,non-specific,197321,7,236,7.104710000000001e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23863,Q#1208 - >seq7855,non-specific,197320,9,206,9.0756e-20,89.8817,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23864,Q#1208 - >seq7855,specific,335306,10,229,8.424760000000001e-18,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23865,Q#1208 - >seq7855,non-specific,197319,13,236,3.26283e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23866,Q#1208 - >seq7855,non-specific,273186,9,237,2.19597e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23867,Q#1208 - >seq7855,non-specific,272954,9,236,5.5323e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23868,Q#1208 - >seq7855,non-specific,197336,9,194,2.11436e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,CompleteHit
23869,Q#1208 - >seq7855,non-specific,333820,514,569,6.93789e-08,53.4502,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23870,Q#1208 - >seq7855,superfamily,333820,514,569,6.93789e-08,53.4502,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23871,Q#1208 - >seq7855,non-specific,197311,7,146,5.71867e-06,48.0569,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23872,Q#1208 - >seq7855,non-specific,236970,9,194,6.99773e-06,48.3518,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23873,Q#1208 - >seq7855,non-specific,339261,108,232,0.00103238,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBb,ORF2,hs0_human,marg,CompleteHit
23874,Q#1208 - >seq7855,non-specific,197314,7,192,0.00187777,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBb,ORF2,hs0_human,marg,C-TerminusTruncated
23875,Q#1208 - >seq7855,non-specific,223496,299,427,0.00577404,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PBb,ORF2,hs0_human,marg,BothTerminiTruncated
23876,Q#1208 - >seq7855,superfamily,223496,299,427,0.00577404,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PBb,ORF2,hs0_human,marg,BothTerminiTruncated
23877,Q#1210 - >seq7857,specific,197310,9,236,1.8935099999999997e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23878,Q#1210 - >seq7857,superfamily,351117,9,236,1.8935099999999997e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23879,Q#1210 - >seq7857,non-specific,197306,9,236,2.95177e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23880,Q#1210 - >seq7857,non-specific,197307,9,236,1.17853e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23881,Q#1210 - >seq7857,non-specific,223780,9,237,1.06639e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23882,Q#1210 - >seq7857,non-specific,197320,9,206,8.284389999999999e-20,89.8817,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23883,Q#1210 - >seq7857,non-specific,197321,7,236,1.17848e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23884,Q#1210 - >seq7857,specific,335306,10,229,7.715880000000001e-18,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23885,Q#1210 - >seq7857,non-specific,197319,13,236,1.06296e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23886,Q#1210 - >seq7857,non-specific,273186,9,237,3.52556e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23887,Q#1210 - >seq7857,non-specific,272954,9,236,1.71239e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23888,Q#1210 - >seq7857,non-specific,197336,9,194,1.9345799999999997e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,CompleteHit
23889,Q#1210 - >seq7857,non-specific,236970,9,194,7.7468e-06,48.3518,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23890,Q#1210 - >seq7857,non-specific,197311,7,146,1.14727e-05,46.9013,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23891,Q#1210 - >seq7857,non-specific,197314,7,192,0.00172463,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23892,Q#1210 - >seq7857,non-specific,339261,108,232,0.0022305,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBb,ORF2,hs0_human,pars,CompleteHit
23893,Q#1210 - >seq7857,non-specific,223496,299,427,0.00373231,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PBb,ORF2,hs0_human,pars,BothTerminiTruncated
23894,Q#1210 - >seq7857,superfamily,223496,299,427,0.00373231,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PBb.ORF2.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PBb,ORF2,hs0_human,pars,BothTerminiTruncated
23895,Q#1211 - >seq7858,non-specific,238827,477,558,3.06824e-23,98.5174,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs0_human.pars.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23896,Q#1211 - >seq7858,superfamily,295487,477,558,3.06824e-23,98.5174,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.pars.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23897,Q#1211 - >seq7858,non-specific,333820,483,538,6.46207e-08,53.065,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.pars.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23898,Q#1211 - >seq7858,superfamily,333820,483,538,6.46207e-08,53.065,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.pars.frame2,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBb,ORF2,hs0_human,pars,C-TerminusTruncated
23899,Q#1212 - >seq7859,non-specific,238827,527,714,3.41047e-24,101.59899999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,N-TerminusTruncated
23900,Q#1212 - >seq7859,superfamily,295487,527,714,3.41047e-24,101.59899999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,N-TerminusTruncated
23901,Q#1212 - >seq7859,non-specific,333820,526,669,4.9137900000000005e-15,73.8658,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,N-TerminusTruncated
23902,Q#1212 - >seq7859,superfamily,333820,526,669,4.9137900000000005e-15,73.8658,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,N-TerminusTruncated
23903,Q#1212 - >seq7859,non-specific,238828,529,665,9.13862e-10,59.522,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,N-TerminusTruncated
23904,Q#1212 - >seq7859,non-specific,275209,530,612,3.9713000000000004e-05,46.681999999999995,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,BothTerminiTruncated
23905,Q#1212 - >seq7859,superfamily,275209,530,612,3.9713000000000004e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,BothTerminiTruncated
23906,Q#1212 - >seq7859,non-specific,238185,597,686,0.00804912,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBb.ORF2.hs0_human.pars.frame1,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBb,ORF2,hs0_human,pars,CompleteHit
23907,Q#1213 - >seq7860,non-specific,335182,67,162,2.56869e-37,126.26299999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,marg,CompleteHit
23908,Q#1213 - >seq7860,superfamily,335182,67,162,2.56869e-37,126.26299999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,marg,CompleteHit
23909,Q#1213 - >seq7860,non-specific,340205,165,228,5.03964e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,marg,CompleteHit
23910,Q#1213 - >seq7860,superfamily,340205,165,228,5.03964e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,marg,CompleteHit
23911,Q#1213 - >seq7860,non-specific,340204,21,63,0.00076889,36.2316,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs0_human,marg,CompleteHit
23912,Q#1213 - >seq7860,superfamily,340204,21,63,0.00076889,36.2316,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs0_human.marg.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBb,ORF1,hs0_human,marg,CompleteHit
23913,Q#1216 - >seq7863,non-specific,335182,67,162,2.8839e-37,125.87799999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,pars,CompleteHit
23914,Q#1216 - >seq7863,superfamily,335182,67,162,2.8839e-37,125.87799999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,pars,CompleteHit
23915,Q#1216 - >seq7863,non-specific,340205,165,228,4.42774e-31,108.963,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,pars,CompleteHit
23916,Q#1216 - >seq7863,superfamily,340205,165,228,4.42774e-31,108.963,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBb,ORF1,hs0_human,pars,CompleteHit
23917,Q#1216 - >seq7863,non-specific,340204,21,63,0.00102593,35.8464,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs0_human,pars,CompleteHit
23918,Q#1216 - >seq7863,superfamily,340204,21,63,0.00102593,35.8464,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBb.ORF1.hs0_human.pars.frame3,1909131028_L1PBb.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBb,ORF1,hs0_human,pars,CompleteHit
23919,Q#1220 - >seq7867,non-specific,197310,31,202,2.4309300000000002e-23,99.7332,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23920,Q#1220 - >seq7867,superfamily,351117,31,202,2.4309300000000002e-23,99.7332,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23921,Q#1220 - >seq7867,non-specific,197306,31,202,3.26729e-08,55.5653,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23922,Q#1220 - >seq7867,non-specific,235175,256,449,1.8035900000000001e-06,51.9884,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23923,Q#1220 - >seq7867,superfamily,235175,256,449,1.8035900000000001e-06,51.9884,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23924,Q#1220 - >seq7867,non-specific,272954,33,215,1.59003e-05,47.7629,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23925,Q#1220 - >seq7867,non-specific,274009,272,497,1.8533e-05,48.9107,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23926,Q#1220 - >seq7867,superfamily,274009,272,497,1.8533e-05,48.9107,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23927,Q#1220 - >seq7867,non-specific,197307,33,202,3.01571e-05,46.8973,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23928,Q#1220 - >seq7867,non-specific,197320,33,215,0.000325041,43.6578,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23929,Q#1220 - >seq7867,non-specific,224117,272,460,0.00058742,43.9348,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23930,Q#1220 - >seq7867,superfamily,224117,272,460,0.00058742,43.9348,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23931,Q#1220 - >seq7867,non-specific,274009,259,380,0.000835349,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23932,Q#1220 - >seq7867,non-specific,197319,33,202,0.0013702,41.4933,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23933,Q#1220 - >seq7867,non-specific,224117,275,450,0.00152823,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23934,Q#1220 - >seq7867,non-specific,336322,227,450,0.00400574,40.9634,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23935,Q#1220 - >seq7867,superfamily,336322,227,450,0.00400574,40.9634,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23936,Q#1220 - >seq7867,non-specific,274008,259,464,0.00828194,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23937,Q#1220 - >seq7867,superfamily,274008,259,464,0.00828194,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23938,Q#1220 - >seq7867,non-specific,223496,248,480,0.00831724,40.1287,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23939,Q#1220 - >seq7867,superfamily,223496,248,480,0.00831724,40.1287,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23940,Q#1220 - >seq7867,non-specific,334125,178,380,0.00969755,39.44,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23941,Q#1220 - >seq7867,superfamily,334125,178,380,0.00969755,39.44,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs2_gorilla.marg.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PB,ORF2,hs2_gorilla,marg,N-TerminusTruncated
23942,Q#1221 - >seq7868,specific,238827,447,698,6.615469999999999e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23943,Q#1221 - >seq7868,superfamily,295487,447,698,6.615469999999999e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23944,Q#1221 - >seq7868,specific,333820,453,676,1.28895e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23945,Q#1221 - >seq7868,superfamily,333820,453,676,1.28895e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23946,Q#1221 - >seq7868,non-specific,238828,453,673,2.2622700000000002e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23947,Q#1221 - >seq7868,non-specific,275209,406,673,1.1840299999999998e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23948,Q#1221 - >seq7868,superfamily,275209,406,673,1.1840299999999998e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,C-TerminusTruncated
23949,Q#1221 - >seq7868,non-specific,239569,477,674,7.988300000000001e-05,44.8711,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23950,Q#1221 - >seq7868,specific,225881,420,616,0.000543187,43.2889,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23951,Q#1221 - >seq7868,superfamily,225881,420,616,0.000543187,43.2889,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,BothTerminiTruncated
23952,Q#1221 - >seq7868,non-specific,238185,592,704,0.000631257,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs2_gorilla.marg.frame3,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs2_gorilla,marg,CompleteHit
23953,Q#1222 - >seq7869,specific,238827,367,618,3.862219999999999e-63,207.52900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23954,Q#1222 - >seq7869,superfamily,295487,367,618,3.862219999999999e-63,207.52900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23955,Q#1222 - >seq7869,specific,333820,373,596,9.53918e-33,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23956,Q#1222 - >seq7869,superfamily,333820,373,596,9.53918e-33,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23957,Q#1222 - >seq7869,non-specific,238828,373,593,1.18771e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23958,Q#1222 - >seq7869,non-specific,275209,326,593,9.90749e-10,60.163999999999994,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23959,Q#1222 - >seq7869,superfamily,275209,326,593,9.90749e-10,60.163999999999994,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23960,Q#1222 - >seq7869,non-specific,239569,397,594,5.43124e-05,44.4859,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,CompleteHit
23961,Q#1222 - >seq7869,specific,225881,340,536,0.000190683,43.6741,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,BothTerminiTruncated
23962,Q#1222 - >seq7869,superfamily,225881,340,536,0.000190683,43.6741,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,BothTerminiTruncated
23963,Q#1222 - >seq7869,non-specific,238185,512,589,0.000593234,39.2564,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs2_gorilla.pars.frame2,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs2_gorilla,pars,C-TerminusTruncated
23964,Q#1223 - >seq7870,non-specific,197310,28,123,5.47926e-13,68.5321,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs2_gorilla.pars.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PB,ORF2,hs2_gorilla,pars,N-TerminusTruncated
23965,Q#1223 - >seq7870,superfamily,351117,28,123,5.47926e-13,68.5321,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs2_gorilla.pars.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs2_gorilla,pars,N-TerminusTruncated
23966,Q#1223 - >seq7870,non-specific,273186,63,124,0.00896258,38.0288,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs2_gorilla.pars.frame1,1909131029_L1PB.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PB,ORF2,hs2_gorilla,pars,N-TerminusTruncated
23967,Q#1227 - >seq7874,non-specific,335182,154,250,1.13702e-39,135.123,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23968,Q#1227 - >seq7874,superfamily,335182,154,250,1.13702e-39,135.123,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23969,Q#1227 - >seq7874,non-specific,340205,253,316,8.413e-31,110.889,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23970,Q#1227 - >seq7874,superfamily,340205,253,316,8.413e-31,110.889,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23971,Q#1227 - >seq7874,non-specific,340204,110,151,4.19842e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23972,Q#1227 - >seq7874,superfamily,340204,110,151,4.19842e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs1_chimp,marg,CompleteHit
23973,Q#1227 - >seq7874,non-specific,224117,63,200,0.00124724,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,N-TerminusTruncated
23974,Q#1227 - >seq7874,superfamily,224117,63,200,0.00124724,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,N-TerminusTruncated
23975,Q#1227 - >seq7874,non-specific,235175,51,235,0.00235589,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23976,Q#1227 - >seq7874,superfamily,235175,51,235,0.00235589,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23977,Q#1227 - >seq7874,non-specific,275316,51,148,0.00319088,39.2332,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23978,Q#1227 - >seq7874,superfamily,275316,51,148,0.00319088,39.2332,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23979,Q#1227 - >seq7874,non-specific,224117,54,147,0.00354797,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23980,Q#1227 - >seq7874,superfamily,224117,54,147,0.00354797,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23981,Q#1227 - >seq7874,non-specific,275316,53,136,0.00543659,38.4628,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23982,Q#1227 - >seq7874,non-specific,313299,74,128,0.00817686,34.8704,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PREC2,ORF1,hs1_chimp,marg,N-TerminusTruncated
23983,Q#1227 - >seq7874,superfamily,313299,74,128,0.00817686,34.8704,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs1_chimp,marg,N-TerminusTruncated
23984,Q#1227 - >seq7874,non-specific,274009,65,147,0.00944587,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23985,Q#1227 - >seq7874,superfamily,274009,65,147,0.00944587,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23986,Q#1227 - >seq7874,non-specific,338612,51,140,0.00954162,37.7207,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23987,Q#1227 - >seq7874,superfamily,338612,51,140,0.00954162,37.7207,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs1_chimp.marg.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs1_chimp,marg,BothTerminiTruncated
23988,Q#1230 - >seq7877,non-specific,335182,154,250,2.3028400000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23989,Q#1230 - >seq7877,superfamily,335182,154,250,2.3028400000000003e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23990,Q#1230 - >seq7877,non-specific,335182,154,250,2.3028400000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23991,Q#1230 - >seq7877,non-specific,340205,253,317,1.91687e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23992,Q#1230 - >seq7877,superfamily,340205,253,317,1.91687e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23993,Q#1230 - >seq7877,non-specific,340205,253,317,1.91687e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23994,Q#1230 - >seq7877,non-specific,340204,110,151,1.6078800000000003e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23995,Q#1230 - >seq7877,superfamily,340204,110,151,1.6078800000000003e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23996,Q#1230 - >seq7877,non-specific,340204,110,151,1.6078800000000003e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,pars,CompleteHit
23997,Q#1230 - >seq7877,non-specific,235175,40,141,0.00105849,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23998,Q#1230 - >seq7877,superfamily,235175,40,141,0.00105849,40.8176,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
23999,Q#1230 - >seq7877,non-specific,235175,40,141,0.00105849,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,C-TerminusTruncated
24000,Q#1230 - >seq7877,non-specific,224117,33,200,0.00140148,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24001,Q#1230 - >seq7877,superfamily,224117,33,200,0.00140148,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24002,Q#1230 - >seq7877,non-specific,224117,33,200,0.00140148,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24003,Q#1230 - >seq7877,non-specific,222878,52,194,0.00248873,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24004,Q#1230 - >seq7877,superfamily,222878,52,194,0.00248873,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24005,Q#1230 - >seq7877,non-specific,222878,52,194,0.00248873,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24006,Q#1230 - >seq7877,non-specific,337766,56,140,0.00350851,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24007,Q#1230 - >seq7877,superfamily,337766,56,140,0.00350851,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24008,Q#1230 - >seq7877,non-specific,337766,56,140,0.00350851,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24009,Q#1230 - >seq7877,non-specific,274008,62,147,0.0083983,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24010,Q#1230 - >seq7877,superfamily,274008,62,147,0.0083983,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24011,Q#1230 - >seq7877,non-specific,274008,62,147,0.0083983,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.pars.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24012,Q#1233 - >seq7880,non-specific,335182,154,250,2.3028400000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24013,Q#1233 - >seq7880,superfamily,335182,154,250,2.3028400000000003e-41,139.36,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24014,Q#1233 - >seq7880,non-specific,335182,154,250,2.3028400000000003e-41,139.36,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24015,Q#1233 - >seq7880,non-specific,340205,253,317,1.91687e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24016,Q#1233 - >seq7880,superfamily,340205,253,317,1.91687e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24017,Q#1233 - >seq7880,non-specific,340205,253,317,1.91687e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24018,Q#1233 - >seq7880,non-specific,340204,110,151,1.6078800000000003e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24019,Q#1233 - >seq7880,superfamily,340204,110,151,1.6078800000000003e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24020,Q#1233 - >seq7880,non-specific,340204,110,151,1.6078800000000003e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs2_gorilla,marg,CompleteHit
24021,Q#1233 - >seq7880,non-specific,235175,40,141,0.00105849,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
24022,Q#1233 - >seq7880,superfamily,235175,40,141,0.00105849,40.8176,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
24023,Q#1233 - >seq7880,non-specific,235175,40,141,0.00105849,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,C-TerminusTruncated
24024,Q#1233 - >seq7880,non-specific,224117,33,200,0.00140148,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24025,Q#1233 - >seq7880,superfamily,224117,33,200,0.00140148,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24026,Q#1233 - >seq7880,non-specific,224117,33,200,0.00140148,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24027,Q#1233 - >seq7880,non-specific,222878,52,194,0.00248873,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24028,Q#1233 - >seq7880,superfamily,222878,52,194,0.00248873,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24029,Q#1233 - >seq7880,non-specific,222878,52,194,0.00248873,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24030,Q#1233 - >seq7880,non-specific,337766,56,140,0.00350851,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24031,Q#1233 - >seq7880,superfamily,337766,56,140,0.00350851,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24032,Q#1233 - >seq7880,non-specific,337766,56,140,0.00350851,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24033,Q#1233 - >seq7880,non-specific,274008,62,147,0.0083983,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24034,Q#1233 - >seq7880,superfamily,274008,62,147,0.0083983,37.7287,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24035,Q#1233 - >seq7880,non-specific,274008,62,147,0.0083983,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs2_gorilla.marg.frame3,1909131031_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24036,Q#1236 - >seq7883,non-specific,335182,154,250,1.7864399999999998e-41,139.745,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24037,Q#1236 - >seq7883,superfamily,335182,154,250,1.7864399999999998e-41,139.745,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24038,Q#1236 - >seq7883,non-specific,340205,253,317,8.56564e-32,113.585,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24039,Q#1236 - >seq7883,superfamily,340205,253,317,8.56564e-32,113.585,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24040,Q#1236 - >seq7883,non-specific,340204,110,151,1.81461e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24041,Q#1236 - >seq7883,superfamily,340204,110,151,1.81461e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs4_gibbon,pars,CompleteHit
24042,Q#1236 - >seq7883,non-specific,224117,33,200,0.00183019,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
24043,Q#1236 - >seq7883,superfamily,224117,33,200,0.00183019,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,N-TerminusTruncated
24044,Q#1236 - >seq7883,non-specific,235175,40,141,0.00191062,39.662,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24045,Q#1236 - >seq7883,superfamily,235175,40,141,0.00191062,39.662,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24046,Q#1236 - >seq7883,non-specific,224117,51,147,0.0019452999999999999,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24047,Q#1236 - >seq7883,superfamily,224117,51,147,0.0019452999999999999,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24048,Q#1236 - >seq7883,non-specific,274008,62,147,0.00315767,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24049,Q#1236 - >seq7883,superfamily,274008,62,147,0.00315767,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24050,Q#1236 - >seq7883,non-specific,222878,52,194,0.00387859,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24051,Q#1236 - >seq7883,superfamily,222878,52,194,0.00387859,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
24052,Q#1236 - >seq7883,non-specific,177432,53,118,0.00581136,38.0801,PHA02607,wac,C,cl28126,fibritin; Provisional,L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24053,Q#1236 - >seq7883,superfamily,332947,53,118,0.00581136,38.0801,cl28126,Fibritin_C superfamily,C, - ,"Fibritin C-terminal region; This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibers to virus particle, and forms the 'whiskers' or fibers on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerisation and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions.",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24054,Q#1236 - >seq7883,non-specific,224495,51,147,0.00666347,37.3451,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24055,Q#1236 - >seq7883,superfamily,224495,51,147,0.00666347,37.3451,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs4_gibbon.pars.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,pars,C-TerminusTruncated
24056,Q#1241 - >seq7888,non-specific,335182,149,245,6.95274e-43,143.21200000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24057,Q#1241 - >seq7888,superfamily,335182,149,245,6.95274e-43,143.21200000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24058,Q#1241 - >seq7888,non-specific,340205,248,312,2.0082599999999997e-31,112.43,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24059,Q#1241 - >seq7888,superfamily,340205,248,312,2.0082599999999997e-31,112.43,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24060,Q#1241 - >seq7888,non-specific,340204,104,146,2.31377e-08,49.3284,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24061,Q#1241 - >seq7888,superfamily,340204,104,146,2.31377e-08,49.3284,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs5_gmonkey,pars,CompleteHit
24062,Q#1241 - >seq7888,non-specific,337766,50,142,0.000407763,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
24063,Q#1241 - >seq7888,superfamily,337766,50,142,0.000407763,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
24064,Q#1241 - >seq7888,non-specific,275316,46,143,0.000683395,41.1592,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24065,Q#1241 - >seq7888,superfamily,275316,46,143,0.000683395,41.1592,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24066,Q#1241 - >seq7888,non-specific,224117,48,143,0.00127844,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24067,Q#1241 - >seq7888,superfamily,224117,48,143,0.00127844,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24068,Q#1241 - >seq7888,non-specific,338612,45,149,0.00140553,40.0319,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24069,Q#1241 - >seq7888,superfamily,338612,45,149,0.00140553,40.0319,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24070,Q#1241 - >seq7888,non-specific,224117,27,195,0.00184419,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
24071,Q#1241 - >seq7888,non-specific,235175,34,143,0.00201181,39.662,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
24072,Q#1241 - >seq7888,superfamily,235175,34,143,0.00201181,39.662,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
24073,Q#1241 - >seq7888,non-specific,222878,45,143,0.00331331,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24074,Q#1241 - >seq7888,superfamily,222878,45,143,0.00331331,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24075,Q#1241 - >seq7888,non-specific,197874,45,148,0.00346088,38.4601,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PREC2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
24076,Q#1241 - >seq7888,superfamily,197874,45,148,0.00346088,38.4601,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PREC2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
24077,Q#1241 - >seq7888,non-specific,224495,45,143,0.00553357,37.3451,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
24078,Q#1241 - >seq7888,superfamily,224495,45,143,0.00553357,37.3451,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
24079,Q#1241 - >seq7888,non-specific,226883,57,159,0.00942978,37.3545,COG4477,EzrA,NC,cl34766,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24080,Q#1241 - >seq7888,superfamily,226883,57,159,0.00942978,37.3545,cl34766,EzrA superfamily,NC, - ,"Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]; Negative regulator of septation ring formation [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.pars.frame3,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
24081,Q#1242 - >seq7889,non-specific,335182,154,250,1.2785199999999998e-42,142.827,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24082,Q#1242 - >seq7889,superfamily,335182,154,250,1.2785199999999998e-42,142.827,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24083,Q#1242 - >seq7889,non-specific,340205,253,317,2.60191e-31,112.044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24084,Q#1242 - >seq7889,superfamily,340205,253,317,2.60191e-31,112.044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Transposase22,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24085,Q#1242 - >seq7889,non-specific,340204,109,151,2.80819e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24086,Q#1242 - >seq7889,superfamily,340204,109,151,2.80819e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Trimerization,L1PREC2,ORF1,hs5_gmonkey,marg,CompleteHit
24087,Q#1242 - >seq7889,non-specific,337766,55,147,0.00048272,41.4443,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1PREC2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
24088,Q#1242 - >seq7889,superfamily,337766,55,147,0.00048272,41.4443,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Flagellar,L1PREC2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
24089,Q#1242 - >seq7889,non-specific,275316,51,148,0.0013545999999999999,40.3888,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Mycoplasma,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24090,Q#1242 - >seq7889,superfamily,275316,51,148,0.0013545999999999999,40.3888,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Mycoplasma,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24091,Q#1242 - >seq7889,non-specific,224117,53,148,0.00142146,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24092,Q#1242 - >seq7889,superfamily,224117,53,148,0.00142146,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24093,Q#1242 - >seq7889,non-specific,338612,50,154,0.00160399,40.0319,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24094,Q#1242 - >seq7889,superfamily,338612,50,154,0.00160399,40.0319,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24095,Q#1242 - >seq7889,non-specific,224117,32,200,0.00199681,39.6976,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
24096,Q#1242 - >seq7889,non-specific,235175,39,148,0.00217791,39.662,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
24097,Q#1242 - >seq7889,superfamily,235175,39,148,0.00217791,39.662,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PREC2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
24098,Q#1242 - >seq7889,non-specific,222878,50,148,0.00361585,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24099,Q#1242 - >seq7889,superfamily,222878,50,148,0.00361585,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PREC2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
24100,Q#1242 - >seq7889,non-specific,197874,50,153,0.00405367,38.4601,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PREC2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
24101,Q#1242 - >seq7889,superfamily,197874,50,153,0.00405367,38.4601,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PREC2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
24102,Q#1242 - >seq7889,non-specific,224495,50,148,0.00631099,37.3451,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PREC2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
24103,Q#1242 - >seq7889,superfamily,224495,50,148,0.00631099,37.3451,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs5_gmonkey.marg.frame1,1909131031_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PREC2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
24104,Q#1247 - >seq7894,non-specific,335182,152,248,3.3926699999999996e-42,141.671,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24105,Q#1247 - >seq7894,superfamily,335182,152,248,3.3926699999999996e-42,141.671,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24106,Q#1247 - >seq7894,non-specific,340205,251,315,3.00888e-32,114.741,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24107,Q#1247 - >seq7894,superfamily,340205,251,315,3.00888e-32,114.741,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24108,Q#1247 - >seq7894,non-specific,340204,108,149,6.731669999999999e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24109,Q#1247 - >seq7894,superfamily,340204,108,149,6.731669999999999e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs0_human,pars,CompleteHit
24110,Q#1247 - >seq7894,non-specific,235175,38,139,0.0005065730000000001,41.588,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,pars,C-TerminusTruncated
24111,Q#1247 - >seq7894,superfamily,235175,38,139,0.0005065730000000001,41.588,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,pars,C-TerminusTruncated
24112,Q#1247 - >seq7894,non-specific,224117,52,145,0.0006836889999999999,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24113,Q#1247 - >seq7894,superfamily,224117,52,145,0.0006836889999999999,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24114,Q#1247 - >seq7894,non-specific,224117,31,198,0.00104854,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,pars,N-TerminusTruncated
24115,Q#1247 - >seq7894,non-specific,222878,50,192,0.00257327,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24116,Q#1247 - >seq7894,superfamily,222878,50,192,0.00257327,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24117,Q#1247 - >seq7894,non-specific,337766,54,145,0.00304102,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs0_human,pars,N-TerminusTruncated
24118,Q#1247 - >seq7894,superfamily,337766,54,145,0.00304102,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs0_human,pars,N-TerminusTruncated
24119,Q#1247 - >seq7894,non-specific,275316,50,146,0.00384044,38.848,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24120,Q#1247 - >seq7894,superfamily,275316,50,146,0.00384044,38.848,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs0_human,pars,BothTerminiTruncated
24121,Q#1247 - >seq7894,non-specific,225087,37,246,0.00681014,38.0689,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs0_human,pars,C-TerminusTruncated
24122,Q#1247 - >seq7894,superfamily,225087,37,246,0.00681014,38.0689,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1PREC2.ORF1.hs0_human.pars.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs0_human,pars,C-TerminusTruncated
24123,Q#1250 - >seq7897,non-specific,335182,152,248,3.40493e-42,141.671,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24124,Q#1250 - >seq7897,superfamily,335182,152,248,3.40493e-42,141.671,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24125,Q#1250 - >seq7897,non-specific,340205,251,315,3.52494e-32,114.35600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24126,Q#1250 - >seq7897,superfamily,340205,251,315,3.52494e-32,114.35600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24127,Q#1250 - >seq7897,non-specific,340204,108,149,6.752330000000001e-06,42.3948,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24128,Q#1250 - >seq7897,superfamily,340204,108,149,6.752330000000001e-06,42.3948,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs0_human,marg,CompleteHit
24129,Q#1250 - >seq7897,non-specific,235175,38,139,0.00047501300000000004,41.588,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,marg,C-TerminusTruncated
24130,Q#1250 - >seq7897,superfamily,235175,38,139,0.00047501300000000004,41.588,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,marg,C-TerminusTruncated
24131,Q#1250 - >seq7897,non-specific,224117,52,145,0.000624614,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24132,Q#1250 - >seq7897,superfamily,224117,52,145,0.000624614,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24133,Q#1250 - >seq7897,non-specific,224117,31,198,0.0009495889999999999,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs0_human,marg,N-TerminusTruncated
24134,Q#1250 - >seq7897,non-specific,222878,50,192,0.00251959,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24135,Q#1250 - >seq7897,superfamily,222878,50,192,0.00251959,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24136,Q#1250 - >seq7897,non-specific,337766,54,145,0.00289791,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs0_human,marg,N-TerminusTruncated
24137,Q#1250 - >seq7897,superfamily,337766,54,145,0.00289791,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PREC2,ORF1,hs0_human,marg,N-TerminusTruncated
24138,Q#1250 - >seq7897,non-specific,275316,50,146,0.00376075,38.848,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24139,Q#1250 - >seq7897,superfamily,275316,50,146,0.00376075,38.848,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs0_human,marg,BothTerminiTruncated
24140,Q#1250 - >seq7897,non-specific,225087,37,246,0.00690567,38.0689,COG2176,PolC,C,cl34415,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs0_human,marg,C-TerminusTruncated
24141,Q#1250 - >seq7897,superfamily,225087,37,246,0.00690567,38.0689,cl34415,PolC superfamily,C, - ,"DNA polymerase III, alpha subunit (gram-positive type)  [Replication, recombination and repair]; DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair].",L1PREC2.ORF1.hs0_human.marg.frame3,1909131031_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs0_human,marg,C-TerminusTruncated
24142,Q#1251 - >seq7898,non-specific,335182,154,250,1.7864399999999998e-41,139.745,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24143,Q#1251 - >seq7898,superfamily,335182,154,250,1.7864399999999998e-41,139.745,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24144,Q#1251 - >seq7898,non-specific,340205,253,317,8.56564e-32,113.585,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24145,Q#1251 - >seq7898,superfamily,340205,253,317,8.56564e-32,113.585,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24146,Q#1251 - >seq7898,non-specific,340204,110,151,1.81461e-05,41.2392,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24147,Q#1251 - >seq7898,superfamily,340204,110,151,1.81461e-05,41.2392,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PREC2,ORF1,hs4_gibbon,marg,CompleteHit
24148,Q#1251 - >seq7898,non-specific,224117,33,200,0.00183019,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,N-TerminusTruncated
24149,Q#1251 - >seq7898,superfamily,224117,33,200,0.00183019,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,N-TerminusTruncated
24150,Q#1251 - >seq7898,non-specific,235175,40,141,0.00191062,39.662,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24151,Q#1251 - >seq7898,superfamily,235175,40,141,0.00191062,39.662,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24152,Q#1251 - >seq7898,non-specific,224117,51,147,0.0019452999999999999,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24153,Q#1251 - >seq7898,superfamily,224117,51,147,0.0019452999999999999,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24154,Q#1251 - >seq7898,non-specific,274008,62,147,0.00315767,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24155,Q#1251 - >seq7898,superfamily,274008,62,147,0.00315767,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24156,Q#1251 - >seq7898,non-specific,222878,52,194,0.00387859,38.8421,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24157,Q#1251 - >seq7898,superfamily,222878,52,194,0.00387859,38.8421,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
24158,Q#1251 - >seq7898,non-specific,177432,53,118,0.00581136,38.0801,PHA02607,wac,C,cl28126,fibritin; Provisional,L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24159,Q#1251 - >seq7898,superfamily,332947,53,118,0.00581136,38.0801,cl28126,Fibritin_C superfamily,C, - ,"Fibritin C-terminal region; This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibers to virus particle, and forms the 'whiskers' or fibers on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerisation and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions.",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24160,Q#1251 - >seq7898,non-specific,224495,51,147,0.00666347,37.3451,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24161,Q#1251 - >seq7898,superfamily,224495,51,147,0.00666347,37.3451,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PREC2.ORF1.hs4_gibbon.marg.frame3,1909131031_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PREC2,ORF1,hs4_gibbon,marg,C-TerminusTruncated
24162,Q#1252 - >seq7899,non-specific,335182,154,250,1.13702e-39,135.123,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24163,Q#1252 - >seq7899,superfamily,335182,154,250,1.13702e-39,135.123,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24164,Q#1252 - >seq7899,non-specific,340205,253,316,8.413e-31,110.889,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24165,Q#1252 - >seq7899,superfamily,340205,253,316,8.413e-31,110.889,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24166,Q#1252 - >seq7899,non-specific,340204,110,151,4.19842e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24167,Q#1252 - >seq7899,superfamily,340204,110,151,4.19842e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PREC2,ORF1,hs1_chimp,pars,CompleteHit
24168,Q#1252 - >seq7899,non-specific,224117,63,200,0.00124724,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,N-TerminusTruncated
24169,Q#1252 - >seq7899,superfamily,224117,63,200,0.00124724,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,N-TerminusTruncated
24170,Q#1252 - >seq7899,non-specific,235175,51,235,0.00235589,39.662,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24171,Q#1252 - >seq7899,superfamily,235175,51,235,0.00235589,39.662,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24172,Q#1252 - >seq7899,non-specific,275316,51,148,0.00319088,39.2332,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24173,Q#1252 - >seq7899,superfamily,275316,51,148,0.00319088,39.2332,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24174,Q#1252 - >seq7899,non-specific,224117,54,147,0.00354797,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24175,Q#1252 - >seq7899,superfamily,224117,54,147,0.00354797,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24176,Q#1252 - >seq7899,non-specific,275316,53,136,0.00543659,38.4628,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24177,Q#1252 - >seq7899,non-specific,313299,74,128,0.00817686,34.8704,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PREC2,ORF1,hs1_chimp,pars,N-TerminusTruncated
24178,Q#1252 - >seq7899,superfamily,313299,74,128,0.00817686,34.8704,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs1_chimp,pars,N-TerminusTruncated
24179,Q#1252 - >seq7899,non-specific,274009,65,147,0.00944587,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24180,Q#1252 - >seq7899,superfamily,274009,65,147,0.00944587,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24181,Q#1252 - >seq7899,non-specific,338612,51,140,0.00954162,37.7207,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24182,Q#1252 - >seq7899,superfamily,338612,51,140,0.00954162,37.7207,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PREC2.ORF1.hs1_chimp.pars.frame3,1909131031_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PREC2,ORF1,hs1_chimp,pars,BothTerminiTruncated
24183,Q#1257 - >seq7904,specific,238827,377,639,1.09959e-54,189.424,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,CompleteHit
24184,Q#1257 - >seq7904,superfamily,295487,377,639,1.09959e-54,189.424,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,CompleteHit
24185,Q#1257 - >seq7904,non-specific,333820,383,605,3.42038e-25,103.52600000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,CompleteHit
24186,Q#1257 - >seq7904,superfamily,333820,383,605,3.42038e-25,103.52600000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,CompleteHit
24187,Q#1257 - >seq7904,non-specific,238828,449,602,2.08209e-06,49.891999999999996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24188,Q#1257 - >seq7904,non-specific,275209,329,602,0.0012537000000000002,42.0596,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24189,Q#1257 - >seq7904,superfamily,275209,329,602,0.0012537000000000002,42.0596,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs4_gibbon.pars.frame2,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24190,Q#1258 - >seq7905,non-specific,197310,5,130,1.2205099999999999e-24,103.585,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24191,Q#1258 - >seq7905,superfamily,351117,5,130,1.2205099999999999e-24,103.585,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24192,Q#1258 - >seq7905,non-specific,197306,5,130,8.38133e-12,65.9657,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24193,Q#1258 - >seq7905,non-specific,197307,5,130,3.94928e-09,58.4533,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24194,Q#1258 - >seq7905,non-specific,197320,5,123,7.93549e-09,57.525,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24195,Q#1258 - >seq7905,non-specific,273186,5,131,1.2113e-07,53.821999999999996,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24196,Q#1258 - >seq7905,non-specific,223780,5,131,2.61926e-07,52.9859,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24197,Q#1258 - >seq7905,non-specific,235175,200,338,5.75786e-07,53.5291,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24198,Q#1258 - >seq7905,superfamily,235175,200,338,5.75786e-07,53.5291,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24199,Q#1258 - >seq7905,non-specific,197319,5,130,8.811879999999999e-07,51.1233,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24200,Q#1258 - >seq7905,non-specific,223496,125,323,3.4145499999999998e-06,50.9143,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24201,Q#1258 - >seq7905,superfamily,223496,125,323,3.4145499999999998e-06,50.9143,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24202,Q#1258 - >seq7905,non-specific,272954,5,130,4.40973e-06,49.3037,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24203,Q#1258 - >seq7905,non-specific,197321,5,130,3.37901e-05,46.3912,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24204,Q#1258 - >seq7905,non-specific,334125,106,305,0.000147399,45.218,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24205,Q#1258 - >seq7905,superfamily,334125,106,305,0.000147399,45.218,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24206,Q#1258 - >seq7905,specific,335306,6,123,0.00028539799999999997,43.3878,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,pars,N-TerminusTruncated
24207,Q#1258 - >seq7905,non-specific,274009,188,329,0.000706811,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24208,Q#1258 - >seq7905,superfamily,274009,188,329,0.000706811,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24209,Q#1258 - >seq7905,non-specific,274009,205,353,0.00155364,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24210,Q#1258 - >seq7905,non-specific,274009,200,353,0.00572384,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24211,Q#1258 - >seq7905,non-specific,223496,157,323,0.00699329,40.1287,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24212,Q#1258 - >seq7905,non-specific,129694,201,455,0.00776944,40.0301,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24213,Q#1258 - >seq7905,superfamily,129694,201,455,0.00776944,40.0301,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24214,Q#1258 - >seq7905,non-specific,274009,188,330,0.00789625,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,BothTerminiTruncated
24215,Q#1258 - >seq7905,non-specific,274009,201,353,0.00935326,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.pars.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24216,Q#1259 - >seq7906,specific,197310,3,166,1.94006e-29,117.45200000000001,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24217,Q#1259 - >seq7906,superfamily,351117,3,166,1.94006e-29,117.45200000000001,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24218,Q#1259 - >seq7906,non-specific,197306,4,166,9.01899e-16,77.9068,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24219,Q#1259 - >seq7906,non-specific,197307,18,166,1.9574900000000004e-10,62.3053,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24220,Q#1259 - >seq7906,non-specific,197319,10,166,2.47862e-09,59.2125,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24221,Q#1259 - >seq7906,non-specific,197320,35,159,2.6843e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24222,Q#1259 - >seq7906,non-specific,273186,18,167,1.6148499999999997e-08,56.5184,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24223,Q#1259 - >seq7906,non-specific,223780,3,167,5.77919e-08,54.9119,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24224,Q#1259 - >seq7906,non-specific,272954,18,166,6.179719999999999e-08,54.6965,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24225,Q#1259 - >seq7906,non-specific,197321,20,166,1.6800900000000002e-06,50.6284,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24226,Q#1259 - >seq7906,non-specific,235175,221,376,8.33283e-06,49.6772,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs4_gibbon,marg,BothTerminiTruncated
24227,Q#1259 - >seq7906,superfamily,235175,221,376,8.33283e-06,49.6772,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs4_gibbon,marg,BothTerminiTruncated
24228,Q#1259 - >seq7906,specific,335306,3,159,0.000121115,44.5434,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24229,Q#1259 - >seq7906,non-specific,274009,224,367,0.000425925,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs4_gibbon,marg,BothTerminiTruncated
24230,Q#1259 - >seq7906,superfamily,274009,224,367,0.000425925,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs4_gibbon,marg,BothTerminiTruncated
24231,Q#1259 - >seq7906,non-specific,334125,142,343,0.000628737,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24232,Q#1259 - >seq7906,superfamily,334125,142,343,0.000628737,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24233,Q#1259 - >seq7906,non-specific,274009,237,445,0.00776518,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs4_gibbon,marg,C-TerminusTruncated
24234,Q#1259 - >seq7906,non-specific,336322,198,382,0.00899251,39.8078,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PB,ORF2,hs4_gibbon,marg,C-TerminusTruncated
24235,Q#1259 - >seq7906,superfamily,336322,198,382,0.00899251,39.8078,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PB.ORF2.hs4_gibbon.marg.frame1,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PB,ORF2,hs4_gibbon,marg,C-TerminusTruncated
24236,Q#1261 - >seq7908,specific,238827,415,693,7.058079999999998e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24237,Q#1261 - >seq7908,superfamily,295487,415,693,7.058079999999998e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24238,Q#1261 - >seq7908,specific,333820,421,654,1.73217e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24239,Q#1261 - >seq7908,superfamily,333820,421,654,1.73217e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24240,Q#1261 - >seq7908,non-specific,238828,493,651,1.22602e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,N-TerminusTruncated
24241,Q#1261 - >seq7908,non-specific,275209,372,717,3.5336199999999996e-06,50.1488,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24242,Q#1261 - >seq7908,superfamily,275209,372,717,3.5336199999999996e-06,50.1488,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,CompleteHit
24243,Q#1261 - >seq7908,non-specific,238185,567,647,0.00161984,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs4_gibbon.marg.frame3,1909131031_L1PB.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs4_gibbon,marg,C-TerminusTruncated
24244,Q#1263 - >seq7910,specific,238827,317,568,3.1103e-58,198.28400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs5_gmonkey,pars,CompleteHit
24245,Q#1263 - >seq7910,superfamily,295487,317,568,3.1103e-58,198.28400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs5_gmonkey,pars,CompleteHit
24246,Q#1263 - >seq7910,specific,333820,323,547,1.41747e-29,115.853,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs5_gmonkey,pars,CompleteHit
24247,Q#1263 - >seq7910,superfamily,333820,323,547,1.41747e-29,115.853,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs5_gmonkey,pars,CompleteHit
24248,Q#1263 - >seq7910,non-specific,238828,389,544,2.45292e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
24249,Q#1263 - >seq7910,non-specific,197310,1,55,1.0378799999999999e-08,56.5909,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
24250,Q#1263 - >seq7910,superfamily,351117,1,55,1.0378799999999999e-08,56.5909,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs5_gmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
24251,Q#1264 - >seq7911,specific,238827,430,700,4.39636e-47,167.85299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs5_gmonkey,marg,CompleteHit
24252,Q#1264 - >seq7911,superfamily,295487,430,700,4.39636e-47,167.85299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs5_gmonkey,marg,CompleteHit
24253,Q#1264 - >seq7911,non-specific,333820,436,679,1.03562e-21,93.5109,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs5_gmonkey,marg,CompleteHit
24254,Q#1264 - >seq7911,superfamily,333820,436,679,1.03562e-21,93.5109,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs5_gmonkey,marg,CompleteHit
24255,Q#1264 - >seq7911,non-specific,197310,39,124,1.95813e-12,68.1469,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
24256,Q#1264 - >seq7911,superfamily,351117,39,124,1.95813e-12,68.1469,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
24257,Q#1264 - >seq7911,non-specific,238828,494,662,2.6910000000000004e-08,55.67,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
24258,Q#1264 - >seq7911,non-specific,274009,185,328,0.0031733,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
24259,Q#1264 - >seq7911,superfamily,274009,185,328,0.0031733,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs5_gmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
24260,Q#1269 - >seq7916,specific,238827,513,781,3.58167e-56,194.047,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24261,Q#1269 - >seq7916,superfamily,295487,513,781,3.58167e-56,194.047,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24262,Q#1269 - >seq7916,specific,197310,12,240,1.0862600000000001e-46,167.528,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24263,Q#1269 - >seq7916,superfamily,351117,12,240,1.0862600000000001e-46,167.528,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24264,Q#1269 - >seq7916,non-specific,197306,12,240,2.4720099999999997e-28,114.501,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24265,Q#1269 - >seq7916,non-specific,333820,519,741,4.2189799999999996e-27,109.304,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24266,Q#1269 - >seq7916,superfamily,333820,519,741,4.2189799999999996e-27,109.304,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24267,Q#1269 - >seq7916,non-specific,197307,12,240,8.039619999999999e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24268,Q#1269 - >seq7916,non-specific,223780,12,241,4.60685e-14,73.4015,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24269,Q#1269 - >seq7916,non-specific,197320,10,210,2.53465e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24270,Q#1269 - >seq7916,non-specific,197321,10,240,3.03115e-12,67.9624,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24271,Q#1269 - >seq7916,non-specific,273186,10,241,1.19542e-11,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24272,Q#1269 - >seq7916,non-specific,238828,519,738,2.00979e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24273,Q#1269 - >seq7916,non-specific,272954,10,240,2.05529e-11,65.4821,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24274,Q#1269 - >seq7916,specific,335306,13,233,1.07242e-10,62.6478,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24275,Q#1269 - >seq7916,non-specific,197319,10,240,2.87124e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24276,Q#1269 - >seq7916,non-specific,275209,470,725,1.19432e-06,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,C-TerminusTruncated
24277,Q#1269 - >seq7916,superfamily,275209,470,725,1.19432e-06,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,C-TerminusTruncated
24278,Q#1269 - >seq7916,non-specific,235175,295,472,2.63666e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs0_human,marg,BothTerminiTruncated
24279,Q#1269 - >seq7916,superfamily,235175,295,472,2.63666e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs0_human,marg,BothTerminiTruncated
24280,Q#1269 - >seq7916,non-specific,197336,10,198,7.89147e-05,45.6811,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24281,Q#1269 - >seq7916,non-specific,339261,112,236,0.00019266900000000002,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24282,Q#1269 - >seq7916,non-specific,239569,542,739,0.0011125,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs0_human,marg,CompleteHit
24283,Q#1269 - >seq7916,non-specific,274009,298,437,0.00207875,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs0_human,marg,BothTerminiTruncated
24284,Q#1269 - >seq7916,superfamily,274009,298,437,0.00207875,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs0_human,marg,BothTerminiTruncated
24285,Q#1269 - >seq7916,non-specific,197311,38,240,0.00227511,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs0_human,marg,CompleteHit
24286,Q#1269 - >seq7916,non-specific,274009,311,459,0.00354148,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.marg.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs0_human,marg,C-TerminusTruncated
24287,Q#1271 - >seq7918,specific,197310,7,161,2.74641e-31,122.845,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24288,Q#1271 - >seq7918,superfamily,351117,7,161,2.74641e-31,122.845,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24289,Q#1271 - >seq7918,non-specific,197306,4,161,4.2831099999999997e-16,78.6772,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24290,Q#1271 - >seq7918,non-specific,197320,31,131,3.2004099999999997e-09,58.6806,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24291,Q#1271 - >seq7918,non-specific,197307,31,161,3.93056e-09,58.4533,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24292,Q#1271 - >seq7918,non-specific,197319,31,161,2.57718e-07,53.0493,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24293,Q#1271 - >seq7918,non-specific,223780,31,162,2.58347e-07,52.9859,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24294,Q#1271 - >seq7918,non-specific,273186,31,162,2.6484000000000003e-07,52.6664,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24295,Q#1271 - >seq7918,non-specific,272954,31,161,2.54414e-06,49.6889,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24296,Q#1271 - >seq7918,non-specific,235175,216,393,1.0318699999999998e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24297,Q#1271 - >seq7918,superfamily,235175,216,393,1.0318699999999998e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24298,Q#1271 - >seq7918,non-specific,197321,31,161,2.1390700000000002e-05,47.1616,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24299,Q#1271 - >seq7918,non-specific,339261,33,157,0.00012426,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24300,Q#1271 - >seq7918,non-specific,335306,37,154,0.000542682,42.6174,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24301,Q#1271 - >seq7918,non-specific,274009,219,358,0.00113124,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24302,Q#1271 - >seq7918,superfamily,274009,219,358,0.00113124,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24303,Q#1271 - >seq7918,non-specific,274009,232,380,0.00201203,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs0_human,pars,C-TerminusTruncated
24304,Q#1271 - >seq7918,non-specific,334125,137,334,0.00226695,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24305,Q#1271 - >seq7918,superfamily,334125,137,334,0.00226695,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB.ORF2.hs0_human.pars.frame2,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB,ORF2,hs0_human,pars,N-TerminusTruncated
24306,Q#1272 - >seq7919,specific,238827,422,653,6.6942500000000005e-50,175.55700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24307,Q#1272 - >seq7919,superfamily,295487,422,653,6.6942500000000005e-50,175.55700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24308,Q#1272 - >seq7919,non-specific,333820,420,631,4.74147e-27,108.919,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24309,Q#1272 - >seq7919,superfamily,333820,420,631,4.74147e-27,108.919,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24310,Q#1272 - >seq7919,non-specific,238828,417,628,3.34386e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24311,Q#1272 - >seq7919,non-specific,275209,478,615,1.67755e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24312,Q#1272 - >seq7919,superfamily,275209,478,615,1.67755e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,BothTerminiTruncated
24313,Q#1272 - >seq7919,non-specific,239569,432,629,0.00140143,41.0191,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs0_human.pars.frame1,1909131031_L1PB.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB,ORF2,hs0_human,pars,CompleteHit
24314,Q#1275 - >seq7922,specific,238827,512,793,3.58045e-42,153.986,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24315,Q#1275 - >seq7922,superfamily,295487,512,793,3.58045e-42,153.986,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24316,Q#1275 - >seq7922,specific,197310,22,221,8.135189999999999e-32,124.38600000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24317,Q#1275 - >seq7922,superfamily,351117,22,221,8.135189999999999e-32,124.38600000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24318,Q#1275 - >seq7922,non-specific,333820,537,770,1.77122e-21,93.1257,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24319,Q#1275 - >seq7922,superfamily,333820,537,770,1.77122e-21,93.1257,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24320,Q#1275 - >seq7922,non-specific,197306,22,221,1.77765e-13,71.3585,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24321,Q#1275 - >seq7922,non-specific,238828,600,767,2.19787e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24322,Q#1275 - >seq7922,non-specific,275209,608,688,0.00017116900000000001,45.1412,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24323,Q#1275 - >seq7922,superfamily,275209,608,688,0.00017116900000000001,45.1412,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24324,Q#1275 - >seq7922,specific,335306,22,214,0.000524782,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs6_sqmonkey,marg,CompleteHit
24325,Q#1275 - >seq7922,non-specific,197320,22,177,0.00130714,41.7318,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24326,Q#1275 - >seq7922,non-specific,238185,664,763,0.00158764,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PB,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24327,Q#1275 - >seq7922,non-specific,223496,296,523,0.00628479,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ATPase_DNARepair_Exonuclease,L1PB,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24328,Q#1275 - >seq7922,superfamily,223496,296,523,0.00628479,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB.ORF2.hs6_sqmonkey.marg.frame1,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Other_ATPase_DNArepair,L1PB,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24329,Q#1276 - >seq7923,specific,238827,343,595,7.031260000000001e-54,187.113,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,CompleteHit
24330,Q#1276 - >seq7923,superfamily,295487,343,595,7.031260000000001e-54,187.113,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,CompleteHit
24331,Q#1276 - >seq7923,specific,333820,349,572,3.5767199999999994e-30,117.779,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,CompleteHit
24332,Q#1276 - >seq7923,superfamily,333820,349,572,3.5767199999999994e-30,117.779,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,CompleteHit
24333,Q#1276 - >seq7923,non-specific,238828,419,569,1.72679e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24334,Q#1276 - >seq7923,non-specific,197310,4,79,1.6268700000000002e-08,56.2057,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24335,Q#1276 - >seq7923,superfamily,351117,4,79,1.6268700000000002e-08,56.2057,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24336,Q#1276 - >seq7923,non-specific,275209,300,569,5.82625e-06,49.3784,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24337,Q#1276 - >seq7923,superfamily,275209,300,569,5.82625e-06,49.3784,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24338,Q#1276 - >seq7923,non-specific,238185,487,565,5.9038e-05,42.7232,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs6_sqmonkey.pars.frame3,1909131031_L1PB.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24339,Q#1279 - >seq7926,specific,197310,3,230,7.97983e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24340,Q#1279 - >seq7926,superfamily,351117,3,230,7.97983e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24341,Q#1279 - >seq7926,non-specific,197306,3,230,3.51312e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24342,Q#1279 - >seq7926,non-specific,223780,3,231,7.15439e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24343,Q#1279 - >seq7926,non-specific,197320,3,200,4.08699e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24344,Q#1279 - >seq7926,non-specific,197307,3,230,1.6633400000000003e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24345,Q#1279 - >seq7926,specific,335306,4,223,1.0932500000000001e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24346,Q#1279 - >seq7926,non-specific,197319,7,230,9.959549999999999e-17,81.1689,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24347,Q#1279 - >seq7926,non-specific,273186,3,231,5.571e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24348,Q#1279 - >seq7926,non-specific,197321,1,230,5.64222e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24349,Q#1279 - >seq7926,non-specific,272954,3,230,6.620660000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24350,Q#1279 - >seq7926,non-specific,197336,3,188,1.3184200000000002e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24351,Q#1279 - >seq7926,non-specific,197322,2,230,4.38676e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24352,Q#1279 - >seq7926,non-specific,236970,3,183,5.338179999999999e-07,52.2038,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24353,Q#1279 - >seq7926,non-specific,197311,24,230,5.365830000000001e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24354,Q#1279 - >seq7926,non-specific,334125,206,404,3.28634e-05,47.5292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
24355,Q#1279 - >seq7926,superfamily,334125,206,404,3.28634e-05,47.5292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
24356,Q#1279 - >seq7926,non-specific,235175,304,456,0.000657493,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
24357,Q#1279 - >seq7926,superfamily,235175,304,456,0.000657493,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
24358,Q#1279 - >seq7926,non-specific,274009,301,450,0.00119111,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24359,Q#1279 - >seq7926,superfamily,274009,301,450,0.00119111,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24360,Q#1279 - >seq7926,non-specific,339261,102,226,0.00169194,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24361,Q#1279 - >seq7926,non-specific,274009,295,462,0.00560267,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
24362,Q#1279 - >seq7926,non-specific,274009,288,428,0.00636076,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs2_gorilla.marg.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
24363,Q#1280 - >seq7927,specific,238827,508,770,5.596669999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24364,Q#1280 - >seq7927,superfamily,295487,508,770,5.596669999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24365,Q#1280 - >seq7927,specific,197310,9,236,3.96219e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24366,Q#1280 - >seq7927,superfamily,351117,9,236,3.96219e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24367,Q#1280 - >seq7927,specific,333820,514,770,1.41104e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24368,Q#1280 - >seq7927,superfamily,333820,514,770,1.41104e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24369,Q#1280 - >seq7927,non-specific,197306,9,236,1.3580499999999998e-32,126.82700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24370,Q#1280 - >seq7927,non-specific,197320,9,206,4.6645299999999995e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24371,Q#1280 - >seq7927,non-specific,223780,9,237,7.30002e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24372,Q#1280 - >seq7927,non-specific,197307,9,236,3.5838500000000004e-18,85.4173,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24373,Q#1280 - >seq7927,specific,335306,10,229,5.3412699999999995e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24374,Q#1280 - >seq7927,non-specific,273186,9,237,1.82198e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24375,Q#1280 - >seq7927,non-specific,272954,9,236,1.16323e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24376,Q#1280 - >seq7927,non-specific,197319,13,236,1.47445e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24377,Q#1280 - >seq7927,non-specific,197321,7,236,3.1502600000000004e-14,73.7404,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24378,Q#1280 - >seq7927,non-specific,238828,514,735,7.44358e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24379,Q#1280 - >seq7927,non-specific,197336,9,194,1.5005100000000002e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24380,Q#1280 - >seq7927,non-specific,275209,464,722,1.99732e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,C-TerminusTruncated
24381,Q#1280 - >seq7927,superfamily,275209,464,722,1.99732e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,C-TerminusTruncated
24382,Q#1280 - >seq7927,non-specific,197322,8,236,2.14221e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24383,Q#1280 - >seq7927,non-specific,236970,9,189,1.62727e-06,50.663000000000004,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,pars,C-TerminusTruncated
24384,Q#1280 - >seq7927,non-specific,197311,30,236,6.33054e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24385,Q#1280 - >seq7927,non-specific,238185,654,768,0.000105791,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24386,Q#1280 - >seq7927,non-specific,334125,212,409,0.000559899,43.6772,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs1_chimp,pars,N-TerminusTruncated
24387,Q#1280 - >seq7927,superfamily,334125,212,409,0.000559899,43.6772,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs1_chimp,pars,N-TerminusTruncated
24388,Q#1280 - >seq7927,non-specific,339261,108,232,0.00058189,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24389,Q#1280 - >seq7927,non-specific,274009,307,455,0.00227187,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,pars,C-TerminusTruncated
24390,Q#1280 - >seq7927,superfamily,274009,307,455,0.00227187,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,pars,C-TerminusTruncated
24391,Q#1280 - >seq7927,non-specific,235175,291,467,0.00283606,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,pars,BothTerminiTruncated
24392,Q#1280 - >seq7927,superfamily,235175,291,467,0.00283606,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,pars,BothTerminiTruncated
24393,Q#1280 - >seq7927,non-specific,239569,523,736,0.00496812,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs1_chimp,pars,CompleteHit
24394,Q#1280 - >seq7927,non-specific,274009,294,433,0.00688041,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.pars.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,pars,BothTerminiTruncated
24395,Q#1281 - >seq7928,non-specific,130009,400,686,0.00156655,42.2774,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs1_chimp.marg.frame1,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24396,Q#1281 - >seq7928,superfamily,130009,400,686,0.00156655,42.2774,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs1_chimp.marg.frame1,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24397,Q#1282 - >seq7929,specific,238827,467,729,3.3506499999999996e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24398,Q#1282 - >seq7929,superfamily,295487,467,729,3.3506499999999996e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24399,Q#1282 - >seq7929,specific,333820,473,729,5.84615e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24400,Q#1282 - >seq7929,superfamily,333820,473,729,5.84615e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24401,Q#1282 - >seq7929,non-specific,238828,473,694,2.73229e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24402,Q#1282 - >seq7929,non-specific,275209,423,681,1.62663e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24403,Q#1282 - >seq7929,superfamily,275209,423,681,1.62663e-09,60.9344,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24404,Q#1282 - >seq7929,non-specific,238185,613,727,3.54115e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24405,Q#1282 - >seq7929,non-specific,239569,482,695,0.00495951,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs1_chimp.marg.frame2,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24406,Q#1283 - >seq7930,specific,197310,3,230,4.647699999999998e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24407,Q#1283 - >seq7930,superfamily,351117,3,230,4.647699999999998e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24408,Q#1283 - >seq7930,non-specific,197306,3,230,2.00797e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24409,Q#1283 - >seq7930,non-specific,223780,3,231,8.62961e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24410,Q#1283 - >seq7930,non-specific,197320,3,200,2.86949e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24411,Q#1283 - >seq7930,non-specific,197307,3,230,4.0111599999999994e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24412,Q#1283 - >seq7930,specific,335306,4,223,5.18746e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24413,Q#1283 - >seq7930,non-specific,197319,7,230,1.49064e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24414,Q#1283 - >seq7930,non-specific,273186,3,231,5.252930000000001e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24415,Q#1283 - >seq7930,non-specific,272954,3,230,8.516400000000001e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24416,Q#1283 - >seq7930,non-specific,197321,1,230,1.32585e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24417,Q#1283 - >seq7930,non-specific,197336,3,188,1.45679e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24418,Q#1283 - >seq7930,non-specific,197322,2,230,2.0785999999999998e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24419,Q#1283 - >seq7930,non-specific,236970,3,183,3.0618300000000004e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24420,Q#1283 - >seq7930,non-specific,197311,24,230,3.6204e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24421,Q#1283 - >seq7930,non-specific,334125,206,403,1.91925e-05,48.2996,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs1_chimp,marg,N-TerminusTruncated
24422,Q#1283 - >seq7930,superfamily,334125,206,403,1.91925e-05,48.2996,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs1_chimp,marg,N-TerminusTruncated
24423,Q#1283 - >seq7930,non-specific,235175,285,436,0.000273973,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,BothTerminiTruncated
24424,Q#1283 - >seq7930,superfamily,235175,285,436,0.000273973,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,BothTerminiTruncated
24425,Q#1283 - >seq7930,non-specific,339261,102,226,0.0006238940000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs1_chimp,marg,CompleteHit
24426,Q#1283 - >seq7930,non-specific,274009,301,449,0.0011794000000000002,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24427,Q#1283 - >seq7930,superfamily,274009,301,449,0.0011794000000000002,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24428,Q#1283 - >seq7930,non-specific,274009,295,461,0.00234043,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,BothTerminiTruncated
24429,Q#1283 - >seq7930,non-specific,274009,288,427,0.0030423000000000004,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs1_chimp,marg,BothTerminiTruncated
24430,Q#1283 - >seq7930,non-specific,235850,299,470,0.0070208,39.6144,PRK06669,fliH,C,cl35503,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24431,Q#1283 - >seq7930,superfamily,235850,299,470,0.0070208,39.6144,cl35503,fliH superfamily,C, - ,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs1_chimp.marg.frame3,1909131033_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs1_chimp,marg,C-TerminusTruncated
24432,Q#1284 - >seq7931,specific,238827,453,714,1.2917599999999997e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24433,Q#1284 - >seq7931,superfamily,295487,453,714,1.2917599999999997e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24434,Q#1284 - >seq7931,specific,333820,459,683,2.38292e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24435,Q#1284 - >seq7931,superfamily,333820,459,683,2.38292e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24436,Q#1284 - >seq7931,non-specific,238828,459,680,1.6531799999999998e-14,73.7744,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24437,Q#1284 - >seq7931,non-specific,275209,409,667,6.85102e-10,62.09,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24438,Q#1284 - >seq7931,superfamily,275209,409,667,6.85102e-10,62.09,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24439,Q#1284 - >seq7931,non-specific,238185,599,676,0.00315682,38.1008,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24440,Q#1284 - >seq7931,non-specific,239569,468,681,0.00324125,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs2_gorilla.pars.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24441,Q#1286 - >seq7933,specific,197310,3,230,4.6866800000000004e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24442,Q#1286 - >seq7933,superfamily,351117,3,230,4.6866800000000004e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24443,Q#1286 - >seq7933,non-specific,197306,3,230,1.0856499999999999e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24444,Q#1286 - >seq7933,non-specific,223780,3,231,7.1913e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24445,Q#1286 - >seq7933,non-specific,197320,3,200,4.10794e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24446,Q#1286 - >seq7933,non-specific,197307,3,230,5.22102e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24447,Q#1286 - >seq7933,specific,335306,4,223,1.0986900000000001e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24448,Q#1286 - >seq7933,non-specific,197319,7,230,1.71366e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24449,Q#1286 - >seq7933,non-specific,273186,3,231,5.5994e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24450,Q#1286 - >seq7933,non-specific,197321,1,230,9.608189999999999e-16,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24451,Q#1286 - >seq7933,non-specific,272954,3,230,1.83808e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24452,Q#1286 - >seq7933,non-specific,197336,3,188,1.32506e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24453,Q#1286 - >seq7933,non-specific,197322,2,230,4.40925e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24454,Q#1286 - >seq7933,non-specific,236970,3,183,2.20414e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24455,Q#1286 - >seq7933,non-specific,197311,24,230,8.27003e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24456,Q#1286 - >seq7933,non-specific,130009,437,731,0.00362471,41.1218,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24457,Q#1286 - >seq7933,superfamily,130009,437,731,0.00362471,41.1218,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24458,Q#1286 - >seq7933,non-specific,339261,102,226,0.00618979,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs2_gorilla.pars.frame3,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs2_gorilla,pars,CompleteHit
24459,Q#1287 - >seq7934,non-specific,130009,401,695,0.00351317,41.1218,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs2_gorilla.marg.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24460,Q#1287 - >seq7934,superfamily,130009,401,695,0.00351317,41.1218,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs2_gorilla.marg.frame1,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24461,Q#1288 - >seq7935,specific,238827,469,730,2.5636899999999997e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24462,Q#1288 - >seq7935,superfamily,295487,469,730,2.5636899999999997e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24463,Q#1288 - >seq7935,specific,333820,475,699,9.61843e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24464,Q#1288 - >seq7935,superfamily,333820,475,699,9.61843e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24465,Q#1288 - >seq7935,non-specific,238828,475,696,1.1555e-14,74.5448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24466,Q#1288 - >seq7935,non-specific,275209,425,683,6.0717e-10,62.09,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24467,Q#1288 - >seq7935,superfamily,275209,425,683,6.0717e-10,62.09,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24468,Q#1288 - >seq7935,non-specific,238185,615,692,0.00148945,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24469,Q#1288 - >seq7935,non-specific,239569,484,697,0.00502666,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs2_gorilla.marg.frame2,1909131033_L1PBa1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs2_gorilla,marg,CompleteHit
24470,Q#1289 - >seq7936,non-specific,130009,401,686,0.00192602,42.2774,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs0_human.pars.frame1,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF2,hs0_human,pars,C-TerminusTruncated
24471,Q#1289 - >seq7936,superfamily,130009,401,686,0.00192602,42.2774,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs0_human.pars.frame1,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF2,hs0_human,pars,C-TerminusTruncated
24472,Q#1290 - >seq7937,non-specific,240274,196,454,7.421310000000001e-05,46.5217,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1PB.ORF2.hs3_orang.pars.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB,ORF2,hs3_orang,pars,C-TerminusTruncated
24473,Q#1290 - >seq7937,superfamily,240274,196,454,7.421310000000001e-05,46.5217,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1PB.ORF2.hs3_orang.pars.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB,ORF2,hs3_orang,pars,C-TerminusTruncated
24474,Q#1291 - >seq7938,specific,197310,3,229,6.558779999999999e-57,196.418,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24475,Q#1291 - >seq7938,superfamily,351117,3,229,6.558779999999999e-57,196.418,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24476,Q#1291 - >seq7938,non-specific,197306,3,229,1.61228e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24477,Q#1291 - >seq7938,non-specific,223780,3,230,4.0811199999999995e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24478,Q#1291 - >seq7938,non-specific,197320,3,222,2.0276e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24479,Q#1291 - >seq7938,non-specific,197307,3,229,8.32374e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24480,Q#1291 - >seq7938,non-specific,197321,1,229,4.71577e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24481,Q#1291 - >seq7938,specific,335306,4,222,5.0094400000000004e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24482,Q#1291 - >seq7938,non-specific,197319,7,229,1.06884e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24483,Q#1291 - >seq7938,non-specific,273186,3,230,3.27756e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24484,Q#1291 - >seq7938,non-specific,272954,3,229,7.358880000000001e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24485,Q#1291 - >seq7938,non-specific,197336,3,187,1.38561e-08,56.8519,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24486,Q#1291 - >seq7938,non-specific,334125,205,403,2.1444e-05,47.9144,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs0_human,pars,N-TerminusTruncated
24487,Q#1291 - >seq7938,superfamily,334125,205,403,2.1444e-05,47.9144,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs0_human,pars,N-TerminusTruncated
24488,Q#1291 - >seq7938,non-specific,236970,3,242,3.5749899999999995e-05,46.81100000000001,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24489,Q#1291 - >seq7938,non-specific,235175,299,455,0.000259938,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,BothTerminiTruncated
24490,Q#1291 - >seq7938,superfamily,235175,299,455,0.000259938,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,BothTerminiTruncated
24491,Q#1291 - >seq7938,non-specific,339261,101,225,0.0005559180000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24492,Q#1291 - >seq7938,non-specific,197311,31,229,0.000867122,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24493,Q#1291 - >seq7938,non-specific,274009,304,461,0.0011775,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,BothTerminiTruncated
24494,Q#1291 - >seq7938,superfamily,274009,304,461,0.0011775,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,BothTerminiTruncated
24495,Q#1291 - >seq7938,non-specific,274009,300,449,0.00479682,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,C-TerminusTruncated
24496,Q#1291 - >seq7938,non-specific,274009,287,427,0.00763909,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.pars.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,pars,BothTerminiTruncated
24497,Q#1292 - >seq7939,non-specific,130009,402,687,0.001928,42.2774,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs0_human.marg.frame1,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs0_human,marg,C-TerminusTruncated
24498,Q#1292 - >seq7939,superfamily,130009,402,687,0.001928,42.2774,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs0_human.marg.frame1,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs0_human,marg,C-TerminusTruncated
24499,Q#1293 - >seq7940,specific,238827,468,730,8.809139999999998e-67,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24500,Q#1293 - >seq7940,superfamily,295487,468,730,8.809139999999998e-67,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24501,Q#1293 - >seq7940,specific,333820,474,698,4.7703199999999994e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24502,Q#1293 - >seq7940,superfamily,333820,474,698,4.7703199999999994e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24503,Q#1293 - >seq7940,non-specific,238828,474,695,1.3675499999999999e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24504,Q#1293 - >seq7940,non-specific,275209,424,682,9.291139999999999e-10,61.7048,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,C-TerminusTruncated
24505,Q#1293 - >seq7940,superfamily,275209,424,682,9.291139999999999e-10,61.7048,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,C-TerminusTruncated
24506,Q#1293 - >seq7940,non-specific,238185,614,728,0.000309645,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs0_human.marg.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24507,Q#1294 - >seq7941,specific,197310,3,230,2.8117199999999996e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24508,Q#1294 - >seq7941,superfamily,351117,3,230,2.8117199999999996e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24509,Q#1294 - >seq7941,non-specific,197306,3,230,5.70983e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24510,Q#1294 - >seq7941,non-specific,223780,3,231,2.26408e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24511,Q#1294 - >seq7941,non-specific,197320,3,223,1.1532199999999999e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24512,Q#1294 - >seq7941,non-specific,197307,3,230,3.30309e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24513,Q#1294 - >seq7941,specific,335306,4,223,2.18621e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24514,Q#1294 - >seq7941,non-specific,197319,7,230,5.3318699999999997e-17,81.9393,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24515,Q#1294 - >seq7941,non-specific,197321,1,230,1.02263e-16,81.0592,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24516,Q#1294 - >seq7941,non-specific,273186,3,231,2.0680400000000002e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24517,Q#1294 - >seq7941,non-specific,272954,3,230,5.0763e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24518,Q#1294 - >seq7941,non-specific,197336,3,188,1.31576e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24519,Q#1294 - >seq7941,non-specific,197322,2,230,1.07808e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24520,Q#1294 - >seq7941,non-specific,236970,3,243,4.20774e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24521,Q#1294 - >seq7941,non-specific,197311,24,230,8.68555e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24522,Q#1294 - >seq7941,non-specific,334125,206,404,2.2414899999999998e-05,47.9144,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs0_human,marg,N-TerminusTruncated
24523,Q#1294 - >seq7941,superfamily,334125,206,404,2.2414899999999998e-05,47.9144,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs0_human,marg,N-TerminusTruncated
24524,Q#1294 - >seq7941,non-specific,235175,300,456,0.000260204,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,BothTerminiTruncated
24525,Q#1294 - >seq7941,superfamily,235175,300,456,0.000260204,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,BothTerminiTruncated
24526,Q#1294 - >seq7941,non-specific,339261,102,226,0.000567281,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs0_human,marg,CompleteHit
24527,Q#1294 - >seq7941,non-specific,274009,305,462,0.00116876,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,BothTerminiTruncated
24528,Q#1294 - >seq7941,superfamily,274009,305,462,0.00116876,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,BothTerminiTruncated
24529,Q#1294 - >seq7941,non-specific,274009,301,450,0.00488357,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,C-TerminusTruncated
24530,Q#1294 - >seq7941,non-specific,274009,288,428,0.00764673,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs0_human.marg.frame3,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs0_human,marg,BothTerminiTruncated
24531,Q#1295 - >seq7942,specific,197310,19,179,2.82588e-33,128.623,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24532,Q#1295 - >seq7942,superfamily,351117,19,179,2.82588e-33,128.623,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24533,Q#1295 - >seq7942,non-specific,197306,19,179,1.5481499999999998e-16,79.8328,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24534,Q#1295 - >seq7942,non-specific,197320,25,172,8.102860000000001e-10,60.2214,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24535,Q#1295 - >seq7942,non-specific,197307,25,179,2.4836999999999996e-09,58.8385,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24536,Q#1295 - >seq7942,non-specific,197319,25,179,4.65884e-09,58.0569,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24537,Q#1295 - >seq7942,non-specific,223780,25,180,1.51176e-07,53.7563,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24538,Q#1295 - >seq7942,non-specific,273186,25,180,7.589699999999999e-07,51.5108,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24539,Q#1295 - >seq7942,non-specific,272954,33,179,2.44109e-05,46.9925,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24540,Q#1295 - >seq7942,non-specific,197321,49,179,3.89748e-05,46.006,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24541,Q#1295 - >seq7942,non-specific,235175,233,426,0.000232737,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs3_orang,pars,BothTerminiTruncated
24542,Q#1295 - >seq7942,superfamily,235175,233,426,0.000232737,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB,ORF2,hs3_orang,pars,BothTerminiTruncated
24543,Q#1295 - >seq7942,specific,335306,55,172,0.00100272,41.4618,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,pars,N-TerminusTruncated
24544,Q#1295 - >seq7942,non-specific,339261,51,175,0.00868323,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB.ORF2.hs3_orang.pars.frame2,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24545,Q#1296 - >seq7943,specific,238827,407,665,7.47371e-66,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24546,Q#1296 - >seq7943,superfamily,295487,407,665,7.47371e-66,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24547,Q#1296 - >seq7943,specific,333820,413,642,2.17008e-34,129.72,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24548,Q#1296 - >seq7943,superfamily,333820,413,642,2.17008e-34,129.72,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24549,Q#1296 - >seq7943,non-specific,238828,413,634,1.14977e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24550,Q#1296 - >seq7943,non-specific,275209,352,634,7.88524e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,C-TerminusTruncated
24551,Q#1296 - >seq7943,superfamily,275209,352,634,7.88524e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,C-TerminusTruncated
24552,Q#1296 - >seq7943,non-specific,238185,553,630,0.00029346200000000003,40.7972,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,C-TerminusTruncated
24553,Q#1296 - >seq7943,non-specific,239569,422,666,0.000718934,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs3_orang.pars.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB,ORF2,hs3_orang,pars,CompleteHit
24554,Q#1297 - >seq7944,specific,197310,56,206,8.853489999999999e-33,127.08200000000001,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24555,Q#1297 - >seq7944,superfamily,351117,56,206,8.853489999999999e-33,127.08200000000001,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24556,Q#1297 - >seq7944,non-specific,197306,34,206,1.80813e-15,77.1364,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24557,Q#1297 - >seq7944,non-specific,197320,60,199,1.7685499999999999e-09,59.451,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24558,Q#1297 - >seq7944,non-specific,197307,58,206,1.23e-08,56.9125,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24559,Q#1297 - >seq7944,non-specific,223780,59,207,2.62746e-07,52.9859,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24560,Q#1297 - >seq7944,non-specific,273186,76,207,2.2333900000000002e-06,50.3552,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24561,Q#1297 - >seq7944,non-specific,197319,76,206,2.68462e-06,49.9677,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24562,Q#1297 - >seq7944,non-specific,272954,59,206,1.25436e-05,47.7629,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24563,Q#1297 - >seq7944,non-specific,197321,58,206,0.000132378,44.8504,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24564,Q#1297 - >seq7944,non-specific,235175,275,453,0.000291332,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs3_orang,marg,BothTerminiTruncated
24565,Q#1297 - >seq7944,superfamily,235175,275,453,0.000291332,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PB,ORF2,hs3_orang,marg,BothTerminiTruncated
24566,Q#1297 - >seq7944,specific,335306,82,199,0.00119041,41.4618,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PB,ORF2,hs3_orang,marg,N-TerminusTruncated
24567,Q#1297 - >seq7944,non-specific,339261,78,202,0.00472363,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB.ORF2.hs3_orang.marg.frame1,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24568,Q#1299 - >seq7946,specific,238827,456,708,9.065649999999998e-67,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24569,Q#1299 - >seq7946,superfamily,295487,456,708,9.065649999999998e-67,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24570,Q#1299 - >seq7946,specific,333820,462,691,9.233899999999999e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24571,Q#1299 - >seq7946,superfamily,333820,462,691,9.233899999999999e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24572,Q#1299 - >seq7946,non-specific,238828,462,683,1.3431e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24573,Q#1299 - >seq7946,non-specific,275209,413,683,3.0788000000000006e-09,59.7788,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,C-TerminusTruncated
24574,Q#1299 - >seq7946,superfamily,275209,413,683,3.0788000000000006e-09,59.7788,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,C-TerminusTruncated
24575,Q#1299 - >seq7946,non-specific,238185,602,679,9.56243e-05,42.338,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,C-TerminusTruncated
24576,Q#1299 - >seq7946,non-specific,239569,471,684,0.00054583,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB.ORF2.hs3_orang.marg.frame3,1909131033_L1PB.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB,ORF2,hs3_orang,marg,CompleteHit
24577,Q#1301 - >seq7948,specific,238827,467,729,1.0043899999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24578,Q#1301 - >seq7948,superfamily,295487,467,729,1.0043899999999998e-66,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24579,Q#1301 - >seq7948,specific,333820,473,697,4.76134e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24580,Q#1301 - >seq7948,superfamily,333820,473,697,4.76134e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24581,Q#1301 - >seq7948,non-specific,238828,473,694,1.3520400000000001e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24582,Q#1301 - >seq7948,non-specific,275209,423,681,9.27206e-10,61.7048,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,C-TerminusTruncated
24583,Q#1301 - >seq7948,superfamily,275209,423,681,9.27206e-10,61.7048,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,C-TerminusTruncated
24584,Q#1301 - >seq7948,non-specific,238185,613,727,0.000303134,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs0_human.pars.frame2,1909131033_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs0_human,pars,CompleteHit
24585,Q#1305 - >seq7952,specific,238827,505,767,9.106499999999998e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24586,Q#1305 - >seq7952,superfamily,295487,505,767,9.106499999999998e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24587,Q#1305 - >seq7952,specific,197310,9,232,6.2126e-55,191.02599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24588,Q#1305 - >seq7952,superfamily,351117,9,232,6.2126e-55,191.02599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24589,Q#1305 - >seq7952,specific,333820,511,735,1.36764e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24590,Q#1305 - >seq7952,superfamily,333820,511,735,1.36764e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24591,Q#1305 - >seq7952,non-specific,197306,9,232,8.228669999999999e-28,113.345,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24592,Q#1305 - >seq7952,non-specific,197320,9,203,2.59304e-17,82.9481,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24593,Q#1305 - >seq7952,non-specific,223780,9,233,9.217e-17,81.4907,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24594,Q#1305 - >seq7952,non-specific,197307,9,232,1.54964e-16,80.4097,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24595,Q#1305 - >seq7952,specific,335306,10,225,1.14655e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24596,Q#1305 - >seq7952,non-specific,238828,511,732,4.2077799999999996e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24597,Q#1305 - >seq7952,non-specific,197321,7,232,6.06152e-13,69.8884,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24598,Q#1305 - >seq7952,non-specific,273186,9,233,1.06576e-11,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24599,Q#1305 - >seq7952,non-specific,272954,9,204,1.56452e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24600,Q#1305 - >seq7952,non-specific,197319,13,232,3.44546e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24601,Q#1305 - >seq7952,non-specific,275209,464,791,1.53519e-07,54.7712,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24602,Q#1305 - >seq7952,superfamily,275209,464,791,1.53519e-07,54.7712,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24603,Q#1305 - >seq7952,non-specific,197311,7,143,1.72598e-06,49.9829,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24604,Q#1305 - >seq7952,non-specific,197336,9,191,1.30055e-05,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24605,Q#1305 - >seq7952,non-specific,236970,9,191,0.00010895700000000001,45.2702,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24606,Q#1305 - >seq7952,non-specific,274009,306,452,0.00059984,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24607,Q#1305 - >seq7952,superfamily,274009,306,452,0.00059984,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24608,Q#1305 - >seq7952,specific,311990,1236,1254,0.000730615,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24609,Q#1305 - >seq7952,superfamily,311990,1236,1254,0.000730615,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24610,Q#1305 - >seq7952,non-specific,238185,651,765,0.00125349,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24611,Q#1305 - >seq7952,non-specific,334125,210,406,0.00179799,42.1364,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24612,Q#1305 - >seq7952,superfamily,334125,210,406,0.00179799,42.1364,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24613,Q#1305 - >seq7952,non-specific,235175,305,444,0.00302124,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24614,Q#1305 - >seq7952,superfamily,235175,305,444,0.00302124,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24615,Q#1305 - >seq7952,non-specific,197314,7,189,0.00415916,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24616,Q#1305 - >seq7952,non-specific,339261,105,228,0.00449423,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24617,Q#1305 - >seq7952,non-specific,239569,520,780,0.00893783,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB3.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs6_sqmonkey,marg,CompleteHit
24618,Q#1306 - >seq7953,specific,311990,1139,1157,0.00230041,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs6_sqmonkey.pars.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24619,Q#1306 - >seq7953,superfamily,311990,1139,1157,0.00230041,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs6_sqmonkey.pars.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24620,Q#1307 - >seq7954,specific,197310,3,229,5.7668899999999995e-56,194.107,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24621,Q#1307 - >seq7954,superfamily,351117,3,229,5.7668899999999995e-56,194.107,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24622,Q#1307 - >seq7954,specific,238827,501,756,1.59927e-55,192.12099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24623,Q#1307 - >seq7954,superfamily,295487,501,756,1.59927e-55,192.12099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24624,Q#1307 - >seq7954,non-specific,197306,3,229,8.71138e-31,121.82,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24625,Q#1307 - >seq7954,non-specific,333820,507,756,6.28724e-28,111.615,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24626,Q#1307 - >seq7954,superfamily,333820,507,756,6.28724e-28,111.615,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24627,Q#1307 - >seq7954,non-specific,197320,3,202,7.05357e-17,81.4073,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24628,Q#1307 - >seq7954,non-specific,223780,3,230,5.201649999999999e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24629,Q#1307 - >seq7954,specific,335306,4,222,6.432680000000001e-16,78.0557,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24630,Q#1307 - >seq7954,non-specific,197307,3,229,1.99278e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24631,Q#1307 - >seq7954,non-specific,197321,1,229,5.08646e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24632,Q#1307 - >seq7954,non-specific,273186,3,230,1.35803e-11,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24633,Q#1307 - >seq7954,non-specific,238828,548,721,4.58062e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24634,Q#1307 - >seq7954,non-specific,197319,7,229,2.65866e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24635,Q#1307 - >seq7954,non-specific,272954,3,201,4.2872200000000004e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24636,Q#1307 - >seq7954,non-specific,275209,571,784,7.17475e-08,55.9268,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24637,Q#1307 - >seq7954,superfamily,275209,571,784,7.17475e-08,55.9268,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24638,Q#1307 - >seq7954,non-specific,197322,2,229,1.0584100000000001e-05,48.8526,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24639,Q#1307 - >seq7954,non-specific,236970,3,188,1.38079e-05,47.9666,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24640,Q#1307 - >seq7954,non-specific,235175,284,460,1.50339e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24641,Q#1307 - >seq7954,superfamily,235175,284,460,1.50339e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24642,Q#1307 - >seq7954,non-specific,197336,3,229,6.999090000000001e-05,45.6811,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24643,Q#1307 - >seq7954,non-specific,238185,640,754,0.000518682,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24644,Q#1307 - >seq7954,non-specific,339261,103,225,0.0007005410000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24645,Q#1307 - >seq7954,non-specific,197311,33,229,0.00118223,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,pars,CompleteHit
24646,Q#1307 - >seq7954,non-specific,214019,300,405,0.00322501,39.6802,cd12926,iSH2_PIK3R2,N,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24647,Q#1307 - >seq7954,superfamily,355389,300,405,0.00322501,39.6802,cl25402,iSH2_PI3K_IA_R superfamily,N, - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24648,Q#1307 - >seq7954,non-specific,214017,254,374,0.00573658,38.906,cd12924,iSH2_PIK3R1,C,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1PA17.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24649,Q#1308 - >seq7955,specific,238827,480,716,3.7156700000000003e-53,185.187,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24650,Q#1308 - >seq7955,superfamily,295487,480,716,3.7156700000000003e-53,185.187,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24651,Q#1308 - >seq7955,specific,333820,472,716,1.35883e-28,113.541,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24652,Q#1308 - >seq7955,superfamily,333820,472,716,1.35883e-28,113.541,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24653,Q#1308 - >seq7955,non-specific,238828,508,681,5.9010400000000005e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24654,Q#1308 - >seq7955,non-specific,275209,531,744,3.4329e-08,56.6972,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24655,Q#1308 - >seq7955,superfamily,275209,531,744,3.4329e-08,56.6972,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24656,Q#1308 - >seq7955,non-specific,238185,600,714,0.000152655,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs6_sqmonkey.marg.frame1,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24657,Q#1309 - >seq7956,specific,311990,1166,1184,0.000993425,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs6_sqmonkey.marg.frame2,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24658,Q#1309 - >seq7956,superfamily,311990,1166,1184,0.000993425,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs6_sqmonkey.marg.frame2,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24659,Q#1310 - >seq7957,specific,197310,8,235,3.5472300000000003e-56,194.49200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24660,Q#1310 - >seq7957,superfamily,351117,8,235,3.5472300000000003e-56,194.49200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24661,Q#1310 - >seq7957,non-specific,197306,8,235,3.81914e-31,122.59,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24662,Q#1310 - >seq7957,non-specific,197320,8,208,5.1660699999999995e-17,81.7925,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24663,Q#1310 - >seq7957,non-specific,197307,8,235,7.08437e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24664,Q#1310 - >seq7957,non-specific,223780,8,236,6.639069999999999e-16,78.7943,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24665,Q#1310 - >seq7957,specific,335306,9,228,1.15961e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24666,Q#1310 - >seq7957,non-specific,197321,6,235,2.5364e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24667,Q#1310 - >seq7957,non-specific,273186,8,236,1.88036e-11,65.378,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24668,Q#1310 - >seq7957,non-specific,197319,12,235,3.81741e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24669,Q#1310 - >seq7957,non-specific,272954,8,207,1.97495e-09,59.3189,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24670,Q#1310 - >seq7957,non-specific,235175,290,467,1.13628e-06,52.7588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24671,Q#1310 - >seq7957,superfamily,235175,290,467,1.13628e-06,52.7588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24672,Q#1310 - >seq7957,non-specific,197322,7,235,5.3398e-06,49.623000000000005,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24673,Q#1310 - >seq7957,non-specific,236970,8,194,1.13206e-05,48.3518,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24674,Q#1310 - >seq7957,non-specific,197336,8,235,5.6849300000000005e-05,46.0663,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24675,Q#1310 - >seq7957,non-specific,238827,508,536,5.8801099999999995e-05,45.3598,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24676,Q#1310 - >seq7957,superfamily,295487,508,536,5.8801099999999995e-05,45.3598,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24677,Q#1310 - >seq7957,non-specific,197311,38,235,0.0007966560000000001,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24678,Q#1310 - >seq7957,non-specific,224117,262,465,0.00179949,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24679,Q#1310 - >seq7957,superfamily,224117,262,465,0.00179949,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
24680,Q#1310 - >seq7957,non-specific,223266,216,463,0.00503854,40.7182,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24681,Q#1310 - >seq7957,superfamily,223266,216,463,0.00503854,40.7182,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
24682,Q#1310 - >seq7957,non-specific,339261,108,231,0.00537807,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs6_sqmonkey.marg.frame3,1909131033_L1PA17.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs6_sqmonkey,marg,CompleteHit
24683,Q#1313 - >seq7960,non-specific,335182,154,251,3.894919999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24684,Q#1313 - >seq7960,superfamily,335182,154,251,3.894919999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24685,Q#1313 - >seq7960,non-specific,340205,254,318,1.12989e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24686,Q#1313 - >seq7960,superfamily,340205,254,318,1.12989e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24687,Q#1313 - >seq7960,non-specific,340204,109,151,1.0943099999999999e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24688,Q#1313 - >seq7960,superfamily,340204,109,151,1.0943099999999999e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA5,ORF1,hs2_gorilla,pars,CompleteHit
24689,Q#1313 - >seq7960,non-specific,222878,30,195,0.000317168,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24690,Q#1313 - >seq7960,superfamily,222878,30,195,0.000317168,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24691,Q#1313 - >seq7960,non-specific,274008,48,161,0.000376005,42.3511,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24692,Q#1313 - >seq7960,superfamily,274008,48,161,0.000376005,42.3511,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24693,Q#1313 - >seq7960,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24694,Q#1313 - >seq7960,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24695,Q#1313 - >seq7960,non-specific,235175,51,154,0.000982601,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24696,Q#1313 - >seq7960,superfamily,235175,51,154,0.000982601,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,pars,BothTerminiTruncated
24697,Q#1313 - >seq7960,non-specific,313022,4,151,0.00305229,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24698,Q#1313 - >seq7960,superfamily,313022,4,151,0.00305229,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs2_gorilla.pars.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA5,ORF1,hs2_gorilla,pars,N-TerminusTruncated
24699,Q#1318 - >seq7965,non-specific,335182,157,254,7.365219999999998e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24700,Q#1318 - >seq7965,superfamily,335182,157,254,7.365219999999998e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24701,Q#1318 - >seq7965,non-specific,335182,157,254,7.365219999999998e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24702,Q#1318 - >seq7965,non-specific,340205,257,321,4.48372e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24703,Q#1318 - >seq7965,superfamily,340205,257,321,4.48372e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24704,Q#1318 - >seq7965,non-specific,340205,257,321,4.48372e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24705,Q#1318 - >seq7965,non-specific,340204,112,154,3.65976e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24706,Q#1318 - >seq7965,superfamily,340204,112,154,3.65976e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24707,Q#1318 - >seq7965,non-specific,340204,112,154,3.65976e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,pars,CompleteHit
24708,Q#1318 - >seq7965,non-specific,179385,61,146,0.000560568,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24709,Q#1318 - >seq7965,superfamily,179385,61,146,0.000560568,41.5642,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24710,Q#1318 - >seq7965,non-specific,179385,61,146,0.000560568,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24711,Q#1318 - >seq7965,non-specific,224117,66,151,0.00245291,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24712,Q#1318 - >seq7965,superfamily,224117,66,151,0.00245291,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24713,Q#1318 - >seq7965,non-specific,224117,66,151,0.00245291,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24714,Q#1318 - >seq7965,non-specific,337766,52,130,0.00301398,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24715,Q#1318 - >seq7965,superfamily,337766,52,130,0.00301398,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24716,Q#1318 - >seq7965,non-specific,337766,52,130,0.00301398,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24717,Q#1318 - >seq7965,non-specific,313022,71,154,0.00344158,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24718,Q#1318 - >seq7965,superfamily,313022,71,154,0.00344158,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24719,Q#1318 - >seq7965,non-specific,313022,71,154,0.00344158,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24720,Q#1318 - >seq7965,non-specific,274765,48,128,0.0044521000000000005,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24721,Q#1318 - >seq7965,superfamily,274765,48,128,0.0044521000000000005,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24722,Q#1318 - >seq7965,non-specific,274765,48,128,0.0044521000000000005,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24723,Q#1318 - >seq7965,non-specific,235175,55,143,0.0051881,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24724,Q#1318 - >seq7965,superfamily,235175,55,143,0.0051881,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24725,Q#1318 - >seq7965,non-specific,235175,55,143,0.0051881,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24726,Q#1318 - >seq7965,non-specific,309330,58,157,0.00599449,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24727,Q#1318 - >seq7965,superfamily,309330,58,157,0.00599449,37.0643,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24728,Q#1318 - >seq7965,non-specific,309330,58,157,0.00599449,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,pars,N-TerminusTruncated
24729,Q#1318 - >seq7965,non-specific,224117,66,157,0.00666798,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24730,Q#1318 - >seq7965,non-specific,224117,66,157,0.00666798,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24731,Q#1318 - >seq7965,non-specific,337663,73,149,0.00753108,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24732,Q#1318 - >seq7965,superfamily,337663,73,149,0.00753108,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24733,Q#1318 - >seq7965,non-specific,337663,73,149,0.00753108,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,pars,C-TerminusTruncated
24734,Q#1318 - >seq7965,non-specific,335556,66,150,0.00910414,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24735,Q#1318 - >seq7965,superfamily,335556,66,150,0.00910414,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24736,Q#1318 - >seq7965,non-specific,335556,66,150,0.00910414,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24737,Q#1318 - >seq7965,non-specific,179385,66,145,0.00912885,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24738,Q#1318 - >seq7965,non-specific,179385,66,145,0.00912885,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.pars.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,pars,BothTerminiTruncated
24739,Q#1321 - >seq7968,non-specific,335182,157,254,7.365219999999998e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24740,Q#1321 - >seq7968,superfamily,335182,157,254,7.365219999999998e-46,151.30100000000002,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24741,Q#1321 - >seq7968,non-specific,335182,157,254,7.365219999999998e-46,151.30100000000002,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24742,Q#1321 - >seq7968,non-specific,340205,257,321,4.48372e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24743,Q#1321 - >seq7968,superfamily,340205,257,321,4.48372e-33,117.052,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24744,Q#1321 - >seq7968,non-specific,340205,257,321,4.48372e-33,117.052,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24745,Q#1321 - >seq7968,non-specific,340204,112,154,3.65976e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24746,Q#1321 - >seq7968,superfamily,340204,112,154,3.65976e-08,48.9432,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24747,Q#1321 - >seq7968,non-specific,340204,112,154,3.65976e-08,48.9432,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8,ORF1,hs1_chimp,marg,CompleteHit
24748,Q#1321 - >seq7968,non-specific,179385,61,146,0.000560568,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24749,Q#1321 - >seq7968,superfamily,179385,61,146,0.000560568,41.5642,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24750,Q#1321 - >seq7968,non-specific,179385,61,146,0.000560568,41.5642,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24751,Q#1321 - >seq7968,non-specific,224117,66,151,0.00245291,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24752,Q#1321 - >seq7968,superfamily,224117,66,151,0.00245291,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24753,Q#1321 - >seq7968,non-specific,224117,66,151,0.00245291,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24754,Q#1321 - >seq7968,non-specific,337766,52,130,0.00301398,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24755,Q#1321 - >seq7968,superfamily,337766,52,130,0.00301398,38.7479,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24756,Q#1321 - >seq7968,non-specific,337766,52,130,0.00301398,38.7479,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24757,Q#1321 - >seq7968,non-specific,313022,71,154,0.00344158,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24758,Q#1321 - >seq7968,superfamily,313022,71,154,0.00344158,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24759,Q#1321 - >seq7968,non-specific,313022,71,154,0.00344158,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24760,Q#1321 - >seq7968,non-specific,274765,48,128,0.0044521000000000005,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24761,Q#1321 - >seq7968,superfamily,274765,48,128,0.0044521000000000005,38.4698,cl26990,conj_TIGR03752 superfamily,C, - ,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24762,Q#1321 - >seq7968,non-specific,274765,48,128,0.0044521000000000005,38.4698,TIGR03752,conj_TIGR03752,C,cl26990,"integrating conjugative element protein, PFL_4705 family; Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions]",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24763,Q#1321 - >seq7968,non-specific,235175,55,143,0.0051881,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24764,Q#1321 - >seq7968,superfamily,235175,55,143,0.0051881,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24765,Q#1321 - >seq7968,non-specific,235175,55,143,0.0051881,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24766,Q#1321 - >seq7968,non-specific,309330,58,157,0.00599449,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24767,Q#1321 - >seq7968,superfamily,309330,58,157,0.00599449,37.0643,cl25897,IncA superfamily,N, - ,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24768,Q#1321 - >seq7968,non-specific,309330,58,157,0.00599449,37.0643,pfam04156,IncA,N,cl25897,"IncA protein; Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,marg,N-TerminusTruncated
24769,Q#1321 - >seq7968,non-specific,224117,66,157,0.00666798,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24770,Q#1321 - >seq7968,non-specific,224117,66,157,0.00666798,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24771,Q#1321 - >seq7968,non-specific,337663,73,149,0.00753108,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24772,Q#1321 - >seq7968,superfamily,337663,73,149,0.00753108,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24773,Q#1321 - >seq7968,non-specific,337663,73,149,0.00753108,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF1,hs1_chimp,marg,C-TerminusTruncated
24774,Q#1321 - >seq7968,non-specific,335556,66,150,0.00910414,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24775,Q#1321 - >seq7968,superfamily,335556,66,150,0.00910414,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24776,Q#1321 - >seq7968,non-specific,335556,66,150,0.00910414,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24777,Q#1321 - >seq7968,non-specific,179385,66,145,0.00912885,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24778,Q#1321 - >seq7968,non-specific,179385,66,145,0.00912885,37.7122,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8.ORF1.hs1_chimp.marg.frame3,1909131033_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF1,hs1_chimp,marg,BothTerminiTruncated
24779,Q#1323 - >seq7970,specific,238827,505,767,2.2932199999999995e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24780,Q#1323 - >seq7970,superfamily,295487,505,767,2.2932199999999995e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24781,Q#1323 - >seq7970,specific,333820,511,735,7.528729999999998e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24782,Q#1323 - >seq7970,superfamily,333820,511,735,7.528729999999998e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24783,Q#1323 - >seq7970,specific,197310,78,233,3.96019e-31,122.46,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24784,Q#1323 - >seq7970,superfamily,351117,78,233,3.96019e-31,122.46,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24785,Q#1323 - >seq7970,non-specific,197306,77,233,2.58628e-15,76.7512,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24786,Q#1323 - >seq7970,non-specific,238828,511,732,2.41396e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24787,Q#1323 - >seq7970,non-specific,197320,104,204,9.97895e-10,60.6066,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24788,Q#1323 - >seq7970,non-specific,197307,87,233,9.86427e-09,57.2977,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24789,Q#1323 - >seq7970,non-specific,223780,89,234,4.76893e-08,55.2971,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24790,Q#1323 - >seq7970,non-specific,275209,464,791,9.6226e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24791,Q#1323 - >seq7970,superfamily,275209,464,791,9.6226e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24792,Q#1323 - >seq7970,non-specific,197319,104,233,1.65767e-06,50.7381,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24793,Q#1323 - >seq7970,non-specific,272954,88,205,1.9040399999999998e-05,47.3777,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24794,Q#1323 - >seq7970,non-specific,197321,104,233,1.91553e-05,47.5468,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24795,Q#1323 - >seq7970,non-specific,273186,84,234,6.27669e-05,45.7328,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24796,Q#1323 - >seq7970,specific,335306,110,226,0.000122719,44.5434,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
24797,Q#1323 - >seq7970,non-specific,274009,307,452,0.000493932,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24798,Q#1323 - >seq7970,superfamily,274009,307,452,0.000493932,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24799,Q#1323 - >seq7970,specific,311990,1228,1246,0.00069083,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24800,Q#1323 - >seq7970,superfamily,311990,1228,1246,0.00069083,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24801,Q#1323 - >seq7970,non-specific,235175,306,444,0.0008329860000000001,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24802,Q#1323 - >seq7970,superfamily,235175,306,444,0.0008329860000000001,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24803,Q#1323 - >seq7970,non-specific,238185,651,765,0.00102394,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24804,Q#1323 - >seq7970,non-specific,223496,296,422,0.00240656,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24805,Q#1323 - >seq7970,superfamily,223496,296,422,0.00240656,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24806,Q#1323 - >seq7970,non-specific,339261,106,229,0.0045917,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24807,Q#1323 - >seq7970,non-specific,274009,297,429,0.00559272,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB3,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
24808,Q#1323 - >seq7970,non-specific,239569,520,780,0.00583656,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB3.ORF2.hs6_sqmonkey.pars.frame2,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs6_sqmonkey,pars,CompleteHit
24809,Q#1325 - >seq7972,non-specific,197310,9,86,2.0468e-10,61.9837,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24810,Q#1325 - >seq7972,superfamily,351117,9,86,2.0468e-10,61.9837,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24811,Q#1325 - >seq7972,non-specific,197306,9,82,1.64448e-05,47.4761,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24812,Q#1325 - >seq7972,non-specific,223780,9,42,0.00038050000000000003,43.3559,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24813,Q#1325 - >seq7972,non-specific,197321,7,48,0.00045967699999999997,42.9244,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24814,Q#1325 - >seq7972,non-specific,197307,9,48,0.00127089,41.8897,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24815,Q#1325 - >seq7972,specific,335306,10,74,0.00227671,40.6914,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24816,Q#1325 - >seq7972,non-specific,273186,9,42,0.00252375,40.7252,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24817,Q#1325 - >seq7972,non-specific,197320,9,42,0.00597905,39.8058,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs6_sqmonkey.pars.frame3,1909131033_L1PB3.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round2.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24818,Q#1326 - >seq7973,non-specific,335182,154,251,3.894919999999999e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24819,Q#1326 - >seq7973,superfamily,335182,154,251,3.894919999999999e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24820,Q#1326 - >seq7973,non-specific,340205,254,318,1.12989e-32,115.896,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24821,Q#1326 - >seq7973,superfamily,340205,254,318,1.12989e-32,115.896,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24822,Q#1326 - >seq7973,non-specific,340204,109,151,1.0943099999999999e-10,55.8768,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24823,Q#1326 - >seq7973,superfamily,340204,109,151,1.0943099999999999e-10,55.8768,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA5,ORF1,hs2_gorilla,marg,CompleteHit
24824,Q#1326 - >seq7973,non-specific,222878,30,195,0.000317168,42.3089,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24825,Q#1326 - >seq7973,superfamily,222878,30,195,0.000317168,42.3089,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24826,Q#1326 - >seq7973,non-specific,274008,48,161,0.000376005,42.3511,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24827,Q#1326 - >seq7973,superfamily,274008,48,161,0.000376005,42.3511,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24828,Q#1326 - >seq7973,non-specific,274009,40,148,0.000413542,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24829,Q#1326 - >seq7973,superfamily,274009,40,148,0.000413542,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24830,Q#1326 - >seq7973,non-specific,235175,51,154,0.000982601,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24831,Q#1326 - >seq7973,superfamily,235175,51,154,0.000982601,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF1,hs2_gorilla,marg,BothTerminiTruncated
24832,Q#1326 - >seq7973,non-specific,313022,4,151,0.00305229,39.0614,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24833,Q#1326 - >seq7973,superfamily,313022,4,151,0.00305229,39.0614,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1PA5.ORF1.hs2_gorilla.marg.frame3,1909131033_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round2.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PA5,ORF1,hs2_gorilla,marg,N-TerminusTruncated
24834,Q#1327 - >seq7974,non-specific,197310,46,293,8.041969999999999e-26,106.667,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs6_sqmonkey,marg,CompleteHit
24835,Q#1327 - >seq7974,superfamily,351117,46,293,8.041969999999999e-26,106.667,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs6_sqmonkey,marg,CompleteHit
24836,Q#1327 - >seq7974,non-specific,197306,43,271,2.53077e-18,85.2256,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs6_sqmonkey,marg,CompleteHit
24837,Q#1337 - >seq7984,non-specific,340205,130,185,1.7823e-07,46.1752,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs7_bushaby.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs7_bushaby,marg,CompleteHit
24838,Q#1337 - >seq7984,superfamily,340205,130,185,1.7823e-07,46.1752,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs7_bushaby.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs7_bushaby,marg,CompleteHit
24839,Q#1341 - >seq7988,non-specific,340205,31,49,0.00142256,32.308,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs7_bushaby.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs7_bushaby,pars,C-TerminusTruncated
24840,Q#1341 - >seq7988,superfamily,340205,31,49,0.00142256,32.308,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs7_bushaby.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs7_bushaby,pars,C-TerminusTruncated
24841,Q#1343 - >seq7990,non-specific,238827,636,789,5.08644e-07,51.1378,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs6_sqmonkey.marg.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24842,Q#1343 - >seq7990,superfamily,295487,636,789,5.08644e-07,51.1378,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs6_sqmonkey.marg.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24843,Q#1347 - >seq7994,non-specific,340205,22,51,0.000290921,34.234,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs9_pika.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs9_pika,pars,C-TerminusTruncated
24844,Q#1347 - >seq7994,superfamily,340205,22,51,0.000290921,34.234,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs9_pika.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs9_pika,pars,C-TerminusTruncated
24845,Q#1357 - >seq8004,non-specific,340205,22,60,8.3076e-06,38.4712,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs9_pika.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs9_pika,marg,C-TerminusTruncated
24846,Q#1357 - >seq8004,superfamily,340205,22,60,8.3076e-06,38.4712,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs9_pika.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs9_pika,marg,C-TerminusTruncated
24847,Q#1360 - >seq8007,specific,197310,11,228,1.8198599999999998e-28,113.6,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs6_sqmonkey,pars,CompleteHit
24848,Q#1360 - >seq8007,superfamily,351117,11,228,1.8198599999999998e-28,113.6,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs6_sqmonkey,pars,CompleteHit
24849,Q#1360 - >seq8007,non-specific,197306,8,211,7.42075e-20,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs6_sqmonkey,pars,CompleteHit
24850,Q#1360 - >seq8007,non-specific,238827,449,540,3.53986e-11,63.07899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24851,Q#1360 - >seq8007,superfamily,295487,449,540,3.53986e-11,63.07899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24852,Q#1365 - >seq8012,specific,197310,3,230,4.97383e-58,199.885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24853,Q#1365 - >seq8012,superfamily,351117,3,230,4.97383e-58,199.885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24854,Q#1365 - >seq8012,non-specific,197306,3,230,2.0485599999999997e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24855,Q#1365 - >seq8012,non-specific,223780,3,231,2.33201e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24856,Q#1365 - >seq8012,non-specific,197320,3,223,1.18759e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24857,Q#1365 - >seq8012,non-specific,197307,3,230,1.7923400000000002e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24858,Q#1365 - >seq8012,specific,335306,4,223,2.2494e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24859,Q#1365 - >seq8012,non-specific,197319,7,230,1.85384e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24860,Q#1365 - >seq8012,non-specific,273186,3,231,2.12935e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24861,Q#1365 - >seq8012,non-specific,197321,1,230,3.65417e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24862,Q#1365 - >seq8012,non-specific,272954,3,230,1.45771e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24863,Q#1365 - >seq8012,non-specific,197336,3,188,1.35428e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24864,Q#1365 - >seq8012,non-specific,197322,2,230,1.1103299999999998e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24865,Q#1365 - >seq8012,non-specific,236970,3,183,2.35643e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
24866,Q#1365 - >seq8012,non-specific,197311,24,230,1.1690399999999999e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24867,Q#1365 - >seq8012,non-specific,339261,102,226,0.00183702,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
24868,Q#1370 - >seq8017,non-specific,333820,491,605,0.00446655,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24869,Q#1370 - >seq8017,superfamily,333820,491,605,0.00446655,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24870,Q#1370 - >seq8017,non-specific,238185,572,604,0.00476322,36.56,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24871,Q#1370 - >seq8017,superfamily,295487,572,604,0.00476322,36.56,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4b,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
24872,Q#1371 - >seq8018,specific,197310,9,226,1.11788e-53,184.862,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24873,Q#1371 - >seq8018,superfamily,351117,9,226,1.11788e-53,184.862,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24874,Q#1371 - >seq8018,non-specific,197306,9,221,1.6822399999999996e-31,122.975,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24875,Q#1371 - >seq8018,non-specific,197320,9,205,1.7753799999999996e-18,85.6445,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24876,Q#1371 - >seq8018,non-specific,223780,9,231,9.30778e-18,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24877,Q#1371 - >seq8018,non-specific,197307,9,217,5.833559999999999e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24878,Q#1371 - >seq8018,specific,335306,10,209,6.62733e-14,71.5073,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24879,Q#1371 - >seq8018,non-specific,272954,9,206,2.22489e-13,70.4897,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24880,Q#1371 - >seq8018,non-specific,197321,7,193,3.30798e-13,69.8884,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24881,Q#1371 - >seq8018,non-specific,197319,13,217,1.98107e-10,61.5237,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24882,Q#1371 - >seq8018,non-specific,273186,9,207,5.82909e-10,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24883,Q#1371 - >seq8018,non-specific,197336,9,190,8.93353e-09,56.8519,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24884,Q#1371 - >seq8018,non-specific,236970,9,193,1.2911400000000001e-05,47.1962,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24885,Q#1371 - >seq8018,non-specific,197311,37,203,7.0215e-05,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
24886,Q#1371 - >seq8018,non-specific,197318,9,148,0.00784014,38.4315,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4b.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
24887,Q#1372 - >seq8019,non-specific,340205,236,301,2.73158e-27,101.259,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
24888,Q#1372 - >seq8019,superfamily,340205,236,301,2.73158e-27,101.259,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
24889,Q#1372 - >seq8019,non-specific,335182,209,233,0.00252648,36.5119,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
24890,Q#1372 - >seq8019,superfamily,335182,209,233,0.00252648,36.5119,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
24891,Q#1374 - >seq8021,non-specific,335182,31,68,6.7682100000000005e-06,42.6751,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs3_orang,marg,C-TerminusTruncated
24892,Q#1374 - >seq8021,superfamily,335182,31,68,6.7682100000000005e-06,42.6751,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs3_orang,marg,C-TerminusTruncated
24893,Q#1375 - >seq8022,non-specific,340205,71,134,3.1661e-34,113.97,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,pars,CompleteHit
24894,Q#1375 - >seq8022,superfamily,340205,71,134,3.1661e-34,113.97,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,pars,CompleteHit
24895,Q#1375 - >seq8022,non-specific,335182,27,68,3.44819e-13,61.1647,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,pars,N-TerminusTruncated
24896,Q#1375 - >seq8022,superfamily,335182,27,68,3.44819e-13,61.1647,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,pars,N-TerminusTruncated
24897,Q#1377 - >seq8024,non-specific,335182,1,37,0.00011166799999999999,38.8231,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs3_orang,pars,C-TerminusTruncated
24898,Q#1377 - >seq8024,superfamily,335182,1,37,0.00011166799999999999,38.8231,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs3_orang,pars,C-TerminusTruncated
24899,Q#1380 - >seq8027,specific,238827,760,1024,9.200659999999999e-63,212.922,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24900,Q#1380 - >seq8027,superfamily,295487,760,1024,9.200659999999999e-63,212.922,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24901,Q#1380 - >seq8027,specific,197310,259,486,3.1741799999999996e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24902,Q#1380 - >seq8027,superfamily,351117,259,486,3.1741799999999996e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24903,Q#1380 - >seq8027,specific,333820,766,1024,9.87075e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24904,Q#1380 - >seq8027,superfamily,333820,766,1024,9.87075e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24905,Q#1380 - >seq8027,non-specific,197306,259,486,1.14571e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24906,Q#1380 - >seq8027,non-specific,340205,148,211,1.37166e-31,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24907,Q#1380 - >seq8027,superfamily,340205,148,211,1.37166e-31,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24908,Q#1380 - >seq8027,non-specific,197307,259,486,3.4101700000000004e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24909,Q#1380 - >seq8027,non-specific,197320,259,479,5.83242e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24910,Q#1380 - >seq8027,non-specific,223780,259,487,7.351e-17,81.8759,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24911,Q#1380 - >seq8027,non-specific,238828,766,987,8.41932e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24912,Q#1380 - >seq8027,specific,335306,260,479,1.57789e-13,71.1221,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24913,Q#1380 - >seq8027,non-specific,197321,257,486,1.3033700000000001e-12,69.118,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24914,Q#1380 - >seq8027,non-specific,273186,259,487,2.53618e-12,68.4596,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24915,Q#1380 - >seq8027,non-specific,272954,259,486,1.0120600000000001e-10,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24916,Q#1380 - >seq8027,non-specific,197319,263,486,9.105369999999999e-10,60.7533,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24917,Q#1380 - >seq8027,non-specific,275209,717,974,5.65013e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24918,Q#1380 - >seq8027,superfamily,275209,717,974,5.65013e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24919,Q#1380 - >seq8027,non-specific,197336,259,444,3.6479300000000002e-06,49.9183,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24920,Q#1380 - >seq8027,non-specific,339261,358,482,0.00235024,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24921,Q#1380 - >seq8027,non-specific,197311,257,486,0.00238523,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,marg,CompleteHit
24922,Q#1380 - >seq8027,non-specific,238185,906,983,0.00288655,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24923,Q#1380 - >seq8027,non-specific,274009,557,751,0.00298764,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24924,Q#1380 - >seq8027,superfamily,274009,557,751,0.00298764,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4b,ORF2,hs2_gorilla,marg,C-TerminusTruncated
24925,Q#1381 - >seq8028,non-specific,197310,408,481,1.01408e-14,75.0805,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24926,Q#1381 - >seq8028,superfamily,351117,408,481,1.01408e-14,75.0805,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24927,Q#1381 - >seq8028,non-specific,197306,379,481,4.61092e-06,49.4021,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24928,Q#1381 - >seq8028,non-specific,197321,415,481,0.000579256,42.9244,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24929,Q#1381 - >seq8028,non-specific,223496,508,674,0.0009478939999999999,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24930,Q#1381 - >seq8028,superfamily,223496,508,674,0.0009478939999999999,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24931,Q#1381 - >seq8028,non-specific,197307,421,481,0.0010884,41.8897,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24932,Q#1381 - >seq8028,non-specific,235175,508,708,0.00183377,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24933,Q#1381 - >seq8028,superfamily,235175,508,708,0.00183377,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24934,Q#1381 - >seq8028,non-specific,274009,551,681,0.00624587,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24935,Q#1381 - >seq8028,superfamily,274009,551,681,0.00624587,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,BothTerminiTruncated
24936,Q#1381 - >seq8028,non-specific,224117,511,721,0.00807536,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24937,Q#1381 - >seq8028,superfamily,224117,511,721,0.00807536,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
24938,Q#1382 - >seq8029,non-specific,274009,204,426,0.000137291,45.8291,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4b,ORF2,hs2_gorilla,pars,BothTerminiTruncated
24939,Q#1382 - >seq8029,superfamily,274009,204,426,0.000137291,45.8291,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4b,ORF2,hs2_gorilla,pars,BothTerminiTruncated
24940,Q#1382 - >seq8029,non-specific,274009,286,443,0.00131796,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24941,Q#1382 - >seq8029,non-specific,240741,364,426,0.00766898,36.1859,cd12295,RRM_YRA2, - ,cl17169,"RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins; This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).",L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24942,Q#1382 - >seq8029,superfamily,354314,364,426,0.00766898,36.1859,cl17169,RRM_SF superfamily, - , - ,"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).",L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24943,Q#1382 - >seq8029,non-specific,235600,225,424,0.00870117,39.9108,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1ME4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24944,Q#1382 - >seq8029,superfamily,235600,225,424,0.00870117,39.9108,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1ME4b.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1ME4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24945,Q#1384 - >seq8031,specific,238827,488,752,2.4032799999999994e-62,210.99599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24946,Q#1384 - >seq8031,superfamily,295487,488,752,2.4032799999999994e-62,210.99599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24947,Q#1384 - >seq8031,specific,197310,10,234,4.35863e-53,185.248,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24948,Q#1384 - >seq8031,superfamily,351117,10,234,4.35863e-53,185.248,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24949,Q#1384 - >seq8031,specific,333820,494,725,3.07651e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24950,Q#1384 - >seq8031,superfamily,333820,494,725,3.07651e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24951,Q#1384 - >seq8031,non-specific,197306,10,234,3.13689e-30,119.89399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24952,Q#1384 - >seq8031,non-specific,197307,10,234,8.58719e-20,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24953,Q#1384 - >seq8031,non-specific,223780,10,235,1.60049e-17,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24954,Q#1384 - >seq8031,non-specific,197320,10,227,4.05118e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24955,Q#1384 - >seq8031,specific,335306,11,227,7.499910000000001e-14,71.8925,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24956,Q#1384 - >seq8031,non-specific,238828,494,715,9.54062e-14,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24957,Q#1384 - >seq8031,non-specific,273186,10,235,1.3605700000000001e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24958,Q#1384 - >seq8031,non-specific,272954,10,234,3.8412300000000006e-12,67.4081,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24959,Q#1384 - >seq8031,non-specific,197321,8,234,1.60529e-11,65.6512,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24960,Q#1384 - >seq8031,non-specific,197319,14,234,2.5899e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24961,Q#1384 - >seq8031,non-specific,236970,10,234,1.55464e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24962,Q#1384 - >seq8031,non-specific,275209,528,819,3.81309e-08,56.312,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,N-TerminusTruncated
24963,Q#1384 - >seq8031,superfamily,275209,528,819,3.81309e-08,56.312,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,N-TerminusTruncated
24964,Q#1384 - >seq8031,non-specific,197336,10,192,1.36645e-06,50.6887,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24965,Q#1384 - >seq8031,non-specific,197311,8,234,4.43058e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24966,Q#1384 - >seq8031,non-specific,339261,106,230,0.00200097,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1ME4b,ORF2,hs2_gorilla,pars,CompleteHit
24967,Q#1384 - >seq8031,non-specific,238185,634,711,0.00269538,38.1008,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs2_gorilla,pars,C-TerminusTruncated
24968,Q#1386 - >seq8033,non-specific,234767,104,290,0.00333556,39.436,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1ME4b.ORF1.hs2_gorilla.marg.frame2,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1ME4b,ORF1,hs2_gorilla,marg,C-TerminusTruncated
24969,Q#1386 - >seq8033,superfamily,234767,104,290,0.00333556,39.436,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1ME4b.ORF1.hs2_gorilla.marg.frame2,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1ME4b,ORF1,hs2_gorilla,marg,C-TerminusTruncated
24970,Q#1387 - >seq8034,non-specific,340205,270,332,9.566619999999999e-18,76.60600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,marg,CompleteHit
24971,Q#1387 - >seq8034,superfamily,340205,270,332,9.566619999999999e-18,76.60600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,marg,CompleteHit
24972,Q#1387 - >seq8034,non-specific,335182,167,267,6.24475e-17,75.4171,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,marg,CompleteHit
24973,Q#1387 - >seq8034,superfamily,335182,167,267,6.24475e-17,75.4171,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs2_gorilla.marg.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,marg,CompleteHit
24974,Q#1389 - >seq8036,non-specific,340205,99,156,5.4738e-17,70.828,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs2_gorilla.pars.frame2,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs2_gorilla,pars,CompleteHit
24975,Q#1389 - >seq8036,superfamily,340205,99,156,5.4738e-17,70.828,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs2_gorilla.pars.frame2,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs2_gorilla,pars,CompleteHit
24976,Q#1390 - >seq8037,non-specific,335182,10,98,1.1031799999999999e-16,71.1799,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,pars,CompleteHit
24977,Q#1390 - >seq8037,superfamily,335182,10,98,1.1031799999999999e-16,71.1799,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs2_gorilla.pars.frame1,1909181109_L1ME4b.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs2_gorilla,pars,CompleteHit
24978,Q#1392 - >seq8039,non-specific,340205,112,175,9.01207e-34,114.741,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,marg,CompleteHit
24979,Q#1392 - >seq8039,superfamily,340205,112,175,9.01207e-34,114.741,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,marg,CompleteHit
24980,Q#1392 - >seq8039,non-specific,335182,59,109,1.44591e-14,66.1723,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,marg,N-TerminusTruncated
24981,Q#1392 - >seq8039,superfamily,335182,59,109,1.44591e-14,66.1723,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4b,ORF1,hs3_orang,marg,N-TerminusTruncated
24982,Q#1394 - >seq8041,specific,238827,466,727,1.0547999999999998e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24983,Q#1394 - >seq8041,superfamily,295487,466,727,1.0547999999999998e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24984,Q#1394 - >seq8041,specific,333820,472,693,6.13166e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24985,Q#1394 - >seq8041,superfamily,333820,472,693,6.13166e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24986,Q#1394 - >seq8041,non-specific,238828,472,693,1.4848e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24987,Q#1394 - >seq8041,non-specific,275209,543,693,7.22401e-07,52.46,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,BothTerminiTruncated
24988,Q#1394 - >seq8041,superfamily,275209,543,693,7.22401e-07,52.46,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs3_orang.pars.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,pars,BothTerminiTruncated
24989,Q#1395 - >seq8042,specific,197310,9,236,3.0111599999999997e-53,186.018,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24990,Q#1395 - >seq8042,superfamily,351117,9,236,3.0111599999999997e-53,186.018,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24991,Q#1395 - >seq8042,non-specific,197306,9,236,8.22692e-27,109.87799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24992,Q#1395 - >seq8042,non-specific,197320,9,206,2.0474200000000003e-16,79.8665,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24993,Q#1395 - >seq8042,non-specific,223780,9,205,3.06248e-15,76.4831,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24994,Q#1395 - >seq8042,specific,335306,10,229,5.0829099999999996e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24995,Q#1395 - >seq8042,non-specific,197307,9,205,1.4041300000000002e-13,71.5501,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24996,Q#1395 - >seq8042,non-specific,197321,7,194,3.25676e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24997,Q#1395 - >seq8042,non-specific,272954,9,205,8.10192e-11,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24998,Q#1395 - >seq8042,non-specific,273186,9,205,4.866520000000001e-09,58.0592,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
24999,Q#1395 - >seq8042,non-specific,197336,9,194,1.89521e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
25000,Q#1395 - >seq8042,non-specific,197319,13,194,5.60966e-08,54.9753,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,pars,CompleteHit
25001,Q#1395 - >seq8042,non-specific,224117,266,400,0.00113045,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4b,ORF2,hs3_orang,pars,BothTerminiTruncated
25002,Q#1395 - >seq8042,superfamily,224117,266,400,0.00113045,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4b,ORF2,hs3_orang,pars,BothTerminiTruncated
25003,Q#1397 - >seq8044,non-specific,335182,156,242,1.0915700000000001e-20,85.04700000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
25004,Q#1397 - >seq8044,superfamily,335182,156,242,1.0915700000000001e-20,85.04700000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
25005,Q#1397 - >seq8044,non-specific,340204,110,153,1.39861e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
25006,Q#1397 - >seq8044,superfamily,340204,110,153,1.39861e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4b.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4b,ORF1,hs6_sqmonkey,marg,CompleteHit
25007,Q#1398 - >seq8045,non-specific,340205,155,218,9.404680000000001e-30,105.49600000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,CompleteHit
25008,Q#1398 - >seq8045,superfamily,340205,155,218,9.404680000000001e-30,105.49600000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,CompleteHit
25009,Q#1398 - >seq8045,non-specific,335182,128,152,0.00106699,37.2823,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25010,Q#1398 - >seq8045,superfamily,335182,128,152,0.00106699,37.2823,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25011,Q#1400 - >seq8047,non-specific,335182,60,146,3.15098e-22,86.973,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,CompleteHit
25012,Q#1400 - >seq8047,superfamily,335182,60,146,3.15098e-22,86.973,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs6_sqmonkey,pars,CompleteHit
25013,Q#1403 - >seq8050,specific,197310,258,484,1.0756899999999999e-58,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25014,Q#1403 - >seq8050,superfamily,351117,258,484,1.0756899999999999e-58,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25015,Q#1403 - >seq8050,specific,238827,744,1004,9.2829e-56,192.891,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25016,Q#1403 - >seq8050,superfamily,295487,744,1004,9.2829e-56,192.891,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25017,Q#1403 - >seq8050,non-specific,197306,258,484,3.9419499999999995e-33,128.753,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25018,Q#1403 - >seq8050,specific,340205,147,210,1.26509e-32,120.904,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25019,Q#1403 - >seq8050,superfamily,340205,147,210,1.26509e-32,120.904,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25020,Q#1403 - >seq8050,non-specific,333820,750,969,1.3976899999999999e-27,110.845,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25021,Q#1403 - >seq8050,superfamily,333820,750,969,1.3976899999999999e-27,110.845,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25022,Q#1403 - >seq8050,non-specific,197320,258,477,7.0588300000000005e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25023,Q#1403 - >seq8050,non-specific,197307,258,484,1.0416e-18,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25024,Q#1403 - >seq8050,non-specific,223780,258,477,1.62809e-18,86.8835,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25025,Q#1403 - >seq8050,specific,335306,259,477,3.1197399999999997e-15,76.1297,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25026,Q#1403 - >seq8050,non-specific,272954,258,484,3.04804e-13,70.8749,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25027,Q#1403 - >seq8050,non-specific,197321,256,484,5.45922e-13,70.2736,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25028,Q#1403 - >seq8050,non-specific,273186,258,485,3.08157e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25029,Q#1403 - >seq8050,non-specific,197319,262,484,5.70021e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25030,Q#1403 - >seq8050,non-specific,238828,798,958,2.7852999999999997e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25031,Q#1403 - >seq8050,non-specific,197336,258,439,1.8587900000000002e-08,56.8519,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25032,Q#1403 - >seq8050,non-specific,236970,258,442,9.54716e-06,48.736999999999995,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25033,Q#1403 - >seq8050,non-specific,197311,286,484,1.7410299999999998e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25034,Q#1403 - >seq8050,non-specific,275209,701,1021,2.3013400000000002e-05,48.2228,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25035,Q#1403 - >seq8050,superfamily,275209,701,1021,2.3013400000000002e-05,48.2228,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,CompleteHit
25036,Q#1403 - >seq8050,non-specific,238185,890,967,0.00144194,39.2564,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25037,Q#1405 - >seq8052,specific,238827,451,708,5.631350000000001e-57,192.891,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
25038,Q#1405 - >seq8052,superfamily,295487,451,708,5.631350000000001e-57,192.891,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
25039,Q#1405 - >seq8052,non-specific,333820,457,674,5.89977e-26,105.06700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
25040,Q#1405 - >seq8052,superfamily,333820,457,674,5.89977e-26,105.06700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,CompleteHit
25041,Q#1405 - >seq8052,non-specific,238828,505,663,9.75563e-11,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25042,Q#1405 - >seq8052,non-specific,238185,595,672,0.000454021,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,C-TerminusTruncated
25043,Q#1405 - >seq8052,non-specific,275209,528,663,0.00235589,40.5188,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,BothTerminiTruncated
25044,Q#1405 - >seq8052,superfamily,275209,528,663,0.00235589,40.5188,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4b,ORF2,hs4_gibbon,pars,BothTerminiTruncated
25045,Q#1408 - >seq8055,non-specific,340205,124,185,1.0700299999999998e-30,107.037,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,marg,CompleteHit
25046,Q#1408 - >seq8055,superfamily,340205,124,185,1.0700299999999998e-30,107.037,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,marg,CompleteHit
25047,Q#1408 - >seq8055,non-specific,335182,32,118,3.45536e-22,86.2026,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,marg,CompleteHit
25048,Q#1408 - >seq8055,superfamily,335182,32,118,3.45536e-22,86.2026,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs4_gibbon.marg.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,marg,CompleteHit
25049,Q#1411 - >seq8058,non-specific,340205,111,172,3.94393e-31,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,pars,CompleteHit
25050,Q#1411 - >seq8058,superfamily,340205,111,172,3.94393e-31,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,pars,CompleteHit
25051,Q#1411 - >seq8058,non-specific,335182,22,105,2.6097299999999997e-24,91.2102,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,pars,CompleteHit
25052,Q#1411 - >seq8058,superfamily,335182,22,105,2.6097299999999997e-24,91.2102,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs4_gibbon.pars.frame1,1909181109_L1ME4b.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4b,ORF1,hs4_gibbon,pars,CompleteHit
25053,Q#1412 - >seq8059,specific,197310,9,236,3.1246099999999996e-52,183.322,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25054,Q#1412 - >seq8059,superfamily,351117,9,236,3.1246099999999996e-52,183.322,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25055,Q#1412 - >seq8059,non-specific,197306,9,236,2.04487e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25056,Q#1412 - >seq8059,non-specific,197320,9,206,2.2793400000000006e-16,79.8665,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25057,Q#1412 - >seq8059,non-specific,223780,9,205,3.41076e-15,76.4831,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25058,Q#1412 - >seq8059,specific,335306,10,229,5.7490299999999995e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25059,Q#1412 - >seq8059,non-specific,197307,9,205,1.63685e-13,71.5501,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25060,Q#1412 - >seq8059,non-specific,197321,7,194,3.72499e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25061,Q#1412 - >seq8059,non-specific,272954,9,205,1.2462899999999998e-10,63.1709,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25062,Q#1412 - >seq8059,non-specific,273186,9,205,5.40716e-09,58.0592,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25063,Q#1412 - >seq8059,non-specific,197336,9,194,2.1051e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25064,Q#1412 - >seq8059,non-specific,197319,13,194,4.3943000000000005e-08,55.3605,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25065,Q#1412 - >seq8059,non-specific,224117,266,400,0.00113544,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4b,ORF2,hs3_orang,marg,BothTerminiTruncated
25066,Q#1412 - >seq8059,superfamily,224117,266,400,0.00113544,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4b,ORF2,hs3_orang,marg,BothTerminiTruncated
25067,Q#1414 - >seq8061,specific,238827,466,727,6.996239999999998e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25068,Q#1414 - >seq8061,superfamily,295487,466,727,6.996239999999998e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25069,Q#1414 - >seq8061,specific,333820,472,727,8.583939999999998e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25070,Q#1414 - >seq8061,superfamily,333820,472,727,8.583939999999998e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25071,Q#1414 - >seq8061,non-specific,238828,472,724,1.5135e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25072,Q#1414 - >seq8061,non-specific,275209,543,693,1.21781e-06,51.6896,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,BothTerminiTruncated
25073,Q#1414 - >seq8061,superfamily,275209,543,693,1.21781e-06,51.6896,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,BothTerminiTruncated
25074,Q#1414 - >seq8061,non-specific,238185,612,727,0.00014729,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4b,ORF2,hs3_orang,marg,CompleteHit
25075,Q#1414 - >seq8061,non-specific,224117,293,434,0.0069369,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4b,ORF2,hs3_orang,marg,N-TerminusTruncated
25076,Q#1414 - >seq8061,superfamily,224117,293,434,0.0069369,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4b.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME4b,ORF2,hs3_orang,marg,N-TerminusTruncated
25077,Q#1416 - >seq8063,non-specific,340205,113,160,0.00195828,35.0044,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs10_snmole.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs10_snmole,marg,CompleteHit
25078,Q#1416 - >seq8063,superfamily,340205,113,160,0.00195828,35.0044,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs10_snmole.marg.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs10_snmole,marg,CompleteHit
25079,Q#1421 - >seq8068,non-specific,335182,163,260,1.85614e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25080,Q#1421 - >seq8068,superfamily,335182,163,260,1.85614e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25081,Q#1421 - >seq8068,non-specific,340205,263,327,2.2396999999999995e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25082,Q#1421 - >seq8068,superfamily,340205,263,327,2.2396999999999995e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25083,Q#1421 - >seq8068,specific,340204,118,160,1.23308e-13,64.3512,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25084,Q#1421 - >seq8068,superfamily,340204,118,160,1.23308e-13,64.3512,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1PA3,ORF1,hs4_gibbon,marg,CompleteHit
25085,Q#1421 - >seq8068,non-specific,224117,39,157,0.0032256999999999997,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
25086,Q#1421 - >seq8068,superfamily,224117,39,157,0.0032256999999999997,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
25087,Q#1421 - >seq8068,non-specific,274009,34,157,0.00382264,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
25088,Q#1421 - >seq8068,superfamily,274009,34,157,0.00382264,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,BothTerminiTruncated
25089,Q#1421 - >seq8068,non-specific,235175,35,149,0.00411588,38.8916,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
25090,Q#1421 - >seq8068,superfamily,235175,35,149,0.00411588,38.8916,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
25091,Q#1421 - >seq8068,non-specific,335623,56,155,0.009012299999999999,37.1538,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other,L1PA3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
25092,Q#1421 - >seq8068,superfamily,335623,56,155,0.009012299999999999,37.1538,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other,L1PA3,ORF1,hs4_gibbon,marg,C-TerminusTruncated
25093,Q#1422 - >seq8069,non-specific,273690,24,78,0.00530517,33.8585,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
25094,Q#1422 - >seq8069,superfamily,355611,24,78,0.00530517,33.8585,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs4_gibbon,pars,C-TerminusTruncated
25095,Q#1425 - >seq8072,specific,238827,510,772,4.027589999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25096,Q#1425 - >seq8072,superfamily,295487,510,772,4.027589999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25097,Q#1425 - >seq8072,non-specific,238827,510,772,4.027589999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25098,Q#1425 - >seq8072,specific,197310,9,236,8.658889999999997e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25099,Q#1425 - >seq8072,superfamily,351117,9,236,8.658889999999997e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25100,Q#1425 - >seq8072,non-specific,197310,9,236,8.658889999999997e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25101,Q#1425 - >seq8072,non-specific,197306,9,236,2.6641099999999998e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25102,Q#1425 - >seq8072,non-specific,197306,9,236,2.6641099999999998e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25103,Q#1425 - >seq8072,specific,333820,516,772,2.4349599999999995e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25104,Q#1425 - >seq8072,superfamily,333820,516,772,2.4349599999999995e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25105,Q#1425 - >seq8072,non-specific,333820,516,772,2.4349599999999995e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25106,Q#1425 - >seq8072,non-specific,197307,9,236,3.56089e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25107,Q#1425 - >seq8072,non-specific,197307,9,236,3.56089e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25108,Q#1425 - >seq8072,non-specific,223780,9,238,2.07619e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25109,Q#1425 - >seq8072,non-specific,223780,9,238,2.07619e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25110,Q#1425 - >seq8072,non-specific,197320,8,236,3.2301599999999997e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25111,Q#1425 - >seq8072,non-specific,197320,8,236,3.2301599999999997e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25112,Q#1425 - >seq8072,non-specific,197321,7,236,3.76241e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25113,Q#1425 - >seq8072,non-specific,197321,7,236,3.76241e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25114,Q#1425 - >seq8072,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25115,Q#1425 - >seq8072,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25116,Q#1425 - >seq8072,non-specific,273186,9,237,2.03473e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25117,Q#1425 - >seq8072,non-specific,273186,9,237,2.03473e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25118,Q#1425 - >seq8072,non-specific,272954,9,236,3.77264e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25119,Q#1425 - >seq8072,non-specific,272954,9,236,3.77264e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25120,Q#1425 - >seq8072,non-specific,197319,8,236,3.67568e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25121,Q#1425 - >seq8072,non-specific,197319,8,236,3.67568e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25122,Q#1425 - >seq8072,non-specific,197336,7,235,6.78813e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25123,Q#1425 - >seq8072,non-specific,197336,7,235,6.78813e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25124,Q#1425 - >seq8072,non-specific,238828,516,737,1.88416e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25125,Q#1425 - >seq8072,non-specific,238828,516,737,1.88416e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25126,Q#1425 - >seq8072,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25127,Q#1425 - >seq8072,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25128,Q#1425 - >seq8072,non-specific,275209,467,800,3.65054e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25129,Q#1425 - >seq8072,superfamily,275209,467,800,3.65054e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25130,Q#1425 - >seq8072,non-specific,275209,467,800,3.65054e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25131,Q#1425 - >seq8072,non-specific,236970,9,238,2.85067e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25132,Q#1425 - >seq8072,non-specific,236970,9,238,2.85067e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25133,Q#1425 - >seq8072,non-specific,339261,108,232,3.09543e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25134,Q#1425 - >seq8072,non-specific,339261,108,232,3.09543e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25135,Q#1425 - >seq8072,non-specific,197317,139,229,1.332e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,N-TerminusTruncated
25136,Q#1425 - >seq8072,non-specific,197317,139,229,1.332e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,N-TerminusTruncated
25137,Q#1425 - >seq8072,non-specific,197311,7,236,3.6224000000000002e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25138,Q#1425 - >seq8072,non-specific,197311,7,236,3.6224000000000002e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25139,Q#1425 - >seq8072,non-specific,238185,656,772,0.000174205,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25140,Q#1425 - >seq8072,non-specific,238185,656,772,0.000174205,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25141,Q#1425 - >seq8072,non-specific,274009,305,453,0.000187755,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25142,Q#1425 - >seq8072,superfamily,274009,305,453,0.000187755,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25143,Q#1425 - >seq8072,non-specific,274009,305,453,0.000187755,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25144,Q#1425 - >seq8072,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,N-TerminusTruncated
25145,Q#1425 - >seq8072,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,marg,N-TerminusTruncated
25146,Q#1425 - >seq8072,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25147,Q#1425 - >seq8072,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25148,Q#1425 - >seq8072,non-specific,235175,301,469,0.00395048,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,BothTerminiTruncated
25149,Q#1425 - >seq8072,superfamily,235175,301,469,0.00395048,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,BothTerminiTruncated
25150,Q#1425 - >seq8072,non-specific,235175,301,469,0.00395048,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,marg,BothTerminiTruncated
25151,Q#1425 - >seq8072,non-specific,239569,525,748,0.00749042,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25152,Q#1425 - >seq8072,non-specific,239569,525,748,0.00749042,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25153,Q#1425 - >seq8072,specific,311990,1241,1259,0.008587000000000001,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25154,Q#1425 - >seq8072,superfamily,311990,1241,1259,0.008587000000000001,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25155,Q#1425 - >seq8072,non-specific,311990,1241,1259,0.008587000000000001,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,marg,CompleteHit
25156,Q#1425 - >seq8072,non-specific,293702,337,451,0.00922042,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25157,Q#1425 - >seq8072,superfamily,293702,337,451,0.00922042,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25158,Q#1425 - >seq8072,non-specific,293702,337,451,0.00922042,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,marg,C-TerminusTruncated
25159,Q#1428 - >seq8075,specific,238827,510,772,4.027589999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25160,Q#1428 - >seq8075,superfamily,295487,510,772,4.027589999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25161,Q#1428 - >seq8075,non-specific,238827,510,772,4.027589999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25162,Q#1428 - >seq8075,specific,197310,9,236,8.658889999999997e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25163,Q#1428 - >seq8075,superfamily,351117,9,236,8.658889999999997e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25164,Q#1428 - >seq8075,non-specific,197310,9,236,8.658889999999997e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25165,Q#1428 - >seq8075,non-specific,197306,9,236,2.6641099999999998e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25166,Q#1428 - >seq8075,non-specific,197306,9,236,2.6641099999999998e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25167,Q#1428 - >seq8075,specific,333820,516,772,2.4349599999999995e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25168,Q#1428 - >seq8075,superfamily,333820,516,772,2.4349599999999995e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25169,Q#1428 - >seq8075,non-specific,333820,516,772,2.4349599999999995e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25170,Q#1428 - >seq8075,non-specific,197307,9,236,3.56089e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25171,Q#1428 - >seq8075,non-specific,197307,9,236,3.56089e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25172,Q#1428 - >seq8075,non-specific,223780,9,238,2.07619e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25173,Q#1428 - >seq8075,non-specific,223780,9,238,2.07619e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25174,Q#1428 - >seq8075,non-specific,197320,8,236,3.2301599999999997e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25175,Q#1428 - >seq8075,non-specific,197320,8,236,3.2301599999999997e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25176,Q#1428 - >seq8075,non-specific,197321,7,236,3.76241e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25177,Q#1428 - >seq8075,non-specific,197321,7,236,3.76241e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25178,Q#1428 - >seq8075,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25179,Q#1428 - >seq8075,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25180,Q#1428 - >seq8075,non-specific,273186,9,237,2.03473e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25181,Q#1428 - >seq8075,non-specific,273186,9,237,2.03473e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25182,Q#1428 - >seq8075,non-specific,272954,9,236,3.77264e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25183,Q#1428 - >seq8075,non-specific,272954,9,236,3.77264e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25184,Q#1428 - >seq8075,non-specific,197319,8,236,3.67568e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25185,Q#1428 - >seq8075,non-specific,197319,8,236,3.67568e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25186,Q#1428 - >seq8075,non-specific,197336,7,235,6.78813e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25187,Q#1428 - >seq8075,non-specific,197336,7,235,6.78813e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25188,Q#1428 - >seq8075,non-specific,238828,516,737,1.88416e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25189,Q#1428 - >seq8075,non-specific,238828,516,737,1.88416e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25190,Q#1428 - >seq8075,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25191,Q#1428 - >seq8075,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25192,Q#1428 - >seq8075,non-specific,275209,467,800,3.65054e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25193,Q#1428 - >seq8075,superfamily,275209,467,800,3.65054e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25194,Q#1428 - >seq8075,non-specific,275209,467,800,3.65054e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25195,Q#1428 - >seq8075,non-specific,236970,9,238,2.85067e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25196,Q#1428 - >seq8075,non-specific,236970,9,238,2.85067e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25197,Q#1428 - >seq8075,non-specific,339261,108,232,3.09543e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25198,Q#1428 - >seq8075,non-specific,339261,108,232,3.09543e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25199,Q#1428 - >seq8075,non-specific,197317,139,229,1.332e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,N-TerminusTruncated
25200,Q#1428 - >seq8075,non-specific,197317,139,229,1.332e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,N-TerminusTruncated
25201,Q#1428 - >seq8075,non-specific,197311,7,236,3.6224000000000002e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25202,Q#1428 - >seq8075,non-specific,197311,7,236,3.6224000000000002e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25203,Q#1428 - >seq8075,non-specific,238185,656,772,0.000174205,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25204,Q#1428 - >seq8075,non-specific,238185,656,772,0.000174205,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25205,Q#1428 - >seq8075,non-specific,274009,305,453,0.000187755,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25206,Q#1428 - >seq8075,superfamily,274009,305,453,0.000187755,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25207,Q#1428 - >seq8075,non-specific,274009,305,453,0.000187755,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25208,Q#1428 - >seq8075,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,N-TerminusTruncated
25209,Q#1428 - >seq8075,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs3_orang,pars,N-TerminusTruncated
25210,Q#1428 - >seq8075,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25211,Q#1428 - >seq8075,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25212,Q#1428 - >seq8075,non-specific,235175,301,469,0.00395048,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,BothTerminiTruncated
25213,Q#1428 - >seq8075,superfamily,235175,301,469,0.00395048,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,BothTerminiTruncated
25214,Q#1428 - >seq8075,non-specific,235175,301,469,0.00395048,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs3_orang,pars,BothTerminiTruncated
25215,Q#1428 - >seq8075,non-specific,239569,525,748,0.00749042,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25216,Q#1428 - >seq8075,non-specific,239569,525,748,0.00749042,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25217,Q#1428 - >seq8075,specific,311990,1241,1259,0.008587000000000001,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25218,Q#1428 - >seq8075,superfamily,311990,1241,1259,0.008587000000000001,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25219,Q#1428 - >seq8075,non-specific,311990,1241,1259,0.008587000000000001,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs3_orang,pars,CompleteHit
25220,Q#1428 - >seq8075,non-specific,293702,337,451,0.00922042,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25221,Q#1428 - >seq8075,superfamily,293702,337,451,0.00922042,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25222,Q#1428 - >seq8075,non-specific,293702,337,451,0.00922042,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs3_orang,pars,C-TerminusTruncated
25223,Q#1431 - >seq8078,non-specific,335182,154,251,4.52865e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25224,Q#1431 - >seq8078,superfamily,335182,154,251,4.52865e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25225,Q#1431 - >seq8078,non-specific,335182,154,251,4.52865e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25226,Q#1431 - >seq8078,non-specific,340205,254,318,9.96438e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25227,Q#1431 - >seq8078,superfamily,340205,254,318,9.96438e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25228,Q#1431 - >seq8078,non-specific,340205,254,318,9.96438e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25229,Q#1431 - >seq8078,non-specific,340204,109,151,2.49805e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25230,Q#1431 - >seq8078,superfamily,340204,109,151,2.49805e-13,63.1956,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25231,Q#1431 - >seq8078,non-specific,340204,109,151,2.49805e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,marg,CompleteHit
25232,Q#1431 - >seq8078,non-specific,335623,52,146,0.000363262,41.391000000000005,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25233,Q#1431 - >seq8078,superfamily,335623,52,146,0.000363262,41.391000000000005,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25234,Q#1431 - >seq8078,non-specific,335623,52,146,0.000363262,41.391000000000005,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25235,Q#1431 - >seq8078,non-specific,235175,52,140,0.000463509,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25236,Q#1431 - >seq8078,superfamily,235175,52,140,0.000463509,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25237,Q#1431 - >seq8078,non-specific,235175,52,140,0.000463509,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25238,Q#1431 - >seq8078,non-specific,273690,53,194,0.00091868,40.4069,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25239,Q#1431 - >seq8078,superfamily,355611,53,194,0.00091868,40.4069,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25240,Q#1431 - >seq8078,non-specific,273690,53,194,0.00091868,40.4069,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25241,Q#1431 - >seq8078,non-specific,235316,51,172,0.00224321,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25242,Q#1431 - >seq8078,superfamily,235316,51,172,0.00224321,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25243,Q#1431 - >seq8078,non-specific,235316,51,172,0.00224321,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25244,Q#1431 - >seq8078,non-specific,235175,30,154,0.00460272,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25245,Q#1431 - >seq8078,non-specific,235175,30,154,0.00460272,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25246,Q#1431 - >seq8078,non-specific,224117,40,180,0.00612667,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25247,Q#1431 - >seq8078,superfamily,224117,40,180,0.00612667,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25248,Q#1431 - >seq8078,non-specific,224117,40,180,0.00612667,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25249,Q#1431 - >seq8078,non-specific,337663,48,139,0.00661763,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25250,Q#1431 - >seq8078,superfamily,337663,48,139,0.00661763,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25251,Q#1431 - >seq8078,non-specific,337663,48,139,0.00661763,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs3_orang,marg,C-TerminusTruncated
25252,Q#1431 - >seq8078,non-specific,335556,47,130,0.00950719,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25253,Q#1431 - >seq8078,superfamily,335556,47,130,0.00950719,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25254,Q#1431 - >seq8078,non-specific,335556,47,130,0.00950719,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.marg.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,marg,BothTerminiTruncated
25255,Q#1434 - >seq8081,non-specific,335182,154,251,4.52865e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25256,Q#1434 - >seq8081,superfamily,335182,154,251,4.52865e-48,156.694,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25257,Q#1434 - >seq8081,non-specific,335182,154,251,4.52865e-48,156.694,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25258,Q#1434 - >seq8081,non-specific,340205,254,318,9.96438e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25259,Q#1434 - >seq8081,superfamily,340205,254,318,9.96438e-34,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25260,Q#1434 - >seq8081,non-specific,340205,254,318,9.96438e-34,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25261,Q#1434 - >seq8081,non-specific,340204,109,151,2.49805e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25262,Q#1434 - >seq8081,superfamily,340204,109,151,2.49805e-13,63.1956,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25263,Q#1434 - >seq8081,non-specific,340204,109,151,2.49805e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs3_orang,pars,CompleteHit
25264,Q#1434 - >seq8081,non-specific,335623,52,146,0.000363262,41.391000000000005,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25265,Q#1434 - >seq8081,superfamily,335623,52,146,0.000363262,41.391000000000005,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25266,Q#1434 - >seq8081,non-specific,335623,52,146,0.000363262,41.391000000000005,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25267,Q#1434 - >seq8081,non-specific,235175,52,140,0.000463509,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25268,Q#1434 - >seq8081,superfamily,235175,52,140,0.000463509,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25269,Q#1434 - >seq8081,non-specific,235175,52,140,0.000463509,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25270,Q#1434 - >seq8081,non-specific,273690,53,194,0.00091868,40.4069,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25271,Q#1434 - >seq8081,superfamily,355611,53,194,0.00091868,40.4069,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25272,Q#1434 - >seq8081,non-specific,273690,53,194,0.00091868,40.4069,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25273,Q#1434 - >seq8081,non-specific,235316,51,172,0.00224321,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25274,Q#1434 - >seq8081,superfamily,235316,51,172,0.00224321,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25275,Q#1434 - >seq8081,non-specific,235316,51,172,0.00224321,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25276,Q#1434 - >seq8081,non-specific,235175,30,154,0.00460272,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25277,Q#1434 - >seq8081,non-specific,235175,30,154,0.00460272,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25278,Q#1434 - >seq8081,non-specific,224117,40,180,0.00612667,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25279,Q#1434 - >seq8081,superfamily,224117,40,180,0.00612667,38.1568,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25280,Q#1434 - >seq8081,non-specific,224117,40,180,0.00612667,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25281,Q#1434 - >seq8081,non-specific,337663,48,139,0.00661763,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25282,Q#1434 - >seq8081,superfamily,337663,48,139,0.00661763,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25283,Q#1434 - >seq8081,non-specific,337663,48,139,0.00661763,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs3_orang,pars,C-TerminusTruncated
25284,Q#1434 - >seq8081,non-specific,335556,47,130,0.00950719,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25285,Q#1434 - >seq8081,superfamily,335556,47,130,0.00950719,36.3569,cl38147,Mnd1 superfamily,NC, - ,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25286,Q#1434 - >seq8081,non-specific,335556,47,130,0.00950719,36.3569,pfam03962,Mnd1,NC,cl38147,Mnd1 family; This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.,L1PA3.ORF1.hs3_orang.pars.frame3,1909181109_L1PA3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF1,hs3_orang,pars,BothTerminiTruncated
25287,Q#1438 - >seq8085,non-specific,130141,203,313,0.00980255,39.8029,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA3.ORF2.hs4_gibbon.pars.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25288,Q#1438 - >seq8085,superfamily,130141,203,313,0.00980255,39.8029,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA3.ORF2.hs4_gibbon.pars.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25289,Q#1441 - >seq8088,specific,238827,500,762,2.9534399999999993e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25290,Q#1441 - >seq8088,superfamily,295487,500,762,2.9534399999999993e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25291,Q#1441 - >seq8088,specific,197310,61,226,6.32793e-39,145.187,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25292,Q#1441 - >seq8088,superfamily,351117,61,226,6.32793e-39,145.187,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25293,Q#1441 - >seq8088,specific,333820,506,762,2.27792e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25294,Q#1441 - >seq8088,superfamily,333820,506,762,2.27792e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25295,Q#1441 - >seq8088,non-specific,197306,61,226,4.51158e-33,128.368,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25296,Q#1441 - >seq8088,non-specific,197307,61,226,3.1460500000000004e-14,73.8613,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25297,Q#1441 - >seq8088,non-specific,223780,62,228,3.3778400000000004e-13,71.0903,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25298,Q#1441 - >seq8088,non-specific,197320,62,226,9.673430000000001e-13,69.4662,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25299,Q#1441 - >seq8088,non-specific,238828,506,727,1.8851e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25300,Q#1441 - >seq8088,non-specific,275209,457,790,3.78106e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25301,Q#1441 - >seq8088,superfamily,275209,457,790,3.78106e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25302,Q#1441 - >seq8088,non-specific,197321,61,226,5.00116e-10,61.413999999999994,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25303,Q#1441 - >seq8088,non-specific,273186,61,227,5.9962799999999995e-09,58.0592,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25304,Q#1441 - >seq8088,non-specific,339261,98,222,2.1654299999999996e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25305,Q#1441 - >seq8088,non-specific,335306,62,219,2.92231e-07,52.6326,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25306,Q#1441 - >seq8088,non-specific,197322,81,226,6.645869999999999e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25307,Q#1441 - >seq8088,non-specific,197319,62,226,4.53251e-06,49.1973,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25308,Q#1441 - >seq8088,non-specific,272954,62,226,5.9946300000000006e-06,48.9185,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25309,Q#1441 - >seq8088,non-specific,197317,129,219,8.00216e-06,48.7524,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25310,Q#1441 - >seq8088,non-specific,236970,62,228,3.23376e-05,46.81100000000001,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25311,Q#1441 - >seq8088,non-specific,197311,62,226,4.4492299999999994e-05,45.7457,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
25312,Q#1441 - >seq8088,non-specific,238185,646,762,0.00018141599999999997,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25313,Q#1441 - >seq8088,non-specific,274009,295,443,0.00108025,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25314,Q#1441 - >seq8088,superfamily,274009,295,443,0.00108025,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25315,Q#1441 - >seq8088,non-specific,235175,291,459,0.006456100000000001,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
25316,Q#1441 - >seq8088,superfamily,235175,291,459,0.006456100000000001,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
25317,Q#1441 - >seq8088,non-specific,239569,515,738,0.00684248,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25318,Q#1441 - >seq8088,specific,311990,1231,1249,0.00894854,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25319,Q#1441 - >seq8088,superfamily,311990,1231,1249,0.00894854,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA3,ORF2,hs4_gibbon,marg,CompleteHit
25320,Q#1441 - >seq8088,non-specific,293702,327,441,0.008982500000000001,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25321,Q#1441 - >seq8088,superfamily,293702,327,441,0.008982500000000001,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs4_gibbon.marg.frame1,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25322,Q#1442 - >seq8089,specific,238827,706,968,9.952469999999999e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25323,Q#1442 - >seq8089,superfamily,295487,706,968,9.952469999999999e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25324,Q#1442 - >seq8089,specific,333820,712,968,2.7701599999999997e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25325,Q#1442 - >seq8089,superfamily,333820,712,968,2.7701599999999997e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25326,Q#1442 - >seq8089,non-specific,238828,712,933,4.95376e-10,60.6776,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25327,Q#1442 - >seq8089,non-specific,275209,783,996,2.32209e-07,54.386,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
25328,Q#1442 - >seq8089,superfamily,275209,783,996,2.32209e-07,54.386,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4b,ORF2,hs1_chimp,marg,N-TerminusTruncated
25329,Q#1444 - >seq8091,specific,238827,469,737,8.72839e-67,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25330,Q#1444 - >seq8091,superfamily,295487,469,737,8.72839e-67,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25331,Q#1444 - >seq8091,specific,333820,475,699,2.2175e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25332,Q#1444 - >seq8091,superfamily,333820,475,699,2.2175e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25333,Q#1444 - >seq8091,non-specific,238828,475,696,1.27176e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25334,Q#1444 - >seq8091,non-specific,275209,424,696,7.51811e-07,52.46,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
25335,Q#1444 - >seq8091,superfamily,275209,424,696,7.51811e-07,52.46,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
25336,Q#1444 - >seq8091,non-specific,239569,484,697,0.000347115,42.9451,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,CompleteHit
25337,Q#1444 - >seq8091,non-specific,238185,615,692,0.000946287,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1PBa1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
25338,Q#1445 - >seq8092,specific,197310,3,230,1.8883299999999997e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25339,Q#1445 - >seq8092,superfamily,351117,3,230,1.8883299999999997e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25340,Q#1445 - >seq8092,non-specific,197306,3,230,7.0195000000000005e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25341,Q#1445 - >seq8092,non-specific,223780,3,231,2.2312900000000005e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25342,Q#1445 - >seq8092,non-specific,197320,3,223,1.13662e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25343,Q#1445 - >seq8092,non-specific,197307,3,230,1.37914e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25344,Q#1445 - >seq8092,specific,335306,4,223,2.15571e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25345,Q#1445 - >seq8092,non-specific,273186,3,231,2.03844e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25346,Q#1445 - >seq8092,non-specific,197319,7,230,2.9528e-16,79.6281,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25347,Q#1445 - >seq8092,non-specific,197321,1,230,5.446680000000001e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25348,Q#1445 - >seq8092,non-specific,272954,3,230,6.57425e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25349,Q#1445 - >seq8092,non-specific,197336,3,188,1.29716e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25350,Q#1445 - >seq8092,non-specific,197322,2,230,1.0625100000000001e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25351,Q#1445 - >seq8092,non-specific,236970,3,243,6.24071e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25352,Q#1445 - >seq8092,non-specific,197311,24,230,8.56797e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25353,Q#1445 - >seq8092,non-specific,339261,102,226,0.000284784,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25354,Q#1446 - >seq8093,specific,238827,472,724,5.43997e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25355,Q#1446 - >seq8093,superfamily,295487,472,724,5.43997e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25356,Q#1446 - >seq8093,specific,333820,478,702,5.5057e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25357,Q#1446 - >seq8093,superfamily,333820,478,702,5.5057e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25358,Q#1446 - >seq8093,non-specific,238828,478,699,3.2254299999999997e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25359,Q#1446 - >seq8093,non-specific,275209,420,699,2.17619e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
25360,Q#1446 - >seq8093,superfamily,275209,420,699,2.17619e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
25361,Q#1446 - >seq8093,non-specific,239569,487,700,0.000224671,43.7155,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,CompleteHit
25362,Q#1446 - >seq8093,non-specific,238185,618,695,0.000360584,40.7972,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs6_sqmonkey.pars.frame2,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
25363,Q#1448 - >seq8095,non-specific,335182,156,252,3.02662e-35,123.182,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25364,Q#1448 - >seq8095,superfamily,335182,156,252,3.02662e-35,123.182,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25365,Q#1448 - >seq8095,non-specific,340205,255,318,4.75625e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25366,Q#1448 - >seq8095,superfamily,340205,255,318,4.75625e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25367,Q#1448 - >seq8095,non-specific,340204,111,153,3.823680000000001e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25368,Q#1448 - >seq8095,superfamily,340204,111,153,3.823680000000001e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs6_sqmonkey,marg,CompleteHit
25369,Q#1448 - >seq8095,non-specific,274009,60,203,4.14741e-06,48.1403,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25370,Q#1448 - >seq8095,superfamily,274009,60,203,4.14741e-06,48.1403,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25371,Q#1448 - >seq8095,non-specific,235175,49,156,8.150779999999999e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25372,Q#1448 - >seq8095,superfamily,235175,49,156,8.150779999999999e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25373,Q#1448 - >seq8095,non-specific,224117,28,177,0.000165296,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25374,Q#1448 - >seq8095,superfamily,224117,28,177,0.000165296,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25375,Q#1448 - >seq8095,non-specific,237177,42,149,0.000176215,42.843,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25376,Q#1448 - >seq8095,superfamily,237177,42,149,0.000176215,42.843,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25377,Q#1448 - >seq8095,non-specific,274008,41,202,0.00018952200000000002,43.1215,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25378,Q#1448 - >seq8095,superfamily,274008,41,202,0.00018952200000000002,43.1215,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25379,Q#1448 - >seq8095,non-specific,223250,47,170,0.0009015830000000001,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25380,Q#1448 - >seq8095,superfamily,223250,47,170,0.0009015830000000001,40.6593,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25381,Q#1448 - >seq8095,non-specific,274008,45,150,0.00185543,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25382,Q#1448 - >seq8095,non-specific,235461,47,170,0.00206928,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25383,Q#1448 - >seq8095,superfamily,235461,47,170,0.00206928,39.281,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25384,Q#1448 - >seq8095,non-specific,274091,65,150,0.00213538,39.6014,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25385,Q#1448 - >seq8095,superfamily,274091,65,150,0.00213538,39.6014,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25386,Q#1448 - >seq8095,non-specific,310273,60,194,0.00237421,39.3434,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25387,Q#1448 - >seq8095,superfamily,310273,60,194,0.00237421,39.3434,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25388,Q#1448 - >seq8095,non-specific,337663,79,183,0.00302812,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25389,Q#1448 - >seq8095,superfamily,337663,79,183,0.00302812,38.5599,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25390,Q#1448 - >seq8095,non-specific,275056,60,152,0.00309145,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25391,Q#1448 - >seq8095,superfamily,275056,60,152,0.00309145,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25392,Q#1448 - >seq8095,non-specific,129694,80,146,0.00377867,38.8745,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25393,Q#1448 - >seq8095,superfamily,129694,80,146,0.00377867,38.8745,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25394,Q#1448 - >seq8095,non-specific,274386,27,147,0.00446164,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25395,Q#1448 - >seq8095,superfamily,274386,27,147,0.00446164,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25396,Q#1448 - >seq8095,non-specific,235175,60,144,0.00486684,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25397,Q#1448 - >seq8095,non-specific,226400,79,149,0.00616485,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25398,Q#1448 - >seq8095,superfamily,226400,79,149,0.00616485,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25399,Q#1448 - >seq8095,non-specific,313406,73,236,0.00632753,38.0946,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25400,Q#1448 - >seq8095,superfamily,313406,73,236,0.00632753,38.0946,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25401,Q#1448 - >seq8095,non-specific,112704,2,148,0.00784362,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25402,Q#1448 - >seq8095,superfamily,112704,2,148,0.00784362,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25403,Q#1448 - >seq8095,non-specific,227278,76,201,0.00912775,37.3941,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25404,Q#1448 - >seq8095,superfamily,227278,76,201,0.00912775,37.3941,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25405,Q#1451 - >seq8098,non-specific,112704,2,90,0.0047871,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25406,Q#1451 - >seq8098,superfamily,112704,2,90,0.0047871,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25407,Q#1452 - >seq8099,non-specific,335182,148,244,6.927199999999999e-36,124.723,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25408,Q#1452 - >seq8099,superfamily,335182,148,244,6.927199999999999e-36,124.723,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25409,Q#1452 - >seq8099,non-specific,340205,247,310,2.49674e-23,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25410,Q#1452 - >seq8099,superfamily,340205,247,310,2.49674e-23,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25411,Q#1452 - >seq8099,non-specific,340204,103,145,6.05293e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25412,Q#1452 - >seq8099,superfamily,340204,103,145,6.05293e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1PBa1,ORF1,hs6_sqmonkey,pars,CompleteHit
25413,Q#1452 - >seq8099,non-specific,129694,13,138,0.00178228,40.0301,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other_DNARepair,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25414,Q#1452 - >seq8099,superfamily,129694,13,138,0.00178228,40.0301,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other_DNARepair,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25415,Q#1452 - >seq8099,non-specific,274009,74,195,0.00296553,39.2807,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25416,Q#1452 - >seq8099,superfamily,274009,74,195,0.00296553,39.2807,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25417,Q#1452 - >seq8099,non-specific,237177,74,141,0.00557292,38.2206,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25418,Q#1452 - >seq8099,superfamily,237177,74,141,0.00557292,38.2206,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25419,Q#1452 - >seq8099,non-specific,227278,74,193,0.00660205,37.7793,COG4942,EnvC,C,cl34844,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25420,Q#1452 - >seq8099,superfamily,227278,74,193,0.00660205,37.7793,cl34844,EnvC superfamily,C, - ,"Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Membrane-bound metallopeptidase [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25421,Q#1452 - >seq8099,non-specific,274008,76,194,0.00947326,37.7287,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25422,Q#1452 - >seq8099,superfamily,274008,76,194,0.00947326,37.7287,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PBa1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PBa1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25423,Q#1453 - >seq8100,non-specific,335182,148,243,4.5261800000000004e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25424,Q#1453 - >seq8100,superfamily,335182,148,243,4.5261800000000004e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25425,Q#1453 - >seq8100,non-specific,335182,148,243,4.5261800000000004e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25426,Q#1453 - >seq8100,non-specific,340205,246,309,1.61955e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25427,Q#1453 - >seq8100,superfamily,340205,246,309,1.61955e-27,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25428,Q#1453 - >seq8100,non-specific,340205,246,309,1.61955e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25429,Q#1453 - >seq8100,non-specific,274008,19,140,1.3652e-05,46.5883,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25430,Q#1453 - >seq8100,superfamily,274008,19,140,1.3652e-05,46.5883,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25431,Q#1453 - >seq8100,non-specific,274008,19,140,1.3652e-05,46.5883,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25432,Q#1453 - >seq8100,non-specific,340204,102,144,5.29663e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25433,Q#1453 - >seq8100,superfamily,340204,102,144,5.29663e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25434,Q#1453 - >seq8100,non-specific,340204,102,144,5.29663e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,marg,CompleteHit
25435,Q#1453 - >seq8100,non-specific,274009,24,141,7.46553e-05,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25436,Q#1453 - >seq8100,superfamily,274009,24,141,7.46553e-05,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25437,Q#1453 - >seq8100,non-specific,274009,24,141,7.46553e-05,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25438,Q#1453 - >seq8100,non-specific,224117,23,141,0.000649607,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25439,Q#1453 - >seq8100,superfamily,224117,23,141,0.000649607,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25440,Q#1453 - >seq8100,non-specific,224117,23,141,0.000649607,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25441,Q#1453 - >seq8100,non-specific,274009,23,146,0.0009103010000000001,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25442,Q#1453 - >seq8100,non-specific,274009,23,146,0.0009103010000000001,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25443,Q#1453 - >seq8100,non-specific,224117,24,141,0.00113779,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25444,Q#1453 - >seq8100,non-specific,224117,24,141,0.00113779,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25445,Q#1453 - >seq8100,non-specific,314569,84,133,0.00152022,39.321999999999996,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25446,Q#1453 - >seq8100,superfamily,327698,84,133,0.00152022,39.321999999999996,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25447,Q#1453 - >seq8100,non-specific,314569,84,133,0.00152022,39.321999999999996,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25448,Q#1453 - >seq8100,non-specific,223571,52,114,0.00204979,39.5051,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25449,Q#1453 - >seq8100,superfamily,223571,52,114,0.00204979,39.5051,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25450,Q#1453 - >seq8100,non-specific,223571,52,114,0.00204979,39.5051,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25451,Q#1453 - >seq8100,non-specific,235175,44,234,0.00245916,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25452,Q#1453 - >seq8100,superfamily,235175,44,234,0.00245916,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25453,Q#1453 - >seq8100,non-specific,235175,44,234,0.00245916,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25454,Q#1453 - >seq8100,non-specific,335555,25,117,0.00437878,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25455,Q#1453 - >seq8100,superfamily,354396,25,117,0.00437878,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PB2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25456,Q#1453 - >seq8100,non-specific,335555,25,117,0.00437878,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
25457,Q#1453 - >seq8100,non-specific,222878,45,141,0.00448003,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25458,Q#1453 - >seq8100,superfamily,222878,45,141,0.00448003,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25459,Q#1453 - >seq8100,non-specific,222878,45,141,0.00448003,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25460,Q#1453 - >seq8100,non-specific,224117,40,141,0.00548938,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25461,Q#1453 - >seq8100,non-specific,224117,40,141,0.00548938,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25462,Q#1453 - >seq8100,non-specific,188306,32,141,0.00807145,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25463,Q#1453 - >seq8100,superfamily,188306,32,141,0.00807145,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25464,Q#1453 - >seq8100,non-specific,188306,32,141,0.00807145,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25465,Q#1453 - >seq8100,non-specific,224117,34,141,0.00864319,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25466,Q#1453 - >seq8100,non-specific,224117,34,141,0.00864319,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
25467,Q#1453 - >seq8100,non-specific,311007,43,141,0.00872516,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25468,Q#1453 - >seq8100,superfamily,311007,43,141,0.00872516,37.3841,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25469,Q#1453 - >seq8100,non-specific,311007,43,141,0.00872516,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.marg.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
25470,Q#1456 - >seq8103,non-specific,335182,148,243,4.5261800000000004e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25471,Q#1456 - >seq8103,superfamily,335182,148,243,4.5261800000000004e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25472,Q#1456 - >seq8103,non-specific,335182,148,243,4.5261800000000004e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25473,Q#1456 - >seq8103,non-specific,340205,246,309,1.61955e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25474,Q#1456 - >seq8103,superfamily,340205,246,309,1.61955e-27,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25475,Q#1456 - >seq8103,non-specific,340205,246,309,1.61955e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25476,Q#1456 - >seq8103,non-specific,274008,19,140,1.3652e-05,46.5883,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25477,Q#1456 - >seq8103,superfamily,274008,19,140,1.3652e-05,46.5883,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25478,Q#1456 - >seq8103,non-specific,274008,19,140,1.3652e-05,46.5883,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25479,Q#1456 - >seq8103,non-specific,340204,102,144,5.29663e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25480,Q#1456 - >seq8103,superfamily,340204,102,144,5.29663e-05,39.6984,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25481,Q#1456 - >seq8103,non-specific,340204,102,144,5.29663e-05,39.6984,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs6_sqmonkey,pars,CompleteHit
25482,Q#1456 - >seq8103,non-specific,274009,24,141,7.46553e-05,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25483,Q#1456 - >seq8103,superfamily,274009,24,141,7.46553e-05,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25484,Q#1456 - >seq8103,non-specific,274009,24,141,7.46553e-05,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25485,Q#1456 - >seq8103,non-specific,224117,23,141,0.000649607,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25486,Q#1456 - >seq8103,superfamily,224117,23,141,0.000649607,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25487,Q#1456 - >seq8103,non-specific,224117,23,141,0.000649607,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25488,Q#1456 - >seq8103,non-specific,274009,23,146,0.0009103010000000001,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25489,Q#1456 - >seq8103,non-specific,274009,23,146,0.0009103010000000001,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25490,Q#1456 - >seq8103,non-specific,224117,24,141,0.00113779,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25491,Q#1456 - >seq8103,non-specific,224117,24,141,0.00113779,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25492,Q#1456 - >seq8103,non-specific,314569,84,133,0.00152022,39.321999999999996,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25493,Q#1456 - >seq8103,superfamily,327698,84,133,0.00152022,39.321999999999996,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25494,Q#1456 - >seq8103,non-specific,314569,84,133,0.00152022,39.321999999999996,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25495,Q#1456 - >seq8103,non-specific,223571,52,114,0.00204979,39.5051,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25496,Q#1456 - >seq8103,superfamily,223571,52,114,0.00204979,39.5051,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25497,Q#1456 - >seq8103,non-specific,223571,52,114,0.00204979,39.5051,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25498,Q#1456 - >seq8103,non-specific,235175,44,234,0.00245916,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25499,Q#1456 - >seq8103,superfamily,235175,44,234,0.00245916,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25500,Q#1456 - >seq8103,non-specific,235175,44,234,0.00245916,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25501,Q#1456 - >seq8103,non-specific,335555,25,117,0.00437878,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25502,Q#1456 - >seq8103,superfamily,354396,25,117,0.00437878,38.3956,cl19219,FapA superfamily,N, - ,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Flagellar,L1PB2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25503,Q#1456 - >seq8103,non-specific,335555,25,117,0.00437878,38.3956,pfam03961,FapA,N,cl19219,"Flagellar Assembly Protein A; Members of this family include FapA (flagellar assembly protein A), found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25504,Q#1456 - >seq8103,non-specific,222878,45,141,0.00448003,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25505,Q#1456 - >seq8103,superfamily,222878,45,141,0.00448003,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25506,Q#1456 - >seq8103,non-specific,222878,45,141,0.00448003,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25507,Q#1456 - >seq8103,non-specific,224117,40,141,0.00548938,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25508,Q#1456 - >seq8103,non-specific,224117,40,141,0.00548938,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25509,Q#1456 - >seq8103,non-specific,188306,32,141,0.00807145,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25510,Q#1456 - >seq8103,superfamily,188306,32,141,0.00807145,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25511,Q#1456 - >seq8103,non-specific,188306,32,141,0.00807145,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25512,Q#1456 - >seq8103,non-specific,224117,34,141,0.00864319,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25513,Q#1456 - >seq8103,non-specific,224117,34,141,0.00864319,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
25514,Q#1456 - >seq8103,non-specific,311007,43,141,0.00872516,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25515,Q#1456 - >seq8103,superfamily,311007,43,141,0.00872516,37.3841,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25516,Q#1456 - >seq8103,non-specific,311007,43,141,0.00872516,37.3841,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25517,Q#1459 - >seq8106,non-specific,197310,9,71,1.02308e-13,71.9989,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25518,Q#1459 - >seq8106,superfamily,351117,9,71,1.02308e-13,71.9989,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25519,Q#1459 - >seq8106,non-specific,197306,9,70,4.475380000000001e-12,67.1213,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25520,Q#1459 - >seq8106,non-specific,223780,9,43,2.82682e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25521,Q#1459 - >seq8106,specific,335306,10,130,4.4024700000000006e-05,46.0842,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25522,Q#1459 - >seq8106,non-specific,197321,7,49,4.6041099999999995e-05,46.3912,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25523,Q#1459 - >seq8106,non-specific,197307,9,49,0.000209915,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25524,Q#1459 - >seq8106,non-specific,197336,7,43,0.000232141,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25525,Q#1459 - >seq8106,non-specific,197320,8,43,0.000803715,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25526,Q#1459 - >seq8106,non-specific,273186,9,43,0.00144509,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25527,Q#1459 - >seq8106,non-specific,272954,9,43,0.00893032,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.marg.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
25528,Q#1461 - >seq8108,specific,238827,427,689,4.2553899999999994e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25529,Q#1461 - >seq8108,superfamily,295487,427,689,4.2553899999999994e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25530,Q#1461 - >seq8108,specific,333820,433,689,3.23075e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25531,Q#1461 - >seq8108,superfamily,333820,433,689,3.23075e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25532,Q#1461 - >seq8108,specific,197310,4,153,1.76492e-33,129.394,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25533,Q#1461 - >seq8108,superfamily,351117,4,153,1.76492e-33,129.394,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25534,Q#1461 - >seq8108,non-specific,197306,8,153,1.21046e-30,121.434,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25535,Q#1461 - >seq8108,non-specific,197307,8,153,2.8653200000000004e-13,70.7797,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25536,Q#1461 - >seq8108,non-specific,223780,8,155,1.18842e-11,66.0827,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25537,Q#1461 - >seq8108,non-specific,197320,23,153,2.22962e-11,65.229,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25538,Q#1461 - >seq8108,non-specific,238828,433,654,2.42554e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25539,Q#1461 - >seq8108,non-specific,275209,384,717,4.13156e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25540,Q#1461 - >seq8108,superfamily,275209,384,717,4.13156e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25541,Q#1461 - >seq8108,non-specific,273186,23,154,1.92252e-08,56.5184,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25542,Q#1461 - >seq8108,non-specific,339261,25,149,2.24098e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25543,Q#1461 - >seq8108,non-specific,197321,23,153,2.27334e-08,56.4064,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25544,Q#1461 - >seq8108,non-specific,197322,8,153,6.2023e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25545,Q#1461 - >seq8108,non-specific,335306,29,146,3.2334e-06,49.551,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25546,Q#1461 - >seq8108,non-specific,197317,56,146,7.34703e-06,48.7524,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25547,Q#1461 - >seq8108,non-specific,272954,8,153,1.2336500000000001e-05,48.1481,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25548,Q#1461 - >seq8108,non-specific,197319,1,153,1.3186099999999999e-05,48.0417,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25549,Q#1461 - >seq8108,non-specific,238185,573,689,0.000188013,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25550,Q#1461 - >seq8108,non-specific,236970,8,155,0.00037814,43.3442,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25551,Q#1461 - >seq8108,non-specific,274009,222,370,0.00102575,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
25552,Q#1461 - >seq8108,superfamily,274009,222,370,0.00102575,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
25553,Q#1461 - >seq8108,non-specific,197311,19,153,0.00163589,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
25554,Q#1461 - >seq8108,non-specific,239569,442,665,0.00782997,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25555,Q#1461 - >seq8108,non-specific,293702,254,368,0.00892693,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
25556,Q#1461 - >seq8108,superfamily,293702,254,368,0.00892693,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
25557,Q#1461 - >seq8108,specific,311990,1158,1176,0.00958564,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25558,Q#1461 - >seq8108,superfamily,311990,1158,1176,0.00958564,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs4_gibbon,pars,CompleteHit
25559,Q#1461 - >seq8108,non-specific,235175,218,386,0.00978253,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
25560,Q#1461 - >seq8108,superfamily,235175,218,386,0.00978253,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs4_gibbon.pars.frame3,1909181109_L1PA3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
25561,Q#1462 - >seq8109,non-specific,335182,62,159,4.5539099999999995e-38,128.189,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,marg,CompleteHit
25562,Q#1462 - >seq8109,superfamily,335182,62,159,4.5539099999999995e-38,128.189,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,marg,CompleteHit
25563,Q#1462 - >seq8109,non-specific,340205,162,225,1.03815e-28,103.185,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,marg,CompleteHit
25564,Q#1462 - >seq8109,superfamily,340205,162,225,1.03815e-28,103.185,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,marg,CompleteHit
25565,Q#1463 - >seq8110,non-specific,340205,161,224,8.18059e-30,105.881,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,CompleteHit
25566,Q#1463 - >seq8110,superfamily,340205,161,224,8.18059e-30,105.881,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,CompleteHit
25567,Q#1463 - >seq8110,non-specific,335182,116,158,1.27521e-07,48.0679,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25568,Q#1463 - >seq8110,superfamily,335182,116,158,1.27521e-07,48.0679,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame3,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
25569,Q#1468 - >seq8115,non-specific,340205,270,335,8.468749999999999e-22,88.162,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs0_human.marg.frame1,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs0_human,marg,CompleteHit
25570,Q#1468 - >seq8115,superfamily,340205,270,335,8.468749999999999e-22,88.162,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs0_human.marg.frame1,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs0_human,marg,CompleteHit
25571,Q#1468 - >seq8115,non-specific,335182,171,262,1.0932700000000001e-07,49.2235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs0_human.marg.frame1,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs0_human,marg,CompleteHit
25572,Q#1468 - >seq8115,superfamily,335182,171,262,1.0932700000000001e-07,49.2235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs0_human.marg.frame1,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF1,hs0_human,marg,CompleteHit
25573,Q#1470 - >seq8117,non-specific,340205,149,211,5.3579e-25,93.1696,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs0_human.pars.frame2,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs0_human,pars,CompleteHit
25574,Q#1470 - >seq8117,superfamily,340205,149,211,5.3579e-25,93.1696,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF1.hs0_human.pars.frame2,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs0_human,pars,CompleteHit
25575,Q#1470 - >seq8117,non-specific,335182,80,146,1.30857e-07,48.0679,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs0_human.pars.frame2,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs0_human,pars,N-TerminusTruncated
25576,Q#1470 - >seq8117,superfamily,335182,80,146,1.30857e-07,48.0679,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4b.ORF1.hs0_human.pars.frame2,1909181109_L1ME4b.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1ME4b,ORF1,hs0_human,pars,N-TerminusTruncated
25577,Q#1483 - >seq8130,non-specific,234767,107,294,0.00900648,39.0508,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1ME4b.ORF2.hs10_snmole.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1ME4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
25578,Q#1483 - >seq8130,superfamily,234767,107,294,0.00900648,39.0508,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1ME4b.ORF2.hs10_snmole.pars.frame1,1909181109_L1ME4b.RM_HPGPNRMPCCSOTSJMCMMRHCCOOOSVCTOPBOCECFCMAOLPPEMMESC_1709081337.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1ME4b,ORF2,hs10_snmole,pars,C-TerminusTruncated
25579,Q#1485 - >seq8132,specific,197310,9,236,3.152389999999999e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25580,Q#1485 - >seq8132,superfamily,351117,9,236,3.152389999999999e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25581,Q#1485 - >seq8132,non-specific,197306,9,236,1.06784e-53,186.918,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25582,Q#1485 - >seq8132,specific,238827,509,768,1.38154e-53,185.572,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25583,Q#1485 - >seq8132,superfamily,295487,509,768,1.38154e-53,185.572,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25584,Q#1485 - >seq8132,non-specific,333820,515,709,3.5514999999999996e-28,112.001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25585,Q#1485 - >seq8132,superfamily,333820,515,709,3.5514999999999996e-28,112.001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25586,Q#1485 - >seq8132,non-specific,197307,9,236,1.0503599999999999e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25587,Q#1485 - >seq8132,non-specific,223780,9,238,1.42243e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25588,Q#1485 - >seq8132,non-specific,197321,7,236,3.7593399999999997e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25589,Q#1485 - >seq8132,non-specific,197320,8,236,1.4797399999999998e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25590,Q#1485 - >seq8132,specific,335306,10,229,2.2053800000000002e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25591,Q#1485 - >seq8132,non-specific,273186,9,237,5.0202100000000005e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25592,Q#1485 - >seq8132,non-specific,197319,8,236,2.20977e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25593,Q#1485 - >seq8132,non-specific,272954,9,236,3.28668e-13,70.4897,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25594,Q#1485 - >seq8132,non-specific,197336,7,235,4.72949e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25595,Q#1485 - >seq8132,non-specific,238828,515,709,2.09248e-10,61.448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25596,Q#1485 - >seq8132,non-specific,197322,9,236,1.77146e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25597,Q#1485 - >seq8132,non-specific,339261,108,232,2.04606e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25598,Q#1485 - >seq8132,non-specific,197311,7,236,2.40089e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25599,Q#1485 - >seq8132,non-specific,275209,466,705,2.78508e-07,53.6156,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25600,Q#1485 - >seq8132,superfamily,275209,466,705,2.78508e-07,53.6156,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25601,Q#1485 - >seq8132,non-specific,197317,139,229,3.12615e-05,46.4412,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,pars,N-TerminusTruncated
25602,Q#1485 - >seq8132,non-specific,238185,655,729,0.00169752,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4c,ORF2,hs3_orang,pars,CompleteHit
25603,Q#1485 - >seq8132,non-specific,274009,305,452,0.00585666,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25604,Q#1485 - >seq8132,superfamily,274009,305,452,0.00585666,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4c,ORF2,hs3_orang,pars,C-TerminusTruncated
25605,Q#1486 - >seq8133,specific,197310,62,232,2.0250299999999997e-38,143.261,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25606,Q#1486 - >seq8133,superfamily,351117,62,232,2.0250299999999997e-38,143.261,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25607,Q#1486 - >seq8133,non-specific,197306,64,232,4.2896e-35,133.761,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25608,Q#1486 - >seq8133,non-specific,238827,507,586,8.291470000000001e-24,100.443,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25609,Q#1486 - >seq8133,superfamily,295487,507,586,8.291470000000001e-24,100.443,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25610,Q#1486 - >seq8133,non-specific,197307,64,232,2.4216799999999997e-13,70.7797,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25611,Q#1486 - >seq8133,non-specific,223780,68,234,1.38704e-11,65.6975,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25612,Q#1486 - >seq8133,non-specific,197320,68,232,6.45982e-10,60.6066,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25613,Q#1486 - >seq8133,non-specific,197321,62,232,3.63273e-09,58.3324,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25614,Q#1486 - >seq8133,non-specific,333820,513,567,1.59306e-08,54.99100000000001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25615,Q#1486 - >seq8133,superfamily,333820,513,567,1.59306e-08,54.99100000000001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25616,Q#1486 - >seq8133,non-specific,273186,67,233,3.72084e-08,55.3628,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25617,Q#1486 - >seq8133,non-specific,339261,104,228,1.68948e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME4c,ORF2,hs3_orang,marg,CompleteHit
25618,Q#1486 - >seq8133,non-specific,335306,36,225,2.01838e-06,49.551,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,CompleteHit
25619,Q#1486 - >seq8133,non-specific,197319,62,232,4.15964e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25620,Q#1486 - >seq8133,non-specific,272954,64,232,2.22075e-05,46.9925,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25621,Q#1486 - >seq8133,non-specific,197317,135,225,3.1341e-05,46.4412,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25622,Q#1486 - >seq8133,non-specific,197311,68,232,7.09225e-05,44.5901,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25623,Q#1486 - >seq8133,non-specific,197322,87,232,0.00016958200000000002,44.6154,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25624,Q#1486 - >seq8133,non-specific,274009,302,450,0.00159136,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25625,Q#1486 - >seq8133,superfamily,274009,302,450,0.00159136,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25626,Q#1486 - >seq8133,non-specific,336322,307,461,0.00646415,39.8078,pfam06160,EzrA,NC,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25627,Q#1486 - >seq8133,superfamily,336322,307,461,0.00646415,39.8078,cl38199,EzrA superfamily,NC, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_CellDiv,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25628,Q#1486 - >seq8133,non-specific,235175,292,461,0.00687742,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25629,Q#1486 - >seq8133,superfamily,235175,292,461,0.00687742,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25630,Q#1486 - >seq8133,non-specific,224117,302,424,0.00923288,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25631,Q#1486 - >seq8133,superfamily,224117,302,424,0.00923288,39.6976,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4c.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME4c,ORF2,hs3_orang,marg,BothTerminiTruncated
25632,Q#1487 - >seq8134,specific,238827,546,729,2.90342e-37,139.349,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25633,Q#1487 - >seq8134,superfamily,295487,546,729,2.90342e-37,139.349,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25634,Q#1487 - >seq8134,non-specific,333820,547,729,3.97721e-22,94.2813,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25635,Q#1487 - >seq8134,superfamily,333820,547,729,3.97721e-22,94.2813,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25636,Q#1487 - >seq8134,non-specific,238828,546,694,1.52432e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25637,Q#1487 - >seq8134,non-specific,275209,548,757,4.60661e-09,59.0084,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25638,Q#1487 - >seq8134,superfamily,275209,548,757,4.60661e-09,59.0084,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,N-TerminusTruncated
25639,Q#1487 - >seq8134,non-specific,238185,613,729,2.43252e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4c.ORF2.hs3_orang.marg.frame2,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4c,ORF2,hs3_orang,marg,CompleteHit
25640,Q#1488 - >seq8135,non-specific,335182,62,133,3.00526e-20,81.9655,pfam02994,Transposase_22,C,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25641,Q#1488 - >seq8135,superfamily,335182,62,133,3.00526e-20,81.9655,cl25509,Transposase_22 superfamily,C, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA15-16.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1PA15-16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA15-16,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
25642,Q#1491 - >seq8138,non-specific,238827,431,542,7.185110000000001e-06,48.0562,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEg.ORF2.hs2_gorilla.marg.frame1,1909181109_L1MEg.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25643,Q#1491 - >seq8138,superfamily,295487,431,542,7.185110000000001e-06,48.0562,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEg.ORF2.hs2_gorilla.marg.frame1,1909181109_L1MEg.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MEg,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25644,Q#1495 - >seq8142,specific,238827,363,597,1.4934399999999998e-28,113.925,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MEg.ORF2.hs1_chimp.marg.frame3,1909181109_L1MEg.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MEg,ORF2,hs1_chimp,marg,CompleteHit
25645,Q#1495 - >seq8142,superfamily,295487,363,597,1.4934399999999998e-28,113.925,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MEg.ORF2.hs1_chimp.marg.frame3,1909181109_L1MEg.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MEg,ORF2,hs1_chimp,marg,CompleteHit
25646,Q#1495 - >seq8142,non-specific,333820,363,597,9.79563e-09,55.7614,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEg.ORF2.hs1_chimp.marg.frame3,1909181109_L1MEg.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MEg,ORF2,hs1_chimp,marg,CompleteHit
25647,Q#1495 - >seq8142,superfamily,333820,363,597,9.79563e-09,55.7614,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MEg.ORF2.hs1_chimp.marg.frame3,1909181109_L1MEg.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MEg,ORF2,hs1_chimp,marg,CompleteHit
25648,Q#1507 - >seq8154,non-specific,197310,9,76,1.31711e-12,68.1469,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25649,Q#1507 - >seq8154,superfamily,351117,9,76,1.31711e-12,68.1469,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25650,Q#1507 - >seq8154,non-specific,197306,9,73,2.4662e-10,61.3433,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25651,Q#1507 - >seq8154,non-specific,223780,9,46,0.0011587,41.4299,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25652,Q#1507 - >seq8154,non-specific,197321,7,52,0.00383596,39.8428,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25653,Q#1507 - >seq8154,non-specific,197307,9,52,0.00759818,38.8081,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4c.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4c,ORF2,hs3_orang,marg,C-TerminusTruncated
25654,Q#1509 - >seq8156,specific,197310,259,400,3.41152e-39,145.957,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25655,Q#1509 - >seq8156,superfamily,351117,259,400,3.41152e-39,145.957,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25656,Q#1509 - >seq8156,non-specific,340205,148,211,5.89556e-32,118.59299999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25657,Q#1509 - >seq8156,superfamily,340205,148,211,5.89556e-32,118.59299999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4b,ORF2,hs1_chimp,marg,CompleteHit
25658,Q#1509 - >seq8156,non-specific,197306,259,411,1.9293e-25,106.412,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25659,Q#1509 - >seq8156,non-specific,223780,259,401,1.58308e-13,71.8607,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25660,Q#1509 - >seq8156,non-specific,197307,259,395,6.47748e-13,70.0093,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25661,Q#1509 - >seq8156,non-specific,197321,257,370,1.00031e-11,66.4216,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25662,Q#1509 - >seq8156,non-specific,197320,259,401,1.10118e-11,66.3846,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25663,Q#1509 - >seq8156,specific,335306,260,393,2.29787e-09,58.7958,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25664,Q#1509 - >seq8156,non-specific,272954,259,412,2.56695e-09,59.3189,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25665,Q#1509 - >seq8156,non-specific,273186,259,395,2.60868e-08,56.1332,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25666,Q#1509 - >seq8156,non-specific,197336,259,413,2.9314400000000002e-08,56.0815,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25667,Q#1509 - >seq8156,non-specific,197319,263,395,3.68505e-07,52.6641,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25668,Q#1509 - >seq8156,non-specific,236970,259,401,6.27271e-05,46.0406,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25669,Q#1509 - >seq8156,non-specific,197311,257,395,0.00490967,39.5825,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,marg,C-TerminusTruncated
25670,Q#1519 - >seq8166,non-specific,197310,8,221,0.00018565,44.2645,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME3.ORF2.hs7_bushaby.marg.frame1,1909181109_L1ME3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME3,ORF2,hs7_bushaby,marg,CompleteHit
25671,Q#1519 - >seq8166,superfamily,351117,8,221,0.00018565,44.2645,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME3.ORF2.hs7_bushaby.marg.frame1,1909181109_L1ME3.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME3,ORF2,hs7_bushaby,marg,CompleteHit
25672,Q#1525 - >seq8172,non-specific,238827,541,579,0.00194201,40.7374,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME3.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1ME3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
25673,Q#1525 - >seq8172,superfamily,295487,541,579,0.00194201,40.7374,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME3.ORF2.hs6_sqmonkey.marg.frame1,1909181109_L1ME3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
25674,Q#1529 - >seq8176,non-specific,335182,51,112,0.00273391,35.7415,pfam02994,Transposase_22,N,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs0_human.marg.frame3,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs0_human,marg,N-TerminusTruncated
25675,Q#1529 - >seq8176,superfamily,335182,51,112,0.00273391,35.7415,cl25509,Transposase_22 superfamily,N, - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MD2.ORF1.hs0_human.marg.frame3,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MD2,ORF1,hs0_human,marg,N-TerminusTruncated
25676,Q#1532 - >seq8179,non-specific,340205,115,178,1.12581e-09,51.9532,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs0_human.marg.frame1,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs0_human,marg,CompleteHit
25677,Q#1532 - >seq8179,superfamily,340205,115,178,1.12581e-09,51.9532,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs0_human.marg.frame1,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MD2,ORF1,hs0_human,marg,CompleteHit
25678,Q#1536 - >seq8183,non-specific,335182,153,249,1.6159e-33,118.945,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25679,Q#1536 - >seq8183,superfamily,335182,153,249,1.6159e-33,118.945,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25680,Q#1536 - >seq8183,non-specific,340205,252,315,5.368189999999999e-23,90.088,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25681,Q#1536 - >seq8183,superfamily,340205,252,315,5.368189999999999e-23,90.088,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25682,Q#1536 - >seq8183,non-specific,340204,109,151,3.9782499999999996e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25683,Q#1536 - >seq8183,superfamily,340204,109,151,3.9782499999999996e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs1_chimp,pars,CompleteHit
25684,Q#1536 - >seq8183,non-specific,235175,47,153,0.000164371,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25685,Q#1536 - >seq8183,superfamily,235175,47,153,0.000164371,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25686,Q#1536 - >seq8183,non-specific,237177,40,147,0.000259856,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25687,Q#1536 - >seq8183,superfamily,237177,40,147,0.000259856,42.4578,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25688,Q#1536 - >seq8183,non-specific,336159,58,143,0.00132157,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
25689,Q#1536 - >seq8183,superfamily,336159,58,143,0.00132157,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
25690,Q#1536 - >seq8183,non-specific,224117,26,153,0.00137209,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25691,Q#1536 - >seq8183,superfamily,224117,26,153,0.00137209,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25692,Q#1536 - >seq8183,non-specific,235461,45,166,0.00224407,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25693,Q#1536 - >seq8183,superfamily,235461,45,166,0.00224407,39.281,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25694,Q#1536 - >seq8183,non-specific,274008,43,148,0.00344964,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25695,Q#1536 - >seq8183,superfamily,274008,43,148,0.00344964,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25696,Q#1536 - >seq8183,non-specific,224117,47,148,0.00349187,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25697,Q#1536 - >seq8183,non-specific,275056,58,150,0.00453701,37.2949,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
25698,Q#1536 - >seq8183,superfamily,275056,58,150,0.00453701,37.2949,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,N-TerminusTruncated
25699,Q#1536 - >seq8183,non-specific,224117,39,147,0.00499305,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25700,Q#1536 - >seq8183,non-specific,222878,60,148,0.00524718,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25701,Q#1536 - >seq8183,superfamily,222878,60,148,0.00524718,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25702,Q#1536 - >seq8183,non-specific,310273,58,146,0.00762306,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25703,Q#1536 - >seq8183,superfamily,310273,58,146,0.00762306,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25704,Q#1536 - >seq8183,non-specific,226400,77,147,0.00767773,37.0054,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25705,Q#1536 - >seq8183,superfamily,226400,77,147,0.00767773,37.0054,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,pars,C-TerminusTruncated
25706,Q#1536 - >seq8183,non-specific,274009,31,148,0.00939588,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25707,Q#1536 - >seq8183,superfamily,274009,31,148,0.00939588,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,pars,BothTerminiTruncated
25708,Q#1556 - >seq8203,non-specific,340205,42,69,5.61605e-06,40.012,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs0_human.pars.frame3,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs0_human,pars,C-TerminusTruncated
25709,Q#1556 - >seq8203,superfamily,340205,42,69,5.61605e-06,40.012,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MD2.ORF1.hs0_human.pars.frame3,1909181109_L1MD2.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MD2,ORF1,hs0_human,pars,C-TerminusTruncated
25710,Q#1563 - >seq8210,non-specific,340205,46,95,4.719880000000001e-06,40.3972,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs2_gorilla.pars.frame2,1909181109_L1MCb.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs2_gorilla,pars,CompleteHit
25711,Q#1563 - >seq8210,superfamily,340205,46,95,4.719880000000001e-06,40.3972,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MCb.ORF1.hs2_gorilla.pars.frame2,1909181109_L1MCb.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1MCb,ORF1,hs2_gorilla,pars,CompleteHit
25712,Q#1565 - >seq8212,non-specific,340205,231,280,1.93428e-17,75.0652,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs0_human.marg.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,marg,C-TerminusTruncated
25713,Q#1565 - >seq8212,superfamily,340205,231,280,1.93428e-17,75.0652,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs0_human.marg.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,marg,C-TerminusTruncated
25714,Q#1565 - >seq8212,non-specific,335182,141,228,5.158239999999999e-09,52.6903,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs0_human.marg.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,marg,CompleteHit
25715,Q#1565 - >seq8212,superfamily,335182,141,228,5.158239999999999e-09,52.6903,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs0_human.marg.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,marg,CompleteHit
25716,Q#1568 - >seq8215,non-specific,340205,221,268,1.36944e-14,66.976,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs0_human.pars.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,pars,C-TerminusTruncated
25717,Q#1568 - >seq8215,superfamily,340205,221,268,1.36944e-14,66.976,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs0_human.pars.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,pars,C-TerminusTruncated
25718,Q#1568 - >seq8215,non-specific,335182,130,218,2.1801100000000002e-09,53.8459,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs0_human.pars.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,pars,CompleteHit
25719,Q#1568 - >seq8215,superfamily,335182,130,218,2.1801100000000002e-09,53.8459,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs0_human.pars.frame3,1909181109_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA7,ORF1,hs0_human,pars,CompleteHit
25720,Q#1575 - >seq8222,non-specific,340205,158,221,3.55914e-23,88.5472,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,pars,CompleteHit
25721,Q#1575 - >seq8222,superfamily,340205,158,221,3.55914e-23,88.5472,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,pars,CompleteHit
25722,Q#1575 - >seq8222,non-specific,335182,70,155,4.4333e-16,70.7947,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,pars,CompleteHit
25723,Q#1575 - >seq8222,superfamily,335182,70,155,4.4333e-16,70.7947,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs6_sqmonkey.pars.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,pars,CompleteHit
25724,Q#1576 - >seq8223,specific,238827,469,716,1.1460099999999997e-57,197.514,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25725,Q#1576 - >seq8223,superfamily,295487,469,716,1.1460099999999997e-57,197.514,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25726,Q#1576 - >seq8223,specific,333820,475,698,1.9790199999999998e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25727,Q#1576 - >seq8223,superfamily,333820,475,698,1.9790199999999998e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25728,Q#1576 - >seq8223,non-specific,197310,9,208,6.02632e-23,98.5776,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25729,Q#1576 - >seq8223,superfamily,351117,9,208,6.02632e-23,98.5776,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25730,Q#1576 - >seq8223,non-specific,197306,9,214,1.94595e-12,67.8917,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25731,Q#1576 - >seq8223,non-specific,238828,475,695,5.25363e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25732,Q#1576 - >seq8223,non-specific,197307,9,139,2.6588e-06,49.5937,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
25733,Q#1576 - >seq8223,non-specific,275209,546,695,3.37978e-06,50.1488,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
25734,Q#1576 - >seq8223,superfamily,275209,546,695,3.37978e-06,50.1488,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,BothTerminiTruncated
25735,Q#1576 - >seq8223,non-specific,223780,9,138,4.79149e-06,49.1339,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
25736,Q#1576 - >seq8223,non-specific,197321,7,48,5.7584099999999996e-05,45.6208,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
25737,Q#1576 - >seq8223,non-specific,197320,9,138,0.00017403700000000001,44.043,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,C-TerminusTruncated
25738,Q#1576 - >seq8223,specific,335306,10,198,0.000960508,41.4618,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25739,Q#1576 - >seq8223,non-specific,238185,615,698,0.00217476,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4b.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25740,Q#1581 - >seq8228,non-specific,238827,617,729,1.2413e-11,65.3902,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs2_gorilla.marg.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,marg,N-TerminusTruncated
25741,Q#1581 - >seq8228,superfamily,295487,617,729,1.2413e-11,65.3902,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs2_gorilla.marg.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,marg,N-TerminusTruncated
25742,Q#1581 - >seq8228,non-specific,333820,597,697,0.00135184,40.7386,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs2_gorilla.marg.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,marg,N-TerminusTruncated
25743,Q#1581 - >seq8228,superfamily,333820,597,697,0.00135184,40.7386,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs2_gorilla.marg.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,marg,N-TerminusTruncated
25744,Q#1583 - >seq8230,non-specific,238827,525,630,3.34867e-07,52.2934,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs2_gorilla.marg.frame1,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25745,Q#1583 - >seq8230,superfamily,295487,525,630,3.34867e-07,52.2934,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs2_gorilla.marg.frame1,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25746,Q#1584 - >seq8231,non-specific,238827,340,595,5.1864e-17,80.7982,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,pars,CompleteHit
25747,Q#1584 - >seq8231,superfamily,295487,340,595,5.1864e-17,80.7982,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,pars,CompleteHit
25748,Q#1584 - >seq8231,non-specific,333820,346,563,1.81772e-08,54.99100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,pars,CompleteHit
25749,Q#1584 - >seq8231,superfamily,333820,346,563,1.81772e-08,54.99100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,pars,CompleteHit
25750,Q#1584 - >seq8231,non-specific,238828,414,547,2.13181e-05,46.4253,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC,ORF2,hs2_gorilla,pars,N-TerminusTruncated
25751,Q#1584 - >seq8231,non-specific,197310,26,78,0.00550534,39.2569,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC,ORF2,hs2_gorilla,pars,N-TerminusTruncated
25752,Q#1584 - >seq8231,superfamily,351117,26,78,0.00550534,39.2569,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC,ORF2,hs2_gorilla,pars,N-TerminusTruncated
25753,Q#1584 - >seq8231,non-specific,311007,152,329,0.00691854,39.6953,pfam06785,UPF0242,C,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC,ORF2,hs2_gorilla,pars,C-TerminusTruncated
25754,Q#1584 - >seq8231,superfamily,311007,152,329,0.00691854,39.6953,cl26473,UPF0242 superfamily,C, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1MC.ORF2.hs2_gorilla.pars.frame3,1909181109_L1MC.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MC,ORF2,hs2_gorilla,pars,C-TerminusTruncated
25755,Q#1594 - >seq8241,non-specific,350482,853,995,0.00020004,43.8566,cd14634,R-PTPc-T-2,C,cl28904,"PTP domain of receptor-type tyrosine-protein phosphatase T, repeat 2; Receptor-type tyrosine-protein phosphatase T (PTPRT), also known as receptor-type tyrosine-protein phosphatase rho (RPTP-rho or PTPrho), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRT is highly expressed in the nervous system and it plays a critical role in regulation of synaptic formation and neuronal development. It dephosphorylates a specific tyrosine residue in syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, and regulates its binding to syntaxin 1. PTPRT has been identified as a potential candidate gene for autism spectrum disorder (ASD) susceptibility. It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment  with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain.",L1MC.ORF2.hs1_chimp.marg.frame2,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1MC,ORF2,hs1_chimp,marg,C-TerminusTruncated
25756,Q#1594 - >seq8241,superfamily,355780,853,995,0.00020004,43.8566,cl28904,PTP_DSP_cys superfamily,C, - ,"cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily; This superfamily is composed of cys-based phosphatases, which includes classical protein tyrosine phosphatases (PTPs) as well as dual-specificity phosphatases (DUSPs or DSPs). They are characterized by a CxxxxxR conserved catalytic loop (where C is the catalytic cysteine, x is any amino acid, and R is an arginine). PTPs are part of the tyrosine phosphorylation/dephosphorylation regulatory mechanism, and are important in the response of the cells to physiologic and pathologic changes in their environment. DUSPs show more substrate diversity (including RNA and lipids) and include pTyr, pSer, and pThr phosphatases.",L1MC.ORF2.hs1_chimp.marg.frame2,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1MC,ORF2,hs1_chimp,marg,C-TerminusTruncated
25757,Q#1595 - >seq8242,non-specific,238827,480,749,3.99634e-16,78.487,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs1_chimp,marg,CompleteHit
25758,Q#1595 - >seq8242,superfamily,295487,480,749,3.99634e-16,78.487,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs1_chimp,marg,CompleteHit
25759,Q#1595 - >seq8242,non-specific,333820,615,719,0.00232879,40.3534,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25760,Q#1595 - >seq8242,superfamily,333820,615,719,0.00232879,40.3534,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25761,Q#1595 - >seq8242,non-specific,129694,149,382,0.00345434,41.5709,TIGR00606,rad50,N,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_DNARepair,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25762,Q#1595 - >seq8242,superfamily,129694,149,382,0.00345434,41.5709,cl31018,rad50 superfamily,N, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_DNARepair,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25763,Q#1595 - >seq8242,non-specific,197310,4,138,0.00805896,39.2569,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25764,Q#1595 - >seq8242,superfamily,351117,4,138,0.00805896,39.2569,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC.ORF2.hs1_chimp.marg.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MC,ORF2,hs1_chimp,marg,N-TerminusTruncated
25765,Q#1598 - >seq8245,non-specific,238827,323,583,9.751339999999999e-20,88.5022,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC.ORF2.hs1_chimp.pars.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs1_chimp,pars,CompleteHit
25766,Q#1598 - >seq8245,superfamily,295487,323,583,9.751339999999999e-20,88.5022,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC.ORF2.hs1_chimp.pars.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs1_chimp,pars,CompleteHit
25767,Q#1598 - >seq8245,non-specific,333820,329,552,2.27766e-08,54.6058,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs1_chimp.pars.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs1_chimp,pars,CompleteHit
25768,Q#1598 - >seq8245,superfamily,333820,329,552,2.27766e-08,54.6058,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC.ORF2.hs1_chimp.pars.frame1,1909181109_L1MC.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC,ORF2,hs1_chimp,pars,CompleteHit
25769,Q#1601 - >seq8248,non-specific,335182,152,248,1.4061700000000002e-33,118.945,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25770,Q#1601 - >seq8248,superfamily,335182,152,248,1.4061700000000002e-33,118.945,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25771,Q#1601 - >seq8248,non-specific,340205,251,314,5.990129999999999e-23,89.7028,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25772,Q#1601 - >seq8248,superfamily,340205,251,314,5.990129999999999e-23,89.7028,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25773,Q#1601 - >seq8248,non-specific,340204,108,150,3.88843e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25774,Q#1601 - >seq8248,superfamily,340204,108,150,3.88843e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs1_chimp,marg,CompleteHit
25775,Q#1601 - >seq8248,non-specific,235175,46,152,0.000166247,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25776,Q#1601 - >seq8248,superfamily,235175,46,152,0.000166247,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25777,Q#1601 - >seq8248,non-specific,237177,39,146,0.000269977,42.0726,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25778,Q#1601 - >seq8248,superfamily,237177,39,146,0.000269977,42.0726,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25779,Q#1601 - >seq8248,non-specific,336159,57,142,0.001361,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
25780,Q#1601 - >seq8248,superfamily,336159,57,142,0.001361,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
25781,Q#1601 - >seq8248,non-specific,224117,25,152,0.00138822,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25782,Q#1601 - >seq8248,superfamily,224117,25,152,0.00138822,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25783,Q#1601 - >seq8248,non-specific,235461,44,165,0.00225173,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25784,Q#1601 - >seq8248,superfamily,235461,44,165,0.00225173,39.281,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25785,Q#1601 - >seq8248,non-specific,274008,42,147,0.00349078,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25786,Q#1601 - >seq8248,superfamily,274008,42,147,0.00349078,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25787,Q#1601 - >seq8248,non-specific,224117,46,147,0.00353356,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25788,Q#1601 - >seq8248,non-specific,275056,57,149,0.00451671,37.2949,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
25789,Q#1601 - >seq8248,superfamily,275056,57,149,0.00451671,37.2949,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,N-TerminusTruncated
25790,Q#1601 - >seq8248,non-specific,224117,38,146,0.004965600000000001,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25791,Q#1601 - >seq8248,non-specific,222878,59,147,0.00512824,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25792,Q#1601 - >seq8248,superfamily,222878,59,147,0.00512824,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25793,Q#1601 - >seq8248,non-specific,226400,76,146,0.00730468,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25794,Q#1601 - >seq8248,superfamily,226400,76,146,0.00730468,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25795,Q#1601 - >seq8248,non-specific,310273,57,145,0.00764925,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25796,Q#1601 - >seq8248,superfamily,310273,57,145,0.00764925,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs1_chimp,marg,C-TerminusTruncated
25797,Q#1601 - >seq8248,non-specific,274009,30,147,0.00934535,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25798,Q#1601 - >seq8248,superfamily,274009,30,147,0.00934535,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs1_chimp,marg,BothTerminiTruncated
25799,Q#1602 - >seq8249,non-specific,340205,175,238,2.93227e-23,88.9324,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,marg,CompleteHit
25800,Q#1602 - >seq8249,superfamily,340205,175,238,2.93227e-23,88.9324,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA7.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,marg,CompleteHit
25801,Q#1602 - >seq8249,non-specific,335182,78,172,7.7698e-17,73.1059,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,marg,CompleteHit
25802,Q#1602 - >seq8249,superfamily,335182,78,172,7.7698e-17,73.1059,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA7.ORF1.hs6_sqmonkey.marg.frame1,1909181109_L1MA7.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1MA7,ORF1,hs6_sqmonkey,marg,CompleteHit
25803,Q#1603 - >seq8250,specific,197310,64,230,1.19523e-35,135.55700000000002,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25804,Q#1603 - >seq8250,superfamily,351117,64,230,1.19523e-35,135.55700000000002,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25805,Q#1603 - >seq8250,non-specific,197306,64,230,6.83165e-17,81.3736,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25806,Q#1603 - >seq8250,non-specific,197320,67,223,1.5597500000000001e-09,59.8362,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25807,Q#1603 - >seq8250,non-specific,197307,83,230,3.82678e-09,58.4533,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25808,Q#1603 - >seq8250,non-specific,223780,67,231,1.89888e-07,53.3711,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25809,Q#1603 - >seq8250,non-specific,272954,84,230,2.22262e-06,50.0741,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25810,Q#1603 - >seq8250,non-specific,197319,85,230,3.0053600000000002e-06,49.9677,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25811,Q#1603 - >seq8250,non-specific,273186,100,231,9.415439999999999e-06,48.4292,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25812,Q#1603 - >seq8250,non-specific,197321,85,230,0.000214158,44.08,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25813,Q#1603 - >seq8250,specific,335306,67,223,0.00195209,41.0766,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,N-TerminusTruncated
25814,Q#1603 - >seq8250,non-specific,339261,102,226,0.00345615,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs1_chimp.pars.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1ME4a,ORF2,hs1_chimp,pars,CompleteHit
25815,Q#1608 - >seq8255,non-specific,238827,131,198,0.00228758,38.8114,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs7_bushaby.marg.frame1,1909181109_L1ME4a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs7_bushaby,marg,C-TerminusTruncated
25816,Q#1608 - >seq8255,superfamily,295487,131,198,0.00228758,38.8114,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs7_bushaby.marg.frame1,1909181109_L1ME4a.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs7_bushaby,marg,C-TerminusTruncated
25817,Q#1618 - >seq8265,specific,197310,3,230,1.2537599999999999e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25818,Q#1618 - >seq8265,superfamily,351117,3,230,1.2537599999999999e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25819,Q#1618 - >seq8265,specific,238827,489,595,3.32644e-35,133.571,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25820,Q#1618 - >seq8265,superfamily,295487,489,595,3.32644e-35,133.571,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25821,Q#1618 - >seq8265,non-specific,197306,3,230,6.8891299999999995e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25822,Q#1618 - >seq8265,non-specific,197320,3,223,6.4096099999999995e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25823,Q#1618 - >seq8265,non-specific,197307,3,230,5.46708e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25824,Q#1618 - >seq8265,non-specific,223780,3,231,1.09973e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25825,Q#1618 - >seq8265,specific,335306,4,223,1.6198199999999998e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25826,Q#1618 - >seq8265,non-specific,197321,1,230,5.4033600000000005e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25827,Q#1618 - >seq8265,non-specific,273186,3,231,1.29228e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25828,Q#1618 - >seq8265,non-specific,272954,3,230,1.4108499999999998e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25829,Q#1618 - >seq8265,non-specific,197319,7,230,1.43887e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25830,Q#1618 - >seq8265,non-specific,333820,495,602,1.2143e-14,73.0954,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25831,Q#1618 - >seq8265,superfamily,333820,495,602,1.2143e-14,73.0954,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25832,Q#1618 - >seq8265,non-specific,197336,3,188,4.02192e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25833,Q#1618 - >seq8265,non-specific,197322,2,230,4.9557699999999996e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25834,Q#1618 - >seq8265,non-specific,236970,3,183,9.025269999999999e-08,54.515,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25835,Q#1618 - >seq8265,non-specific,197311,1,230,4.4660500000000004e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25836,Q#1618 - >seq8265,non-specific,339261,102,226,0.000994862,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs5_gmonkey,marg,CompleteHit
25837,Q#1618 - >seq8265,non-specific,275209,434,597,0.00896605,39.7484,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25838,Q#1618 - >seq8265,superfamily,275209,434,597,0.00896605,39.7484,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25839,Q#1619 - >seq8266,non-specific,238827,620,727,8.699559999999998e-25,103.525,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
25840,Q#1619 - >seq8266,superfamily,295487,620,727,8.699559999999998e-25,103.525,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
25841,Q#1619 - >seq8266,non-specific,333820,602,705,1.51191e-13,70.0138,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
25842,Q#1619 - >seq8266,superfamily,333820,602,705,1.51191e-13,70.0138,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
25843,Q#1619 - >seq8266,non-specific,238828,559,702,3.54404e-09,58.3664,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
25844,Q#1619 - >seq8266,non-specific,238185,621,698,0.000100625,42.338,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.marg.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
25845,Q#1621 - >seq8268,specific,197310,3,230,1.9108699999999997e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25846,Q#1621 - >seq8268,superfamily,351117,3,230,1.9108699999999997e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25847,Q#1621 - >seq8268,specific,238827,488,594,1.61809e-35,134.341,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25848,Q#1621 - >seq8268,superfamily,295487,488,594,1.61809e-35,134.341,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25849,Q#1621 - >seq8268,non-specific,197306,3,230,3.51918e-34,131.45,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25850,Q#1621 - >seq8268,non-specific,197320,3,223,6.110579999999999e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25851,Q#1621 - >seq8268,non-specific,197307,3,230,7.4045e-20,90.0397,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25852,Q#1621 - >seq8268,non-specific,223780,3,231,1.04819e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25853,Q#1621 - >seq8268,specific,335306,4,223,1.54641e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25854,Q#1621 - >seq8268,non-specific,197321,1,230,6.64456e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25855,Q#1621 - >seq8268,non-specific,273186,3,231,1.23233e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25856,Q#1621 - >seq8268,non-specific,272954,3,230,2.13291e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25857,Q#1621 - >seq8268,non-specific,197319,7,230,2.55347e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25858,Q#1621 - >seq8268,non-specific,333820,494,601,8.79368e-15,73.4806,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25859,Q#1621 - >seq8268,superfamily,333820,494,601,8.79368e-15,73.4806,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25860,Q#1621 - >seq8268,non-specific,197336,3,188,3.83824e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25861,Q#1621 - >seq8268,non-specific,197322,2,230,4.72463e-08,55.7862,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25862,Q#1621 - >seq8268,non-specific,236970,3,183,8.93174e-08,54.515,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25863,Q#1621 - >seq8268,non-specific,197311,1,230,3.78554e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25864,Q#1621 - >seq8268,non-specific,339261,102,226,0.0005770069999999999,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs5_gmonkey,pars,CompleteHit
25865,Q#1621 - >seq8268,non-specific,275209,433,596,0.00918106,39.3632,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25866,Q#1621 - >seq8268,superfamily,275209,433,596,0.00918106,39.3632,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25867,Q#1622 - >seq8269,non-specific,238827,618,733,7.2455e-25,103.91,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
25868,Q#1622 - >seq8269,superfamily,295487,618,733,7.2455e-25,103.91,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
25869,Q#1622 - >seq8269,non-specific,333820,600,703,1.6028399999999999e-13,70.0138,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
25870,Q#1622 - >seq8269,superfamily,333820,600,703,1.6028399999999999e-13,70.0138,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
25871,Q#1622 - >seq8269,non-specific,238828,558,700,4.9508900000000005e-09,57.596000000000004,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
25872,Q#1622 - >seq8269,non-specific,238185,619,696,9.54519e-05,42.338,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
25873,Q#1622 - >seq8269,non-specific,274009,341,467,0.00317205,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
25874,Q#1622 - >seq8269,superfamily,274009,341,467,0.00317205,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF2.hs5_gmonkey.pars.frame2,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1ME4a,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
25875,Q#1627 - >seq8274,non-specific,197310,47,172,4.428030000000001e-10,60.8281,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4b.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25876,Q#1627 - >seq8274,superfamily,351117,47,172,4.428030000000001e-10,60.8281,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4b.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1ME4b,ORF2,hs1_chimp,pars,CompleteHit
25877,Q#1627 - >seq8274,non-specific,224117,184,442,0.000898565,43.1644,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME4b,ORF2,hs1_chimp,pars,N-TerminusTruncated
25878,Q#1627 - >seq8274,superfamily,224117,184,442,0.000898565,43.1644,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4b.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4b.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1ME4b,ORF2,hs1_chimp,pars,N-TerminusTruncated
25879,Q#1628 - >seq8275,specific,238827,484,694,1.56931e-52,183.261,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
25880,Q#1628 - >seq8275,superfamily,295487,484,694,1.56931e-52,183.261,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
25881,Q#1628 - >seq8275,non-specific,333820,490,699,5.18309e-27,108.919,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,CompleteHit
25882,Q#1628 - >seq8275,superfamily,333820,490,699,5.18309e-27,108.919,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,CompleteHit
25883,Q#1628 - >seq8275,non-specific,238828,490,739,4.60264e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,CompleteHit
25884,Q#1628 - >seq8275,non-specific,275209,442,701,3.85358e-07,53.2304,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
25885,Q#1628 - >seq8275,superfamily,275209,442,701,3.85358e-07,53.2304,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
25886,Q#1628 - >seq8275,non-specific,238185,629,689,0.0007976410000000001,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs1_chimp.pars.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
25887,Q#1630 - >seq8277,non-specific,335182,159,255,1.9097100000000003e-39,134.738,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25888,Q#1630 - >seq8277,superfamily,335182,159,255,1.9097100000000003e-39,134.738,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25889,Q#1630 - >seq8277,non-specific,340205,258,321,4.1788e-29,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25890,Q#1630 - >seq8277,superfamily,340205,258,321,4.1788e-29,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25891,Q#1630 - >seq8277,non-specific,340204,115,156,1.05319e-06,44.706,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25892,Q#1630 - >seq8277,superfamily,340204,115,156,1.05319e-06,44.706,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Trimerization,L1ME4a,ORF1,hs0_human,marg,CompleteHit
25893,Q#1630 - >seq8277,non-specific,226447,54,130,0.00010347399999999999,40.9186,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other,L1ME4a,ORF1,hs0_human,marg,N-TerminusTruncated
25894,Q#1630 - >seq8277,superfamily,352825,54,130,0.00010347399999999999,40.9186,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,marg,N-TerminusTruncated
25895,Q#1630 - >seq8277,non-specific,237049,32,147,0.00151176,40.2367,PRK12300,leuS,N,cl36101,leucyl-tRNA synthetase; Reviewed,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,marg,N-TerminusTruncated
25896,Q#1630 - >seq8277,superfamily,237049,32,147,0.00151176,40.2367,cl36101,leuS superfamily,N, - ,leucyl-tRNA synthetase; Reviewed,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,marg,N-TerminusTruncated
25897,Q#1630 - >seq8277,non-specific,224117,47,240,0.00847302,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4a,ORF1,hs0_human,marg,BothTerminiTruncated
25898,Q#1630 - >seq8277,superfamily,224117,47,240,0.00847302,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1ME4a,ORF1,hs0_human,marg,BothTerminiTruncated
25899,Q#1630 - >seq8277,non-specific,235600,47,189,0.0085387,37.5996,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME4a,ORF1,hs0_human,marg,C-TerminusTruncated
25900,Q#1630 - >seq8277,superfamily,235600,47,189,0.0085387,37.5996,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Other_ATPase,L1ME4a,ORF1,hs0_human,marg,C-TerminusTruncated
25901,Q#1630 - >seq8277,non-specific,274009,56,206,0.00920519,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4a,ORF1,hs0_human,marg,BothTerminiTruncated
25902,Q#1630 - >seq8277,superfamily,274009,56,206,0.00920519,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs0_human.marg.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,ChromSeg,L1ME4a,ORF1,hs0_human,marg,BothTerminiTruncated
25903,Q#1631 - >seq8278,non-specific,340205,267,291,8.49844e-05,39.6268,pfam17490,Tnp_22_dsRBD,N,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.pars.frame3,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25904,Q#1631 - >seq8278,superfamily,340205,267,291,8.49844e-05,39.6268,cl38762,Tnp_22_dsRBD superfamily,N, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.pars.frame3,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25905,Q#1633 - >seq8280,non-specific,335182,150,246,3.6095e-39,133.582,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,pars,CompleteHit
25906,Q#1633 - >seq8280,superfamily,335182,150,246,3.6095e-39,133.582,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,pars,CompleteHit
25907,Q#1633 - >seq8280,non-specific,340205,249,287,2.44972e-16,71.9836,pfam17490,Tnp_22_dsRBD,C,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,pars,C-TerminusTruncated
25908,Q#1633 - >seq8280,superfamily,340205,249,287,2.44972e-16,71.9836,cl38762,Tnp_22_dsRBD superfamily,C, - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs0_human,pars,C-TerminusTruncated
25909,Q#1633 - >seq8280,non-specific,340204,106,147,1.18818e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME4a,ORF1,hs0_human,pars,CompleteHit
25910,Q#1633 - >seq8280,superfamily,340204,106,147,1.18818e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME4a,ORF1,hs0_human,pars,CompleteHit
25911,Q#1633 - >seq8280,non-specific,274009,40,203,0.00010346,43.9031,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25912,Q#1633 - >seq8280,superfamily,274009,40,203,0.00010346,43.9031,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25913,Q#1633 - >seq8280,non-specific,112704,3,142,0.0018452000000000002,38.8411,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME4a,ORF1,hs0_human,pars,C-TerminusTruncated
25914,Q#1633 - >seq8280,superfamily,112704,3,142,0.0018452000000000002,38.8411,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other,L1ME4a,ORF1,hs0_human,pars,C-TerminusTruncated
25915,Q#1633 - >seq8280,non-specific,214360,39,130,0.00757726,37.7876,CHL00094,dnaK,N,cl33328,heat shock protein 70,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25916,Q#1633 - >seq8280,superfamily,214360,39,130,0.00757726,37.7876,cl33328,dnaK superfamily,N, - ,heat shock protein 70,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,pars,N-TerminusTruncated
25917,Q#1633 - >seq8280,non-specific,235505,37,177,0.00961291,37.5426,PRK05563,PRK05563,NC,cl35337,DNA polymerase III subunits gamma and tau; Validated,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1ME4a,ORF1,hs0_human,pars,BothTerminiTruncated
25918,Q#1633 - >seq8280,superfamily,235505,37,177,0.00961291,37.5426,cl35337,PRK05563 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1ME4a.ORF1.hs0_human.pars.frame1,1909181109_L1ME4a.RM_hs_1709082029.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1ME4a,ORF1,hs0_human,pars,BothTerminiTruncated
25919,Q#1647 - >seq8294,non-specific,335182,156,252,3.59426e-30,110.085,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25920,Q#1647 - >seq8294,superfamily,335182,156,252,3.59426e-30,110.085,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25921,Q#1647 - >seq8294,non-specific,340205,255,318,2.49417e-24,93.5548,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25922,Q#1647 - >seq8294,superfamily,340205,255,318,2.49417e-24,93.5548,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25923,Q#1647 - >seq8294,non-specific,340204,111,153,1.5338399999999999e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25924,Q#1647 - >seq8294,superfamily,340204,111,153,1.5338399999999999e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs5_gmonkey,marg,CompleteHit
25925,Q#1647 - >seq8294,non-specific,235175,49,156,5.7603699999999995e-06,47.7512,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25926,Q#1647 - >seq8294,superfamily,235175,49,156,5.7603699999999995e-06,47.7512,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25927,Q#1647 - >seq8294,non-specific,237177,42,149,1.0756500000000001e-05,46.695,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25928,Q#1647 - >seq8294,superfamily,237177,42,149,1.0756500000000001e-05,46.695,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25929,Q#1647 - >seq8294,non-specific,336159,60,145,0.000236445,42.7417,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25930,Q#1647 - >seq8294,superfamily,336159,60,145,0.000236445,42.7417,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25931,Q#1647 - >seq8294,non-specific,224117,49,161,0.0006194659999999999,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25932,Q#1647 - >seq8294,superfamily,224117,49,161,0.0006194659999999999,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25933,Q#1647 - >seq8294,non-specific,274009,33,150,0.000709497,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25934,Q#1647 - >seq8294,superfamily,274009,33,150,0.000709497,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25935,Q#1647 - >seq8294,non-specific,188306,43,150,0.000957445,40.6794,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25936,Q#1647 - >seq8294,superfamily,188306,43,150,0.000957445,40.6794,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25937,Q#1647 - >seq8294,non-specific,274386,1,147,0.00139604,40.0346,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25938,Q#1647 - >seq8294,superfamily,274386,1,147,0.00139604,40.0346,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25939,Q#1647 - >seq8294,non-specific,274008,45,150,0.00151798,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25940,Q#1647 - >seq8294,superfamily,274008,45,150,0.00151798,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25941,Q#1647 - >seq8294,non-specific,224117,41,149,0.00306109,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25942,Q#1647 - >seq8294,non-specific,310273,60,148,0.0035218000000000003,38.9582,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25943,Q#1647 - >seq8294,superfamily,310273,60,148,0.0035218000000000003,38.9582,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25944,Q#1647 - >seq8294,non-specific,188306,34,149,0.00427418,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25945,Q#1647 - >seq8294,non-specific,222878,62,150,0.00447309,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25946,Q#1647 - >seq8294,superfamily,222878,62,150,0.00447309,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25947,Q#1647 - >seq8294,non-specific,130673,83,149,0.00503254,38.494,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25948,Q#1647 - >seq8294,superfamily,130673,83,149,0.00503254,38.494,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25949,Q#1647 - >seq8294,non-specific,224117,49,150,0.00525544,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25950,Q#1647 - >seq8294,non-specific,274008,60,145,0.00556684,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25951,Q#1647 - >seq8294,non-specific,335541,50,136,0.00658888,36.4107,pfam03938,OmpH,C,cl38144,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25952,Q#1647 - >seq8294,superfamily,335541,50,136,0.00658888,36.4107,cl38144,OmpH superfamily,C, - ,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
25953,Q#1647 - >seq8294,non-specific,274091,65,150,0.00802933,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25954,Q#1647 - >seq8294,superfamily,274091,65,150,0.00802933,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25955,Q#1647 - >seq8294,non-specific,274009,33,150,0.00823363,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25956,Q#1647 - >seq8294,non-specific,235175,41,150,0.00828894,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25957,Q#1647 - >seq8294,non-specific,224117,41,149,0.00894117,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
25958,Q#1647 - >seq8294,non-specific,226447,50,125,0.00995443,35.1406,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25959,Q#1647 - >seq8294,superfamily,352825,50,125,0.00995443,35.1406,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1ME4a.ORF1.hs5_gmonkey.marg.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
25960,Q#1651 - >seq8298,non-specific,112704,2,74,0.00771643,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,pars,C-TerminusTruncated
25961,Q#1651 - >seq8298,superfamily,112704,2,74,0.00771643,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,pars,C-TerminusTruncated
25962,Q#1652 - >seq8299,non-specific,335182,146,242,1.30969e-30,110.855,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25963,Q#1652 - >seq8299,superfamily,335182,146,242,1.30969e-30,110.855,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25964,Q#1652 - >seq8299,non-specific,340205,245,308,1.0167700000000003e-24,94.3252,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25965,Q#1652 - >seq8299,superfamily,340205,245,308,1.0167700000000003e-24,94.3252,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25966,Q#1652 - >seq8299,non-specific,340204,102,144,1.50358e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25967,Q#1652 - >seq8299,superfamily,340204,102,144,1.50358e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs3_orang.pars.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame1,Trimerization,L1ME4a,ORF1,hs3_orang,pars,CompleteHit
25968,Q#1653 - >seq8300,specific,238827,494,752,4.761999999999999e-63,213.692,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25969,Q#1653 - >seq8300,superfamily,295487,494,752,4.761999999999999e-63,213.692,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25970,Q#1653 - >seq8300,specific,197310,9,236,6.89103e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25971,Q#1653 - >seq8300,superfamily,351117,9,236,6.89103e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25972,Q#1653 - >seq8300,specific,333820,500,724,1.8155199999999997e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25973,Q#1653 - >seq8300,superfamily,333820,500,724,1.8155199999999997e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25974,Q#1653 - >seq8300,non-specific,197306,9,236,1.6951900000000002e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25975,Q#1653 - >seq8300,non-specific,197320,9,229,2.37925e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25976,Q#1653 - >seq8300,non-specific,223780,9,237,9.260469999999999e-21,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25977,Q#1653 - >seq8300,non-specific,197307,9,236,3.20778e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25978,Q#1653 - >seq8300,specific,335306,10,229,1.35964e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25979,Q#1653 - >seq8300,non-specific,273186,9,237,1.20569e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25980,Q#1653 - >seq8300,non-specific,197319,13,236,1.51712e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25981,Q#1653 - >seq8300,non-specific,197321,7,236,4.18755e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25982,Q#1653 - >seq8300,non-specific,272954,9,236,2.37558e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25983,Q#1653 - >seq8300,non-specific,238828,500,721,2.28983e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25984,Q#1653 - >seq8300,non-specific,197336,9,194,1.71433e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25985,Q#1653 - >seq8300,non-specific,197322,8,236,9.93892e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25986,Q#1653 - >seq8300,non-specific,236970,9,189,1.68887e-06,50.663000000000004,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25987,Q#1653 - >seq8300,non-specific,275209,440,721,2.3221e-06,50.9192,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25988,Q#1653 - >seq8300,superfamily,275209,440,721,2.3221e-06,50.9192,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25989,Q#1653 - >seq8300,non-specific,197311,7,236,0.000120846,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25990,Q#1653 - >seq8300,non-specific,239569,509,753,0.000724479,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25991,Q#1653 - >seq8300,non-specific,238185,640,717,0.00113068,39.2564,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,marg,C-TerminusTruncated
25992,Q#1653 - >seq8300,non-specific,339261,108,232,0.0023611,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs2_gorilla,marg,CompleteHit
25993,Q#1656 - >seq8303,specific,238827,493,751,1.0595599999999998e-62,212.53599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25994,Q#1656 - >seq8303,superfamily,295487,493,751,1.0595599999999998e-62,212.53599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25995,Q#1656 - >seq8303,specific,197310,9,236,7.671729999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25996,Q#1656 - >seq8303,superfamily,351117,9,236,7.671729999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25997,Q#1656 - >seq8303,non-specific,197306,9,236,5.037689999999999e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25998,Q#1656 - >seq8303,specific,333820,499,723,6.66183e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
25999,Q#1656 - >seq8303,superfamily,333820,499,723,6.66183e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26000,Q#1656 - >seq8303,non-specific,197320,9,229,2.36985e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26001,Q#1656 - >seq8303,non-specific,223780,9,237,1.5095399999999998e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26002,Q#1656 - >seq8303,non-specific,197307,9,236,5.22948e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26003,Q#1656 - >seq8303,specific,335306,10,229,1.35443e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26004,Q#1656 - >seq8303,non-specific,273186,9,237,1.6075600000000002e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26005,Q#1656 - >seq8303,non-specific,197319,13,236,3.69353e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26006,Q#1656 - >seq8303,non-specific,197321,7,236,7.75548e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26007,Q#1656 - >seq8303,non-specific,272954,9,236,2.8014099999999996e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26008,Q#1656 - >seq8303,non-specific,238828,499,720,3.32786e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26009,Q#1656 - >seq8303,non-specific,197336,9,194,1.7077e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26010,Q#1656 - >seq8303,non-specific,197322,8,236,9.89978e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26011,Q#1656 - >seq8303,non-specific,236970,9,189,1.1398899999999998e-06,51.4334,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
26012,Q#1656 - >seq8303,non-specific,275209,439,720,4.62605e-06,50.1488,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
26013,Q#1656 - >seq8303,superfamily,275209,439,720,4.62605e-06,50.1488,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
26014,Q#1656 - >seq8303,non-specific,197311,7,236,9.46785e-05,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26015,Q#1656 - >seq8303,non-specific,239569,508,752,0.000776624,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26016,Q#1656 - >seq8303,non-specific,339261,108,232,0.000805904,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs2_gorilla,pars,CompleteHit
26017,Q#1656 - >seq8303,non-specific,238185,639,716,0.00160019,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME4a,ORF2,hs2_gorilla,pars,C-TerminusTruncated
26018,Q#1659 - >seq8306,non-specific,335182,55,151,8.377599999999999e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26019,Q#1659 - >seq8306,superfamily,335182,55,151,8.377599999999999e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26020,Q#1659 - >seq8306,non-specific,335182,55,151,8.377599999999999e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26021,Q#1659 - >seq8306,non-specific,340205,154,217,1.1664100000000001e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26022,Q#1659 - >seq8306,superfamily,340205,154,217,1.1664100000000001e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26023,Q#1659 - >seq8306,non-specific,340205,154,217,1.1664100000000001e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26024,Q#1659 - >seq8306,non-specific,340204,11,53,1.02711e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26025,Q#1659 - >seq8306,superfamily,340204,11,53,1.02711e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26026,Q#1659 - >seq8306,non-specific,340204,11,53,1.02711e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.marg.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,marg,CompleteHit
26027,Q#1662 - >seq8309,non-specific,335182,55,151,8.377599999999999e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26028,Q#1662 - >seq8309,superfamily,335182,55,151,8.377599999999999e-30,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26029,Q#1662 - >seq8309,non-specific,335182,55,151,8.377599999999999e-30,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26030,Q#1662 - >seq8309,non-specific,340205,154,217,1.1664100000000001e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26031,Q#1662 - >seq8309,superfamily,340205,154,217,1.1664100000000001e-25,94.7104,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26032,Q#1662 - >seq8309,non-specific,340205,154,217,1.1664100000000001e-25,94.7104,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26033,Q#1662 - >seq8309,non-specific,340204,11,53,1.02711e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26034,Q#1662 - >seq8309,superfamily,340204,11,53,1.02711e-07,47.0172,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26035,Q#1662 - >seq8309,non-specific,340204,11,53,1.02711e-07,47.0172,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs2_gorilla.pars.frame3,1909181109_L1ME4a.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs2_gorilla,pars,CompleteHit
26036,Q#1665 - >seq8312,specific,197310,9,232,8.08562e-56,193.33700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26037,Q#1665 - >seq8312,superfamily,351117,9,232,8.08562e-56,193.33700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26038,Q#1665 - >seq8312,non-specific,197306,9,232,1.07005e-30,121.434,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26039,Q#1665 - >seq8312,non-specific,197320,9,225,5.384020000000001e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26040,Q#1665 - >seq8312,non-specific,197307,9,232,1.6324700000000003e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26041,Q#1665 - >seq8312,non-specific,223780,9,233,6.82777e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26042,Q#1665 - >seq8312,non-specific,273186,9,233,2.32115e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26043,Q#1665 - >seq8312,non-specific,272954,9,232,3.76474e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26044,Q#1665 - >seq8312,non-specific,197319,13,232,2.79659e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26045,Q#1665 - >seq8312,non-specific,197321,7,232,4.38911e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26046,Q#1665 - >seq8312,specific,335306,10,225,6.48879e-15,74.9741,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26047,Q#1665 - >seq8312,non-specific,197336,9,190,2.67042e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26048,Q#1665 - >seq8312,non-specific,236970,9,185,3.55062e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26049,Q#1665 - >seq8312,non-specific,197311,7,142,4.978819999999999e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26050,Q#1665 - >seq8312,non-specific,139971,7,232,0.00286727,40.8328,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26051,Q#1665 - >seq8312,non-specific,339261,104,228,0.00414108,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26052,Q#1665 - >seq8312,non-specific,197318,9,232,0.00928464,39.2019,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1ME4a.ORF2.hs1_chimp.marg.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26053,Q#1666 - >seq8313,specific,238827,485,695,1.5114899999999998e-52,183.646,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26054,Q#1666 - >seq8313,superfamily,295487,485,695,1.5114899999999998e-52,183.646,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26055,Q#1666 - >seq8313,non-specific,333820,491,700,4.8493199999999996e-27,108.919,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26056,Q#1666 - >seq8313,superfamily,333820,491,700,4.8493199999999996e-27,108.919,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26057,Q#1666 - >seq8313,non-specific,238828,491,740,4.2720900000000003e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,CompleteHit
26058,Q#1666 - >seq8313,non-specific,275209,442,702,1.44391e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26059,Q#1666 - >seq8313,superfamily,275209,442,702,1.44391e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26060,Q#1666 - >seq8313,non-specific,238185,630,690,0.00071024,40.0268,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs1_chimp.marg.frame2,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26061,Q#1667 - >seq8314,non-specific,197310,9,70,2.55844e-11,64.6801,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26062,Q#1667 - >seq8314,superfamily,351117,9,70,2.55844e-11,64.6801,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26063,Q#1667 - >seq8314,non-specific,197306,9,71,7.969869999999999e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26064,Q#1667 - >seq8314,specific,335306,10,67,0.000106103,44.5434,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26065,Q#1667 - >seq8314,non-specific,223780,9,43,0.000274218,43.7411,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26066,Q#1667 - >seq8314,non-specific,197321,7,49,0.00030253,43.6948,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26067,Q#1667 - >seq8314,non-specific,197307,9,64,0.00139609,41.5045,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26068,Q#1667 - >seq8314,non-specific,197320,9,43,0.00209203,40.9614,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26069,Q#1667 - >seq8314,non-specific,273186,9,43,0.00378894,40.34,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs1_chimp.pars.frame3,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs1_chimp,pars,C-TerminusTruncated
26070,Q#1670 - >seq8317,non-specific,335182,154,250,1.70254e-29,108.15899999999999,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26071,Q#1670 - >seq8317,superfamily,335182,154,250,1.70254e-29,108.15899999999999,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26072,Q#1670 - >seq8317,non-specific,340205,253,316,4.4250099999999995e-24,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26073,Q#1670 - >seq8317,superfamily,340205,253,316,4.4250099999999995e-24,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26074,Q#1670 - >seq8317,non-specific,340204,110,152,1.5543200000000002e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26075,Q#1670 - >seq8317,superfamily,340204,110,152,1.5543200000000002e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs3_orang,marg,CompleteHit
26076,Q#1670 - >seq8317,non-specific,237177,42,148,4.64901e-06,47.8506,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26077,Q#1670 - >seq8317,superfamily,237177,42,148,4.64901e-06,47.8506,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26078,Q#1670 - >seq8317,non-specific,235175,49,154,8.04877e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26079,Q#1670 - >seq8317,superfamily,235175,49,154,8.04877e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26080,Q#1670 - >seq8317,non-specific,188306,43,149,0.00035574900000000004,41.835,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26081,Q#1670 - >seq8317,superfamily,188306,43,149,0.00035574900000000004,41.835,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26082,Q#1670 - >seq8317,non-specific,274008,41,148,0.00047346800000000006,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26083,Q#1670 - >seq8317,superfamily,274008,41,148,0.00047346800000000006,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26084,Q#1670 - >seq8317,non-specific,336159,60,144,0.00145087,40.0453,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs3_orang,marg,N-TerminusTruncated
26085,Q#1670 - >seq8317,superfamily,336159,60,144,0.00145087,40.0453,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs3_orang,marg,N-TerminusTruncated
26086,Q#1670 - >seq8317,non-specific,224117,49,149,0.00154591,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26087,Q#1670 - >seq8317,superfamily,224117,49,149,0.00154591,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26088,Q#1670 - >seq8317,non-specific,274386,11,146,0.00260354,39.2642,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26089,Q#1670 - >seq8317,superfamily,274386,11,146,0.00260354,39.2642,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26090,Q#1670 - >seq8317,non-specific,337663,62,146,0.00324677,38.5599,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26091,Q#1670 - >seq8317,superfamily,337663,62,146,0.00324677,38.5599,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26092,Q#1670 - >seq8317,non-specific,274009,33,149,0.00340665,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26093,Q#1670 - >seq8317,superfamily,274009,33,149,0.00340665,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26094,Q#1670 - >seq8317,non-specific,224117,24,148,0.00366784,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26095,Q#1670 - >seq8317,non-specific,224495,41,148,0.00672033,37.3451,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26096,Q#1670 - >seq8317,superfamily,224495,41,148,0.00672033,37.3451,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26097,Q#1670 - >seq8317,non-specific,335541,50,135,0.009010700000000002,36.0255,pfam03938,OmpH,C,cl38144,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26098,Q#1670 - >seq8317,superfamily,335541,50,135,0.009010700000000002,36.0255,cl38144,OmpH superfamily,C, - ,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26099,Q#1670 - >seq8317,non-specific,235461,47,128,0.00926889,37.355,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26100,Q#1670 - >seq8317,superfamily,235461,47,128,0.00926889,37.355,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26101,Q#1670 - >seq8317,non-specific,112704,2,147,0.00966562,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26102,Q#1670 - >seq8317,superfamily,112704,2,147,0.00966562,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs3_orang,marg,C-TerminusTruncated
26103,Q#1670 - >seq8317,non-specific,310273,86,146,0.00996491,37.4174,pfam05557,MAD,NC,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26104,Q#1670 - >seq8317,superfamily,310273,86,146,0.00996491,37.4174,cl37733,MAD superfamily,NC, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs3_orang,marg,BothTerminiTruncated
26105,Q#1671 - >seq8318,non-specific,240274,657,992,0.00658714,40.3585,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1ME4a.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26106,Q#1671 - >seq8318,superfamily,240274,657,992,0.00658714,40.3585,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1ME4a.ORF2.hs1_chimp.marg.frame1,1909181109_L1ME4a.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Unusual,L1ME4a,ORF2,hs1_chimp,marg,C-TerminusTruncated
26107,Q#1672 - >seq8319,specific,238827,481,743,3.7006599999999993e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26108,Q#1672 - >seq8319,superfamily,295487,481,743,3.7006599999999993e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26109,Q#1672 - >seq8319,specific,333820,487,743,1.9041700000000001e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26110,Q#1672 - >seq8319,superfamily,333820,487,743,1.9041700000000001e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26111,Q#1672 - >seq8319,non-specific,238828,553,708,5.08286e-13,69.5372,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,N-TerminusTruncated
26112,Q#1672 - >seq8319,non-specific,275209,558,767,2.5600799999999997e-07,54.0008,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,N-TerminusTruncated
26113,Q#1672 - >seq8319,superfamily,275209,558,767,2.5600799999999997e-07,54.0008,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,N-TerminusTruncated
26114,Q#1672 - >seq8319,non-specific,238185,627,741,1.03725e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26115,Q#1672 - >seq8319,non-specific,239569,496,718,2.63444e-05,46.4119,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs3_orang.pars.frame2,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26116,Q#1675 - >seq8322,non-specific,335182,153,249,2.1020199999999998e-30,110.47,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26117,Q#1675 - >seq8322,superfamily,335182,153,249,2.1020199999999998e-30,110.47,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26118,Q#1675 - >seq8322,non-specific,340205,252,315,2.11846e-24,93.94,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26119,Q#1675 - >seq8322,superfamily,340205,252,315,2.11846e-24,93.94,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26120,Q#1675 - >seq8322,non-specific,340204,108,150,1.2982599999999999e-06,44.3208,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26121,Q#1675 - >seq8322,superfamily,340204,108,150,1.2982599999999999e-06,44.3208,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs5_gmonkey,pars,CompleteHit
26122,Q#1675 - >seq8322,non-specific,235175,46,153,5.2556399999999995e-06,47.7512,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26123,Q#1675 - >seq8322,superfamily,235175,46,153,5.2556399999999995e-06,47.7512,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26124,Q#1675 - >seq8322,non-specific,237177,39,146,9.91041e-06,46.695,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26125,Q#1675 - >seq8322,superfamily,237177,39,146,9.91041e-06,46.695,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26126,Q#1675 - >seq8322,non-specific,336159,57,142,0.000228182,42.7417,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
26127,Q#1675 - >seq8322,superfamily,336159,57,142,0.000228182,42.7417,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
26128,Q#1675 - >seq8322,non-specific,224117,46,158,0.000592847,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26129,Q#1675 - >seq8322,superfamily,224117,46,158,0.000592847,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26130,Q#1675 - >seq8322,non-specific,274009,30,147,0.000679064,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26131,Q#1675 - >seq8322,superfamily,274009,30,147,0.000679064,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26132,Q#1675 - >seq8322,non-specific,188306,40,147,0.00086206,40.6794,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26133,Q#1675 - >seq8322,superfamily,188306,40,147,0.00086206,40.6794,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26134,Q#1675 - >seq8322,non-specific,274008,42,147,0.00149222,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26135,Q#1675 - >seq8322,superfamily,274008,42,147,0.00149222,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26136,Q#1675 - >seq8322,non-specific,224117,38,146,0.00293273,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26137,Q#1675 - >seq8322,non-specific,310273,57,147,0.00331647,38.9582,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26138,Q#1675 - >seq8322,superfamily,310273,57,147,0.00331647,38.9582,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26139,Q#1675 - >seq8322,non-specific,188306,31,146,0.00375187,38.7534,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26140,Q#1675 - >seq8322,non-specific,274386,8,144,0.00409284,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26141,Q#1675 - >seq8322,superfamily,274386,8,144,0.00409284,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26142,Q#1675 - >seq8322,non-specific,224117,46,147,0.0049497,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26143,Q#1675 - >seq8322,non-specific,222878,59,147,0.00506608,38.4569,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26144,Q#1675 - >seq8322,superfamily,222878,59,147,0.00506608,38.4569,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26145,Q#1675 - >seq8322,non-specific,130673,80,146,0.005307,38.494,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26146,Q#1675 - >seq8322,superfamily,130673,80,146,0.005307,38.494,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26147,Q#1675 - >seq8322,non-specific,274008,57,142,0.00542915,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26148,Q#1675 - >seq8322,non-specific,235175,38,147,0.00767394,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26149,Q#1675 - >seq8322,non-specific,335541,47,133,0.00786262,36.0255,pfam03938,OmpH,C,cl38144,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26150,Q#1675 - >seq8322,superfamily,335541,47,133,0.00786262,36.0255,cl38144,OmpH superfamily,C, - ,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26151,Q#1675 - >seq8322,non-specific,274009,30,147,0.00789313,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26152,Q#1675 - >seq8322,non-specific,224117,38,146,0.00857194,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
26153,Q#1675 - >seq8322,non-specific,274091,62,147,0.0090147,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
26154,Q#1675 - >seq8322,superfamily,274091,62,147,0.0090147,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
26155,Q#1675 - >seq8322,non-specific,223250,44,156,0.00963149,37.1925,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26156,Q#1675 - >seq8322,superfamily,223250,44,156,0.00963149,37.1925,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs5_gmonkey.pars.frame3,1909181109_L1ME4a.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
26157,Q#1676 - >seq8323,non-specific,197310,9,65,5.8274199999999994e-12,66.6061,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26158,Q#1676 - >seq8323,superfamily,351117,9,65,5.8274199999999994e-12,66.6061,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26159,Q#1676 - >seq8323,non-specific,197306,9,90,2.03572e-08,56.3357,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26160,Q#1676 - >seq8323,non-specific,223780,9,43,0.000284757,43.7411,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26161,Q#1676 - >seq8323,specific,335306,10,53,0.000287486,43.3878,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26162,Q#1676 - >seq8323,non-specific,197321,7,49,0.000389786,43.3096,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26163,Q#1676 - >seq8323,non-specific,197307,9,76,0.000700621,42.6601,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26164,Q#1676 - >seq8323,non-specific,197320,9,43,0.00217172,40.9614,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26165,Q#1676 - >seq8323,non-specific,273186,9,43,0.0039329000000000005,40.34,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26166,Q#1676 - >seq8323,non-specific,197336,9,59,0.00865844,39.1327,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26167,Q#1677 - >seq8324,specific,238827,469,731,9.611939999999998e-70,232.567,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26168,Q#1677 - >seq8324,superfamily,295487,469,731,9.611939999999998e-70,232.567,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26169,Q#1677 - >seq8324,specific,333820,475,731,1.0495199999999999e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26170,Q#1677 - >seq8324,superfamily,333820,475,731,1.0495199999999999e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26171,Q#1677 - >seq8324,non-specific,238828,475,696,1.13268e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26172,Q#1677 - >seq8324,non-specific,275209,425,696,5.82503e-10,62.09,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26173,Q#1677 - >seq8324,superfamily,275209,425,696,5.82503e-10,62.09,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,C-TerminusTruncated
26174,Q#1677 - >seq8324,non-specific,238185,615,731,2.47291e-06,46.9604,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26175,Q#1677 - >seq8324,non-specific,239569,484,706,0.000190792,43.7155,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs4_gibbon.marg.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26176,Q#1678 - >seq8325,specific,197310,37,229,1.1219699999999999e-41,152.891,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26177,Q#1678 - >seq8325,superfamily,351117,37,229,1.1219699999999999e-41,152.891,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26178,Q#1678 - >seq8325,non-specific,197306,56,229,1.0681099999999999e-19,89.4628,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26179,Q#1678 - >seq8325,non-specific,197320,47,222,7.22242e-13,69.8514,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26180,Q#1678 - >seq8325,non-specific,223780,52,230,1.1412299999999999e-10,63.3863,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26181,Q#1678 - >seq8325,non-specific,197307,82,229,7.438939999999999e-10,60.7645,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26182,Q#1678 - >seq8325,non-specific,197319,65,229,2.16337e-08,56.1309,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26183,Q#1678 - >seq8325,non-specific,272954,56,229,2.1484300000000001e-07,53.1557,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26184,Q#1678 - >seq8325,non-specific,273186,47,230,9.00285e-07,51.5108,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26185,Q#1678 - >seq8325,specific,335306,54,222,1.262e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26186,Q#1678 - >seq8325,non-specific,197321,62,229,1.64469e-05,47.5468,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease,L1ME4a,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26187,Q#1678 - >seq8325,non-specific,339261,101,225,0.00041633400000000003,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs4_gibbon.marg.frame1,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1ME4a,ORF2,hs4_gibbon,marg,CompleteHit
26188,Q#1679 - >seq8326,specific,197310,3,230,8.250169999999999e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26189,Q#1679 - >seq8326,superfamily,351117,3,230,8.250169999999999e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26190,Q#1679 - >seq8326,non-specific,197306,3,230,4.2865199999999995e-34,131.064,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26191,Q#1679 - >seq8326,non-specific,197320,3,223,1.35704e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26192,Q#1679 - >seq8326,non-specific,223780,3,231,6.09455e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26193,Q#1679 - >seq8326,non-specific,197307,3,230,9.85965e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26194,Q#1679 - >seq8326,specific,335306,4,223,7.980429999999999e-18,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26195,Q#1679 - >seq8326,non-specific,273186,3,231,1.31711e-16,80.786,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26196,Q#1679 - >seq8326,non-specific,197321,1,230,3.52006e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26197,Q#1679 - >seq8326,non-specific,272954,3,230,1.71083e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26198,Q#1679 - >seq8326,non-specific,197319,7,230,2.18733e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26199,Q#1679 - >seq8326,non-specific,197336,3,188,6.09589e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26200,Q#1679 - >seq8326,non-specific,197322,2,230,1.09208e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26201,Q#1679 - >seq8326,non-specific,236970,3,243,8.895920000000001e-08,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26202,Q#1679 - >seq8326,non-specific,197311,1,230,7.75904e-05,44.9753,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26203,Q#1679 - >seq8326,non-specific,339261,102,226,0.000132173,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26204,Q#1680 - >seq8327,specific,238827,488,745,2.5332699999999993e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26205,Q#1680 - >seq8327,superfamily,295487,488,745,2.5332699999999993e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26206,Q#1680 - >seq8327,specific,333820,494,718,4.412e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26207,Q#1680 - >seq8327,superfamily,333820,494,718,4.412e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26208,Q#1680 - >seq8327,non-specific,238828,494,715,6.897569999999999e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26209,Q#1680 - >seq8327,non-specific,275209,444,715,3.67116e-10,62.8604,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
26210,Q#1680 - >seq8327,superfamily,275209,444,715,3.67116e-10,62.8604,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,C-TerminusTruncated
26211,Q#1680 - >seq8327,non-specific,239569,503,725,0.000195277,43.7155,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26212,Q#1680 - >seq8327,non-specific,238185,634,745,0.00026823900000000003,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs4_gibbon.pars.frame2,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME4a,ORF2,hs4_gibbon,pars,CompleteHit
26213,Q#1684 - >seq8331,specific,197310,3,230,3.1680699999999995e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26214,Q#1684 - >seq8331,superfamily,351117,3,230,3.1680699999999995e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26215,Q#1684 - >seq8331,non-specific,197306,3,230,1.6766299999999997e-34,132.22,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26216,Q#1684 - >seq8331,non-specific,223780,3,231,2.6443299999999997e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26217,Q#1684 - >seq8331,non-specific,197320,3,223,7.83883e-22,96.0449,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26218,Q#1684 - >seq8331,non-specific,197307,3,230,9.15967e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26219,Q#1684 - >seq8331,specific,335306,4,223,1.00583e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26220,Q#1684 - >seq8331,non-specific,197319,7,230,1.20449e-16,80.7837,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26221,Q#1684 - >seq8331,non-specific,273186,3,231,1.8885199999999999e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26222,Q#1684 - >seq8331,non-specific,197321,1,230,3.91314e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26223,Q#1684 - >seq8331,non-specific,272954,3,230,6.32498e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26224,Q#1684 - >seq8331,non-specific,197336,3,188,1.40869e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26225,Q#1684 - >seq8331,non-specific,197322,2,230,4.9351099999999995e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26226,Q#1684 - >seq8331,non-specific,236970,3,243,2.77879e-07,52.9742,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26227,Q#1684 - >seq8331,non-specific,197311,24,230,5.68794e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26228,Q#1684 - >seq8331,non-specific,339261,102,226,8.76066e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs3_orang.pars.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs3_orang,pars,CompleteHit
26229,Q#1685 - >seq8332,non-specific,335182,156,252,6.69028e-29,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26230,Q#1685 - >seq8332,superfamily,335182,156,252,6.69028e-29,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26231,Q#1685 - >seq8332,non-specific,340205,255,318,4.71298e-24,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26232,Q#1685 - >seq8332,superfamily,340205,255,318,4.71298e-24,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26233,Q#1685 - >seq8332,non-specific,340204,111,153,1.88518e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26234,Q#1685 - >seq8332,superfamily,340204,111,153,1.88518e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Trimerization,L1ME4a,ORF1,hs4_gibbon,marg,CompleteHit
26235,Q#1685 - >seq8332,non-specific,237177,42,149,6.603279999999999e-06,47.4654,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26236,Q#1685 - >seq8332,superfamily,237177,42,149,6.603279999999999e-06,47.4654,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26237,Q#1685 - >seq8332,non-specific,235175,49,156,8.49162e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26238,Q#1685 - >seq8332,superfamily,235175,49,156,8.49162e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26239,Q#1685 - >seq8332,non-specific,336159,60,145,7.27587e-05,44.2825,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26240,Q#1685 - >seq8332,superfamily,336159,60,145,7.27587e-05,44.2825,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26241,Q#1685 - >seq8332,non-specific,274009,60,164,0.000295922,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26242,Q#1685 - >seq8332,superfamily,274009,60,164,0.000295922,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26243,Q#1685 - >seq8332,non-specific,224117,28,163,0.000315926,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26244,Q#1685 - >seq8332,superfamily,224117,28,163,0.000315926,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26245,Q#1685 - >seq8332,non-specific,274009,33,150,0.000513443,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26246,Q#1685 - >seq8332,non-specific,310273,60,165,0.0007076280000000001,40.8842,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26247,Q#1685 - >seq8332,superfamily,310273,60,165,0.0007076280000000001,40.8842,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26248,Q#1685 - >seq8332,non-specific,224117,49,150,0.000750785,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26249,Q#1685 - >seq8332,non-specific,188306,43,150,0.000900185,40.6794,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26250,Q#1685 - >seq8332,superfamily,188306,43,150,0.000900185,40.6794,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26251,Q#1685 - >seq8332,non-specific,222878,62,150,0.000986925,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26252,Q#1685 - >seq8332,superfamily,222878,62,150,0.000986925,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26253,Q#1685 - >seq8332,non-specific,275056,60,152,0.00114937,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26254,Q#1685 - >seq8332,superfamily,275056,60,152,0.00114937,39.2209,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26255,Q#1685 - >seq8332,non-specific,274008,60,145,0.00147875,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26256,Q#1685 - >seq8332,superfamily,274008,60,145,0.00147875,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26257,Q#1685 - >seq8332,non-specific,224117,33,149,0.00179789,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26258,Q#1685 - >seq8332,non-specific,224117,41,149,0.00203151,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26259,Q#1685 - >seq8332,non-specific,274008,45,150,0.00209652,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26260,Q#1685 - >seq8332,non-specific,224117,43,164,0.00306109,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26261,Q#1685 - >seq8332,non-specific,223250,47,165,0.0037391999999999994,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26262,Q#1685 - >seq8332,superfamily,223250,47,165,0.0037391999999999994,38.7333,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26263,Q#1685 - >seq8332,non-specific,224117,46,149,0.00445341,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26264,Q#1685 - >seq8332,non-specific,188306,34,149,0.00518614,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26265,Q#1685 - >seq8332,non-specific,130673,49,149,0.00553706,38.494,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26266,Q#1685 - >seq8332,superfamily,130673,49,149,0.00553706,38.494,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26267,Q#1685 - >seq8332,non-specific,274386,11,147,0.00555874,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26268,Q#1685 - >seq8332,superfamily,274386,11,147,0.00555874,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26269,Q#1685 - >seq8332,non-specific,226447,50,125,0.00589693,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26270,Q#1685 - >seq8332,superfamily,352825,50,125,0.00589693,35.911,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26271,Q#1685 - >seq8332,non-specific,274008,49,149,0.00645557,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26272,Q#1685 - >seq8332,non-specific,337663,62,147,0.00769267,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26273,Q#1685 - >seq8332,superfamily,337663,62,147,0.00769267,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26274,Q#1685 - >seq8332,non-specific,224495,33,149,0.00791298,36.9599,COG1579,COG1579,NC,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26275,Q#1685 - >seq8332,superfamily,224495,33,149,0.00791298,36.9599,cl34310,COG1579 superfamily,NC, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,BothTerminiTruncated
26276,Q#1685 - >seq8332,non-specific,274091,65,150,0.00876473,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26277,Q#1685 - >seq8332,superfamily,274091,65,150,0.00876473,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,marg,N-TerminusTruncated
26278,Q#1685 - >seq8332,non-specific,335541,50,136,0.00952314,36.0255,pfam03938,OmpH,C,cl38144,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26279,Q#1685 - >seq8332,superfamily,335541,50,136,0.00952314,36.0255,cl38144,OmpH superfamily,C, - ,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs4_gibbon.marg.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs4_gibbon,marg,C-TerminusTruncated
26280,Q#1686 - >seq8333,specific,197310,3,230,2.2139799999999997e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26281,Q#1686 - >seq8333,superfamily,351117,3,230,2.2139799999999997e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26282,Q#1686 - >seq8333,non-specific,197306,3,230,2.02772e-34,132.22,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26283,Q#1686 - >seq8333,non-specific,223780,3,231,2.71726e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26284,Q#1686 - >seq8333,non-specific,197320,3,223,8.05364e-22,96.0449,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26285,Q#1686 - >seq8333,non-specific,197307,3,230,2.1697400000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26286,Q#1686 - >seq8333,specific,335306,4,223,1.03254e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26287,Q#1686 - >seq8333,non-specific,273186,3,231,1.93999e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26288,Q#1686 - >seq8333,non-specific,197319,7,230,2.3492799999999997e-16,80.0133,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26289,Q#1686 - >seq8333,non-specific,197321,1,230,4.1348699999999994e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26290,Q#1686 - >seq8333,non-specific,272954,3,230,1.04008e-15,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26291,Q#1686 - >seq8333,non-specific,197336,3,188,1.4465899999999999e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26292,Q#1686 - >seq8333,non-specific,197322,2,230,5.07112e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26293,Q#1686 - >seq8333,non-specific,236970,3,243,8.24957e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26294,Q#1686 - >seq8333,non-specific,197311,24,230,5.83442e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26295,Q#1686 - >seq8333,non-specific,339261,102,226,0.00017826599999999998,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME4a.ORF2.hs3_orang.marg.frame3,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26296,Q#1689 - >seq8336,non-specific,335182,156,252,6.69028e-29,106.618,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26297,Q#1689 - >seq8336,superfamily,335182,156,252,6.69028e-29,106.618,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26298,Q#1689 - >seq8336,non-specific,340205,255,318,4.71298e-24,92.7844,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26299,Q#1689 - >seq8336,superfamily,340205,255,318,4.71298e-24,92.7844,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26300,Q#1689 - >seq8336,non-specific,340204,111,153,1.88518e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26301,Q#1689 - >seq8336,superfamily,340204,111,153,1.88518e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1ME4a,ORF1,hs4_gibbon,pars,CompleteHit
26302,Q#1689 - >seq8336,non-specific,237177,42,149,6.603279999999999e-06,47.4654,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26303,Q#1689 - >seq8336,superfamily,237177,42,149,6.603279999999999e-06,47.4654,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26304,Q#1689 - >seq8336,non-specific,235175,49,156,8.49162e-06,47.36600000000001,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26305,Q#1689 - >seq8336,superfamily,235175,49,156,8.49162e-06,47.36600000000001,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26306,Q#1689 - >seq8336,non-specific,336159,60,145,7.27587e-05,44.2825,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26307,Q#1689 - >seq8336,superfamily,336159,60,145,7.27587e-05,44.2825,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26308,Q#1689 - >seq8336,non-specific,274009,60,164,0.000295922,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26309,Q#1689 - >seq8336,superfamily,274009,60,164,0.000295922,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26310,Q#1689 - >seq8336,non-specific,224117,28,163,0.000315926,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26311,Q#1689 - >seq8336,superfamily,224117,28,163,0.000315926,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26312,Q#1689 - >seq8336,non-specific,274009,33,150,0.000513443,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26313,Q#1689 - >seq8336,non-specific,310273,60,165,0.0007076280000000001,40.8842,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26314,Q#1689 - >seq8336,superfamily,310273,60,165,0.0007076280000000001,40.8842,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26315,Q#1689 - >seq8336,non-specific,224117,49,150,0.000750785,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26316,Q#1689 - >seq8336,non-specific,188306,43,150,0.000900185,40.6794,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26317,Q#1689 - >seq8336,superfamily,188306,43,150,0.000900185,40.6794,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26318,Q#1689 - >seq8336,non-specific,222878,62,150,0.000986925,40.3829,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26319,Q#1689 - >seq8336,superfamily,222878,62,150,0.000986925,40.3829,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26320,Q#1689 - >seq8336,non-specific,275056,60,152,0.00114937,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26321,Q#1689 - >seq8336,superfamily,275056,60,152,0.00114937,39.2209,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26322,Q#1689 - >seq8336,non-specific,274008,60,145,0.00147875,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26323,Q#1689 - >seq8336,superfamily,274008,60,145,0.00147875,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26324,Q#1689 - >seq8336,non-specific,224117,33,149,0.00179789,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26325,Q#1689 - >seq8336,non-specific,224117,41,149,0.00203151,39.6976,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26326,Q#1689 - >seq8336,non-specific,274008,45,150,0.00209652,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26327,Q#1689 - >seq8336,non-specific,224117,43,164,0.00306109,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26328,Q#1689 - >seq8336,non-specific,223250,47,165,0.0037391999999999994,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26329,Q#1689 - >seq8336,superfamily,223250,47,165,0.0037391999999999994,38.7333,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26330,Q#1689 - >seq8336,non-specific,224117,46,149,0.00445341,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26331,Q#1689 - >seq8336,non-specific,188306,34,149,0.00518614,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26332,Q#1689 - >seq8336,non-specific,130673,49,149,0.00553706,38.494,TIGR01612,235kDa-fam,NC,cl31124,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26333,Q#1689 - >seq8336,superfamily,130673,49,149,0.00553706,38.494,cl31124,235kDa-fam superfamily,NC, - ,"reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26334,Q#1689 - >seq8336,non-specific,274386,11,147,0.00555874,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26335,Q#1689 - >seq8336,superfamily,274386,11,147,0.00555874,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26336,Q#1689 - >seq8336,non-specific,226447,50,125,0.00589693,35.911,COG3937,PhaF,N,cl07863,"Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]; Uncharacterized conserved protein [Function unknown].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26337,Q#1689 - >seq8336,superfamily,352825,50,125,0.00589693,35.911,cl07863,Phasin superfamily,N, - ,Poly(hydroxyalcanoate) granule associated protein (phasin); Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26338,Q#1689 - >seq8336,non-specific,274008,49,149,0.00645557,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26339,Q#1689 - >seq8336,non-specific,337663,62,147,0.00769267,37.4043,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26340,Q#1689 - >seq8336,superfamily,337663,62,147,0.00769267,37.4043,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26341,Q#1689 - >seq8336,non-specific,224495,33,149,0.00791298,36.9599,COG1579,COG1579,NC,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26342,Q#1689 - >seq8336,superfamily,224495,33,149,0.00791298,36.9599,cl34310,COG1579 superfamily,NC, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,BothTerminiTruncated
26343,Q#1689 - >seq8336,non-specific,274091,65,150,0.00876473,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26344,Q#1689 - >seq8336,superfamily,274091,65,150,0.00876473,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1ME4a,ORF1,hs4_gibbon,pars,N-TerminusTruncated
26345,Q#1689 - >seq8336,non-specific,335541,50,136,0.00952314,36.0255,pfam03938,OmpH,C,cl38144,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26346,Q#1689 - >seq8336,superfamily,335541,50,136,0.00952314,36.0255,cl38144,OmpH superfamily,C, - ,Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.,L1ME4a.ORF1.hs4_gibbon.pars.frame3,1909181109_L1ME4a.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round3.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1ME4a,ORF1,hs4_gibbon,pars,C-TerminusTruncated
26347,Q#1692 - >seq8339,specific,238827,454,716,2.9873699999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26348,Q#1692 - >seq8339,superfamily,295487,454,716,2.9873699999999994e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26349,Q#1692 - >seq8339,specific,333820,460,716,1.38586e-34,130.49,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26350,Q#1692 - >seq8339,superfamily,333820,460,716,1.38586e-34,130.49,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26351,Q#1692 - >seq8339,non-specific,238828,526,681,3.22819e-13,69.9224,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,N-TerminusTruncated
26352,Q#1692 - >seq8339,non-specific,275209,531,740,1.92133e-07,54.386,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,N-TerminusTruncated
26353,Q#1692 - >seq8339,superfamily,275209,531,740,1.92133e-07,54.386,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,N-TerminusTruncated
26354,Q#1692 - >seq8339,non-specific,238185,600,714,4.37364e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26355,Q#1692 - >seq8339,non-specific,239569,469,691,3.4721e-05,46.0267,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1ME4a.ORF2.hs3_orang.marg.frame1,1909181109_L1ME4a.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round3.marginal_IndelAndChars_N1.frame1,RT,L1ME4a,ORF2,hs3_orang,marg,CompleteHit
26356,Q#1693 - >seq8340,specific,197310,9,236,1.9059699999999998e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26357,Q#1693 - >seq8340,superfamily,351117,9,236,1.9059699999999998e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26358,Q#1693 - >seq8340,specific,238827,525,765,6.720509999999999e-52,181.72,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26359,Q#1693 - >seq8340,superfamily,295487,525,765,6.720509999999999e-52,181.72,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26360,Q#1693 - >seq8340,non-specific,197306,9,236,2.71648e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26361,Q#1693 - >seq8340,non-specific,333820,525,765,5.08053e-26,106.223,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26362,Q#1693 - >seq8340,superfamily,333820,525,765,5.08053e-26,106.223,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26363,Q#1693 - >seq8340,non-specific,197307,9,236,4.96459e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26364,Q#1693 - >seq8340,specific,335306,10,229,8.282360000000001e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26365,Q#1693 - >seq8340,non-specific,223780,9,229,3.02271e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26366,Q#1693 - >seq8340,non-specific,197320,9,229,3.88242e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26367,Q#1693 - >seq8340,non-specific,197321,7,236,2.433e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26368,Q#1693 - >seq8340,non-specific,273186,9,237,3.59735e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26369,Q#1693 - >seq8340,non-specific,197319,9,236,4.9638800000000005e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26370,Q#1693 - >seq8340,non-specific,272954,9,236,6.868380000000001e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26371,Q#1693 - >seq8340,non-specific,238828,577,730,1.8446199999999998e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
26372,Q#1693 - >seq8340,non-specific,197336,9,229,4.17003e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26373,Q#1693 - >seq8340,non-specific,236970,9,207,2.57042e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26374,Q#1693 - >seq8340,non-specific,197311,30,236,2.05329e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26375,Q#1693 - >seq8340,non-specific,275209,582,789,7.18571e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
26376,Q#1693 - >seq8340,superfamily,275209,582,789,7.18571e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
26377,Q#1693 - >seq8340,non-specific,238185,651,765,1.78332e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26378,Q#1693 - >seq8340,non-specific,197322,8,236,2.10646e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26379,Q#1693 - >seq8340,non-specific,339261,108,232,0.000192438,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26380,Q#1693 - >seq8340,non-specific,197318,9,236,0.000447756,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26381,Q#1693 - >seq8340,specific,311990,1232,1250,0.00356135,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26382,Q#1693 - >seq8340,superfamily,311990,1232,1250,0.00356135,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs4_gibbon,pars,CompleteHit
26383,Q#1693 - >seq8340,non-specific,235175,291,468,0.00365849,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
26384,Q#1693 - >seq8340,superfamily,235175,291,468,0.00365849,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
26385,Q#1695 - >seq8342,specific,311990,1125,1143,0.0007891819999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26386,Q#1695 - >seq8342,superfamily,311990,1125,1143,0.0007891819999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26387,Q#1697 - >seq8344,specific,311990,1115,1133,0.000829835,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26388,Q#1697 - >seq8344,superfamily,311990,1115,1133,0.000829835,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26389,Q#1698 - >seq8345,specific,197310,9,236,7.475929999999999e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26390,Q#1698 - >seq8345,superfamily,351117,9,236,7.475929999999999e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26391,Q#1698 - >seq8345,specific,238827,547,768,7.93255e-45,161.305,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26392,Q#1698 - >seq8345,superfamily,295487,547,768,7.93255e-45,161.305,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26393,Q#1698 - >seq8345,non-specific,197306,9,236,1.24628e-29,118.353,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26394,Q#1698 - >seq8345,non-specific,333820,552,768,9.69266e-22,93.8961,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26395,Q#1698 - >seq8345,superfamily,333820,552,768,9.69266e-22,93.8961,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26396,Q#1698 - >seq8345,specific,335306,10,229,4.61443e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26397,Q#1698 - >seq8345,non-specific,197320,9,229,4.29275e-18,85.2593,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26398,Q#1698 - >seq8345,non-specific,197307,9,236,5.8789599999999996e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26399,Q#1698 - >seq8345,non-specific,223780,9,229,4.84159e-17,82.2611,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26400,Q#1698 - >seq8345,non-specific,197321,7,236,1.67619e-13,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26401,Q#1698 - >seq8345,non-specific,273186,9,237,4.28821e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26402,Q#1698 - >seq8345,non-specific,272954,9,236,1.42132e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26403,Q#1698 - >seq8345,non-specific,197319,9,236,1.6445799999999998e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26404,Q#1698 - >seq8345,non-specific,238828,578,733,2.53753e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,N-TerminusTruncated
26405,Q#1698 - >seq8345,non-specific,197336,9,229,1.63272e-07,53.7703,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26406,Q#1698 - >seq8345,non-specific,275209,583,792,4.10306e-07,53.6156,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,N-TerminusTruncated
26407,Q#1698 - >seq8345,superfamily,275209,583,792,4.10306e-07,53.6156,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,N-TerminusTruncated
26408,Q#1698 - >seq8345,non-specific,235175,291,469,2.7523200000000004e-06,51.6032,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,marg,BothTerminiTruncated
26409,Q#1698 - >seq8345,superfamily,235175,291,469,2.7523200000000004e-06,51.6032,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,marg,BothTerminiTruncated
26410,Q#1698 - >seq8345,non-specific,197311,7,236,3.4921e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26411,Q#1698 - >seq8345,non-specific,236970,9,207,1.4523800000000001e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26412,Q#1698 - >seq8345,non-specific,238185,652,768,8.73398e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26413,Q#1698 - >seq8345,non-specific,334125,212,412,0.000316574,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MA4A,ORF2,hs3_orang,marg,N-TerminusTruncated
26414,Q#1698 - >seq8345,superfamily,334125,212,412,0.000316574,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1MA4A,ORF2,hs3_orang,marg,N-TerminusTruncated
26415,Q#1698 - >seq8345,non-specific,339261,108,232,0.000357173,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MA4A,ORF2,hs3_orang,marg,CompleteHit
26416,Q#1698 - >seq8345,non-specific,274009,307,452,0.0016768,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,marg,C-TerminusTruncated
26417,Q#1698 - >seq8345,superfamily,274009,307,452,0.0016768,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs3_orang.marg.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,marg,C-TerminusTruncated
26418,Q#1699 - >seq8346,non-specific,240274,223,517,0.00432641,41.1289,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs3_orang.marg.frame1,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MA4A,ORF2,hs3_orang,marg,C-TerminusTruncated
26419,Q#1699 - >seq8346,superfamily,240274,223,517,0.00432641,41.1289,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs3_orang.marg.frame1,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MA4A,ORF2,hs3_orang,marg,C-TerminusTruncated
26420,Q#1702 - >seq8349,specific,238827,510,772,1.1645099999999997e-63,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26421,Q#1702 - >seq8349,superfamily,295487,510,772,1.1645099999999997e-63,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26422,Q#1702 - >seq8349,specific,197310,9,236,6.04224e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26423,Q#1702 - >seq8349,superfamily,351117,9,236,6.04224e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26424,Q#1702 - >seq8349,specific,333820,516,772,4.4455e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26425,Q#1702 - >seq8349,superfamily,333820,516,772,4.4455e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26426,Q#1702 - >seq8349,non-specific,197306,9,236,1.00505e-24,104.1,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26427,Q#1702 - >seq8349,non-specific,197307,9,236,3.961e-14,73.4761,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26428,Q#1702 - >seq8349,non-specific,223780,9,229,8.213430000000001e-14,72.6311,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26429,Q#1702 - >seq8349,non-specific,197320,9,229,1.0496600000000001e-13,72.1626,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26430,Q#1702 - >seq8349,specific,335306,10,229,2.66683e-13,70.3517,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26431,Q#1702 - >seq8349,non-specific,238828,516,737,9.44463e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26432,Q#1702 - >seq8349,non-specific,197319,9,236,1.51725e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26433,Q#1702 - >seq8349,non-specific,197321,7,236,1.5395899999999999e-09,59.8732,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26434,Q#1702 - >seq8349,non-specific,272954,9,236,2.01474e-09,59.7041,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26435,Q#1702 - >seq8349,non-specific,273186,9,237,3.3103899999999998e-09,58.8296,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26436,Q#1702 - >seq8349,non-specific,275209,467,796,8.10036e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26437,Q#1702 - >seq8349,superfamily,275209,467,796,8.10036e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26438,Q#1702 - >seq8349,non-specific,339261,108,232,0.000125003,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26439,Q#1702 - >seq8349,non-specific,238185,656,772,0.00022554099999999997,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26440,Q#1702 - >seq8349,non-specific,236970,9,207,0.000399189,43.7294,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26441,Q#1702 - >seq8349,non-specific,197311,72,236,0.000488802,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
26442,Q#1702 - >seq8349,non-specific,197336,9,229,0.00068339,42.5995,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26443,Q#1702 - >seq8349,specific,311990,1247,1265,0.00447342,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26444,Q#1702 - >seq8349,superfamily,311990,1247,1265,0.00447342,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs2_gorilla,marg,CompleteHit
26445,Q#1702 - >seq8349,non-specific,334125,212,412,0.00497903,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
26446,Q#1702 - >seq8349,superfamily,334125,212,412,0.00497903,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
26447,Q#1706 - >seq8353,specific,238827,498,760,8.884979999999999e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26448,Q#1706 - >seq8353,superfamily,295487,498,760,8.884979999999999e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26449,Q#1706 - >seq8353,specific,197310,20,227,6.464109999999999e-50,176.773,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26450,Q#1706 - >seq8353,superfamily,351117,20,227,6.464109999999999e-50,176.773,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26451,Q#1706 - >seq8353,specific,333820,504,760,4.122899999999999e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26452,Q#1706 - >seq8353,superfamily,333820,504,760,4.122899999999999e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26453,Q#1706 - >seq8353,non-specific,197306,20,227,1.4324600000000002e-20,92.1592,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26454,Q#1706 - >seq8353,non-specific,238828,504,725,7.98133e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26455,Q#1706 - >seq8353,non-specific,197320,48,220,1.24315e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26456,Q#1706 - >seq8353,non-specific,197307,30,227,1.63163e-09,59.6089,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26457,Q#1706 - >seq8353,specific,335306,19,220,2.42617e-09,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26458,Q#1706 - >seq8353,non-specific,275209,455,784,6.96014e-09,59.0084,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26459,Q#1706 - >seq8353,superfamily,275209,455,784,6.96014e-09,59.0084,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26460,Q#1706 - >seq8353,non-specific,223780,44,220,2.29467e-08,56.4527,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26461,Q#1706 - >seq8353,non-specific,197319,97,227,4.79521e-07,52.2789,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
26462,Q#1706 - >seq8353,non-specific,272954,14,227,2.51966e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26463,Q#1706 - >seq8353,non-specific,273186,97,228,1.64825e-05,47.6588,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
26464,Q#1706 - >seq8353,non-specific,197321,30,227,4.28995e-05,46.3912,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26465,Q#1706 - >seq8353,non-specific,339261,99,223,0.000116024,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26466,Q#1706 - >seq8353,non-specific,238185,644,760,0.000244604,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26467,Q#1706 - >seq8353,non-specific,197311,63,227,0.00048043900000000004,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
26468,Q#1706 - >seq8353,specific,311990,1227,1245,0.00440447,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26469,Q#1706 - >seq8353,superfamily,311990,1227,1245,0.00440447,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26470,Q#1706 - >seq8353,non-specific,334125,203,400,0.00638809,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MA4A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
26471,Q#1706 - >seq8353,superfamily,334125,203,400,0.00638809,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MA4A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
26472,Q#1706 - >seq8353,non-specific,236970,48,198,0.00890522,39.4922,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4A,ORF2,hs2_gorilla,pars,CompleteHit
26473,Q#1706 - >seq8353,non-specific,235175,255,457,0.00982836,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA4A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
26474,Q#1706 - >seq8353,superfamily,235175,255,457,0.00982836,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA4A.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA4A,ORF2,hs2_gorilla,pars,BothTerminiTruncated
26475,Q#1707 - >seq8354,specific,197310,9,236,3.8624599999999994e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26476,Q#1707 - >seq8354,superfamily,351117,9,236,3.8624599999999994e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26477,Q#1707 - >seq8354,specific,238827,526,771,2.4108e-45,162.846,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26478,Q#1707 - >seq8354,superfamily,295487,526,771,2.4108e-45,162.846,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26479,Q#1707 - >seq8354,non-specific,197306,9,236,9.688229999999999e-31,121.82,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26480,Q#1707 - >seq8354,non-specific,333820,526,771,6.965160000000001e-23,96.9777,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26481,Q#1707 - >seq8354,superfamily,333820,526,771,6.965160000000001e-23,96.9777,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26482,Q#1707 - >seq8354,specific,335306,10,229,9.04444e-19,86.5301,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26483,Q#1707 - >seq8354,non-specific,197320,9,229,1.8845e-17,83.3333,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26484,Q#1707 - >seq8354,non-specific,223780,9,229,1.09415e-15,78.4091,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26485,Q#1707 - >seq8354,non-specific,197307,9,236,1.0443799999999998e-14,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26486,Q#1707 - >seq8354,non-specific,197321,7,236,8.92683e-12,66.4216,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26487,Q#1707 - >seq8354,non-specific,273186,9,237,2.0290300000000002e-10,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26488,Q#1707 - >seq8354,non-specific,238828,580,735,3.3474800000000004e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,N-TerminusTruncated
26489,Q#1707 - >seq8354,non-specific,197319,9,236,3.3568599999999997e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26490,Q#1707 - >seq8354,non-specific,272954,9,236,3.6957199999999996e-08,55.8521,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26491,Q#1707 - >seq8354,non-specific,275209,585,795,1.62637e-06,51.6896,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,N-TerminusTruncated
26492,Q#1707 - >seq8354,superfamily,275209,585,795,1.62637e-06,51.6896,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,N-TerminusTruncated
26493,Q#1707 - >seq8354,non-specific,235175,304,467,3.3813e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,marg,BothTerminiTruncated
26494,Q#1707 - >seq8354,superfamily,235175,304,467,3.3813e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,marg,BothTerminiTruncated
26495,Q#1707 - >seq8354,non-specific,339261,108,232,0.000173891,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26496,Q#1707 - >seq8354,non-specific,197311,37,236,0.000192757,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26497,Q#1707 - >seq8354,non-specific,334125,212,410,0.000223445,44.8328,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs1_chimp,marg,N-TerminusTruncated
26498,Q#1707 - >seq8354,superfamily,334125,212,410,0.000223445,44.8328,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs1_chimp,marg,N-TerminusTruncated
26499,Q#1707 - >seq8354,non-specific,223496,319,500,0.00159104,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4A,ORF2,hs1_chimp,marg,BothTerminiTruncated
26500,Q#1707 - >seq8354,superfamily,223496,319,500,0.00159104,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA4A,ORF2,hs1_chimp,marg,BothTerminiTruncated
26501,Q#1707 - >seq8354,non-specific,197336,9,229,0.0021914,41.0587,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26502,Q#1707 - >seq8354,non-specific,238185,654,771,0.00472417,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26503,Q#1707 - >seq8354,non-specific,274009,306,500,0.00493371,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,marg,C-TerminusTruncated
26504,Q#1707 - >seq8354,superfamily,274009,306,500,0.00493371,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,marg,C-TerminusTruncated
26505,Q#1709 - >seq8356,specific,197310,9,236,8.747569999999998e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26506,Q#1709 - >seq8356,superfamily,351117,9,236,8.747569999999998e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26507,Q#1709 - >seq8356,specific,238827,546,767,8.0815e-45,161.305,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26508,Q#1709 - >seq8356,superfamily,295487,546,767,8.0815e-45,161.305,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26509,Q#1709 - >seq8356,non-specific,197306,9,236,1.29437e-29,118.353,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26510,Q#1709 - >seq8356,non-specific,333820,551,767,9.59097e-22,93.8961,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26511,Q#1709 - >seq8356,superfamily,333820,551,767,9.59097e-22,93.8961,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26512,Q#1709 - >seq8356,specific,335306,10,229,4.65585e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26513,Q#1709 - >seq8356,non-specific,197320,9,229,4.25107e-18,85.2593,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26514,Q#1709 - >seq8356,non-specific,197307,9,236,5.7126199999999994e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26515,Q#1709 - >seq8356,non-specific,223780,9,229,4.7951000000000006e-17,82.2611,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26516,Q#1709 - >seq8356,non-specific,197321,7,236,1.7074e-13,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26517,Q#1709 - >seq8356,non-specific,273186,9,237,4.32735e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26518,Q#1709 - >seq8356,non-specific,272954,9,236,1.42096e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26519,Q#1709 - >seq8356,non-specific,197319,9,236,1.6595599999999998e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26520,Q#1709 - >seq8356,non-specific,238828,577,732,2.56018e-10,61.8332,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,N-TerminusTruncated
26521,Q#1709 - >seq8356,non-specific,197336,9,229,1.64738e-07,53.7703,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26522,Q#1709 - >seq8356,non-specific,275209,582,791,3.99782e-07,53.6156,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,N-TerminusTruncated
26523,Q#1709 - >seq8356,superfamily,275209,582,791,3.99782e-07,53.6156,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,N-TerminusTruncated
26524,Q#1709 - >seq8356,non-specific,235175,291,468,1.84877e-06,52.3736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,pars,BothTerminiTruncated
26525,Q#1709 - >seq8356,superfamily,235175,291,468,1.84877e-06,52.3736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,pars,BothTerminiTruncated
26526,Q#1709 - >seq8356,non-specific,197311,7,236,3.6562800000000003e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26527,Q#1709 - >seq8356,non-specific,236970,9,207,1.4653699999999998e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26528,Q#1709 - >seq8356,non-specific,334125,212,411,4.7797100000000004e-05,47.144,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1MA4A,ORF2,hs3_orang,pars,N-TerminusTruncated
26529,Q#1709 - >seq8356,superfamily,334125,212,411,4.7797100000000004e-05,47.144,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1MA4A,ORF2,hs3_orang,pars,N-TerminusTruncated
26530,Q#1709 - >seq8356,non-specific,238185,651,767,9.0669e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26531,Q#1709 - >seq8356,non-specific,339261,108,232,0.00040440699999999997,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MA4A,ORF2,hs3_orang,pars,CompleteHit
26532,Q#1709 - >seq8356,non-specific,274009,306,451,0.000437369,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,pars,C-TerminusTruncated
26533,Q#1709 - >seq8356,superfamily,274009,306,451,0.000437369,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4A.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA4A,ORF2,hs3_orang,pars,C-TerminusTruncated
26534,Q#1711 - >seq8358,non-specific,238827,516,641,2.1009799999999997e-22,96.5914,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26535,Q#1711 - >seq8358,superfamily,295487,516,641,2.1009799999999997e-22,96.5914,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26536,Q#1711 - >seq8358,non-specific,333820,519,641,7.50553e-12,65.0062,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26537,Q#1711 - >seq8358,superfamily,333820,519,641,7.50553e-12,65.0062,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26538,Q#1711 - >seq8358,non-specific,238828,545,634,4.16263e-07,52.2032,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26539,Q#1711 - >seq8358,non-specific,275209,550,634,6.45236e-05,46.2968,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26540,Q#1711 - >seq8358,superfamily,275209,550,634,6.45236e-05,46.2968,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26541,Q#1712 - >seq8359,specific,197310,9,236,8.44672e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26542,Q#1712 - >seq8359,superfamily,351117,9,236,8.44672e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26543,Q#1712 - >seq8359,specific,238827,528,770,8.887119999999999e-55,189.81,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26544,Q#1712 - >seq8359,superfamily,295487,528,770,8.887119999999999e-55,189.81,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26545,Q#1712 - >seq8359,non-specific,197306,9,236,5.67519e-31,122.205,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26546,Q#1712 - >seq8359,specific,333820,528,770,1.00735e-28,113.927,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26547,Q#1712 - >seq8359,superfamily,333820,528,770,1.00735e-28,113.927,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26548,Q#1712 - >seq8359,non-specific,197307,9,236,4.95546e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26549,Q#1712 - >seq8359,specific,335306,10,229,8.26749e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26550,Q#1712 - >seq8359,non-specific,223780,9,229,3.9313200000000003e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26551,Q#1712 - >seq8359,non-specific,197320,9,229,6.77448e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26552,Q#1712 - >seq8359,non-specific,197321,7,236,2.3832899999999997e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26553,Q#1712 - >seq8359,non-specific,273186,9,237,4.8961599999999995e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26554,Q#1712 - >seq8359,non-specific,197319,9,236,3.8825300000000004e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26555,Q#1712 - >seq8359,non-specific,272954,9,236,7.051230000000001e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26556,Q#1712 - >seq8359,non-specific,238828,582,735,2.0986300000000002e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26557,Q#1712 - >seq8359,non-specific,197336,9,229,5.43878e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26558,Q#1712 - >seq8359,non-specific,236970,9,207,2.83549e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26559,Q#1712 - >seq8359,non-specific,197311,30,236,3.11739e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26560,Q#1712 - >seq8359,non-specific,275209,587,794,7.4283699999999995e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26561,Q#1712 - >seq8359,superfamily,275209,587,794,7.4283699999999995e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
26562,Q#1712 - >seq8359,non-specific,238185,656,770,1.2413399999999999e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26563,Q#1712 - >seq8359,non-specific,197322,8,236,2.10266e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26564,Q#1712 - >seq8359,non-specific,339261,108,232,0.00036004099999999996,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26565,Q#1712 - >seq8359,non-specific,197318,9,236,0.0006351369999999999,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26566,Q#1712 - >seq8359,non-specific,235175,291,468,0.00180682,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
26567,Q#1712 - >seq8359,superfamily,235175,291,468,0.00180682,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
26568,Q#1714 - >seq8361,specific,311990,1122,1140,0.00101288,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26569,Q#1714 - >seq8361,superfamily,311990,1122,1140,0.00101288,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA4A,ORF2,hs1_chimp,marg,CompleteHit
26570,Q#1717 - >seq8364,specific,197310,9,236,1.0257e-57,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26571,Q#1717 - >seq8364,superfamily,351117,9,236,1.0257e-57,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26572,Q#1717 - >seq8364,specific,238827,524,767,4.47417e-54,187.88400000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26573,Q#1717 - >seq8364,superfamily,295487,524,767,4.47417e-54,187.88400000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26574,Q#1717 - >seq8364,specific,333820,524,767,1.30565e-29,116.62299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26575,Q#1717 - >seq8364,superfamily,333820,524,767,1.30565e-29,116.62299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26576,Q#1717 - >seq8364,non-specific,197306,9,236,3.72392e-27,111.419,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26577,Q#1717 - >seq8364,specific,335306,10,229,2.35828e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26578,Q#1717 - >seq8364,non-specific,197320,9,229,1.6119999999999999e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26579,Q#1717 - >seq8364,non-specific,223780,9,229,2.20801e-14,74.5571,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26580,Q#1717 - >seq8364,non-specific,197307,9,236,4.498130000000001e-14,73.4761,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26581,Q#1717 - >seq8364,non-specific,273186,9,237,6.6074e-10,61.1408,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26582,Q#1717 - >seq8364,non-specific,238828,578,732,9.243989999999999e-10,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,N-TerminusTruncated
26583,Q#1717 - >seq8364,non-specific,197319,9,236,1.6419500000000001e-09,59.5977,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26584,Q#1717 - >seq8364,non-specific,272954,9,236,2.59778e-09,59.3189,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26585,Q#1717 - >seq8364,non-specific,197321,7,236,2.8730300000000004e-09,59.1028,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26586,Q#1717 - >seq8364,non-specific,275209,583,795,2.30012e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,N-TerminusTruncated
26587,Q#1717 - >seq8364,superfamily,275209,583,795,2.30012e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,N-TerminusTruncated
26588,Q#1717 - >seq8364,non-specific,339261,108,232,0.00032454799999999997,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26589,Q#1717 - >seq8364,non-specific,235175,304,466,0.000538915,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs0_human,pars,BothTerminiTruncated
26590,Q#1717 - >seq8364,superfamily,235175,304,466,0.000538915,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs0_human,pars,BothTerminiTruncated
26591,Q#1717 - >seq8364,non-specific,197311,37,236,0.000815315,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26592,Q#1717 - >seq8364,non-specific,223496,319,498,0.00107251,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4A,ORF2,hs0_human,pars,BothTerminiTruncated
26593,Q#1717 - >seq8364,superfamily,223496,319,498,0.00107251,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA4A,ORF2,hs0_human,pars,BothTerminiTruncated
26594,Q#1717 - >seq8364,non-specific,197336,9,229,0.00120822,41.8291,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26595,Q#1717 - >seq8364,non-specific,238185,652,767,0.0034113,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26596,Q#1717 - >seq8364,specific,311990,1233,1251,0.00412853,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26597,Q#1717 - >seq8364,superfamily,311990,1233,1251,0.00412853,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs0_human.pars.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4A,ORF2,hs0_human,pars,CompleteHit
26598,Q#1720 - >seq8367,specific,197310,9,237,6.29556e-40,147.88299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26599,Q#1720 - >seq8367,superfamily,351117,9,237,6.29556e-40,147.88299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26600,Q#1720 - >seq8367,non-specific,197306,9,237,5.819e-22,96.0112,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26601,Q#1720 - >seq8367,specific,335306,10,230,4.87451e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26602,Q#1720 - >seq8367,non-specific,197307,9,237,1.91051e-10,62.3053,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26603,Q#1720 - >seq8367,non-specific,197320,9,230,1.86275e-09,59.451,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26604,Q#1720 - >seq8367,non-specific,223780,9,230,2.8960300000000002e-08,56.0675,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26605,Q#1720 - >seq8367,non-specific,273186,9,238,5.15787e-08,55.3628,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26606,Q#1720 - >seq8367,non-specific,197321,7,237,6.505319999999999e-08,54.8656,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26607,Q#1720 - >seq8367,non-specific,197319,9,237,6.569100000000001e-07,51.8937,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26608,Q#1720 - >seq8367,non-specific,272954,9,237,1.66452e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26609,Q#1720 - >seq8367,non-specific,235175,292,470,0.000223743,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26610,Q#1720 - >seq8367,superfamily,235175,292,470,0.000223743,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26611,Q#1720 - >seq8367,non-specific,197336,9,43,0.00117569,41.8291,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26612,Q#1720 - >seq8367,non-specific,197318,9,237,0.00931299,39.2019,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26613,Q#1721 - >seq8368,specific,311990,1172,1190,0.00023185599999999998,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs4_gibbon.marg.frame2,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26614,Q#1721 - >seq8368,superfamily,311990,1172,1190,0.00023185599999999998,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs4_gibbon.marg.frame2,1909181135_L1MA4A.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4A,ORF2,hs4_gibbon,marg,CompleteHit
26615,Q#1722 - >seq8369,specific,238827,513,721,1.7910899999999998e-35,134.341,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26616,Q#1722 - >seq8369,superfamily,295487,513,721,1.7910899999999998e-35,134.341,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26617,Q#1722 - >seq8369,non-specific,333820,487,699,3.10369e-20,89.2737,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26618,Q#1722 - >seq8369,superfamily,333820,487,699,3.10369e-20,89.2737,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26619,Q#1722 - >seq8369,non-specific,238828,540,696,1.1236200000000002e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
26620,Q#1722 - >seq8369,non-specific,275209,545,696,3.22905e-07,53.6156,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26621,Q#1722 - >seq8369,superfamily,275209,545,696,3.22905e-07,53.6156,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26622,Q#1722 - >seq8369,specific,311990,1201,1219,0.00116078,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26623,Q#1722 - >seq8369,superfamily,311990,1201,1219,0.00116078,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4A,ORF2,hs6_sqmonkey,marg,CompleteHit
26624,Q#1723 - >seq8370,specific,197310,9,237,6.65994e-39,144.80200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26625,Q#1723 - >seq8370,superfamily,351117,9,237,6.65994e-39,144.80200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26626,Q#1723 - >seq8370,non-specific,197306,9,237,1.2481e-21,95.2408,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26627,Q#1723 - >seq8370,specific,335306,10,230,4.78422e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26628,Q#1723 - >seq8370,non-specific,197307,9,237,2.62269e-10,61.9201,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26629,Q#1723 - >seq8370,non-specific,197320,9,230,1.7813499999999999e-09,59.451,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26630,Q#1723 - >seq8370,non-specific,223780,9,230,2.6714400000000002e-08,56.0675,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26631,Q#1723 - >seq8370,non-specific,238827,512,559,5.2293199999999995e-08,54.6046,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26632,Q#1723 - >seq8370,superfamily,295487,512,559,5.2293199999999995e-08,54.6046,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26633,Q#1723 - >seq8370,non-specific,273186,9,238,6.8646e-08,54.9776,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26634,Q#1723 - >seq8370,non-specific,197321,7,237,7.01126e-08,54.8656,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26635,Q#1723 - >seq8370,non-specific,197319,9,237,9.222660000000001e-07,51.5085,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26636,Q#1723 - >seq8370,non-specific,272954,9,237,2.85157e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26637,Q#1723 - >seq8370,non-specific,235175,292,470,0.00022277400000000002,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26638,Q#1723 - >seq8370,superfamily,235175,292,470,0.00022277400000000002,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26639,Q#1723 - >seq8370,non-specific,197336,9,43,0.00120951,41.8291,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26640,Q#1724 - >seq8371,non-specific,238827,635,700,7.37484e-07,51.1378,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
26641,Q#1724 - >seq8371,superfamily,295487,635,700,7.37484e-07,51.1378,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
26642,Q#1724 - >seq8371,specific,311990,1190,1208,0.00144136,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26643,Q#1724 - >seq8371,superfamily,311990,1190,1208,0.00144136,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4A,ORF2,hs6_sqmonkey,pars,CompleteHit
26644,Q#1725 - >seq8372,specific,197310,9,237,1.22437e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26645,Q#1725 - >seq8372,superfamily,351117,9,237,1.22437e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26646,Q#1725 - >seq8372,specific,238827,528,770,1.6734099999999997e-44,160.534,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26647,Q#1725 - >seq8372,superfamily,295487,528,770,1.6734099999999997e-44,160.534,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26648,Q#1725 - >seq8372,non-specific,197306,9,237,1.1696700000000001e-29,118.353,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26649,Q#1725 - >seq8372,non-specific,333820,528,740,2.16735e-24,101.6,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26650,Q#1725 - >seq8372,superfamily,333820,528,740,2.16735e-24,101.6,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26651,Q#1725 - >seq8372,specific,335306,10,230,3.66557e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26652,Q#1725 - >seq8372,non-specific,197307,9,237,3.9044500000000003e-16,79.2541,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26653,Q#1725 - >seq8372,non-specific,223780,9,230,6.216599999999999e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26654,Q#1725 - >seq8372,non-specific,197320,9,230,6.21711e-16,78.7109,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26655,Q#1725 - >seq8372,non-specific,197321,7,237,1.16741e-11,66.0364,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26656,Q#1725 - >seq8372,non-specific,273186,9,238,1.38306e-11,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26657,Q#1725 - >seq8372,non-specific,197319,9,237,5.04441e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26658,Q#1725 - >seq8372,non-specific,238828,582,737,7.66797e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26659,Q#1725 - >seq8372,non-specific,272954,9,237,1.00309e-10,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26660,Q#1725 - >seq8372,non-specific,275209,587,794,1.93507e-06,51.3044,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26661,Q#1725 - >seq8372,superfamily,275209,587,794,1.93507e-06,51.3044,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26662,Q#1725 - >seq8372,non-specific,235175,301,469,2.93177e-06,51.6032,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26663,Q#1725 - >seq8372,superfamily,235175,301,469,2.93177e-06,51.6032,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26664,Q#1725 - >seq8372,non-specific,197336,9,230,5.6851599999999996e-05,46.0663,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26665,Q#1725 - >seq8372,non-specific,339261,109,233,0.000156093,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26666,Q#1725 - >seq8372,non-specific,334125,213,412,0.000714809,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26667,Q#1725 - >seq8372,superfamily,334125,213,412,0.000714809,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26668,Q#1725 - >seq8372,non-specific,197318,9,237,0.00143463,41.5131,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26669,Q#1725 - >seq8372,non-specific,197311,30,237,0.00318006,40.3529,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26670,Q#1725 - >seq8372,specific,311990,1236,1254,0.00343513,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26671,Q#1725 - >seq8372,superfamily,311990,1236,1254,0.00343513,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs5_gmonkey,marg,CompleteHit
26672,Q#1725 - >seq8372,non-specific,274009,308,452,0.00559076,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26673,Q#1725 - >seq8372,superfamily,274009,308,452,0.00559076,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26674,Q#1725 - >seq8372,non-specific,223496,321,500,0.006707600000000001,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26675,Q#1725 - >seq8372,superfamily,223496,321,500,0.006707600000000001,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA4A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26676,Q#1726 - >seq8373,non-specific,240420,324,424,0.00230256,41.8733,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26677,Q#1726 - >seq8373,superfamily,240420,324,424,0.00230256,41.8733,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26678,Q#1726 - >seq8373,non-specific,240274,225,528,0.00292344,41.8993,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26679,Q#1726 - >seq8373,superfamily,240274,225,528,0.00292344,41.8993,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26680,Q#1728 - >seq8375,specific,197310,9,236,9.943209999999999e-58,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26681,Q#1728 - >seq8375,superfamily,351117,9,236,9.943209999999999e-58,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26682,Q#1728 - >seq8375,specific,238827,527,769,1.57459e-44,160.534,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26683,Q#1728 - >seq8375,superfamily,295487,527,769,1.57459e-44,160.534,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26684,Q#1728 - >seq8375,non-specific,197306,9,236,2.13652e-30,120.664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26685,Q#1728 - >seq8375,non-specific,333820,527,739,2.14091e-24,101.6,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26686,Q#1728 - >seq8375,superfamily,333820,527,739,2.14091e-24,101.6,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26687,Q#1728 - >seq8375,specific,335306,10,229,1.9669099999999997e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26688,Q#1728 - >seq8375,non-specific,197307,9,236,1.39011e-17,83.4913,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26689,Q#1728 - >seq8375,non-specific,223780,9,229,1.0090700000000002e-16,81.4907,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26690,Q#1728 - >seq8375,non-specific,197320,9,229,6.43342e-16,78.7109,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26691,Q#1728 - >seq8375,non-specific,197321,7,236,3.54467e-13,70.6588,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26692,Q#1728 - >seq8375,non-specific,197319,9,236,1.1973e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26693,Q#1728 - >seq8375,non-specific,273186,9,237,5.1361699999999995e-12,67.304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26694,Q#1728 - >seq8375,non-specific,238828,581,736,7.64382e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26695,Q#1728 - >seq8375,non-specific,272954,9,236,1.7928700000000003e-10,62.7857,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26696,Q#1728 - >seq8375,non-specific,235175,300,468,9.51806e-07,53.1439,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26697,Q#1728 - >seq8375,superfamily,235175,300,468,9.51806e-07,53.1439,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26698,Q#1728 - >seq8375,non-specific,275209,586,793,2.69003e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26699,Q#1728 - >seq8375,superfamily,275209,586,793,2.69003e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26700,Q#1728 - >seq8375,non-specific,197336,9,229,5.08893e-06,49.1479,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26701,Q#1728 - >seq8375,non-specific,339261,108,232,0.000267648,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26702,Q#1728 - >seq8375,non-specific,334125,212,411,0.000357055,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26703,Q#1728 - >seq8375,superfamily,334125,212,411,0.000357055,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26704,Q#1728 - >seq8375,non-specific,223496,320,499,0.00279047,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26705,Q#1728 - >seq8375,superfamily,223496,320,499,0.00279047,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA4A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26706,Q#1728 - >seq8375,non-specific,274009,307,451,0.0028068000000000004,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26707,Q#1728 - >seq8375,superfamily,274009,307,451,0.0028068000000000004,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26708,Q#1728 - >seq8375,non-specific,197311,30,236,0.00334978,39.9677,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26709,Q#1728 - >seq8375,non-specific,197318,9,236,0.00662536,39.5871,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26710,Q#1728 - >seq8375,non-specific,226567,658,806,0.00974864,37.8886,COG4081,COG4081, - ,cl01691,Uncharacterized protein [Function unknown]; Uncharacterized protein conserved in archaea [Function unknown].,L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26711,Q#1728 - >seq8375,superfamily,321627,658,806,0.00974864,37.8886,cl01691,DUF1890 superfamily, - , - ,Domain of unknown function (DUF1890); This domain is found in a set of hypothetical archaeal proteins.,L1MA4A.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26712,Q#1729 - >seq8376,specific,311990,1163,1181,0.00024407400000000002,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26713,Q#1729 - >seq8376,superfamily,311990,1163,1181,0.00024407400000000002,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4A,ORF2,hs5_gmonkey,pars,CompleteHit
26714,Q#1729 - >seq8376,non-specific,240420,323,423,0.00193196,42.2585,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26715,Q#1729 - >seq8376,superfamily,240420,323,423,0.00193196,42.2585,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26716,Q#1729 - >seq8376,non-specific,240274,224,527,0.0020747,42.2845,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26717,Q#1729 - >seq8376,superfamily,240274,224,527,0.0020747,42.2845,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MA4A.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA4A.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA4A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26718,Q#1731 - >seq8378,non-specific,238827,476,505,1.30251e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26719,Q#1731 - >seq8378,superfamily,295487,476,505,1.30251e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26720,Q#1731 - >seq8378,non-specific,333820,475,513,0.00530535,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26721,Q#1731 - >seq8378,superfamily,333820,475,513,0.00530535,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA4A.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26722,Q#1732 - >seq8379,specific,197310,9,236,1.11621e-57,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26723,Q#1732 - >seq8379,superfamily,351117,9,236,1.11621e-57,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26724,Q#1732 - >seq8379,specific,238827,526,769,4.3328099999999996e-54,187.88400000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26725,Q#1732 - >seq8379,superfamily,295487,526,769,4.3328099999999996e-54,187.88400000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26726,Q#1732 - >seq8379,specific,333820,526,769,1.27615e-29,116.62299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26727,Q#1732 - >seq8379,superfamily,333820,526,769,1.27615e-29,116.62299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26728,Q#1732 - >seq8379,non-specific,197306,9,236,4.20384e-27,111.03399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26729,Q#1732 - >seq8379,specific,335306,10,229,2.37308e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26730,Q#1732 - >seq8379,non-specific,197320,9,229,1.76597e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26731,Q#1732 - >seq8379,non-specific,223780,9,229,2.3949700000000002e-14,74.1719,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26732,Q#1732 - >seq8379,non-specific,197307,9,236,4.4011900000000005e-14,73.4761,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26733,Q#1732 - >seq8379,non-specific,273186,9,237,7.159930000000001e-10,60.7556,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26734,Q#1732 - >seq8379,non-specific,238828,580,734,9.38902e-10,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,N-TerminusTruncated
26735,Q#1732 - >seq8379,non-specific,197319,9,236,1.6523299999999998e-09,59.5977,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26736,Q#1732 - >seq8379,non-specific,272954,9,236,2.6142100000000002e-09,59.3189,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26737,Q#1732 - >seq8379,non-specific,197321,7,236,2.8911900000000002e-09,59.1028,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26738,Q#1732 - >seq8379,non-specific,275209,585,797,2.17697e-06,51.3044,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,N-TerminusTruncated
26739,Q#1732 - >seq8379,superfamily,275209,585,797,2.17697e-06,51.3044,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,N-TerminusTruncated
26740,Q#1732 - >seq8379,non-specific,339261,108,232,0.000359546,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26741,Q#1732 - >seq8379,non-specific,235175,291,468,0.000481643,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs0_human,marg,BothTerminiTruncated
26742,Q#1732 - >seq8379,superfamily,235175,291,468,0.000481643,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA4A,ORF2,hs0_human,marg,BothTerminiTruncated
26743,Q#1732 - >seq8379,non-specific,197311,37,236,0.000907558,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26744,Q#1732 - >seq8379,non-specific,197336,9,229,0.00132961,41.8291,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26745,Q#1732 - >seq8379,non-specific,238185,654,769,0.00353262,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26746,Q#1732 - >seq8379,specific,311990,1240,1258,0.00407049,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26747,Q#1732 - >seq8379,superfamily,311990,1240,1258,0.00407049,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4A,ORF2,hs0_human,marg,CompleteHit
26748,Q#1732 - >seq8379,non-specific,223496,320,500,0.00952786,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4A,ORF2,hs0_human,marg,BothTerminiTruncated
26749,Q#1732 - >seq8379,superfamily,223496,320,500,0.00952786,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs0_human.marg.frame3,1909181135_L1MA4A.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA4A,ORF2,hs0_human,marg,BothTerminiTruncated
26750,Q#1734 - >seq8381,specific,311990,1170,1188,0.00024508,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs1_chimp.pars.frame2,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
26751,Q#1734 - >seq8381,superfamily,311990,1170,1188,0.00024508,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4A.ORF2.hs1_chimp.pars.frame2,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
26752,Q#1736 - >seq8383,specific,197310,9,236,1.36936e-54,189.87,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26753,Q#1736 - >seq8383,superfamily,351117,9,236,1.36936e-54,189.87,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26754,Q#1736 - >seq8383,non-specific,197306,9,236,3.58226e-29,116.81200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26755,Q#1736 - >seq8383,non-specific,197320,7,229,7.24419e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26756,Q#1736 - >seq8383,specific,335306,10,229,2.4889399999999997e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26757,Q#1736 - >seq8383,non-specific,223780,7,229,4.63019e-18,85.3427,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26758,Q#1736 - >seq8383,non-specific,197307,9,236,5.663330000000001e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26759,Q#1736 - >seq8383,non-specific,272954,7,207,1.2701799999999998e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26760,Q#1736 - >seq8383,non-specific,197319,7,236,2.2653800000000002e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26761,Q#1736 - >seq8383,non-specific,273186,7,237,2.27023e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26762,Q#1736 - >seq8383,non-specific,197321,7,236,7.77348e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26763,Q#1736 - >seq8383,non-specific,197336,7,229,3.5606900000000004e-08,55.6963,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26764,Q#1736 - >seq8383,non-specific,197318,9,236,2.45342e-05,46.9059,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26765,Q#1736 - >seq8383,non-specific,197311,7,236,0.000738191,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,marg,CompleteHit
26766,Q#1736 - >seq8383,non-specific,339261,113,232,0.00227956,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs0_human.marg.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26767,Q#1737 - >seq8384,specific,238827,491,753,3.2112299999999993e-59,202.90599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26768,Q#1737 - >seq8384,superfamily,295487,491,753,3.2112299999999993e-59,202.90599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26769,Q#1737 - >seq8384,specific,333820,497,753,2.38374e-28,112.771,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26770,Q#1737 - >seq8384,superfamily,333820,497,753,2.38374e-28,112.771,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26771,Q#1737 - >seq8384,non-specific,238828,497,718,2.87864e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,CompleteHit
26772,Q#1737 - >seq8384,non-specific,275209,452,718,5.78027e-07,52.8452,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,C-TerminusTruncated
26773,Q#1737 - >seq8384,superfamily,275209,452,718,5.78027e-07,52.8452,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA2,ORF2,hs0_human,marg,C-TerminusTruncated
26774,Q#1737 - >seq8384,specific,311990,1222,1240,0.00276577,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA2,ORF2,hs0_human,marg,CompleteHit
26775,Q#1737 - >seq8384,superfamily,311990,1222,1240,0.00276577,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs0_human.marg.frame2,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA2,ORF2,hs0_human,marg,CompleteHit
26776,Q#1739 - >seq8386,specific,197310,9,228,1.7185199999999998e-46,166.75799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26777,Q#1739 - >seq8386,superfamily,351117,9,228,1.7185199999999998e-46,166.75799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26778,Q#1739 - >seq8386,non-specific,197306,9,211,3.21391e-26,108.338,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26779,Q#1739 - >seq8386,non-specific,197320,7,208,2.10082e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26780,Q#1739 - >seq8386,specific,335306,10,210,2.35028e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26781,Q#1739 - >seq8386,non-specific,223780,7,207,2.5403400000000003e-16,79.9499,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26782,Q#1739 - >seq8386,non-specific,197307,9,208,1.3521599999999999e-15,77.7133,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26783,Q#1739 - >seq8386,non-specific,272954,7,207,1.03524e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26784,Q#1739 - >seq8386,non-specific,197321,7,207,2.98313e-11,64.8808,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26785,Q#1739 - >seq8386,non-specific,273186,7,208,6.34018e-11,63.8372,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26786,Q#1739 - >seq8386,non-specific,197319,7,218,9.882769999999999e-10,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26787,Q#1739 - >seq8386,non-specific,197336,7,204,6.84612e-08,54.9259,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26788,Q#1739 - >seq8386,non-specific,197318,9,148,0.00111367,41.8983,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs0_human,pars,C-TerminusTruncated
26789,Q#1739 - >seq8386,non-specific,197311,7,204,0.002724,40.3529,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs0_human.pars.frame3,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs0_human,pars,CompleteHit
26790,Q#1741 - >seq8388,specific,238827,471,733,7.899439999999998e-60,204.447,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26791,Q#1741 - >seq8388,superfamily,295487,471,733,7.899439999999998e-60,204.447,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26792,Q#1741 - >seq8388,specific,333820,477,733,1.11832e-28,113.541,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26793,Q#1741 - >seq8388,superfamily,333820,477,733,1.11832e-28,113.541,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26794,Q#1741 - >seq8388,non-specific,238828,477,698,1.38789e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26795,Q#1741 - >seq8388,non-specific,275209,548,698,2.19857e-06,50.9192,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26796,Q#1741 - >seq8388,superfamily,275209,548,698,2.19857e-06,50.9192,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26797,Q#1741 - >seq8388,non-specific,235175,271,426,0.00193511,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26798,Q#1741 - >seq8388,superfamily,235175,271,426,0.00193511,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26799,Q#1741 - >seq8388,non-specific,223496,283,514,0.00291022,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26800,Q#1741 - >seq8388,superfamily,223496,283,514,0.00291022,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MA2,ORF2,hs0_human,pars,BothTerminiTruncated
26801,Q#1741 - >seq8388,specific,311990,1187,1205,0.0035679,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs0_human,pars,CompleteHit
26802,Q#1741 - >seq8388,superfamily,311990,1187,1205,0.0035679,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs0_human,pars,CompleteHit
26803,Q#1741 - >seq8388,non-specific,274009,269,462,0.009089100000000001,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs0_human,pars,C-TerminusTruncated
26804,Q#1741 - >seq8388,superfamily,274009,269,462,0.009089100000000001,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs0_human,pars,C-TerminusTruncated
26805,Q#1741 - >seq8388,non-specific,238185,612,733,0.00947691,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs0_human.pars.frame1,1909181135_L1MA2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs0_human,pars,CompleteHit
26806,Q#1742 - >seq8389,specific,197310,9,236,2.0189699999999995e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26807,Q#1742 - >seq8389,superfamily,351117,9,236,2.0189699999999995e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26808,Q#1742 - >seq8389,specific,238827,511,772,1.8446899999999999e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26809,Q#1742 - >seq8389,superfamily,295487,511,772,1.8446899999999999e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26810,Q#1742 - >seq8389,non-specific,197306,9,236,1.8343e-35,135.30200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26811,Q#1742 - >seq8389,specific,333820,517,772,1.58797e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26812,Q#1742 - >seq8389,superfamily,333820,517,772,1.58797e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26813,Q#1742 - >seq8389,non-specific,197320,7,229,4.78502e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26814,Q#1742 - >seq8389,non-specific,223780,7,229,4.67696e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26815,Q#1742 - >seq8389,non-specific,197307,9,236,1.1868499999999999e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26816,Q#1742 - >seq8389,specific,335306,10,229,1.21291e-20,91.9229,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26817,Q#1742 - >seq8389,non-specific,197321,7,236,6.415490000000001e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26818,Q#1742 - >seq8389,non-specific,197319,7,236,1.6048699999999998e-18,86.5617,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26819,Q#1742 - >seq8389,non-specific,272954,7,207,1.10734e-16,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26820,Q#1742 - >seq8389,non-specific,273186,7,237,2.41311e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26821,Q#1742 - >seq8389,non-specific,197336,7,229,2.0481999999999998e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26822,Q#1742 - >seq8389,non-specific,238828,517,737,1.39337e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26823,Q#1742 - >seq8389,non-specific,275209,468,737,1.7705e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26824,Q#1742 - >seq8389,superfamily,275209,468,737,1.7705e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26825,Q#1742 - >seq8389,non-specific,197311,7,236,3.47831e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26826,Q#1742 - >seq8389,non-specific,236970,9,207,7.700799999999999e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26827,Q#1742 - >seq8389,non-specific,339261,108,232,3.43425e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26828,Q#1742 - >seq8389,non-specific,197318,9,236,0.000176553,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26829,Q#1742 - >seq8389,non-specific,238185,658,772,0.00028894,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26830,Q#1742 - >seq8389,non-specific,274009,306,455,0.000744412,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26831,Q#1742 - >seq8389,superfamily,274009,306,455,0.000744412,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
26832,Q#1742 - >seq8389,non-specific,197314,7,236,0.00105942,41.9455,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26833,Q#1742 - >seq8389,non-specific,235175,307,465,0.00142708,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26834,Q#1742 - >seq8389,superfamily,235175,307,465,0.00142708,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
26835,Q#1742 - >seq8389,specific,311990,1241,1259,0.00289084,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26836,Q#1742 - >seq8389,superfamily,311990,1241,1259,0.00289084,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26837,Q#1742 - >seq8389,non-specific,334125,217,412,0.00350623,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
26838,Q#1742 - >seq8389,superfamily,334125,217,412,0.00350623,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
26839,Q#1742 - >seq8389,non-specific,224259,294,465,0.00579048,40.0496,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26840,Q#1742 - >seq8389,superfamily,224259,294,465,0.00579048,40.0496,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs6_sqmonkey,marg,CompleteHit
26841,Q#1745 - >seq8392,specific,197310,9,236,1.9747199999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26842,Q#1745 - >seq8392,superfamily,351117,9,236,1.9747199999999997e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26843,Q#1745 - >seq8392,specific,238827,510,771,1.8942599999999996e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26844,Q#1745 - >seq8392,superfamily,295487,510,771,1.8942599999999996e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26845,Q#1745 - >seq8392,non-specific,197306,9,236,1.76193e-35,135.30200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26846,Q#1745 - >seq8392,specific,333820,516,771,1.5852100000000002e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26847,Q#1745 - >seq8392,superfamily,333820,516,771,1.5852100000000002e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26848,Q#1745 - >seq8392,non-specific,197320,7,229,4.96157e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26849,Q#1745 - >seq8392,non-specific,223780,7,229,4.7128800000000005e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26850,Q#1745 - >seq8392,non-specific,197307,9,236,1.2074200000000001e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26851,Q#1745 - >seq8392,specific,335306,10,229,1.21074e-20,91.9229,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26852,Q#1745 - >seq8392,non-specific,197321,7,236,6.40379e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26853,Q#1745 - >seq8392,non-specific,197319,7,236,1.60194e-18,86.5617,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26854,Q#1745 - >seq8392,non-specific,272954,7,207,1.10532e-16,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26855,Q#1745 - >seq8392,non-specific,273186,7,237,2.4087200000000004e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26856,Q#1745 - >seq8392,non-specific,197336,7,229,2.04449e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26857,Q#1745 - >seq8392,non-specific,238828,516,736,1.39089e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26858,Q#1745 - >seq8392,non-specific,275209,467,736,1.79877e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26859,Q#1745 - >seq8392,superfamily,275209,467,736,1.79877e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26860,Q#1745 - >seq8392,non-specific,197311,7,236,3.5048900000000004e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26861,Q#1745 - >seq8392,non-specific,236970,9,207,7.68704e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26862,Q#1745 - >seq8392,non-specific,339261,108,232,3.4619099999999995e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26863,Q#1745 - >seq8392,non-specific,197318,9,236,0.000168459,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26864,Q#1745 - >seq8392,non-specific,238185,657,771,0.00027744,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26865,Q#1745 - >seq8392,non-specific,197314,7,236,0.00105757,41.9455,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26866,Q#1745 - >seq8392,non-specific,235175,307,464,0.00185272,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26867,Q#1745 - >seq8392,superfamily,235175,307,464,0.00185272,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
26868,Q#1745 - >seq8392,specific,311990,1239,1257,0.00288636,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26869,Q#1745 - >seq8392,superfamily,311990,1239,1257,0.00288636,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA2,ORF2,hs6_sqmonkey,pars,CompleteHit
26870,Q#1745 - >seq8392,non-specific,274009,306,454,0.00971165,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26871,Q#1745 - >seq8392,superfamily,274009,306,454,0.00971165,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
26872,Q#1748 - >seq8395,specific,238827,509,771,2.5524099999999998e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26873,Q#1748 - >seq8395,superfamily,295487,509,771,2.5524099999999998e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26874,Q#1748 - >seq8395,specific,197310,9,236,7.154269999999999e-63,213.752,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26875,Q#1748 - >seq8395,superfamily,351117,9,236,7.154269999999999e-63,213.752,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26876,Q#1748 - >seq8395,non-specific,197306,9,236,1.9441199999999998e-35,135.30200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26877,Q#1748 - >seq8395,specific,333820,515,771,2.2936999999999997e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26878,Q#1748 - >seq8395,superfamily,333820,515,771,2.2936999999999997e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26879,Q#1748 - >seq8395,non-specific,197320,7,229,8.225329999999999e-24,101.823,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26880,Q#1748 - >seq8395,non-specific,223780,7,229,3.29267e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26881,Q#1748 - >seq8395,specific,335306,10,229,5.38687e-21,92.6933,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26882,Q#1748 - >seq8395,non-specific,197307,9,236,2.3437900000000003e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26883,Q#1748 - >seq8395,non-specific,197321,7,236,3.00999e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26884,Q#1748 - >seq8395,non-specific,272954,7,207,7.0444e-17,81.6604,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26885,Q#1748 - >seq8395,non-specific,273186,7,237,2.91426e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26886,Q#1748 - >seq8395,non-specific,197319,7,236,2.82681e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26887,Q#1748 - >seq8395,non-specific,238828,515,736,1.64473e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26888,Q#1748 - >seq8395,non-specific,197336,7,229,1.4737000000000002e-11,65.7115,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26889,Q#1748 - >seq8395,non-specific,275209,466,736,2.2078900000000003e-08,57.4676,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26890,Q#1748 - >seq8395,superfamily,275209,466,736,2.2078900000000003e-08,57.4676,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26891,Q#1748 - >seq8395,non-specific,197311,7,236,2.28464e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26892,Q#1748 - >seq8395,non-specific,236970,9,207,1.7558799999999999e-06,50.663000000000004,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26893,Q#1748 - >seq8395,non-specific,339261,108,232,4.17308e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26894,Q#1748 - >seq8395,non-specific,238185,657,771,0.000147717,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26895,Q#1748 - >seq8395,non-specific,197318,9,236,0.00021737400000000002,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26896,Q#1748 - >seq8395,non-specific,197314,7,236,0.00027473,43.8715,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26897,Q#1748 - >seq8395,non-specific,235175,294,463,0.00191904,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26898,Q#1748 - >seq8395,superfamily,235175,294,463,0.00191904,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26899,Q#1748 - >seq8395,non-specific,334125,217,410,0.00275392,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26900,Q#1748 - >seq8395,superfamily,334125,217,410,0.00275392,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
26901,Q#1748 - >seq8395,non-specific,223496,320,499,0.00398219,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26902,Q#1748 - >seq8395,superfamily,223496,320,499,0.00398219,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26903,Q#1748 - >seq8395,specific,225881,482,679,0.00648785,40.2073,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26904,Q#1748 - >seq8395,superfamily,225881,482,679,0.00648785,40.2073,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
26905,Q#1748 - >seq8395,non-specific,274009,305,453,0.00741926,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26906,Q#1748 - >seq8395,superfamily,274009,305,453,0.00741926,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
26907,Q#1749 - >seq8396,specific,311990,1167,1185,0.00019742799999999998,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26908,Q#1749 - >seq8396,superfamily,311990,1167,1185,0.00019742799999999998,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs5_gmonkey.marg.frame2,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA2,ORF2,hs5_gmonkey,marg,CompleteHit
26909,Q#1751 - >seq8398,specific,238827,604,721,8.698810000000001e-30,118.163,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26910,Q#1751 - >seq8398,superfamily,295487,604,721,8.698810000000001e-30,118.163,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26911,Q#1751 - >seq8398,non-specific,333820,586,721,1.53899e-13,70.0138,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26912,Q#1751 - >seq8398,superfamily,333820,586,721,1.53899e-13,70.0138,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26913,Q#1751 - >seq8398,non-specific,238828,565,686,9.15607e-07,51.0476,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26914,Q#1751 - >seq8398,non-specific,238185,605,721,4.4717e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,CompleteHit
26915,Q#1751 - >seq8398,specific,311990,1188,1206,0.000982093,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4,ORF2,hs3_orang,pars,CompleteHit
26916,Q#1751 - >seq8398,superfamily,311990,1188,1206,0.000982093,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4,ORF2,hs3_orang,pars,CompleteHit
26917,Q#1751 - >seq8398,non-specific,275209,557,740,0.00123375,42.4448,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26918,Q#1751 - >seq8398,superfamily,275209,557,740,0.00123375,42.4448,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs3_orang.pars.frame2,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA4,ORF2,hs3_orang,pars,N-TerminusTruncated
26919,Q#1752 - >seq8399,specific,238827,508,770,3.492399999999999e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26920,Q#1752 - >seq8399,superfamily,295487,508,770,3.492399999999999e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26921,Q#1752 - >seq8399,specific,197310,9,236,1.1094699999999998e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26922,Q#1752 - >seq8399,superfamily,351117,9,236,1.1094699999999998e-62,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26923,Q#1752 - >seq8399,non-specific,197306,9,236,2.1857299999999999e-35,134.916,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26924,Q#1752 - >seq8399,specific,333820,514,770,1.7033e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26925,Q#1752 - >seq8399,superfamily,333820,514,770,1.7033e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26926,Q#1752 - >seq8399,non-specific,197320,7,229,7.14352e-24,102.208,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26927,Q#1752 - >seq8399,non-specific,223780,7,229,2.60183e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26928,Q#1752 - >seq8399,specific,335306,10,229,5.39656e-21,92.6933,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26929,Q#1752 - >seq8399,non-specific,197307,9,236,2.30395e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26930,Q#1752 - >seq8399,non-specific,197321,7,236,3.04412e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26931,Q#1752 - >seq8399,non-specific,272954,7,207,5.8995e-17,82.0456,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26932,Q#1752 - >seq8399,non-specific,273186,7,237,2.65713e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26933,Q#1752 - >seq8399,non-specific,197319,7,236,2.77921e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26934,Q#1752 - >seq8399,non-specific,238828,514,735,1.61691e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26935,Q#1752 - >seq8399,non-specific,197336,7,229,1.47638e-11,65.7115,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26936,Q#1752 - >seq8399,non-specific,197311,7,236,2.81173e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26937,Q#1752 - >seq8399,non-specific,275209,585,735,3.01762e-07,54.0008,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26938,Q#1752 - >seq8399,superfamily,275209,585,735,3.01762e-07,54.0008,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26939,Q#1752 - >seq8399,non-specific,236970,9,207,1.44148e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26940,Q#1752 - >seq8399,non-specific,339261,108,232,5.17121e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26941,Q#1752 - >seq8399,non-specific,238185,656,770,0.000145103,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26942,Q#1752 - >seq8399,non-specific,197318,9,236,0.000178513,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26943,Q#1752 - >seq8399,non-specific,197314,7,236,0.000275215,43.8715,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
26944,Q#1752 - >seq8399,non-specific,235175,306,463,0.00317032,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26945,Q#1752 - >seq8399,superfamily,235175,306,463,0.00317032,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
26946,Q#1752 - >seq8399,non-specific,334125,217,410,0.00446919,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26947,Q#1752 - >seq8399,superfamily,334125,217,410,0.00446919,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
26948,Q#1752 - >seq8399,non-specific,274009,305,499,0.00822625,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26949,Q#1752 - >seq8399,superfamily,274009,305,499,0.00822625,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
26950,Q#1754 - >seq8401,specific,238827,507,769,8.286989999999998e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26951,Q#1754 - >seq8401,superfamily,295487,507,769,8.286989999999998e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26952,Q#1754 - >seq8401,specific,197310,9,236,5.059569999999999e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26953,Q#1754 - >seq8401,superfamily,351117,9,236,5.059569999999999e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26954,Q#1754 - >seq8401,non-specific,197306,9,236,2.8349499999999996e-36,137.613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26955,Q#1754 - >seq8401,specific,333820,513,769,1.86607e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26956,Q#1754 - >seq8401,superfamily,333820,513,769,1.86607e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26957,Q#1754 - >seq8401,non-specific,197320,7,229,5.68944e-25,105.29,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26958,Q#1754 - >seq8401,non-specific,223780,7,229,8.82093e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26959,Q#1754 - >seq8401,non-specific,197307,9,236,5.2843400000000006e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26960,Q#1754 - >seq8401,specific,335306,10,229,2.35658e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26961,Q#1754 - >seq8401,non-specific,197321,7,236,4.0872499999999996e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26962,Q#1754 - >seq8401,non-specific,273186,7,237,2.87825e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26963,Q#1754 - >seq8401,non-specific,272954,7,236,4.98591e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26964,Q#1754 - >seq8401,non-specific,197319,7,236,3.12243e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26965,Q#1754 - >seq8401,non-specific,197336,7,229,7.44478e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26966,Q#1754 - >seq8401,non-specific,238828,513,734,3.83464e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26967,Q#1754 - >seq8401,non-specific,275209,464,734,3.28169e-07,53.6156,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
26968,Q#1754 - >seq8401,superfamily,275209,464,734,3.28169e-07,53.6156,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
26969,Q#1754 - >seq8401,non-specific,197311,7,236,6.02196e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26970,Q#1754 - >seq8401,non-specific,339261,108,232,6.74061e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26971,Q#1754 - >seq8401,non-specific,236970,9,207,2.35233e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26972,Q#1754 - >seq8401,non-specific,238185,653,769,0.000285439,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26973,Q#1754 - >seq8401,non-specific,197318,9,236,0.000372484,43.4391,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26974,Q#1754 - >seq8401,specific,311990,1240,1258,0.00375771,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26975,Q#1754 - >seq8401,superfamily,311990,1240,1258,0.00375771,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs1_chimp,pars,CompleteHit
26976,Q#1754 - >seq8401,non-specific,223496,320,497,0.00683445,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA3,ORF2,hs1_chimp,pars,BothTerminiTruncated
26977,Q#1754 - >seq8401,superfamily,223496,320,497,0.00683445,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA3,ORF2,hs1_chimp,pars,BothTerminiTruncated
26978,Q#1754 - >seq8401,non-specific,334125,212,407,0.00778938,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
26979,Q#1754 - >seq8401,superfamily,334125,212,407,0.00778938,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
26980,Q#1758 - >seq8405,specific,238827,507,769,9.571189999999998e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
26981,Q#1758 - >seq8405,superfamily,295487,507,769,9.571189999999998e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
26982,Q#1758 - >seq8405,specific,197310,9,234,1.2929699999999999e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26983,Q#1758 - >seq8405,superfamily,351117,9,234,1.2929699999999999e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26984,Q#1758 - >seq8405,non-specific,197306,9,234,7.758749999999999e-33,127.598,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26985,Q#1758 - >seq8405,specific,333820,513,769,3.63003e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
26986,Q#1758 - >seq8405,superfamily,333820,513,769,3.63003e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
26987,Q#1758 - >seq8405,non-specific,197320,7,227,5.55155e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26988,Q#1758 - >seq8405,non-specific,223780,7,227,3.40146e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26989,Q#1758 - >seq8405,specific,335306,10,227,4.67956e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26990,Q#1758 - >seq8405,non-specific,197307,9,234,8.47943e-17,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26991,Q#1758 - >seq8405,non-specific,197321,7,234,5.38394e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26992,Q#1758 - >seq8405,non-specific,197319,7,234,9.34534e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26993,Q#1758 - >seq8405,non-specific,272954,7,234,1.8614400000000001e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26994,Q#1758 - >seq8405,non-specific,273186,7,235,8.763659999999999e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26995,Q#1758 - >seq8405,non-specific,238828,513,734,3.11592e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
26996,Q#1758 - >seq8405,non-specific,197336,7,227,2.00505e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
26997,Q#1758 - >seq8405,non-specific,275209,584,734,7.766549999999999e-07,52.46,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,BothTerminiTruncated
26998,Q#1758 - >seq8405,superfamily,275209,584,734,7.766549999999999e-07,52.46,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,BothTerminiTruncated
26999,Q#1758 - >seq8405,non-specific,339261,108,230,3.04776e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
27000,Q#1758 - >seq8405,non-specific,197311,7,234,3.81749e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
27001,Q#1758 - >seq8405,non-specific,236970,9,205,0.000294413,44.1146,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,marg,CompleteHit
27002,Q#1758 - >seq8405,non-specific,238185,653,769,0.000346585,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs0_human,marg,CompleteHit
27003,Q#1758 - >seq8405,non-specific,223496,318,497,0.000465101,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA3,ORF2,hs0_human,marg,BothTerminiTruncated
27004,Q#1758 - >seq8405,superfamily,223496,318,497,0.000465101,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA3,ORF2,hs0_human,marg,BothTerminiTruncated
27005,Q#1758 - >seq8405,non-specific,334125,210,407,0.00247536,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs0_human,marg,N-TerminusTruncated
27006,Q#1758 - >seq8405,superfamily,334125,210,407,0.00247536,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs0_human,marg,N-TerminusTruncated
27007,Q#1758 - >seq8405,specific,311990,1239,1257,0.00394336,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs0_human,marg,CompleteHit
27008,Q#1758 - >seq8405,superfamily,311990,1239,1257,0.00394336,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs0_human,marg,CompleteHit
27009,Q#1758 - >seq8405,non-specific,224117,260,497,0.00585649,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA3,ORF2,hs0_human,marg,N-TerminusTruncated
27010,Q#1758 - >seq8405,superfamily,224117,260,497,0.00585649,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF2.hs0_human.marg.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA3,ORF2,hs0_human,marg,N-TerminusTruncated
27011,Q#1761 - >seq8408,specific,238827,506,766,1.39827e-64,217.929,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27012,Q#1761 - >seq8408,superfamily,295487,506,766,1.39827e-64,217.929,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27013,Q#1761 - >seq8408,specific,197310,9,233,4.873479999999999e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27014,Q#1761 - >seq8408,superfamily,351117,9,233,4.873479999999999e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27015,Q#1761 - >seq8408,specific,333820,512,767,8.778629999999999e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27016,Q#1761 - >seq8408,superfamily,333820,512,767,8.778629999999999e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27017,Q#1761 - >seq8408,non-specific,197306,9,233,1.69612e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27018,Q#1761 - >seq8408,non-specific,197320,7,226,3.59776e-23,99.8969,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27019,Q#1761 - >seq8408,non-specific,223780,7,226,1.27726e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27020,Q#1761 - >seq8408,specific,335306,10,226,1.0569600000000001e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27021,Q#1761 - >seq8408,non-specific,197307,9,233,1.0778099999999999e-16,81.1801,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27022,Q#1761 - >seq8408,non-specific,197321,7,233,8.09594e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27023,Q#1761 - >seq8408,non-specific,272954,7,233,1.5938499999999998e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27024,Q#1761 - >seq8408,non-specific,273186,7,234,5.11697e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27025,Q#1761 - >seq8408,non-specific,197319,7,233,8.95175e-13,69.6129,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27026,Q#1761 - >seq8408,non-specific,238828,512,733,2.9294e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27027,Q#1761 - >seq8408,non-specific,197336,7,226,2.2066e-07,53.3851,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27028,Q#1761 - >seq8408,non-specific,275209,583,733,7.326690000000001e-07,52.46,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,BothTerminiTruncated
27029,Q#1761 - >seq8408,superfamily,275209,583,733,7.326690000000001e-07,52.46,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,BothTerminiTruncated
27030,Q#1761 - >seq8408,non-specific,197311,7,233,1.36106e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27031,Q#1761 - >seq8408,non-specific,339261,108,229,1.7785900000000002e-06,48.1023,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27032,Q#1761 - >seq8408,non-specific,236970,9,204,5.5871499999999995e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs0_human,pars,CompleteHit
27033,Q#1761 - >seq8408,non-specific,223496,317,496,0.000400488,44.7511,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA3,ORF2,hs0_human,pars,BothTerminiTruncated
27034,Q#1761 - >seq8408,superfamily,223496,317,496,0.000400488,44.7511,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA3,ORF2,hs0_human,pars,BothTerminiTruncated
27035,Q#1761 - >seq8408,non-specific,238185,652,767,0.00054526,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs0_human,pars,CompleteHit
27036,Q#1761 - >seq8408,non-specific,334125,209,406,0.00229812,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs0_human,pars,N-TerminusTruncated
27037,Q#1761 - >seq8408,superfamily,334125,209,406,0.00229812,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs0_human,pars,N-TerminusTruncated
27038,Q#1761 - >seq8408,specific,311990,1235,1253,0.00377409,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs0_human,pars,CompleteHit
27039,Q#1761 - >seq8408,superfamily,311990,1235,1253,0.00377409,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs0_human,pars,CompleteHit
27040,Q#1761 - >seq8408,non-specific,224117,259,496,0.005307699999999999,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA3,ORF2,hs0_human,pars,N-TerminusTruncated
27041,Q#1761 - >seq8408,superfamily,224117,259,496,0.005307699999999999,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA3.ORF2.hs0_human.pars.frame3,1909181135_L1MA3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA3,ORF2,hs0_human,pars,N-TerminusTruncated
27042,Q#1764 - >seq8411,specific,238827,509,771,1.7262999999999996e-63,214.84799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27043,Q#1764 - >seq8411,superfamily,295487,509,771,1.7262999999999996e-63,214.84799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27044,Q#1764 - >seq8411,specific,197310,9,237,3.24773e-36,137.09799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27045,Q#1764 - >seq8411,superfamily,351117,9,237,3.24773e-36,137.09799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27046,Q#1764 - >seq8411,specific,333820,515,771,5.03004e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27047,Q#1764 - >seq8411,superfamily,333820,515,771,5.03004e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27048,Q#1764 - >seq8411,non-specific,197306,9,237,4.41158e-23,99.478,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27049,Q#1764 - >seq8411,specific,335306,10,230,9.50892e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27050,Q#1764 - >seq8411,non-specific,197320,7,230,3.32127e-13,70.6218,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27051,Q#1764 - >seq8411,non-specific,197307,9,237,8.40272e-11,63.4609,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27052,Q#1764 - >seq8411,non-specific,223780,7,230,1.0595299999999998e-10,63.3863,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27053,Q#1764 - >seq8411,non-specific,238828,515,736,3.71379e-10,61.0628,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27054,Q#1764 - >seq8411,non-specific,272954,7,208,6.35192e-08,55.0817,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27055,Q#1764 - >seq8411,non-specific,197321,7,237,1.85913e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27056,Q#1764 - >seq8411,non-specific,273186,7,238,2.46033e-07,53.0516,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27057,Q#1764 - >seq8411,non-specific,275209,466,736,1.05642e-06,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
27058,Q#1764 - >seq8411,superfamily,275209,466,736,1.05642e-06,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
27059,Q#1764 - >seq8411,non-specific,197319,7,237,5.31768e-05,46.1157,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27060,Q#1764 - >seq8411,non-specific,197336,7,230,0.000927608,42.2143,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27061,Q#1764 - >seq8411,non-specific,238185,650,771,0.00497505,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27062,Q#1765 - >seq8412,specific,311990,1165,1183,0.00039051300000000005,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27063,Q#1765 - >seq8412,superfamily,311990,1165,1183,0.00039051300000000005,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA3,ORF2,hs6_sqmonkey,marg,CompleteHit
27064,Q#1766 - >seq8413,non-specific,197310,37,121,1.5120699999999997e-09,59.2873,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
27065,Q#1766 - >seq8413,superfamily,351117,37,121,1.5120699999999997e-09,59.2873,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
27066,Q#1767 - >seq8414,non-specific,197310,9,57,5.34586e-11,63.9097,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27067,Q#1767 - >seq8414,superfamily,351117,9,57,5.34586e-11,63.9097,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27068,Q#1767 - >seq8414,non-specific,197306,9,143,5.554069999999999e-08,54.7949,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27069,Q#1767 - >seq8414,non-specific,272954,7,73,3.73957e-05,46.6073,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27070,Q#1767 - >seq8414,non-specific,223780,7,43,4.19225e-05,46.4375,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27071,Q#1767 - >seq8414,non-specific,197321,7,43,8.64243e-05,45.2356,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27072,Q#1767 - >seq8414,non-specific,197320,7,43,0.00018201,44.4282,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27073,Q#1767 - >seq8414,specific,311990,1176,1194,0.000251156,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27074,Q#1767 - >seq8414,superfamily,311990,1176,1194,0.000251156,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27075,Q#1767 - >seq8414,specific,335306,10,193,0.0005375569999999999,42.6174,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27076,Q#1767 - >seq8414,non-specific,197307,9,43,0.000965756,42.2749,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27077,Q#1767 - >seq8414,non-specific,273186,7,53,0.00103491,41.8808,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27078,Q#1767 - >seq8414,non-specific,197336,7,43,0.00510307,39.9031,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27079,Q#1767 - >seq8414,non-specific,197319,7,43,0.00924358,39.1821,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27080,Q#1769 - >seq8416,specific,238827,495,757,2.3716899999999994e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27081,Q#1769 - >seq8416,superfamily,295487,495,757,2.3716899999999994e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27082,Q#1769 - >seq8416,specific,197310,37,224,4.682689999999999e-37,139.79399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27083,Q#1769 - >seq8416,superfamily,351117,37,224,4.682689999999999e-37,139.79399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27084,Q#1769 - >seq8416,specific,333820,501,757,5.21336e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27085,Q#1769 - >seq8416,superfamily,333820,501,757,5.21336e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27086,Q#1769 - >seq8416,non-specific,197306,37,224,7.21413e-15,75.5956,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27087,Q#1769 - >seq8416,non-specific,238828,501,722,3.73615e-10,61.0628,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27088,Q#1769 - >seq8416,non-specific,197320,97,217,4.05675e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
27089,Q#1769 - >seq8416,specific,335306,53,217,8.99018e-07,51.0918,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
27090,Q#1769 - >seq8416,non-specific,223780,41,217,1.83726e-06,50.6747,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27091,Q#1769 - >seq8416,non-specific,275209,453,722,1.5947100000000002e-05,48.2228,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27092,Q#1769 - >seq8416,superfamily,275209,453,722,1.5947100000000002e-05,48.2228,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
27093,Q#1769 - >seq8416,non-specific,197307,82,224,5.3615299999999995e-05,46.1269,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
27094,Q#1769 - >seq8416,non-specific,197319,97,224,0.00038849699999999996,43.4193,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
27095,Q#1769 - >seq8416,non-specific,339261,99,220,0.000824118,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27096,Q#1769 - >seq8416,non-specific,238185,636,757,0.00547351,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA3,ORF2,hs6_sqmonkey,pars,CompleteHit
27097,Q#1769 - >seq8416,non-specific,197321,97,224,0.00885271,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1MA3.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA3,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
27098,Q#1770 - >seq8417,specific,238827,508,770,8.738409999999999e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27099,Q#1770 - >seq8417,superfamily,295487,508,770,8.738409999999999e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27100,Q#1770 - >seq8417,specific,197310,9,235,3.55315e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27101,Q#1770 - >seq8417,superfamily,351117,9,235,3.55315e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27102,Q#1770 - >seq8417,non-specific,197306,9,235,3.72061e-36,137.22799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27103,Q#1770 - >seq8417,specific,333820,514,770,2.54834e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27104,Q#1770 - >seq8417,superfamily,333820,514,770,2.54834e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27105,Q#1770 - >seq8417,non-specific,197320,7,228,9.84366e-22,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27106,Q#1770 - >seq8417,non-specific,223780,7,228,1.82919e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27107,Q#1770 - >seq8417,specific,335306,10,228,5.79276e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27108,Q#1770 - >seq8417,non-specific,197307,9,235,2.9434500000000003e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27109,Q#1770 - >seq8417,non-specific,197321,7,235,5.1072899999999994e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27110,Q#1770 - >seq8417,non-specific,272954,7,235,6.6373199999999995e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27111,Q#1770 - >seq8417,non-specific,273186,7,236,1.17771e-13,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27112,Q#1770 - >seq8417,non-specific,197319,7,235,2.4613000000000003e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27113,Q#1770 - >seq8417,non-specific,238828,514,735,2.40362e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27114,Q#1770 - >seq8417,non-specific,197336,7,228,4.7833599999999995e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27115,Q#1770 - >seq8417,non-specific,275209,465,735,6.78824e-08,55.9268,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
27116,Q#1770 - >seq8417,superfamily,275209,465,735,6.78824e-08,55.9268,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
27117,Q#1770 - >seq8417,non-specific,197311,7,235,5.65209e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27118,Q#1770 - >seq8417,non-specific,339261,107,231,5.90297e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27119,Q#1770 - >seq8417,non-specific,236970,9,206,0.000134473,44.885,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27120,Q#1770 - >seq8417,non-specific,238185,654,770,0.000237768,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27121,Q#1770 - >seq8417,non-specific,223496,319,498,0.00142891,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27122,Q#1770 - >seq8417,superfamily,223496,319,498,0.00142891,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27123,Q#1770 - >seq8417,non-specific,197314,7,235,0.00157268,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27124,Q#1770 - >seq8417,non-specific,334125,211,408,0.00188555,42.1364,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27125,Q#1770 - >seq8417,superfamily,334125,211,408,0.00188555,42.1364,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27126,Q#1770 - >seq8417,specific,311990,1241,1259,0.00341486,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27127,Q#1770 - >seq8417,superfamily,311990,1241,1259,0.00341486,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs5_gmonkey,marg,CompleteHit
27128,Q#1773 - >seq8420,specific,197310,9,235,8.11236e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27129,Q#1773 - >seq8420,superfamily,351117,9,235,8.11236e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27130,Q#1773 - >seq8420,non-specific,197306,9,235,4.6488e-37,139.924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27131,Q#1773 - >seq8420,non-specific,197320,7,228,4.84857e-22,96.8153,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27132,Q#1773 - >seq8420,non-specific,223780,7,228,9.57999e-21,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27133,Q#1773 - >seq8420,non-specific,197307,9,235,6.138330000000001e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27134,Q#1773 - >seq8420,specific,335306,10,228,5.35437e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27135,Q#1773 - >seq8420,non-specific,272954,7,235,2.40861e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27136,Q#1773 - >seq8420,non-specific,197321,7,235,6.78695e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27137,Q#1773 - >seq8420,non-specific,197319,7,235,5.18126e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27138,Q#1773 - >seq8420,non-specific,273186,7,236,2.4496e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27139,Q#1773 - >seq8420,non-specific,197336,7,228,4.41912e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27140,Q#1773 - >seq8420,non-specific,236970,9,228,2.0663000000000002e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27141,Q#1773 - >seq8420,non-specific,197311,7,235,3.9302e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27142,Q#1773 - >seq8420,non-specific,339261,107,231,5.43629e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27143,Q#1773 - >seq8420,non-specific,197314,7,235,0.00145628,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27144,Q#1774 - >seq8421,specific,238827,490,751,1.5469399999999997e-63,214.84799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27145,Q#1774 - >seq8421,superfamily,295487,490,751,1.5469399999999997e-63,214.84799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27146,Q#1774 - >seq8421,specific,333820,496,751,2.35027e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27147,Q#1774 - >seq8421,superfamily,333820,496,751,2.35027e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27148,Q#1774 - >seq8421,non-specific,238828,496,716,1.89047e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27149,Q#1774 - >seq8421,non-specific,275209,447,716,3.20685e-07,53.6156,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27150,Q#1774 - >seq8421,superfamily,275209,447,716,3.20685e-07,53.6156,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27151,Q#1774 - >seq8421,non-specific,238185,636,751,6.0218600000000005e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27152,Q#1774 - >seq8421,specific,311990,1206,1224,0.00193503,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27153,Q#1774 - >seq8421,superfamily,311990,1206,1224,0.00193503,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1MA3.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA3,ORF2,hs5_gmonkey,pars,CompleteHit
27154,Q#1775 - >seq8422,specific,238827,508,770,7.565919999999999e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27155,Q#1775 - >seq8422,superfamily,295487,508,770,7.565919999999999e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27156,Q#1775 - >seq8422,specific,197310,9,236,4.8921399999999995e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27157,Q#1775 - >seq8422,superfamily,351117,9,236,4.8921399999999995e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27158,Q#1775 - >seq8422,non-specific,197306,9,236,2.5597900000000003e-36,137.613,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27159,Q#1775 - >seq8422,specific,333820,514,770,1.7671499999999998e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27160,Q#1775 - >seq8422,superfamily,333820,514,770,1.7671499999999998e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27161,Q#1775 - >seq8422,non-specific,197320,7,229,4.54237e-25,105.675,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27162,Q#1775 - >seq8422,non-specific,223780,7,229,7.97709e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27163,Q#1775 - >seq8422,non-specific,197307,9,236,4.77808e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27164,Q#1775 - >seq8422,specific,335306,10,229,2.36499e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27165,Q#1775 - >seq8422,non-specific,197321,7,236,3.7320699999999996e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27166,Q#1775 - >seq8422,non-specific,273186,7,237,2.78192e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27167,Q#1775 - >seq8422,non-specific,272954,7,236,4.59753e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27168,Q#1775 - >seq8422,non-specific,197319,7,236,2.90714e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27169,Q#1775 - >seq8422,non-specific,197336,7,229,6.681230000000001e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27170,Q#1775 - >seq8422,non-specific,238828,514,735,3.67172e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27171,Q#1775 - >seq8422,non-specific,275209,465,735,3.06972e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27172,Q#1775 - >seq8422,superfamily,275209,465,735,3.06972e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27173,Q#1775 - >seq8422,non-specific,197311,7,236,6.04294e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27174,Q#1775 - >seq8422,non-specific,339261,108,232,6.762919999999999e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27175,Q#1775 - >seq8422,non-specific,236970,9,207,2.15766e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27176,Q#1775 - >seq8422,non-specific,238185,654,770,0.000270105,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27177,Q#1775 - >seq8422,non-specific,197318,9,236,0.00032356,43.8243,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27178,Q#1775 - >seq8422,non-specific,334125,212,408,0.00116469,42.5216,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27179,Q#1775 - >seq8422,superfamily,334125,212,408,0.00116469,42.5216,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27180,Q#1775 - >seq8422,specific,311990,1241,1259,0.00366018,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27181,Q#1775 - >seq8422,superfamily,311990,1241,1259,0.00366018,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs1_chimp,marg,CompleteHit
27182,Q#1776 - >seq8423,specific,197310,9,236,3.8646099999999995e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27183,Q#1776 - >seq8423,superfamily,351117,9,236,3.8646099999999995e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27184,Q#1776 - >seq8423,specific,238827,507,769,9.474639999999998e-47,167.083,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27185,Q#1776 - >seq8423,superfamily,295487,507,769,9.474639999999998e-47,167.083,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27186,Q#1776 - >seq8423,non-specific,197306,9,236,7.591209999999999e-31,121.82,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27187,Q#1776 - >seq8423,non-specific,333820,524,769,1.02027e-22,96.5925,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27188,Q#1776 - >seq8423,superfamily,333820,524,769,1.02027e-22,96.5925,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27189,Q#1776 - >seq8423,specific,335306,10,229,9.359080000000001e-19,86.5301,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27190,Q#1776 - >seq8423,non-specific,197320,9,229,2.37582e-17,82.9481,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27191,Q#1776 - >seq8423,non-specific,223780,9,229,1.94935e-15,77.6387,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27192,Q#1776 - >seq8423,non-specific,197307,9,236,1.1001799999999998e-14,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27193,Q#1776 - >seq8423,non-specific,197321,7,236,9.84716e-12,66.4216,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27194,Q#1776 - >seq8423,non-specific,273186,9,237,2.69242e-10,62.2964,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27195,Q#1776 - >seq8423,non-specific,238828,578,733,3.3029199999999997e-10,61.448,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,N-TerminusTruncated
27196,Q#1776 - >seq8423,non-specific,197319,9,236,3.3734600000000005e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27197,Q#1776 - >seq8423,non-specific,272954,9,236,4.30105e-08,55.4669,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27198,Q#1776 - >seq8423,non-specific,275209,583,793,2.33977e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,N-TerminusTruncated
27199,Q#1776 - >seq8423,superfamily,275209,583,793,2.33977e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,N-TerminusTruncated
27200,Q#1776 - >seq8423,non-specific,339261,108,232,0.000157426,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27201,Q#1776 - >seq8423,non-specific,197311,37,236,0.00021649900000000002,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27202,Q#1776 - >seq8423,non-specific,334125,212,409,0.000963616,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs1_chimp,pars,N-TerminusTruncated
27203,Q#1776 - >seq8423,superfamily,334125,212,409,0.000963616,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA4A,ORF2,hs1_chimp,pars,N-TerminusTruncated
27204,Q#1776 - >seq8423,non-specific,274009,306,499,0.00192023,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,pars,C-TerminusTruncated
27205,Q#1776 - >seq8423,superfamily,274009,306,499,0.00192023,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4A,ORF2,hs1_chimp,pars,C-TerminusTruncated
27206,Q#1776 - >seq8423,non-specific,197336,9,229,0.0023651,41.0587,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27207,Q#1776 - >seq8423,non-specific,238185,652,769,0.00471203,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4A.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA4A.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4A,ORF2,hs1_chimp,pars,CompleteHit
27208,Q#1777 - >seq8424,specific,197310,9,236,3.0197299999999997e-62,211.826,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27209,Q#1777 - >seq8424,superfamily,351117,9,236,3.0197299999999997e-62,211.826,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27210,Q#1777 - >seq8424,non-specific,197306,9,236,4.7432899999999997e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27211,Q#1777 - >seq8424,non-specific,238827,524,603,4.83664e-23,98.5174,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs3_orang,pars,C-TerminusTruncated
27212,Q#1777 - >seq8424,superfamily,295487,524,603,4.83664e-23,98.5174,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs3_orang,pars,C-TerminusTruncated
27213,Q#1777 - >seq8424,non-specific,197307,9,236,3.69418e-22,96.9733,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27214,Q#1777 - >seq8424,non-specific,223780,7,229,1.9817999999999998e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27215,Q#1777 - >seq8424,non-specific,197320,7,229,7.33526e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27216,Q#1777 - >seq8424,specific,335306,10,229,8.69791e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27217,Q#1777 - >seq8424,non-specific,197321,7,236,2.67533e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27218,Q#1777 - >seq8424,non-specific,272954,7,236,6.71343e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27219,Q#1777 - >seq8424,non-specific,273186,7,237,8.3853e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27220,Q#1777 - >seq8424,non-specific,197319,7,236,2.91063e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27221,Q#1777 - >seq8424,non-specific,333820,524,623,1.03687e-09,58.843,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs3_orang,pars,C-TerminusTruncated
27222,Q#1777 - >seq8424,superfamily,333820,524,623,1.03687e-09,58.843,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs3_orang,pars,C-TerminusTruncated
27223,Q#1777 - >seq8424,non-specific,197336,7,229,1.8554700000000003e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27224,Q#1777 - >seq8424,non-specific,236970,9,229,3.07785e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27225,Q#1777 - >seq8424,non-specific,197318,9,236,7.66577e-06,48.4467,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27226,Q#1777 - >seq8424,non-specific,197322,8,236,2.74252e-05,47.3118,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27227,Q#1777 - >seq8424,non-specific,197311,7,236,0.000224949,43.4345,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27228,Q#1777 - >seq8424,non-specific,339261,108,232,0.00948182,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs3_orang.pars.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs3_orang,pars,CompleteHit
27229,Q#1778 - >seq8425,non-specific,238827,490,705,1.01395e-23,100.443,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27230,Q#1778 - >seq8425,superfamily,295487,490,705,1.01395e-23,100.443,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27231,Q#1778 - >seq8425,non-specific,333820,526,705,4.37912e-13,68.8582,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27232,Q#1778 - >seq8425,superfamily,333820,526,705,4.37912e-13,68.8582,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27233,Q#1778 - >seq8425,non-specific,238828,521,682,6.401980000000001e-07,51.4328,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27234,Q#1778 - >seq8425,non-specific,275209,522,729,4.69713e-05,46.681999999999995,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27235,Q#1778 - >seq8425,superfamily,275209,522,729,4.69713e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs1_chimp.marg.frame3,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27236,Q#1782 - >seq8429,specific,238827,441,702,4.7437399999999995e-27,110.073,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,CompleteHit
27237,Q#1782 - >seq8429,superfamily,295487,441,702,4.7437399999999995e-27,110.073,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,CompleteHit
27238,Q#1782 - >seq8429,non-specific,333820,447,695,9.14489e-15,73.4806,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,CompleteHit
27239,Q#1782 - >seq8429,superfamily,333820,447,695,9.14489e-15,73.4806,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,CompleteHit
27240,Q#1782 - >seq8429,non-specific,238828,523,695,7.27148e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27241,Q#1782 - >seq8429,non-specific,275209,524,731,0.00017934,45.1412,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27242,Q#1782 - >seq8429,superfamily,275209,524,731,0.00017934,45.1412,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27243,Q#1782 - >seq8429,non-specific,238185,586,695,0.00271295,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs4_gibbon,pars,CompleteHit
27244,Q#1783 - >seq8430,specific,197310,9,234,1.1260399999999999e-45,164.447,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27245,Q#1783 - >seq8430,superfamily,351117,9,234,1.1260399999999999e-45,164.447,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27246,Q#1783 - >seq8430,specific,238827,573,767,8.4726e-28,112.385,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,N-TerminusTruncated
27247,Q#1783 - >seq8430,superfamily,295487,573,767,8.4726e-28,112.385,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,N-TerminusTruncated
27248,Q#1783 - >seq8430,non-specific,197306,9,234,4.63963e-22,96.3964,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27249,Q#1783 - >seq8430,non-specific,333820,580,767,8.35923e-18,82.3401,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,N-TerminusTruncated
27250,Q#1783 - >seq8430,superfamily,333820,580,767,8.35923e-18,82.3401,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,N-TerminusTruncated
27251,Q#1783 - >seq8430,non-specific,223780,9,227,6.950870000000001e-17,81.8759,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27252,Q#1783 - >seq8430,non-specific,197320,9,219,3.84971e-13,70.6218,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27253,Q#1783 - >seq8430,non-specific,197307,9,234,5.60891e-13,70.0093,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27254,Q#1783 - >seq8430,non-specific,273186,9,235,1.00745e-12,69.23,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27255,Q#1783 - >seq8430,specific,335306,10,227,1.2185600000000002e-10,62.6478,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27256,Q#1783 - >seq8430,non-specific,238828,576,745,6.43797e-10,60.6776,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,N-TerminusTruncated
27257,Q#1783 - >seq8430,non-specific,272954,9,205,1.13788e-08,57.3929,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27258,Q#1783 - >seq8430,non-specific,197321,7,234,2.0699799999999996e-08,56.4064,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27259,Q#1783 - >seq8430,non-specific,197322,8,234,7.806260000000001e-08,55.401,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27260,Q#1783 - >seq8430,non-specific,275209,581,732,2.24167e-07,54.386,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,BothTerminiTruncated
27261,Q#1783 - >seq8430,superfamily,275209,581,732,2.24167e-07,54.386,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,BothTerminiTruncated
27262,Q#1783 - >seq8430,non-specific,197319,9,234,5.19693e-07,52.2789,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27263,Q#1783 - >seq8430,non-specific,197336,9,192,7.4115999999999995e-06,48.7627,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27264,Q#1783 - >seq8430,non-specific,339261,106,230,7.568660000000001e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27265,Q#1783 - >seq8430,non-specific,238185,649,745,0.0013572,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.marg.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs3_orang,marg,CompleteHit
27266,Q#1785 - >seq8432,non-specific,238827,484,519,9.20689e-06,48.0562,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs3_orang.marg.frame1,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs3_orang,marg,C-TerminusTruncated
27267,Q#1785 - >seq8432,superfamily,295487,484,519,9.20689e-06,48.0562,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.marg.frame1,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs3_orang,marg,C-TerminusTruncated
27268,Q#1786 - >seq8433,specific,197310,9,234,4.17416e-46,165.602,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27269,Q#1786 - >seq8433,superfamily,351117,9,234,4.17416e-46,165.602,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27270,Q#1786 - >seq8433,specific,238827,573,767,8.39599e-28,112.385,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,N-TerminusTruncated
27271,Q#1786 - >seq8433,superfamily,295487,573,767,8.39599e-28,112.385,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,N-TerminusTruncated
27272,Q#1786 - >seq8433,non-specific,197306,9,234,2.3143700000000004e-22,97.1668,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27273,Q#1786 - >seq8433,non-specific,333820,580,767,8.285819999999999e-18,82.3401,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,N-TerminusTruncated
27274,Q#1786 - >seq8433,superfamily,333820,580,767,8.285819999999999e-18,82.3401,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,N-TerminusTruncated
27275,Q#1786 - >seq8433,non-specific,223780,9,227,3.18165e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27276,Q#1786 - >seq8433,non-specific,197320,9,219,2.77535e-13,71.007,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27277,Q#1786 - >seq8433,non-specific,197307,9,234,3.3117699999999997e-12,67.6981,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27278,Q#1786 - >seq8433,non-specific,273186,9,235,3.72055e-12,67.6892,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27279,Q#1786 - >seq8433,specific,335306,10,227,5.58948e-11,63.4182,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27280,Q#1786 - >seq8433,non-specific,238828,576,745,6.440250000000001e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,N-TerminusTruncated
27281,Q#1786 - >seq8433,non-specific,197321,7,234,3.76252e-08,55.636,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27282,Q#1786 - >seq8433,non-specific,272954,9,205,7.68642e-08,54.6965,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27283,Q#1786 - >seq8433,non-specific,197319,9,234,1.30503e-07,54.2049,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27284,Q#1786 - >seq8433,non-specific,275209,581,732,2.30039e-07,54.386,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,BothTerminiTruncated
27285,Q#1786 - >seq8433,superfamily,275209,581,732,2.30039e-07,54.386,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,BothTerminiTruncated
27286,Q#1786 - >seq8433,non-specific,197322,8,234,2.4465e-06,50.7786,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27287,Q#1786 - >seq8433,non-specific,339261,107,230,3.4931599999999996e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27288,Q#1786 - >seq8433,non-specific,197336,9,192,6.125319999999999e-06,48.7627,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27289,Q#1786 - >seq8433,non-specific,238185,649,745,0.00134601,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.pars.frame3,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs3_orang,pars,CompleteHit
27290,Q#1789 - >seq8436,non-specific,238827,485,520,9.05972e-06,48.0562,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs3_orang.pars.frame1,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs3_orang,pars,C-TerminusTruncated
27291,Q#1789 - >seq8436,superfamily,295487,485,520,9.05972e-06,48.0562,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs3_orang.pars.frame1,1909181135_L1MC1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs3_orang,pars,C-TerminusTruncated
27292,Q#1791 - >seq8438,specific,238827,487,727,2.81841e-43,157.06799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27293,Q#1791 - >seq8438,superfamily,295487,487,727,2.81841e-43,157.06799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27294,Q#1791 - >seq8438,non-specific,333820,482,705,5.046750000000001e-22,94.6665,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27295,Q#1791 - >seq8438,superfamily,333820,482,705,5.046750000000001e-22,94.6665,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27296,Q#1791 - >seq8438,non-specific,238828,536,705,2.68795e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,N-TerminusTruncated
27297,Q#1791 - >seq8438,non-specific,275209,541,692,4.0890900000000007e-08,56.6972,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,BothTerminiTruncated
27298,Q#1791 - >seq8438,superfamily,275209,541,692,4.0890900000000007e-08,56.6972,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,BothTerminiTruncated
27299,Q#1791 - >seq8438,non-specific,238185,610,705,0.00154043,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27300,Q#1791 - >seq8438,non-specific,239569,495,702,0.00270298,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27301,Q#1791 - >seq8438,non-specific,238843,480,705,0.00863535,39.1888,cd01699,RNA_dep_RNAP, - ,cl02808,"RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.",L1MC1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27302,Q#1792 - >seq8439,specific,197310,9,237,3.92722e-46,165.602,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27303,Q#1792 - >seq8439,superfamily,351117,9,237,3.92722e-46,165.602,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27304,Q#1792 - >seq8439,non-specific,197306,9,237,1.45052e-19,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27305,Q#1792 - >seq8439,non-specific,223780,9,230,1.1888600000000002e-14,75.3275,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27306,Q#1792 - >seq8439,non-specific,197307,9,237,4.31793e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27307,Q#1792 - >seq8439,non-specific,197320,52,222,6.86028e-10,60.9918,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,pars,N-TerminusTruncated
27308,Q#1792 - >seq8439,specific,335306,10,230,1.08026e-09,59.9514,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27309,Q#1792 - >seq8439,non-specific,273186,9,238,3.9966399999999995e-09,58.4444,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27310,Q#1792 - >seq8439,non-specific,197322,8,237,6.39887e-07,52.3194,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27311,Q#1792 - >seq8439,non-specific,272954,9,237,2.2874e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27312,Q#1792 - >seq8439,non-specific,339261,109,233,4.80805e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27313,Q#1792 - >seq8439,non-specific,197321,7,237,6.59663e-06,48.7024,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27314,Q#1792 - >seq8439,non-specific,235175,292,449,0.00542975,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs1_chimp,pars,BothTerminiTruncated
27315,Q#1792 - >seq8439,superfamily,235175,292,449,0.00542975,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs1_chimp,pars,BothTerminiTruncated
27316,Q#1794 - >seq8441,specific,238827,485,725,3.70372e-43,156.68200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27317,Q#1794 - >seq8441,superfamily,295487,485,725,3.70372e-43,156.68200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27318,Q#1794 - >seq8441,non-specific,333820,480,703,6.566210000000001e-22,94.2813,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27319,Q#1794 - >seq8441,superfamily,333820,480,703,6.566210000000001e-22,94.2813,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27320,Q#1794 - >seq8441,non-specific,238828,534,703,2.90676e-12,67.226,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,N-TerminusTruncated
27321,Q#1794 - >seq8441,non-specific,275209,539,690,4.67821e-08,56.312,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,BothTerminiTruncated
27322,Q#1794 - >seq8441,superfamily,275209,539,690,4.67821e-08,56.312,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,BothTerminiTruncated
27323,Q#1794 - >seq8441,non-specific,238185,608,703,0.00157671,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27324,Q#1794 - >seq8441,non-specific,239569,493,700,0.00310787,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27325,Q#1794 - >seq8441,non-specific,238843,478,703,0.00904724,39.1888,cd01699,RNA_dep_RNAP, - ,cl02808,"RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.",L1MC1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1MC1,ORF2,hs1_chimp,pars,CompleteHit
27326,Q#1796 - >seq8443,specific,238827,515,708,6.25632e-31,121.244,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27327,Q#1796 - >seq8443,superfamily,295487,515,708,6.25632e-31,121.244,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27328,Q#1796 - >seq8443,non-specific,333820,527,708,1.21386e-17,81.9549,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27329,Q#1796 - >seq8443,superfamily,333820,527,708,1.21386e-17,81.9549,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27330,Q#1796 - >seq8443,non-specific,238828,518,660,1.8456e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27331,Q#1796 - >seq8443,non-specific,275209,523,736,3.2955899999999998e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27332,Q#1796 - >seq8443,superfamily,275209,523,736,3.2955899999999998e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27333,Q#1796 - >seq8443,non-specific,238185,592,708,0.00013773,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27334,Q#1797 - >seq8444,specific,197310,26,233,8.67959e-33,127.46799999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27335,Q#1797 - >seq8444,superfamily,351117,26,233,8.67959e-33,127.46799999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27336,Q#1797 - >seq8444,non-specific,238827,504,567,7.75584e-11,63.07899999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27337,Q#1797 - >seq8444,superfamily,295487,504,567,7.75584e-11,63.07899999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27338,Q#1797 - >seq8444,specific,335306,36,226,8.485790000000002e-09,57.255,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27339,Q#1797 - >seq8444,non-specific,197306,36,233,1.32434e-07,53.6393,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27340,Q#1797 - >seq8444,non-specific,197320,107,218,3.0114999999999997e-07,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27341,Q#1797 - >seq8444,non-specific,223780,37,222,1.2455e-06,51.0599,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27342,Q#1797 - >seq8444,non-specific,333820,510,560,0.000271493,43.0498,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27343,Q#1797 - >seq8444,superfamily,333820,510,560,0.000271493,43.0498,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27344,Q#1797 - >seq8444,non-specific,339261,107,228,0.000306771,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27345,Q#1797 - >seq8444,non-specific,235175,257,458,0.000438494,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
27346,Q#1797 - >seq8444,superfamily,235175,257,458,0.000438494,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
27347,Q#1797 - >seq8444,non-specific,197322,107,219,0.000505886,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27348,Q#1797 - >seq8444,non-specific,197307,37,226,0.00170332,41.5045,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27349,Q#1797 - >seq8444,non-specific,272954,107,204,0.00400192,40.0589,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27350,Q#1797 - >seq8444,non-specific,235175,250,453,0.00582687,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27351,Q#1797 - >seq8444,non-specific,274009,258,452,0.00585436,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27352,Q#1797 - >seq8444,superfamily,274009,258,452,0.00585436,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1MB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27353,Q#1797 - >seq8444,non-specific,273186,107,234,0.00609169,39.5696,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27354,Q#1797 - >seq8444,non-specific,197321,37,226,0.008483200000000002,39.0724,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,marg,CompleteHit
27355,Q#1798 - >seq8445,specific,197310,9,237,3.73142e-46,165.988,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27356,Q#1798 - >seq8445,superfamily,351117,9,237,3.73142e-46,165.988,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27357,Q#1798 - >seq8445,non-specific,197306,9,237,1.4057500000000002e-19,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27358,Q#1798 - >seq8445,non-specific,223780,9,230,1.31439e-14,74.9423,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27359,Q#1798 - >seq8445,non-specific,197307,9,237,4.07266e-11,64.6165,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27360,Q#1798 - >seq8445,non-specific,197320,52,222,6.90585e-10,60.9918,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs1_chimp,marg,N-TerminusTruncated
27361,Q#1798 - >seq8445,specific,335306,10,230,1.0872899999999999e-09,59.9514,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27362,Q#1798 - >seq8445,non-specific,273186,9,238,4.09799e-09,58.4444,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27363,Q#1798 - >seq8445,non-specific,197322,8,237,6.44178e-07,52.3194,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27364,Q#1798 - >seq8445,non-specific,272954,9,237,2.2403900000000003e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27365,Q#1798 - >seq8445,non-specific,339261,109,233,5.22678e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27366,Q#1798 - >seq8445,non-specific,197321,7,237,6.46126e-06,48.7024,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs1_chimp,marg,CompleteHit
27367,Q#1798 - >seq8445,non-specific,274009,308,451,0.00845457,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs1_chimp,marg,C-TerminusTruncated
27368,Q#1798 - >seq8445,superfamily,274009,308,451,0.00845457,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MC1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs1_chimp,marg,C-TerminusTruncated
27369,Q#1799 - >seq8446,non-specific,238827,478,541,1.04731e-10,62.6938,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27370,Q#1799 - >seq8446,superfamily,295487,478,541,1.04731e-10,62.6938,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27371,Q#1799 - >seq8446,non-specific,333820,484,534,0.000309438,42.6646,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27372,Q#1799 - >seq8446,superfamily,333820,484,534,0.000309438,42.6646,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27373,Q#1799 - >seq8446,non-specific,235175,232,433,0.000371688,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
27374,Q#1799 - >seq8446,superfamily,235175,232,433,0.000371688,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
27375,Q#1799 - >seq8446,non-specific,235175,225,428,0.00533384,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27376,Q#1799 - >seq8446,non-specific,274009,233,427,0.00656608,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27377,Q#1799 - >seq8446,superfamily,274009,233,427,0.00656608,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27378,Q#1801 - >seq8448,non-specific,238827,587,675,1.123e-12,68.0866,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs0_human.pars.frame1,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs0_human,pars,N-TerminusTruncated
27379,Q#1801 - >seq8448,superfamily,295487,587,675,1.123e-12,68.0866,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs0_human.pars.frame1,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs0_human,pars,N-TerminusTruncated
27380,Q#1801 - >seq8448,non-specific,238828,540,656,1.7686900000000003e-06,49.891999999999996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs0_human.pars.frame1,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs0_human,pars,N-TerminusTruncated
27381,Q#1801 - >seq8448,non-specific,333820,507,664,4.5069e-06,48.0574,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.pars.frame1,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs0_human,pars,CompleteHit
27382,Q#1801 - >seq8448,superfamily,333820,507,664,4.5069e-06,48.0574,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.pars.frame1,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MCa,ORF2,hs0_human,pars,CompleteHit
27383,Q#1803 - >seq8450,specific,238827,509,771,4.7469399999999994e-66,222.166,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27384,Q#1803 - >seq8450,superfamily,295487,509,771,4.7469399999999994e-66,222.166,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27385,Q#1803 - >seq8450,specific,197310,9,236,7.337059999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27386,Q#1803 - >seq8450,superfamily,351117,9,236,7.337059999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27387,Q#1803 - >seq8450,non-specific,197306,9,236,3.9187299999999993e-35,134.14600000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27388,Q#1803 - >seq8450,specific,333820,515,771,3.8765199999999995e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27389,Q#1803 - >seq8450,superfamily,333820,515,771,3.8765199999999995e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27390,Q#1803 - >seq8450,non-specific,223780,9,237,7.42816e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27391,Q#1803 - >seq8450,non-specific,197307,9,236,1.90875e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27392,Q#1803 - >seq8450,non-specific,197320,9,229,3.33109e-22,97.2005,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27393,Q#1803 - >seq8450,non-specific,197321,7,236,1.21366e-21,95.6968,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27394,Q#1803 - >seq8450,specific,335306,10,229,1.80887e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27395,Q#1803 - >seq8450,non-specific,273186,9,237,9.491430000000001e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27396,Q#1803 - >seq8450,non-specific,197319,13,236,2.62113e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27397,Q#1803 - >seq8450,non-specific,272954,9,236,9.938960000000001e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27398,Q#1803 - >seq8450,non-specific,197336,9,194,8.99402e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27399,Q#1803 - >seq8450,non-specific,238828,515,736,1.34193e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27400,Q#1803 - >seq8450,non-specific,236970,9,237,5.69506e-11,64.5302,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27401,Q#1803 - >seq8450,non-specific,275209,466,799,3.4952699999999997e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27402,Q#1803 - >seq8450,superfamily,275209,466,799,3.4952699999999997e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27403,Q#1803 - >seq8450,non-specific,235175,291,468,2.0382e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27404,Q#1803 - >seq8450,superfamily,235175,291,468,2.0382e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27405,Q#1803 - >seq8450,non-specific,197311,38,204,0.000290015,43.4345,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27406,Q#1803 - >seq8450,non-specific,238185,655,769,0.000351123,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27407,Q#1803 - >seq8450,non-specific,339261,108,232,0.000436541,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27408,Q#1803 - >seq8450,non-specific,310273,309,512,0.0012814999999999999,42.8102,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA17,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
27409,Q#1803 - >seq8450,superfamily,310273,309,512,0.0012814999999999999,42.8102,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA17,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
27410,Q#1803 - >seq8450,non-specific,223266,211,407,0.00346629,41.4886,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27411,Q#1803 - >seq8450,superfamily,223266,211,407,0.00346629,41.4886,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
27412,Q#1803 - >seq8450,specific,311990,1240,1258,0.00551995,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27413,Q#1803 - >seq8450,superfamily,311990,1240,1258,0.00551995,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs5_gmonkey,marg,CompleteHit
27414,Q#1803 - >seq8450,non-specific,224117,263,466,0.00553974,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27415,Q#1803 - >seq8450,superfamily,224117,263,466,0.00553974,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27416,Q#1803 - >seq8450,non-specific,274009,294,455,0.00621547,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27417,Q#1803 - >seq8450,superfamily,274009,294,455,0.00621547,40.8215,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
27418,Q#1806 - >seq8453,non-specific,197310,9,112,3.19216e-24,102.43,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27419,Q#1806 - >seq8453,superfamily,351117,9,112,3.19216e-24,102.43,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27420,Q#1806 - >seq8453,non-specific,197306,9,122,7.530679999999999e-14,72.5141,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27421,Q#1806 - >seq8453,non-specific,197321,7,94,1.32325e-09,59.8732,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27422,Q#1806 - >seq8453,non-specific,197307,9,102,4.05676e-09,58.4533,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27423,Q#1806 - >seq8453,specific,335306,10,136,2.27659e-08,55.7142,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27424,Q#1806 - >seq8453,non-specific,223780,9,106,5.549840000000001e-08,55.2971,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27425,Q#1806 - >seq8453,non-specific,197336,9,97,3.2339499999999998e-06,49.5331,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27426,Q#1806 - >seq8453,non-specific,197320,9,76,1.15691e-05,47.895,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27427,Q#1806 - >seq8453,non-specific,273186,9,97,0.00016413200000000002,44.5772,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27428,Q#1806 - >seq8453,non-specific,272954,9,98,0.000201858,44.2961,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27429,Q#1806 - >seq8453,specific,311990,1135,1153,0.00120094,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27430,Q#1806 - >seq8453,superfamily,311990,1135,1153,0.00120094,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27431,Q#1807 - >seq8454,specific,238827,502,763,9.343159999999999e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27432,Q#1807 - >seq8454,superfamily,295487,502,763,9.343159999999999e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27433,Q#1807 - >seq8454,specific,333820,508,763,3.3774399999999995e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27434,Q#1807 - >seq8454,superfamily,333820,508,763,3.3774399999999995e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27435,Q#1807 - >seq8454,specific,197310,92,229,1.25062e-28,115.141,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27436,Q#1807 - >seq8454,superfamily,351117,92,229,1.25062e-28,115.141,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27437,Q#1807 - >seq8454,non-specific,197306,101,229,8.27464e-13,69.4325,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27438,Q#1807 - >seq8454,non-specific,238828,508,728,1.51094e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27439,Q#1807 - >seq8454,non-specific,197320,101,222,2.99397e-10,62.1474,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27440,Q#1807 - >seq8454,non-specific,223780,101,230,1.41573e-09,59.9195,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27441,Q#1807 - >seq8454,non-specific,275209,578,791,9.46844e-09,58.6232,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27442,Q#1807 - >seq8454,superfamily,275209,578,791,9.46844e-09,58.6232,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27443,Q#1807 - >seq8454,non-specific,197307,91,229,2.0783400000000003e-08,56.5273,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27444,Q#1807 - >seq8454,non-specific,197319,101,229,4.1736600000000003e-07,52.6641,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27445,Q#1807 - >seq8454,non-specific,197321,99,229,1.9578e-06,50.6284,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27446,Q#1807 - >seq8454,non-specific,273186,101,230,1.07481e-05,48.044,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27447,Q#1807 - >seq8454,specific,335306,105,222,1.43374e-05,47.625,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27448,Q#1807 - >seq8454,non-specific,235175,284,461,3.34092e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
27449,Q#1807 - >seq8454,superfamily,235175,284,461,3.34092e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
27450,Q#1807 - >seq8454,non-specific,238185,647,761,0.00015619899999999999,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27451,Q#1807 - >seq8454,non-specific,236970,100,230,0.000574683,42.958999999999996,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27452,Q#1807 - >seq8454,non-specific,339261,101,225,0.000873705,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA17,ORF2,hs5_gmonkey,pars,CompleteHit
27453,Q#1807 - >seq8454,non-specific,272954,103,229,0.0008903989999999999,42.3701,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27454,Q#1807 - >seq8454,non-specific,310273,302,505,0.00385429,41.2694,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27455,Q#1807 - >seq8454,superfamily,310273,302,505,0.00385429,41.2694,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1PA17,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
27456,Q#1807 - >seq8454,non-specific,223266,204,400,0.00440879,41.1034,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PA17,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
27457,Q#1807 - >seq8454,superfamily,223266,204,400,0.00440879,41.1034,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA17,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
27458,Q#1807 - >seq8454,non-specific,224117,270,459,0.00785705,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27459,Q#1807 - >seq8454,superfamily,224117,270,459,0.00785705,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27460,Q#1807 - >seq8454,non-specific,274009,287,448,0.00789789,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27461,Q#1807 - >seq8454,superfamily,274009,287,448,0.00789789,40.4363,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1PA17.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA17,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
27462,Q#1810 - >seq8457,specific,238827,529,783,5.074279999999999e-29,116.23700000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27463,Q#1810 - >seq8457,superfamily,295487,529,783,5.074279999999999e-29,116.23700000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27464,Q#1810 - >seq8457,non-specific,333820,535,776,2.74245e-16,78.10300000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27465,Q#1810 - >seq8457,superfamily,333820,535,776,2.74245e-16,78.10300000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27466,Q#1810 - >seq8457,non-specific,238828,604,776,3.418e-12,67.226,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27467,Q#1810 - >seq8457,non-specific,197310,9,254,6.86587e-05,45.8053,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27468,Q#1810 - >seq8457,superfamily,351117,9,254,6.86587e-05,45.8053,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27469,Q#1810 - >seq8457,non-specific,275209,605,812,9.108110000000001e-05,46.2968,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27470,Q#1810 - >seq8457,superfamily,275209,605,812,9.108110000000001e-05,46.2968,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27471,Q#1810 - >seq8457,non-specific,238185,667,776,0.00198433,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27472,Q#1810 - >seq8457,non-specific,197306,9,253,0.00933323,39.3869,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MC3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs4_gibbon,marg,CompleteHit
27473,Q#1811 - >seq8458,non-specific,238827,502,693,1.43127e-25,105.836,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,N-TerminusTruncated
27474,Q#1811 - >seq8458,superfamily,295487,502,693,1.43127e-25,105.836,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,N-TerminusTruncated
27475,Q#1811 - >seq8458,non-specific,333820,516,693,5.80907e-14,71.1694,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,N-TerminusTruncated
27476,Q#1811 - >seq8458,superfamily,333820,516,693,5.80907e-14,71.1694,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,N-TerminusTruncated
27477,Q#1811 - >seq8458,non-specific,238828,497,666,2.2399599999999997e-12,67.6112,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,N-TerminusTruncated
27478,Q#1811 - >seq8458,non-specific,275209,497,596,1.17338e-06,51.6896,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,BothTerminiTruncated
27479,Q#1811 - >seq8458,superfamily,275209,497,596,1.17338e-06,51.6896,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs9_pika.marg.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs9_pika,marg,BothTerminiTruncated
27480,Q#1813 - >seq8460,specific,238827,405,612,1.2163899999999998e-28,114.696,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,CompleteHit
27481,Q#1813 - >seq8460,superfamily,295487,405,612,1.2163899999999998e-28,114.696,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,CompleteHit
27482,Q#1813 - >seq8460,non-specific,333820,402,612,8.4321e-13,67.7026,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,CompleteHit
27483,Q#1813 - >seq8460,superfamily,333820,402,612,8.4321e-13,67.7026,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,CompleteHit
27484,Q#1813 - >seq8460,non-specific,238828,429,553,8.31929e-11,62.9888,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,BothTerminiTruncated
27485,Q#1813 - >seq8460,non-specific,275209,434,519,1.15774e-06,51.6896,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,BothTerminiTruncated
27486,Q#1813 - >seq8460,superfamily,275209,434,519,1.15774e-06,51.6896,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs9_pika.pars.frame2,1909181135_L1ME1.RM_HPGPNRMPCCSOTSJMCMMRHCCOOO_1708211255.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs9_pika,pars,BothTerminiTruncated
27487,Q#1815 - >seq8462,specific,197310,34,262,1.6141299999999998e-48,172.53599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27488,Q#1815 - >seq8462,superfamily,351117,34,262,1.6141299999999998e-48,172.53599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27489,Q#1815 - >seq8462,non-specific,197306,34,262,3.9433300000000006e-22,96.3964,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27490,Q#1815 - >seq8462,non-specific,223780,34,255,8.123380000000001e-16,78.4091,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27491,Q#1815 - >seq8462,non-specific,197307,34,262,4.50221e-15,76.1725,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27492,Q#1815 - >seq8462,non-specific,273186,34,263,2.09747e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27493,Q#1815 - >seq8462,specific,335306,35,255,8.60622e-12,65.7294,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27494,Q#1815 - >seq8462,non-specific,197320,34,247,1.55616e-11,65.6142,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27495,Q#1815 - >seq8462,non-specific,197322,108,262,3.0011700000000003e-09,59.6382,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27496,Q#1815 - >seq8462,non-specific,272954,34,233,6.40111e-09,57.7781,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27497,Q#1815 - >seq8462,non-specific,197321,32,262,6.09346e-08,54.8656,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,CompleteHit
27498,Q#1815 - >seq8462,non-specific,238827,529,594,9.087899999999999e-07,50.7526,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs0_human,marg,C-TerminusTruncated
27499,Q#1815 - >seq8462,superfamily,295487,529,594,9.087899999999999e-07,50.7526,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs0_human,marg,C-TerminusTruncated
27500,Q#1815 - >seq8462,non-specific,197319,117,262,5.383930000000001e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27501,Q#1815 - >seq8462,non-specific,339261,134,258,1.10462e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs0_human,marg,CompleteHit
27502,Q#1815 - >seq8462,non-specific,333820,547,585,0.00495004,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs0_human,marg,C-TerminusTruncated
27503,Q#1815 - >seq8462,superfamily,333820,547,585,0.00495004,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.marg.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MCa,ORF2,hs0_human,marg,C-TerminusTruncated
27504,Q#1816 - >seq8463,non-specific,238827,613,701,5.13205e-13,69.2422,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs0_human.marg.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27505,Q#1816 - >seq8463,superfamily,295487,613,701,5.13205e-13,69.2422,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs0_human.marg.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27506,Q#1816 - >seq8463,non-specific,238828,566,682,1.75563e-06,49.891999999999996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MCa.ORF2.hs0_human.marg.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27507,Q#1816 - >seq8463,non-specific,333820,595,690,6.260119999999999e-06,47.6722,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.marg.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27508,Q#1816 - >seq8463,superfamily,333820,595,690,6.260119999999999e-06,47.6722,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.marg.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MCa,ORF2,hs0_human,marg,N-TerminusTruncated
27509,Q#1818 - >seq8465,specific,197310,9,237,4.9908299999999995e-48,170.995,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27510,Q#1818 - >seq8465,superfamily,351117,9,237,4.9908299999999995e-48,170.995,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27511,Q#1818 - >seq8465,non-specific,197306,9,237,2.4882900000000003e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27512,Q#1818 - >seq8465,non-specific,223780,9,230,1.71531e-16,80.3351,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27513,Q#1818 - >seq8465,non-specific,197307,9,237,2.3217500000000003e-15,76.9429,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27514,Q#1818 - >seq8465,non-specific,273186,9,238,1.4930100000000001e-12,68.4596,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27515,Q#1818 - >seq8465,specific,335306,10,230,8.11834e-12,65.7294,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27516,Q#1818 - >seq8465,non-specific,197320,9,222,1.46576e-11,65.6142,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27517,Q#1818 - >seq8465,non-specific,197322,83,237,2.8226999999999998e-09,59.6382,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,N-TerminusTruncated
27518,Q#1818 - >seq8465,non-specific,272954,9,208,3.60052e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27519,Q#1818 - >seq8465,non-specific,197321,7,237,7.0292e-08,54.4804,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,CompleteHit
27520,Q#1818 - >seq8465,non-specific,197319,92,237,4.76561e-06,48.8121,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MCa,ORF2,hs0_human,pars,N-TerminusTruncated
27521,Q#1818 - >seq8465,non-specific,339261,109,233,1.00724e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MCa.ORF2.hs0_human.pars.frame3,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MCa,ORF2,hs0_human,pars,CompleteHit
27522,Q#1819 - >seq8466,non-specific,238827,461,525,5.25788e-07,51.523,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MCa.ORF2.hs0_human.pars.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs0_human,pars,C-TerminusTruncated
27523,Q#1819 - >seq8466,superfamily,295487,461,525,5.25788e-07,51.523,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MCa.ORF2.hs0_human.pars.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs0_human,pars,C-TerminusTruncated
27524,Q#1819 - >seq8466,non-specific,333820,479,514,0.00608826,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.pars.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs0_human,pars,C-TerminusTruncated
27525,Q#1819 - >seq8466,superfamily,333820,479,514,0.00608826,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MCa.ORF2.hs0_human.pars.frame2,1909181135_L1MCa.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MCa,ORF2,hs0_human,pars,C-TerminusTruncated
27526,Q#1822 - >seq8469,specific,238827,535,728,2.1326599999999996e-31,122.785,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27527,Q#1822 - >seq8469,superfamily,295487,535,728,2.1326599999999996e-31,122.785,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27528,Q#1822 - >seq8469,specific,197310,35,214,2.26213e-29,117.45200000000001,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27529,Q#1822 - >seq8469,superfamily,351117,35,214,2.26213e-29,117.45200000000001,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27530,Q#1822 - >seq8469,non-specific,333820,547,728,4.87909e-18,83.1105,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27531,Q#1822 - >seq8469,superfamily,333820,547,728,4.87909e-18,83.1105,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27532,Q#1822 - >seq8469,non-specific,238828,538,680,1.3058399999999999e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27533,Q#1822 - >seq8469,non-specific,275209,543,756,1.7868399999999998e-09,60.9344,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27534,Q#1822 - >seq8469,superfamily,275209,543,756,1.7868399999999998e-09,60.9344,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27535,Q#1822 - >seq8469,specific,335306,35,206,4.8254099999999995e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27536,Q#1822 - >seq8469,non-specific,197320,106,204,3.08169e-07,52.9026,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27537,Q#1822 - >seq8469,non-specific,197306,35,206,3.27802e-07,52.4837,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27538,Q#1822 - >seq8469,non-specific,223780,36,203,3.68342e-06,49.5191,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27539,Q#1822 - >seq8469,non-specific,238185,612,728,9.51818e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs2_gorilla,pars,CompleteHit
27540,Q#1822 - >seq8469,non-specific,339261,106,201,0.000588577,40.7835,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27541,Q#1822 - >seq8469,non-specific,197322,106,214,0.000869132,42.6894,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27542,Q#1822 - >seq8469,non-specific,272954,106,203,0.00252664,40.8293,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27543,Q#1822 - >seq8469,non-specific,273186,106,204,0.005749499999999999,39.5696,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MB3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27544,Q#1823 - >seq8470,specific,197310,29,230,4.09933e-38,142.49,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27545,Q#1823 - >seq8470,superfamily,351117,29,230,4.09933e-38,142.49,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27546,Q#1823 - >seq8470,non-specific,197306,31,213,7.06552e-15,75.5956,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27547,Q#1823 - >seq8470,non-specific,197320,30,203,7.34528e-15,75.6293,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27548,Q#1823 - >seq8470,non-specific,223780,30,202,4.53758e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27549,Q#1823 - >seq8470,specific,335306,30,205,1.3604e-10,62.2626,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27550,Q#1823 - >seq8470,non-specific,238827,503,554,5.45501e-09,57.6862,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27551,Q#1823 - >seq8470,superfamily,295487,503,554,5.45501e-09,57.6862,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27552,Q#1823 - >seq8470,non-specific,197307,30,203,8.444710000000001e-08,54.6013,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27553,Q#1823 - >seq8470,non-specific,272954,30,202,2.7566800000000003e-07,53.1557,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27554,Q#1823 - >seq8470,non-specific,197311,34,199,4.66453e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27555,Q#1823 - >seq8470,non-specific,235175,237,463,1.48285e-06,52.3736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27556,Q#1823 - >seq8470,superfamily,235175,237,463,1.48285e-06,52.3736,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27557,Q#1823 - >seq8470,non-specific,224259,256,462,2.93096e-06,50.45,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27558,Q#1823 - >seq8470,superfamily,224259,256,462,2.93096e-06,50.45,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27559,Q#1823 - >seq8470,non-specific,273186,30,203,1.94586e-05,47.2736,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27560,Q#1823 - >seq8470,non-specific,197321,31,202,2.32596e-05,47.1616,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,CompleteHit
27561,Q#1823 - >seq8470,non-specific,274009,301,496,0.00114971,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27562,Q#1823 - >seq8470,superfamily,274009,301,496,0.00114971,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27563,Q#1823 - >seq8470,non-specific,333820,509,567,0.00175448,40.7386,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27564,Q#1823 - >seq8470,superfamily,333820,509,567,0.00175448,40.7386,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27565,Q#1823 - >seq8470,non-specific,197322,104,217,0.00175506,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27566,Q#1823 - >seq8470,non-specific,224117,227,512,0.00257628,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27567,Q#1823 - >seq8470,superfamily,224117,227,512,0.00257628,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MB3,ORF2,hs1_chimp,marg,N-TerminusTruncated
27568,Q#1823 - >seq8470,non-specific,223496,242,440,0.00417417,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1MB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
27569,Q#1823 - >seq8470,superfamily,223496,242,440,0.00417417,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1MB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
27570,Q#1823 - >seq8470,non-specific,223496,243,580,0.00637744,40.5139,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1MB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
27571,Q#1823 - >seq8470,non-specific,224117,227,473,0.0084186,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.marg.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
27572,Q#1825 - >seq8472,specific,197310,8,235,7.508309999999999e-63,213.752,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27573,Q#1825 - >seq8472,superfamily,351117,8,235,7.508309999999999e-63,213.752,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27574,Q#1825 - >seq8472,specific,238827,533,761,1.9323299999999997e-48,171.705,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27575,Q#1825 - >seq8472,superfamily,295487,533,761,1.9323299999999997e-48,171.705,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27576,Q#1825 - >seq8472,non-specific,197306,8,235,3.54223e-33,128.753,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27577,Q#1825 - >seq8472,non-specific,333820,534,734,1.17501e-25,105.06700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27578,Q#1825 - >seq8472,superfamily,333820,534,734,1.17501e-25,105.06700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27579,Q#1825 - >seq8472,non-specific,223780,6,228,4.5235e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27580,Q#1825 - >seq8472,non-specific,197307,8,235,3.1258000000000003e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27581,Q#1825 - >seq8472,non-specific,197320,6,228,4.66815e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27582,Q#1825 - >seq8472,specific,335306,9,228,5.62958e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27583,Q#1825 - >seq8472,non-specific,197321,6,235,5.92986e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27584,Q#1825 - >seq8472,non-specific,273186,6,236,7.97416e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27585,Q#1825 - >seq8472,non-specific,272954,6,235,1.12141e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27586,Q#1825 - >seq8472,non-specific,197319,6,235,3.57433e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27587,Q#1825 - >seq8472,non-specific,238828,576,731,4.14333e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27588,Q#1825 - >seq8472,non-specific,197336,6,228,2.18274e-07,53.3851,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27589,Q#1825 - >seq8472,non-specific,275209,581,784,1.01562e-05,48.9932,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27590,Q#1825 - >seq8472,superfamily,275209,581,784,1.01562e-05,48.9932,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27591,Q#1825 - >seq8472,non-specific,197311,29,235,1.67835e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27592,Q#1825 - >seq8472,non-specific,197318,8,235,0.000222995,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27593,Q#1825 - >seq8472,non-specific,238185,650,765,0.00091633,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27594,Q#1825 - >seq8472,non-specific,339261,107,231,0.00628454,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA6.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MA6,ORF2,hs4_gibbon,marg,CompleteHit
27595,Q#1826 - >seq8473,specific,197310,9,236,7.082489999999999e-63,213.752,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27596,Q#1826 - >seq8473,superfamily,351117,9,236,7.082489999999999e-63,213.752,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27597,Q#1826 - >seq8473,specific,238827,534,762,9.65803e-49,172.476,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27598,Q#1826 - >seq8473,superfamily,295487,534,762,9.65803e-49,172.476,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27599,Q#1826 - >seq8473,non-specific,197306,9,236,1.82926e-33,129.524,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27600,Q#1826 - >seq8473,non-specific,333820,535,735,8.07654e-26,105.45200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27601,Q#1826 - >seq8473,superfamily,333820,535,735,8.07654e-26,105.45200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27602,Q#1826 - >seq8473,non-specific,223780,7,229,4.6192e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27603,Q#1826 - >seq8473,non-specific,197307,9,236,3.0434699999999997e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27604,Q#1826 - >seq8473,non-specific,197320,7,229,4.721390000000001e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27605,Q#1826 - >seq8473,specific,335306,10,229,5.69207e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27606,Q#1826 - >seq8473,non-specific,197321,7,236,6.467390000000001e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27607,Q#1826 - >seq8473,non-specific,273186,7,237,8.61236e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27608,Q#1826 - >seq8473,non-specific,272954,7,236,1.3303e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27609,Q#1826 - >seq8473,non-specific,197319,7,236,4.3994099999999996e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27610,Q#1826 - >seq8473,non-specific,238828,577,732,3.34364e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27611,Q#1826 - >seq8473,non-specific,197336,7,229,2.20697e-07,53.3851,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27612,Q#1826 - >seq8473,non-specific,275209,582,785,8.69659e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27613,Q#1826 - >seq8473,superfamily,275209,582,785,8.69659e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27614,Q#1826 - >seq8473,non-specific,197311,30,236,1.68075e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27615,Q#1826 - >seq8473,non-specific,197318,9,236,0.000134687,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27616,Q#1826 - >seq8473,non-specific,238185,651,766,0.0009346630000000001,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27617,Q#1826 - >seq8473,non-specific,339261,108,232,0.00593458,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA6.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA6.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA6,ORF2,hs4_gibbon,pars,CompleteHit
27618,Q#1829 - >seq8476,specific,238827,506,725,4.03886e-51,179.40900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,CompleteHit
27619,Q#1829 - >seq8476,superfamily,295487,506,725,4.03886e-51,179.40900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,CompleteHit
27620,Q#1829 - >seq8476,non-specific,333820,512,708,3.96893e-28,112.001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27621,Q#1829 - >seq8476,superfamily,333820,512,708,3.96893e-28,112.001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27622,Q#1829 - >seq8476,non-specific,197310,9,234,2.06033e-19,88.5625,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs4_gibbon,marg,CompleteHit
27623,Q#1829 - >seq8476,superfamily,351117,9,234,2.06033e-19,88.5625,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,marg,CompleteHit
27624,Q#1829 - >seq8476,non-specific,238828,512,708,4.0809e-10,61.0628,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,CompleteHit
27625,Q#1829 - >seq8476,non-specific,275209,463,667,6.27481e-07,52.8452,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27626,Q#1829 - >seq8476,superfamily,275209,463,667,6.27481e-07,52.8452,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27627,Q#1829 - >seq8476,non-specific,197306,142,234,2.61094e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27628,Q#1829 - >seq8476,non-specific,197320,171,227,0.0017394,41.3466,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27629,Q#1829 - >seq8476,non-specific,197307,174,234,0.0040281,40.3489,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
27630,Q#1831 - >seq8478,non-specific,197310,46,129,5.25652e-08,55.0501,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27631,Q#1831 - >seq8478,superfamily,351117,46,129,5.25652e-08,55.0501,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
27632,Q#1833 - >seq8480,non-specific,197310,9,234,2.44284e-19,88.5625,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs4_gibbon,pars,CompleteHit
27633,Q#1833 - >seq8480,superfamily,351117,9,234,2.44284e-19,88.5625,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,pars,CompleteHit
27634,Q#1833 - >seq8480,non-specific,238827,505,544,1.26013e-09,59.6122,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27635,Q#1833 - >seq8480,superfamily,295487,505,544,1.26013e-09,59.6122,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27636,Q#1833 - >seq8480,non-specific,197306,142,234,3.01929e-05,46.7057,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27637,Q#1833 - >seq8480,non-specific,333820,511,559,0.00024003799999999998,43.0498,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27638,Q#1833 - >seq8480,superfamily,333820,511,559,0.00024003799999999998,43.0498,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27639,Q#1833 - >seq8480,non-specific,197320,171,227,0.00221502,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27640,Q#1833 - >seq8480,non-specific,197307,174,234,0.00682397,39.5785,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27641,Q#1834 - >seq8481,specific,238827,489,667,9.630610000000001e-32,123.555,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,CompleteHit
27642,Q#1834 - >seq8481,superfamily,295487,489,667,9.630610000000001e-32,123.555,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,CompleteHit
27643,Q#1834 - >seq8481,non-specific,333820,469,650,4.81725e-17,80.029,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27644,Q#1834 - >seq8481,superfamily,333820,469,650,4.81725e-17,80.029,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27645,Q#1834 - >seq8481,non-specific,238828,520,650,1.06653e-09,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27646,Q#1834 - >seq8481,non-specific,197310,46,129,3.22674e-08,55.4353,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27647,Q#1834 - >seq8481,superfamily,351117,46,129,3.22674e-08,55.4353,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27648,Q#1834 - >seq8481,non-specific,275209,525,609,0.000283223,44.3708,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,BothTerminiTruncated
27649,Q#1834 - >seq8481,superfamily,275209,525,609,0.000283223,44.3708,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA5.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs4_gibbon,pars,BothTerminiTruncated
27650,Q#1835 - >seq8482,non-specific,197310,9,61,5.48321e-12,66.6061,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27651,Q#1835 - >seq8482,superfamily,351117,9,61,5.48321e-12,66.6061,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27652,Q#1835 - >seq8482,non-specific,197306,9,58,1.05691e-07,54.0245,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27653,Q#1835 - >seq8482,non-specific,197321,7,59,5.90956e-06,48.7024,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27654,Q#1835 - >seq8482,non-specific,223780,7,43,1.56415e-05,47.5931,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27655,Q#1835 - >seq8482,non-specific,273186,7,43,5.85804e-05,45.7328,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27656,Q#1835 - >seq8482,non-specific,197307,9,43,0.000268811,43.8157,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27657,Q#1835 - >seq8482,specific,335306,10,165,0.00033732300000000005,43.3878,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27658,Q#1835 - >seq8482,non-specific,197320,7,43,0.000492564,42.8874,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27659,Q#1835 - >seq8482,non-specific,197336,7,43,0.000655271,42.5995,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27660,Q#1835 - >seq8482,non-specific,197319,7,43,0.00281134,40.7229,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27661,Q#1835 - >seq8482,specific,311990,1115,1133,0.00512959,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27662,Q#1835 - >seq8482,superfamily,311990,1115,1133,0.00512959,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27663,Q#1835 - >seq8482,non-specific,272954,7,43,0.007503,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
27664,Q#1836 - >seq8483,specific,238827,518,758,9.789339999999998e-52,181.335,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27665,Q#1836 - >seq8483,superfamily,295487,518,758,9.789339999999998e-52,181.335,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27666,Q#1836 - >seq8483,specific,197310,57,230,2.46409e-36,137.483,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27667,Q#1836 - >seq8483,superfamily,351117,57,230,2.46409e-36,137.483,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27668,Q#1836 - >seq8483,non-specific,333820,518,758,2.4179399999999998e-26,106.993,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27669,Q#1836 - >seq8483,superfamily,333820,518,758,2.4179399999999998e-26,106.993,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27670,Q#1836 - >seq8483,non-specific,197306,66,230,2.12981e-17,82.9144,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27671,Q#1836 - >seq8483,non-specific,238828,568,723,1.3790700000000002e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27672,Q#1836 - >seq8483,non-specific,197320,101,203,4.823259999999999e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27673,Q#1836 - >seq8483,non-specific,275209,573,777,1.07317e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27674,Q#1836 - >seq8483,superfamily,275209,573,777,1.07317e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27675,Q#1836 - >seq8483,non-specific,197307,86,230,4.47254e-07,52.2901,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27676,Q#1836 - >seq8483,specific,335306,57,223,5.43529e-07,51.8622,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27677,Q#1836 - >seq8483,non-specific,223780,86,223,2.1575400000000004e-06,50.2895,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27678,Q#1836 - >seq8483,non-specific,197319,101,230,0.000309422,43.8045,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27679,Q#1836 - >seq8483,non-specific,238185,642,758,0.00041163800000000003,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27680,Q#1836 - >seq8483,non-specific,197311,67,230,0.000490887,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27681,Q#1836 - >seq8483,non-specific,272954,86,202,0.00113914,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
27682,Q#1836 - >seq8483,non-specific,339261,103,226,0.0029888000000000002,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs2_gorilla.marg.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MA5,ORF2,hs2_gorilla,marg,CompleteHit
27683,Q#1838 - >seq8485,non-specific,197310,9,61,5.74067e-12,66.6061,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27684,Q#1838 - >seq8485,superfamily,351117,9,61,5.74067e-12,66.6061,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27685,Q#1838 - >seq8485,non-specific,197306,9,58,1.09549e-07,54.0245,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27686,Q#1838 - >seq8485,non-specific,197321,7,59,5.90368e-06,48.7024,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27687,Q#1838 - >seq8485,non-specific,223780,7,43,1.56259e-05,47.5931,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27688,Q#1838 - >seq8485,non-specific,273186,7,43,5.85224e-05,45.7328,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27689,Q#1838 - >seq8485,non-specific,197307,9,43,0.000273426,43.8157,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27690,Q#1838 - >seq8485,specific,335306,10,165,0.000336995,43.3878,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27691,Q#1838 - >seq8485,non-specific,197320,7,43,0.000492079,42.8874,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27692,Q#1838 - >seq8485,non-specific,197336,7,43,0.000654627,42.5995,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27693,Q#1838 - >seq8485,non-specific,197319,7,43,0.00278358,40.7229,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27694,Q#1838 - >seq8485,specific,311990,1116,1134,0.00512518,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27695,Q#1838 - >seq8485,superfamily,311990,1116,1134,0.00512518,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27696,Q#1838 - >seq8485,non-specific,272954,7,43,0.007495699999999999,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
27697,Q#1839 - >seq8486,specific,238827,519,759,1.1864e-51,180.95,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27698,Q#1839 - >seq8486,superfamily,295487,519,759,1.1864e-51,180.95,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27699,Q#1839 - >seq8486,specific,197310,57,230,3.1009799999999996e-36,137.09799999999998,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27700,Q#1839 - >seq8486,superfamily,351117,57,230,3.1009799999999996e-36,137.09799999999998,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27701,Q#1839 - >seq8486,non-specific,333820,519,759,3.25749e-26,106.60799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27702,Q#1839 - >seq8486,superfamily,333820,519,759,3.25749e-26,106.60799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27703,Q#1839 - >seq8486,non-specific,197306,66,230,2.2523000000000003e-17,82.9144,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27704,Q#1839 - >seq8486,non-specific,238828,569,724,1.49916e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27705,Q#1839 - >seq8486,non-specific,197320,101,203,4.81884e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27706,Q#1839 - >seq8486,non-specific,275209,574,778,1.27906e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27707,Q#1839 - >seq8486,superfamily,275209,574,778,1.27906e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27708,Q#1839 - >seq8486,non-specific,197307,86,230,4.89637e-07,52.2901,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27709,Q#1839 - >seq8486,specific,335306,57,223,5.43045e-07,51.8622,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27710,Q#1839 - >seq8486,non-specific,223780,86,223,2.0977099999999997e-06,50.2895,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27711,Q#1839 - >seq8486,non-specific,197319,101,230,0.000314759,43.8045,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27712,Q#1839 - >seq8486,non-specific,238185,643,759,0.000411297,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27713,Q#1839 - >seq8486,non-specific,197311,67,230,0.000494994,42.6641,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27714,Q#1839 - >seq8486,non-specific,272954,86,202,0.00114837,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
27715,Q#1839 - >seq8486,non-specific,339261,103,226,0.00290112,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs2_gorilla.pars.frame2,1909181135_L1MA5.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MA5,ORF2,hs2_gorilla,pars,CompleteHit
27716,Q#1841 - >seq8488,specific,197310,9,236,5.73275e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27717,Q#1841 - >seq8488,superfamily,351117,9,236,5.73275e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27718,Q#1841 - >seq8488,specific,238827,526,770,1.95868e-58,200.595,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27719,Q#1841 - >seq8488,superfamily,295487,526,770,1.95868e-58,200.595,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27720,Q#1841 - >seq8488,non-specific,197306,9,236,3.7833899999999995e-33,128.753,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27721,Q#1841 - >seq8488,specific,333820,526,770,1.01681e-30,119.705,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27722,Q#1841 - >seq8488,superfamily,333820,526,770,1.01681e-30,119.705,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27723,Q#1841 - >seq8488,non-specific,197307,9,236,2.3486300000000004e-21,94.6621,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27724,Q#1841 - >seq8488,non-specific,223780,7,229,1.77975e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27725,Q#1841 - >seq8488,non-specific,197320,7,229,1.0276000000000001e-19,89.8817,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27726,Q#1841 - >seq8488,specific,335306,10,229,9.24067e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27727,Q#1841 - >seq8488,non-specific,197321,7,236,8.54743e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27728,Q#1841 - >seq8488,non-specific,273186,7,237,2.8292200000000003e-14,73.8524,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27729,Q#1841 - >seq8488,non-specific,272954,7,236,3.35911e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27730,Q#1841 - >seq8488,non-specific,197319,7,236,3.8501599999999997e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27731,Q#1841 - >seq8488,non-specific,238828,580,735,8.76784e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,N-TerminusTruncated
27732,Q#1841 - >seq8488,non-specific,197336,7,229,1.97203e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27733,Q#1841 - >seq8488,non-specific,275209,585,789,2.5627400000000004e-08,57.0824,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,N-TerminusTruncated
27734,Q#1841 - >seq8488,superfamily,275209,585,789,2.5627400000000004e-08,57.0824,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,N-TerminusTruncated
27735,Q#1841 - >seq8488,non-specific,236970,9,229,4.95471e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27736,Q#1841 - >seq8488,non-specific,197318,9,236,9.08006e-06,48.4467,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27737,Q#1841 - >seq8488,non-specific,197322,8,236,2.9151e-05,47.3118,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27738,Q#1841 - >seq8488,non-specific,197311,7,236,0.000238538,43.4345,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27739,Q#1841 - >seq8488,non-specific,238185,654,770,0.000343785,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27740,Q#1841 - >seq8488,non-specific,339261,108,232,0.00289101,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27741,Q#1841 - >seq8488,specific,311990,1239,1257,0.00406733,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27742,Q#1841 - >seq8488,superfamily,311990,1239,1257,0.00406733,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs3_orang.marg.frame3,1909181135_L1MA4.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs3_orang,marg,CompleteHit
27743,Q#1843 - >seq8490,specific,238827,512,773,5.89254e-56,193.27599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27744,Q#1843 - >seq8490,superfamily,295487,512,773,5.89254e-56,193.27599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27745,Q#1843 - >seq8490,specific,197310,6,242,3.6013200000000003e-53,186.018,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27746,Q#1843 - >seq8490,superfamily,351117,6,242,3.6013200000000003e-53,186.018,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27747,Q#1843 - >seq8490,non-specific,197306,6,242,1.7971099999999996e-30,120.664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27748,Q#1843 - >seq8490,non-specific,333820,518,773,1.60863e-27,110.46,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27749,Q#1843 - >seq8490,superfamily,333820,518,773,1.60863e-27,110.46,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27750,Q#1843 - >seq8490,non-specific,197320,4,235,2.29077e-15,77.1701,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27751,Q#1843 - >seq8490,non-specific,223780,4,235,2.09867e-13,71.4755,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27752,Q#1843 - >seq8490,specific,335306,7,235,1.29761e-12,68.4258,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27753,Q#1843 - >seq8490,non-specific,197307,6,235,7.78157e-12,66.5425,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27754,Q#1843 - >seq8490,non-specific,273186,4,243,2.4916499999999997e-07,53.0516,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27755,Q#1843 - >seq8490,non-specific,197321,4,235,2.57011e-07,53.3248,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27756,Q#1843 - >seq8490,non-specific,197319,4,242,2.96402e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27757,Q#1843 - >seq8490,non-specific,272954,4,213,2.30884e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27758,Q#1843 - >seq8490,non-specific,238828,518,739,1.2110699999999999e-05,47.5809,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27759,Q#1843 - >seq8490,non-specific,197311,4,210,5.5052799999999996e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27760,Q#1843 - >seq8490,non-specific,275209,469,765,0.00543079,40.5188,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27761,Q#1843 - >seq8490,superfamily,275209,469,765,0.00543079,40.5188,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27762,Q#1843 - >seq8490,non-specific,339261,114,237,0.00711532,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs3_orang.pars.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27763,Q#1844 - >seq8491,specific,311990,1118,1136,0.00103952,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs3_orang.pars.frame2,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27764,Q#1844 - >seq8491,superfamily,311990,1118,1136,0.00103952,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs3_orang.pars.frame2,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA7,ORF2,hs3_orang,pars,CompleteHit
27765,Q#1848 - >seq8495,specific,197310,33,234,4.19338e-39,145.572,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27766,Q#1848 - >seq8495,superfamily,351117,33,234,4.19338e-39,145.572,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27767,Q#1848 - >seq8495,non-specific,197306,35,217,3.17178e-15,76.366,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27768,Q#1848 - >seq8495,non-specific,197320,34,207,9.03673e-15,75.2441,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27769,Q#1848 - >seq8495,non-specific,223780,34,206,3.2788300000000005e-12,68.0087,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27770,Q#1848 - >seq8495,specific,335306,34,209,1.3237999999999999e-10,62.2626,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27771,Q#1848 - >seq8495,non-specific,197307,34,207,4.82584e-08,55.3717,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27772,Q#1848 - >seq8495,non-specific,238827,508,547,1.33811e-07,53.449,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27773,Q#1848 - >seq8495,superfamily,295487,508,547,1.33811e-07,53.449,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27774,Q#1848 - >seq8495,non-specific,272954,34,206,1.46733e-07,53.9261,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27775,Q#1848 - >seq8495,non-specific,197311,38,203,2.20957e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27776,Q#1848 - >seq8495,non-specific,235175,241,467,3.80279e-06,51.218,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27777,Q#1848 - >seq8495,superfamily,235175,241,467,3.80279e-06,51.218,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27778,Q#1848 - >seq8495,non-specific,224259,260,466,4.92204e-06,49.6796,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27779,Q#1848 - >seq8495,superfamily,224259,260,466,4.92204e-06,49.6796,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27780,Q#1848 - >seq8495,non-specific,273186,34,207,9.517289999999999e-06,48.4292,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27781,Q#1848 - >seq8495,non-specific,197321,35,206,1.63467e-05,47.5468,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27782,Q#1848 - >seq8495,non-specific,274009,305,501,0.0007593989999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27783,Q#1848 - >seq8495,superfamily,274009,305,501,0.0007593989999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27784,Q#1848 - >seq8495,non-specific,197322,108,221,0.00174025,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27785,Q#1848 - >seq8495,non-specific,224117,231,499,0.00210256,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27786,Q#1848 - >seq8495,superfamily,224117,231,499,0.00210256,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27787,Q#1848 - >seq8495,non-specific,224117,220,369,0.00294912,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27788,Q#1848 - >seq8495,non-specific,339261,109,206,0.00379784,38.4723,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
27789,Q#1848 - >seq8495,non-specific,223496,246,444,0.0082934,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1MB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
27790,Q#1848 - >seq8495,superfamily,223496,246,444,0.0082934,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MB3.ORF2.hs1_chimp.pars.frame2,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1MB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
27791,Q#1849 - >seq8496,non-specific,238827,499,714,4.7278000000000004e-24,101.59899999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27792,Q#1849 - >seq8496,superfamily,295487,499,714,4.7278000000000004e-24,101.59899999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,CompleteHit
27793,Q#1849 - >seq8496,non-specific,333820,535,714,3.39398e-13,69.2434,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27794,Q#1849 - >seq8496,superfamily,333820,535,714,3.39398e-13,69.2434,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27795,Q#1849 - >seq8496,non-specific,238828,530,691,7.73133e-07,51.4328,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27796,Q#1849 - >seq8496,non-specific,275209,531,738,0.00010446899999999999,45.9116,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27797,Q#1849 - >seq8496,superfamily,275209,531,738,0.00010446899999999999,45.9116,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs1_chimp.pars.frame1,1909181135_L1MB3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
27798,Q#1850 - >seq8497,specific,238827,508,771,1.76569e-56,194.817,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27799,Q#1850 - >seq8497,superfamily,295487,508,771,1.76569e-56,194.817,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27800,Q#1850 - >seq8497,specific,197310,9,237,1.75211e-55,192.56599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27801,Q#1850 - >seq8497,superfamily,351117,9,237,1.75211e-55,192.56599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27802,Q#1850 - >seq8497,specific,333820,514,771,4.49405e-29,115.08200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27803,Q#1850 - >seq8497,superfamily,333820,514,771,4.49405e-29,115.08200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27804,Q#1850 - >seq8497,non-specific,197306,9,237,1.3972299999999999e-28,115.271,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27805,Q#1850 - >seq8497,non-specific,197320,7,230,3.96635e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27806,Q#1850 - >seq8497,non-specific,223780,7,230,5.04827e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27807,Q#1850 - >seq8497,specific,335306,10,230,1.95127e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27808,Q#1850 - >seq8497,non-specific,197307,9,230,2.77679e-17,82.7209,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27809,Q#1850 - >seq8497,non-specific,273186,7,238,6.79561e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27810,Q#1850 - >seq8497,non-specific,197321,7,230,9.049090000000001e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27811,Q#1850 - >seq8497,non-specific,197319,7,237,2.32826e-11,65.3757,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27812,Q#1850 - >seq8497,non-specific,272954,7,208,5.84853e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27813,Q#1850 - >seq8497,non-specific,238828,584,746,5.70256e-08,54.8996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,N-TerminusTruncated
27814,Q#1850 - >seq8497,non-specific,197336,7,230,6.42558e-08,54.9259,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27815,Q#1850 - >seq8497,non-specific,197311,38,205,4.217100000000001e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27816,Q#1850 - >seq8497,non-specific,275209,585,795,0.00033379199999999996,44.3708,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,N-TerminusTruncated
27817,Q#1850 - >seq8497,superfamily,275209,585,795,0.00033379199999999996,44.3708,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,marg,N-TerminusTruncated
27818,Q#1850 - >seq8497,non-specific,197318,9,231,0.00184276,41.1279,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27819,Q#1850 - >seq8497,non-specific,339261,109,232,0.0099807,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27820,Q#1852 - >seq8499,specific,311990,1119,1137,0.00143993,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27821,Q#1852 - >seq8499,superfamily,311990,1119,1137,0.00143993,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs1_chimp,marg,CompleteHit
27822,Q#1853 - >seq8500,specific,238827,508,769,1.01582e-56,195.588,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27823,Q#1853 - >seq8500,superfamily,295487,508,769,1.01582e-56,195.588,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27824,Q#1853 - >seq8500,specific,197310,9,237,1.6741999999999997e-54,189.87,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27825,Q#1853 - >seq8500,superfamily,351117,9,237,1.6741999999999997e-54,189.87,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27826,Q#1853 - >seq8500,specific,333820,514,769,2.69006e-29,115.46700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27827,Q#1853 - >seq8500,superfamily,333820,514,769,2.69006e-29,115.46700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27828,Q#1853 - >seq8500,non-specific,197306,9,237,5.19912e-29,116.81200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27829,Q#1853 - >seq8500,non-specific,197320,7,230,6.53875e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27830,Q#1853 - >seq8500,non-specific,223780,7,230,9.402310000000001e-18,84.5723,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27831,Q#1853 - >seq8500,specific,335306,10,230,2.5014000000000003e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27832,Q#1853 - >seq8500,non-specific,197307,9,230,1.6142499999999998e-15,77.7133,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27833,Q#1853 - >seq8500,non-specific,197321,7,230,9.28958e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27834,Q#1853 - >seq8500,non-specific,273186,7,238,1.08212e-12,69.23,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27835,Q#1853 - >seq8500,non-specific,197319,7,237,6.21443e-10,61.1385,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27836,Q#1853 - >seq8500,non-specific,272954,7,208,9.23207e-10,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27837,Q#1853 - >seq8500,non-specific,238828,584,744,5.58775e-08,54.8996,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,N-TerminusTruncated
27838,Q#1853 - >seq8500,non-specific,197336,7,230,6.09668e-07,51.8443,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27839,Q#1853 - >seq8500,non-specific,197311,39,205,5.25767e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27840,Q#1853 - >seq8500,non-specific,275209,585,793,0.000189078,45.1412,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,N-TerminusTruncated
27841,Q#1853 - >seq8500,superfamily,275209,585,793,0.000189078,45.1412,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs1_chimp,pars,N-TerminusTruncated
27842,Q#1853 - >seq8500,non-specific,197318,9,231,0.000285415,43.8243,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27843,Q#1853 - >seq8500,non-specific,339261,110,232,0.00338461,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27844,Q#1853 - >seq8500,non-specific,226098,126,238,0.0038345999999999996,40.4616,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MA9.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs1_chimp,pars,N-TerminusTruncated
27845,Q#1855 - >seq8502,specific,311990,1118,1136,0.00145287,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27846,Q#1855 - >seq8502,superfamily,311990,1118,1136,0.00145287,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA9.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA9,ORF2,hs1_chimp,pars,CompleteHit
27847,Q#1856 - >seq8503,specific,197310,7,234,5.657969999999999e-58,199.885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27848,Q#1856 - >seq8503,superfamily,351117,7,234,5.657969999999999e-58,199.885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27849,Q#1856 - >seq8503,specific,238827,525,768,3.7234599999999997e-56,194.047,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,CompleteHit
27850,Q#1856 - >seq8503,superfamily,295487,525,768,3.7234599999999997e-56,194.047,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,CompleteHit
27851,Q#1856 - >seq8503,specific,333820,525,768,5.8808800000000005e-30,117.39299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,CompleteHit
27852,Q#1856 - >seq8503,superfamily,333820,525,768,5.8808800000000005e-30,117.39299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,CompleteHit
27853,Q#1856 - >seq8503,non-specific,197306,7,234,9.75813e-30,118.738,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27854,Q#1856 - >seq8503,non-specific,197320,5,227,6.5363000000000004e-18,84.4889,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27855,Q#1856 - >seq8503,non-specific,223780,5,227,6.850050000000001e-18,84.9575,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27856,Q#1856 - >seq8503,non-specific,197307,7,234,3.23686e-17,82.7209,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27857,Q#1856 - >seq8503,specific,335306,8,227,1.5698e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27858,Q#1856 - >seq8503,non-specific,197321,5,234,2.48613e-12,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27859,Q#1856 - >seq8503,non-specific,272954,5,234,3.87365e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27860,Q#1856 - >seq8503,non-specific,197319,5,234,7.28335e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27861,Q#1856 - >seq8503,non-specific,273186,5,235,8.93771e-12,66.5336,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27862,Q#1856 - >seq8503,non-specific,238828,583,744,9.397540000000001e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,N-TerminusTruncated
27863,Q#1856 - >seq8503,non-specific,236970,8,227,4.77917e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27864,Q#1856 - >seq8503,non-specific,197322,6,234,0.00012281100000000001,45.3858,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27865,Q#1856 - >seq8503,non-specific,275209,584,795,0.0007384889999999999,43.2152,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,N-TerminusTruncated
27866,Q#1856 - >seq8503,superfamily,275209,584,795,0.0007384889999999999,43.2152,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs0_human,marg,N-TerminusTruncated
27867,Q#1856 - >seq8503,non-specific,197311,28,234,0.00108789,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,marg,CompleteHit
27868,Q#1856 - >seq8503,specific,311990,1237,1255,0.00656463,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs0_human,marg,CompleteHit
27869,Q#1856 - >seq8503,superfamily,311990,1237,1255,0.00656463,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs0_human.marg.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs0_human,marg,CompleteHit
27870,Q#1859 - >seq8506,specific,197310,7,234,3.78205e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27871,Q#1859 - >seq8506,superfamily,351117,7,234,3.78205e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27872,Q#1859 - >seq8506,specific,238827,523,766,5.795779999999999e-57,196.358,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,CompleteHit
27873,Q#1859 - >seq8506,superfamily,295487,523,766,5.795779999999999e-57,196.358,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,CompleteHit
27874,Q#1859 - >seq8506,specific,333820,523,766,2.3298099999999997e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,CompleteHit
27875,Q#1859 - >seq8506,superfamily,333820,523,766,2.3298099999999997e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,CompleteHit
27876,Q#1859 - >seq8506,non-specific,197306,7,234,8.8589e-30,118.738,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27877,Q#1859 - >seq8506,non-specific,223780,5,227,4.07088e-18,85.3427,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27878,Q#1859 - >seq8506,non-specific,197320,5,227,5.6114400000000005e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27879,Q#1859 - >seq8506,non-specific,197307,7,234,2.34467e-17,83.1061,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27880,Q#1859 - >seq8506,specific,335306,8,227,1.5250199999999999e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27881,Q#1859 - >seq8506,non-specific,197321,5,234,1.4581399999999999e-12,68.7328,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27882,Q#1859 - >seq8506,non-specific,272954,5,234,3.55664e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27883,Q#1859 - >seq8506,non-specific,197319,5,234,4.52051e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27884,Q#1859 - >seq8506,non-specific,273186,5,235,8.598110000000001e-12,66.5336,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27885,Q#1859 - >seq8506,non-specific,238828,577,742,5.07467e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,N-TerminusTruncated
27886,Q#1859 - >seq8506,non-specific,236970,8,227,5.81132e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27887,Q#1859 - >seq8506,non-specific,197322,6,234,0.000119298,45.3858,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27888,Q#1859 - >seq8506,non-specific,275209,582,793,0.00056217,43.6004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,N-TerminusTruncated
27889,Q#1859 - >seq8506,superfamily,275209,582,793,0.00056217,43.6004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs0_human,pars,N-TerminusTruncated
27890,Q#1859 - >seq8506,non-specific,197311,28,234,0.000904842,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs0_human.pars.frame3,1909181135_L1MA8.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs0_human,pars,CompleteHit
27891,Q#1863 - >seq8510,specific,311990,1123,1141,0.0011742,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs3_orang.marg.frame2,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27892,Q#1863 - >seq8510,superfamily,311990,1123,1141,0.0011742,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs3_orang.marg.frame2,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27893,Q#1864 - >seq8511,specific,238827,515,779,6.67966e-54,187.498,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27894,Q#1864 - >seq8511,superfamily,295487,515,779,6.67966e-54,187.498,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27895,Q#1864 - >seq8511,specific,197310,6,242,4.35052e-53,185.63299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27896,Q#1864 - >seq8511,superfamily,351117,6,242,4.35052e-53,185.63299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27897,Q#1864 - >seq8511,non-specific,197306,6,242,1.96985e-30,120.664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27898,Q#1864 - >seq8511,non-specific,333820,521,745,2.12372e-26,107.37799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27899,Q#1864 - >seq8511,superfamily,333820,521,745,2.12372e-26,107.37799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27900,Q#1864 - >seq8511,non-specific,197320,4,235,2.3692599999999998e-15,77.1701,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27901,Q#1864 - >seq8511,non-specific,223780,4,235,2.17015e-13,71.4755,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27902,Q#1864 - >seq8511,specific,335306,7,235,1.30456e-12,68.4258,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27903,Q#1864 - >seq8511,non-specific,197307,6,235,7.60818e-12,66.5425,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27904,Q#1864 - >seq8511,non-specific,273186,4,243,2.50508e-07,53.0516,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27905,Q#1864 - >seq8511,non-specific,197321,4,235,2.6076999999999997e-07,53.3248,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27906,Q#1864 - >seq8511,non-specific,197319,4,242,2.97997e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27907,Q#1864 - >seq8511,non-specific,272954,4,213,2.32122e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27908,Q#1864 - >seq8511,non-specific,238828,521,742,1.1521600000000002e-05,47.9661,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27909,Q#1864 - >seq8511,non-specific,197311,4,210,6.2997e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27910,Q#1864 - >seq8511,non-specific,275209,472,742,0.00666663,40.1336,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,C-TerminusTruncated
27911,Q#1864 - >seq8511,superfamily,275209,472,742,0.00666663,40.1336,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA7,ORF2,hs3_orang,marg,C-TerminusTruncated
27912,Q#1864 - >seq8511,non-specific,339261,114,237,0.00826303,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs3_orang.marg.frame1,1909181135_L1MA7.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MA7,ORF2,hs3_orang,marg,CompleteHit
27913,Q#1866 - >seq8513,specific,311990,1123,1141,0.000868172,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
27914,Q#1866 - >seq8513,superfamily,311990,1123,1141,0.000868172,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1MA2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs5_gmonkey,pars,CompleteHit
27915,Q#1869 - >seq8516,specific,238827,485,706,3.8729199999999995e-40,147.82299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
27916,Q#1869 - >seq8516,superfamily,295487,485,706,3.8729199999999995e-40,147.82299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
27917,Q#1869 - >seq8516,non-specific,333820,464,674,3.0806100000000002e-21,91.9701,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
27918,Q#1869 - >seq8516,superfamily,333820,464,674,3.0806100000000002e-21,91.9701,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
27919,Q#1869 - >seq8516,non-specific,238828,516,671,3.9994000000000004e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
27920,Q#1869 - >seq8516,non-specific,275209,521,671,3.4005800000000004e-06,50.1488,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
27921,Q#1869 - >seq8516,superfamily,275209,521,671,3.4005800000000004e-06,50.1488,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
27922,Q#1869 - >seq8516,non-specific,238185,590,650,0.0045607,37.3304,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
27923,Q#1870 - >seq8517,specific,197310,9,235,1.4496899999999999e-61,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27924,Q#1870 - >seq8517,superfamily,351117,9,235,1.4496899999999999e-61,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27925,Q#1870 - >seq8517,specific,238827,508,756,9.182499999999999e-59,201.36599999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27926,Q#1870 - >seq8517,superfamily,295487,508,756,9.182499999999999e-59,201.36599999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27927,Q#1870 - >seq8517,non-specific,197306,9,235,2.2076799999999997e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27928,Q#1870 - >seq8517,specific,333820,514,738,5.73786e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27929,Q#1870 - >seq8517,superfamily,333820,514,738,5.73786e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27930,Q#1870 - >seq8517,specific,335306,10,228,3.10879e-20,90.7673,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27931,Q#1870 - >seq8517,non-specific,197320,9,208,4.8925e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27932,Q#1870 - >seq8517,non-specific,223780,9,228,1.11343e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27933,Q#1870 - >seq8517,non-specific,197307,9,235,2.2292900000000003e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27934,Q#1870 - >seq8517,non-specific,197321,7,235,6.854580000000001e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27935,Q#1870 - >seq8517,non-specific,273186,9,236,6.6494699999999996e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27936,Q#1870 - >seq8517,non-specific,272954,9,207,1.0565799999999998e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27937,Q#1870 - >seq8517,non-specific,197319,9,235,1.46184e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27938,Q#1870 - >seq8517,non-specific,238828,514,735,2.5798000000000003e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27939,Q#1870 - >seq8517,non-specific,197336,9,228,1.4077600000000001e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27940,Q#1870 - >seq8517,non-specific,275209,465,735,1.32144e-07,55.1564,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27941,Q#1870 - >seq8517,superfamily,275209,465,735,1.32144e-07,55.1564,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27942,Q#1870 - >seq8517,non-specific,197311,30,235,4.89442e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27943,Q#1870 - >seq8517,non-specific,236970,9,207,7.39336e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27944,Q#1870 - >seq8517,non-specific,197322,8,235,1.1371600000000001e-05,48.4674,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27945,Q#1870 - >seq8517,non-specific,235175,290,467,1.81695e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,marg,BothTerminiTruncated
27946,Q#1870 - >seq8517,superfamily,235175,290,467,1.81695e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,marg,BothTerminiTruncated
27947,Q#1870 - >seq8517,non-specific,339261,108,231,0.000328515,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs3_orang,marg,CompleteHit
27948,Q#1870 - >seq8517,non-specific,197318,9,235,0.000583506,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,marg,CompleteHit
27949,Q#1870 - >seq8517,non-specific,223496,319,498,0.00297345,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M2,ORF2,hs3_orang,marg,BothTerminiTruncated
27950,Q#1870 - >seq8517,superfamily,223496,319,498,0.00297345,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M2,ORF2,hs3_orang,marg,BothTerminiTruncated
27951,Q#1870 - >seq8517,non-specific,334125,213,410,0.00689261,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs3_orang,marg,N-TerminusTruncated
27952,Q#1870 - >seq8517,superfamily,334125,213,410,0.00689261,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs3_orang,marg,N-TerminusTruncated
27953,Q#1870 - >seq8517,non-specific,274009,306,450,0.00784042,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27954,Q#1870 - >seq8517,superfamily,274009,306,450,0.00784042,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M2.ORF2.hs3_orang.marg.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27955,Q#1871 - >seq8518,non-specific,240274,221,517,0.00373327,41.5141,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1M2.ORF2.hs3_orang.marg.frame2,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27956,Q#1871 - >seq8518,superfamily,240274,221,517,0.00373327,41.5141,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1M2.ORF2.hs3_orang.marg.frame2,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1M2,ORF2,hs3_orang,marg,C-TerminusTruncated
27957,Q#1873 - >seq8520,specific,238827,505,774,3.7155099999999993e-59,202.521,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27958,Q#1873 - >seq8520,superfamily,295487,505,774,3.7155099999999993e-59,202.521,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27959,Q#1873 - >seq8520,specific,197310,9,234,5.626479999999999e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27960,Q#1873 - >seq8520,superfamily,351117,9,234,5.626479999999999e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27961,Q#1873 - >seq8520,specific,333820,511,735,2.9095699999999998e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27962,Q#1873 - >seq8520,superfamily,333820,511,735,2.9095699999999998e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27963,Q#1873 - >seq8520,non-specific,197306,9,234,6.7833e-31,121.82,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27964,Q#1873 - >seq8520,non-specific,197320,9,207,3.24838e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27965,Q#1873 - >seq8520,non-specific,223780,9,227,3.4673e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27966,Q#1873 - >seq8520,specific,335306,10,227,2.9918599999999996e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27967,Q#1873 - >seq8520,non-specific,197307,9,234,2.5868200000000002e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27968,Q#1873 - >seq8520,non-specific,273186,9,235,2.0690200000000002e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27969,Q#1873 - >seq8520,non-specific,272954,9,206,6.470019999999999e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27970,Q#1873 - >seq8520,non-specific,197321,7,234,5.66206e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27971,Q#1873 - >seq8520,non-specific,197319,9,234,8.830130000000001e-12,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27972,Q#1873 - >seq8520,non-specific,238828,511,732,1.65976e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27973,Q#1873 - >seq8520,non-specific,197336,9,227,9.2592e-08,54.5407,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27974,Q#1873 - >seq8520,non-specific,236970,9,206,3.10883e-07,52.9742,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27975,Q#1873 - >seq8520,non-specific,197311,30,234,3.2826500000000003e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27976,Q#1873 - >seq8520,non-specific,275209,464,732,4.77386e-07,53.2304,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27977,Q#1873 - >seq8520,superfamily,275209,464,732,4.77386e-07,53.2304,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27978,Q#1873 - >seq8520,non-specific,235175,289,466,7.093769999999999e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,pars,BothTerminiTruncated
27979,Q#1873 - >seq8520,superfamily,235175,289,466,7.093769999999999e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,pars,BothTerminiTruncated
27980,Q#1873 - >seq8520,non-specific,339261,107,230,0.000882104,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs3_orang,pars,CompleteHit
27981,Q#1873 - >seq8520,non-specific,197318,9,234,0.0011232000000000002,41.8983,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs3_orang,pars,CompleteHit
27982,Q#1873 - >seq8520,non-specific,274009,305,449,0.00404196,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27983,Q#1873 - >seq8520,superfamily,274009,305,449,0.00404196,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27984,Q#1873 - >seq8520,non-specific,226567,654,804,0.00412242,38.659,COG4081,COG4081, - ,cl01691,Uncharacterized protein [Function unknown]; Uncharacterized protein conserved in archaea [Function unknown].,L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1M2,ORF2,hs3_orang,pars,CompleteHit
27985,Q#1873 - >seq8520,superfamily,321627,654,804,0.00412242,38.659,cl01691,DUF1890 superfamily, - , - ,Domain of unknown function (DUF1890); This domain is found in a set of hypothetical archaeal proteins.,L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1M2,ORF2,hs3_orang,pars,CompleteHit
27986,Q#1873 - >seq8520,non-specific,334125,212,409,0.00496973,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M2,ORF2,hs3_orang,pars,N-TerminusTruncated
27987,Q#1873 - >seq8520,superfamily,334125,212,409,0.00496973,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M2,ORF2,hs3_orang,pars,N-TerminusTruncated
27988,Q#1873 - >seq8520,non-specific,223496,318,496,0.00772982,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1M2,ORF2,hs3_orang,pars,BothTerminiTruncated
27989,Q#1873 - >seq8520,superfamily,223496,318,496,0.00772982,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs3_orang.pars.frame3,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1M2,ORF2,hs3_orang,pars,BothTerminiTruncated
27990,Q#1874 - >seq8521,non-specific,240274,220,514,0.000969699,43.0549,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1M2.ORF2.hs3_orang.pars.frame2,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27991,Q#1874 - >seq8521,superfamily,240274,220,514,0.000969699,43.0549,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1M2.ORF2.hs3_orang.pars.frame2,1909181135_L1M2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M2,ORF2,hs3_orang,pars,C-TerminusTruncated
27992,Q#1877 - >seq8524,specific,197310,9,236,2.0389799999999997e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27993,Q#1877 - >seq8524,superfamily,351117,9,236,2.0389799999999997e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27994,Q#1877 - >seq8524,specific,238827,509,771,9.634089999999998e-59,201.36599999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27995,Q#1877 - >seq8524,superfamily,295487,509,771,9.634089999999998e-59,201.36599999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27996,Q#1877 - >seq8524,non-specific,197306,9,236,6.272380000000001e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27997,Q#1877 - >seq8524,specific,333820,515,771,3.28652e-29,115.08200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27998,Q#1877 - >seq8524,superfamily,333820,515,771,3.28652e-29,115.08200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
27999,Q#1877 - >seq8524,non-specific,223780,9,229,9.22066e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28000,Q#1877 - >seq8524,non-specific,197307,9,236,1.7456e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28001,Q#1877 - >seq8524,non-specific,197320,9,229,2.9894e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28002,Q#1877 - >seq8524,specific,335306,10,229,3.52669e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28003,Q#1877 - >seq8524,non-specific,273186,9,237,1.20795e-17,83.8676,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28004,Q#1877 - >seq8524,non-specific,197321,7,236,1.8513299999999998e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28005,Q#1877 - >seq8524,non-specific,272954,9,236,5.67977e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28006,Q#1877 - >seq8524,non-specific,197319,9,236,1.74232e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28007,Q#1877 - >seq8524,non-specific,197336,9,229,4.2683800000000003e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28008,Q#1877 - >seq8524,non-specific,238828,515,704,1.70645e-08,56.0552,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
28009,Q#1877 - >seq8524,non-specific,275209,466,795,1.94128e-07,54.386,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28010,Q#1877 - >seq8524,superfamily,275209,466,795,1.94128e-07,54.386,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28011,Q#1877 - >seq8524,non-specific,236970,9,207,9.119130000000001e-06,48.3518,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28012,Q#1877 - >seq8524,non-specific,197311,30,236,1.54004e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28013,Q#1877 - >seq8524,non-specific,197318,9,236,0.00011187799999999999,44.9799,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28014,Q#1877 - >seq8524,non-specific,339261,108,232,0.00013453600000000001,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28015,Q#1877 - >seq8524,non-specific,238185,655,771,0.00803744,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,marg,CompleteHit
28016,Q#1877 - >seq8524,non-specific,223496,320,499,0.00995657,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1M2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
28017,Q#1877 - >seq8524,superfamily,223496,320,499,0.00995657,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs2_gorilla.marg.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1M2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
28018,Q#1880 - >seq8527,specific,238827,508,771,1.2130699999999997e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28019,Q#1880 - >seq8527,superfamily,295487,508,771,1.2130699999999997e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28020,Q#1880 - >seq8527,specific,197310,9,236,1.4779399999999998e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28021,Q#1880 - >seq8527,superfamily,351117,9,236,1.4779399999999998e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28022,Q#1880 - >seq8527,non-specific,197306,9,236,5.897759999999999e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28023,Q#1880 - >seq8527,specific,333820,514,771,3.4926e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28024,Q#1880 - >seq8527,superfamily,333820,514,771,3.4926e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28025,Q#1880 - >seq8527,non-specific,223780,9,229,8.78238e-22,95.7431,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28026,Q#1880 - >seq8527,non-specific,197307,9,236,2.17578e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28027,Q#1880 - >seq8527,non-specific,197320,9,229,2.2937599999999998e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28028,Q#1880 - >seq8527,specific,335306,10,229,2.72716e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28029,Q#1880 - >seq8527,non-specific,273186,9,237,1.3533599999999999e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28030,Q#1880 - >seq8527,non-specific,197321,7,236,1.68552e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28031,Q#1880 - >seq8527,non-specific,272954,9,236,7.0533e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28032,Q#1880 - >seq8527,non-specific,197319,9,236,1.9328000000000002e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28033,Q#1880 - >seq8527,non-specific,197336,9,229,3.2919199999999994e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28034,Q#1880 - >seq8527,non-specific,238828,514,723,2.188e-09,58.3664,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28035,Q#1880 - >seq8527,non-specific,275209,465,795,2.72073e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28036,Q#1880 - >seq8527,superfamily,275209,465,795,2.72073e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28037,Q#1880 - >seq8527,non-specific,236970,9,207,1.0781099999999999e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28038,Q#1880 - >seq8527,non-specific,197311,30,236,1.20152e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28039,Q#1880 - >seq8527,non-specific,197318,9,236,7.522260000000001e-05,45.3651,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28040,Q#1880 - >seq8527,non-specific,339261,108,232,7.66002e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28041,Q#1880 - >seq8527,non-specific,238185,654,771,0.00914886,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28042,Q#1880 - >seq8527,non-specific,239569,523,784,0.00962079,38.3227,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1M2.ORF2.hs2_gorilla.pars.frame2,1909181135_L1M2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs2_gorilla,pars,CompleteHit
28043,Q#1882 - >seq8529,specific,238827,506,769,7.778459999999998e-58,198.669,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28044,Q#1882 - >seq8529,superfamily,295487,506,769,7.778459999999998e-58,198.669,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28045,Q#1882 - >seq8529,specific,197310,7,234,1.1401699999999999e-55,192.952,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28046,Q#1882 - >seq8529,superfamily,351117,7,234,1.1401699999999999e-55,192.952,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28047,Q#1882 - >seq8529,specific,333820,512,736,3.57202e-30,118.164,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28048,Q#1882 - >seq8529,superfamily,333820,512,736,3.57202e-30,118.164,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28049,Q#1882 - >seq8529,non-specific,197306,7,234,5.53495e-27,110.649,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28050,Q#1882 - >seq8529,non-specific,197307,7,234,1.04272e-14,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28051,Q#1882 - >seq8529,specific,335306,8,227,2.3824099999999997e-13,70.3517,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28052,Q#1882 - >seq8529,non-specific,223780,7,227,7.627e-13,69.9347,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28053,Q#1882 - >seq8529,non-specific,197320,7,227,1.24926e-12,69.081,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28054,Q#1882 - >seq8529,non-specific,238828,512,720,2.90755e-10,61.448,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28055,Q#1882 - >seq8529,non-specific,197321,5,234,3.5615200000000003e-09,58.7176,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28056,Q#1882 - >seq8529,non-specific,272954,7,234,3.56354e-09,58.5485,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28057,Q#1882 - >seq8529,non-specific,275209,463,735,7.16821e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,C-TerminusTruncated
28058,Q#1882 - >seq8529,superfamily,275209,463,735,7.16821e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs1_chimp,marg,C-TerminusTruncated
28059,Q#1882 - >seq8529,non-specific,197319,7,234,1.31213e-08,56.9013,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28060,Q#1882 - >seq8529,non-specific,235175,292,465,2.53517e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28061,Q#1882 - >seq8529,superfamily,235175,292,465,2.53517e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28062,Q#1882 - >seq8529,non-specific,223496,318,496,6.74285e-05,47.0623,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28063,Q#1882 - >seq8529,superfamily,223496,318,496,6.74285e-05,47.0623,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28064,Q#1882 - >seq8529,non-specific,197336,7,227,0.00111724,41.8291,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,marg,CompleteHit
28065,Q#1882 - >seq8529,non-specific,334125,210,408,0.00141974,42.1364,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs1_chimp,marg,N-TerminusTruncated
28066,Q#1882 - >seq8529,superfamily,334125,210,408,0.00141974,42.1364,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs1_chimp.marg.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs1_chimp,marg,N-TerminusTruncated
28067,Q#1885 - >seq8532,specific,238827,505,753,6.33274e-58,198.669,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28068,Q#1885 - >seq8532,superfamily,295487,505,753,6.33274e-58,198.669,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28069,Q#1885 - >seq8532,specific,197310,7,234,2.7529100000000002e-55,191.796,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28070,Q#1885 - >seq8532,superfamily,351117,7,234,2.7529100000000002e-55,191.796,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28071,Q#1885 - >seq8532,specific,333820,511,735,8.55061e-31,119.705,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28072,Q#1885 - >seq8532,superfamily,333820,511,735,8.55061e-31,119.705,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28073,Q#1885 - >seq8532,non-specific,197306,7,234,6.46028e-27,110.264,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28074,Q#1885 - >seq8532,non-specific,197307,7,234,4.03239e-15,76.1725,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28075,Q#1885 - >seq8532,non-specific,223780,7,227,1.54417e-13,71.8607,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28076,Q#1885 - >seq8532,specific,335306,8,227,2.1135900000000002e-13,70.3517,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28077,Q#1885 - >seq8532,non-specific,197320,7,227,1.11556e-12,69.081,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28078,Q#1885 - >seq8532,non-specific,238828,511,719,9.64023e-11,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28079,Q#1885 - >seq8532,non-specific,197321,5,234,1.32407e-09,59.8732,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28080,Q#1885 - >seq8532,non-specific,275209,462,734,2.7649099999999997e-09,60.163999999999994,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,C-TerminusTruncated
28081,Q#1885 - >seq8532,superfamily,275209,462,734,2.7649099999999997e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs1_chimp,pars,C-TerminusTruncated
28082,Q#1885 - >seq8532,non-specific,272954,7,234,2.77408e-09,58.9337,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28083,Q#1885 - >seq8532,non-specific,197319,7,234,4.799239999999999e-09,58.0569,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28084,Q#1885 - >seq8532,non-specific,235175,292,464,2.1994299999999997e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28085,Q#1885 - >seq8532,superfamily,235175,292,464,2.1994299999999997e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28086,Q#1885 - >seq8532,non-specific,235175,292,495,0.000152474,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28087,Q#1885 - >seq8532,non-specific,334125,210,407,0.000162628,45.218,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M2,ORF2,hs1_chimp,pars,N-TerminusTruncated
28088,Q#1885 - >seq8532,superfamily,334125,210,407,0.000162628,45.218,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M2,ORF2,hs1_chimp,pars,N-TerminusTruncated
28089,Q#1885 - >seq8532,non-specific,223496,317,495,0.000514245,43.9807,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1M2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28090,Q#1885 - >seq8532,superfamily,223496,317,495,0.000514245,43.9807,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1M2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28091,Q#1885 - >seq8532,non-specific,197336,7,227,0.0009931760000000001,41.8291,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs1_chimp.pars.frame3,1909181135_L1M2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs1_chimp,pars,CompleteHit
28092,Q#1887 - >seq8534,specific,197310,9,236,3.1425199999999994e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28093,Q#1887 - >seq8534,superfamily,351117,9,236,3.1425199999999994e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28094,Q#1887 - >seq8534,non-specific,197306,9,236,2.2996e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28095,Q#1887 - >seq8534,specific,335306,10,229,1.92805e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28096,Q#1887 - >seq8534,non-specific,197307,9,236,3.00013e-17,82.3357,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28097,Q#1887 - >seq8534,non-specific,197320,9,229,1.19546e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28098,Q#1887 - >seq8534,non-specific,223780,9,229,1.39271e-16,80.7203,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28099,Q#1887 - >seq8534,non-specific,197321,7,236,4.48791e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28100,Q#1887 - >seq8534,non-specific,273186,9,237,2.28889e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28101,Q#1887 - >seq8534,non-specific,197319,9,236,1.02698e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28102,Q#1887 - >seq8534,non-specific,272954,9,236,1.43793e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28103,Q#1887 - >seq8534,non-specific,197336,9,229,3.35789e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28104,Q#1887 - >seq8534,non-specific,197311,7,146,7.00414e-05,44.9753,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28105,Q#1887 - >seq8534,non-specific,197318,9,236,0.000923474,41.8983,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28106,Q#1887 - >seq8534,non-specific,339261,108,232,0.00122279,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs4_gibbon,pars,CompleteHit
28107,Q#1887 - >seq8534,non-specific,238827,523,542,0.00134456,41.1226,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28108,Q#1887 - >seq8534,superfamily,295487,523,542,0.00134456,41.1226,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28109,Q#1887 - >seq8534,non-specific,333820,523,560,0.00619011,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28110,Q#1887 - >seq8534,superfamily,333820,523,560,0.00619011,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28111,Q#1891 - >seq8538,non-specific,238827,479,508,4.45869e-06,48.8266,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs0_human.marg.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M2,ORF2,hs0_human,marg,C-TerminusTruncated
28112,Q#1891 - >seq8538,superfamily,295487,479,508,4.45869e-06,48.8266,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.marg.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M2,ORF2,hs0_human,marg,C-TerminusTruncated
28113,Q#1891 - >seq8538,non-specific,197310,84,120,0.00019971,43.8793,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs0_human.marg.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,marg,BothTerminiTruncated
28114,Q#1891 - >seq8538,superfamily,351117,84,120,0.00019971,43.8793,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.marg.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,marg,BothTerminiTruncated
28115,Q#1892 - >seq8539,non-specific,197310,9,83,4.2971800000000004e-19,87.4069,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28116,Q#1892 - >seq8539,superfamily,351117,9,83,4.2971800000000004e-19,87.4069,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28117,Q#1892 - >seq8539,non-specific,197306,9,81,8.373070000000001e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28118,Q#1892 - >seq8539,non-specific,197321,7,80,8.625520000000001e-07,51.3988,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28119,Q#1892 - >seq8539,specific,335306,10,77,7.163789999999999e-06,48.0102,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28120,Q#1892 - >seq8539,non-specific,223780,9,80,3.0108499999999998e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28121,Q#1892 - >seq8539,non-specific,197307,9,80,7.859699999999999e-05,45.3565,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28122,Q#1892 - >seq8539,non-specific,238827,664,726,0.00026083599999999997,43.4338,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28123,Q#1892 - >seq8539,superfamily,295487,664,726,0.00026083599999999997,43.4338,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28124,Q#1892 - >seq8539,non-specific,197320,9,76,0.00130524,41.7318,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28125,Q#1892 - >seq8539,non-specific,273186,9,43,0.00132249,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28126,Q#1892 - >seq8539,non-specific,197336,9,76,0.00351903,40.2883,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs0_human.pars.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28127,Q#1893 - >seq8540,non-specific,238827,470,499,2.93504e-06,49.2118,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs0_human.pars.frame2,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28128,Q#1893 - >seq8540,superfamily,295487,470,499,2.93504e-06,49.2118,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.pars.frame2,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28129,Q#1894 - >seq8541,specific,197310,84,225,9.52027e-31,121.304,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28130,Q#1894 - >seq8541,superfamily,351117,84,225,9.52027e-31,121.304,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28131,Q#1894 - >seq8541,specific,238827,542,705,6.26006e-29,115.46600000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28132,Q#1894 - >seq8541,superfamily,295487,542,705,6.26006e-29,115.46600000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28133,Q#1894 - >seq8541,non-specific,333820,541,699,6.36367e-17,79.6438,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28134,Q#1894 - >seq8541,superfamily,333820,541,699,6.36367e-17,79.6438,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28135,Q#1894 - >seq8541,non-specific,197306,84,225,1.58279e-14,74.0548,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28136,Q#1894 - >seq8541,non-specific,197320,96,197,8.748e-10,60.2214,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28137,Q#1894 - >seq8541,non-specific,238828,569,699,2.3712399999999998e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28138,Q#1894 - >seq8541,non-specific,223780,96,218,7.302389999999999e-08,54.5267,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28139,Q#1894 - >seq8541,non-specific,197319,96,225,3.02653e-07,52.6641,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28140,Q#1894 - >seq8541,non-specific,197307,96,225,3.4424399999999997e-07,52.6753,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28141,Q#1894 - >seq8541,specific,335306,104,218,1.0293e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28142,Q#1894 - >seq8541,non-specific,273186,96,226,3.0934699999999997e-06,49.5848,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28143,Q#1894 - >seq8541,non-specific,275209,574,693,1.59203e-05,48.2228,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,BothTerminiTruncated
28144,Q#1894 - >seq8541,superfamily,275209,574,693,1.59203e-05,48.2228,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,BothTerminiTruncated
28145,Q#1894 - >seq8541,non-specific,272954,96,225,3.84568e-05,46.2221,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28146,Q#1894 - >seq8541,non-specific,339261,98,221,0.000804659,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M2,ORF2,hs0_human,pars,CompleteHit
28147,Q#1894 - >seq8541,non-specific,197321,96,225,0.00100861,41.7688,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28148,Q#1894 - >seq8541,non-specific,197311,92,225,0.00142929,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs0_human,pars,N-TerminusTruncated
28149,Q#1894 - >seq8541,non-specific,238185,643,703,0.00585398,36.9452,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.pars.frame1,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs0_human,pars,C-TerminusTruncated
28150,Q#1895 - >seq8542,non-specific,197310,9,85,4.918069999999999e-18,84.3253,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28151,Q#1895 - >seq8542,superfamily,351117,9,85,4.918069999999999e-18,84.3253,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28152,Q#1895 - >seq8542,non-specific,238827,540,647,9.51653e-08,53.8342,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28153,Q#1895 - >seq8542,superfamily,295487,540,647,9.51653e-08,53.8342,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28154,Q#1895 - >seq8542,non-specific,197321,7,80,1.4481600000000001e-06,50.6284,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28155,Q#1895 - >seq8542,non-specific,197306,9,80,6.9501100000000004e-06,48.6317,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28156,Q#1895 - >seq8542,non-specific,223780,7,82,1.4880399999999999e-05,47.5931,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28157,Q#1895 - >seq8542,specific,335306,10,91,1.66262e-05,47.2398,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28158,Q#1895 - >seq8542,non-specific,197307,9,92,0.000142333,44.5861,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28159,Q#1895 - >seq8542,non-specific,273186,7,76,0.00078502,42.266000000000005,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28160,Q#1895 - >seq8542,non-specific,333820,556,647,0.0059952,38.8126,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28161,Q#1895 - >seq8542,superfamily,333820,556,647,0.0059952,38.8126,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28162,Q#1896 - >seq8543,non-specific,238827,612,699,1.7268099999999997e-10,61.9234,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28163,Q#1896 - >seq8543,superfamily,295487,612,699,1.7268099999999997e-10,61.9234,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28164,Q#1896 - >seq8543,non-specific,333820,619,670,0.00314026,39.9682,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28165,Q#1896 - >seq8543,superfamily,333820,619,670,0.00314026,39.9682,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.marg.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28166,Q#1897 - >seq8544,specific,197310,70,224,3.5770199999999996e-27,110.904,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28167,Q#1897 - >seq8544,superfamily,351117,70,224,3.5770199999999996e-27,110.904,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28168,Q#1897 - >seq8544,non-specific,197306,46,224,2.1380400000000003e-15,76.7512,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28169,Q#1897 - >seq8544,non-specific,197320,94,196,1.01955e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28170,Q#1897 - >seq8544,non-specific,238827,498,557,1.0923200000000002e-08,56.5306,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28171,Q#1897 - >seq8544,superfamily,295487,498,557,1.0923200000000002e-08,56.5306,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28172,Q#1897 - >seq8544,non-specific,223780,79,195,4.1738999999999995e-07,52.6007,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28173,Q#1897 - >seq8544,non-specific,197307,79,196,4.00544e-06,49.5937,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28174,Q#1897 - >seq8544,specific,335306,100,198,3.46173e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28175,Q#1897 - >seq8544,non-specific,272954,79,195,0.000827299,42.3701,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28176,Q#1897 - >seq8544,non-specific,339261,96,220,0.00443926,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1M2,ORF2,hs6_sqmonkey,marg,CompleteHit
28177,Q#1897 - >seq8544,non-specific,235175,279,457,0.007693800000000001,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28178,Q#1897 - >seq8544,superfamily,235175,279,457,0.007693800000000001,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28179,Q#1897 - >seq8544,non-specific,197311,90,134,0.00886819,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.marg.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28180,Q#1899 - >seq8546,non-specific,197310,9,85,2.3345899999999998e-18,84.7105,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28181,Q#1899 - >seq8546,superfamily,351117,9,85,2.3345899999999998e-18,84.7105,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28182,Q#1899 - >seq8546,non-specific,238827,526,633,4.85626e-08,53.8342,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28183,Q#1899 - >seq8546,superfamily,295487,526,633,4.85626e-08,53.8342,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28184,Q#1899 - >seq8546,non-specific,197321,7,80,4.35055e-07,51.3988,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28185,Q#1899 - >seq8546,non-specific,197306,9,80,1.78263e-06,49.4021,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28186,Q#1899 - >seq8546,non-specific,223780,7,82,7.2119e-06,47.9783,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28187,Q#1899 - >seq8546,specific,335306,10,91,9.2014e-06,47.2398,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28188,Q#1899 - >seq8546,non-specific,197307,9,92,3.25234e-05,45.7417,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28189,Q#1899 - >seq8546,non-specific,273186,7,76,0.000310433,43.0364,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28190,Q#1899 - >seq8546,non-specific,333820,542,633,0.00278736,39.1978,pfam00078,RVT_1,NC,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28191,Q#1899 - >seq8546,superfamily,333820,542,633,0.00278736,39.1978,cl37957,RVT_1 superfamily,NC, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28192,Q#1899 - >seq8546,non-specific,272954,7,76,0.00308548,39.6737,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28193,Q#1900 - >seq8547,non-specific,197310,70,206,2.84306e-26,107.43700000000001,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28194,Q#1900 - >seq8547,superfamily,351117,70,206,2.84306e-26,107.43700000000001,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28195,Q#1900 - >seq8547,non-specific,197306,46,208,2.48268e-15,75.9808,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28196,Q#1900 - >seq8547,non-specific,197320,94,196,5.30633e-11,63.303000000000004,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28197,Q#1900 - >seq8547,non-specific,238827,470,529,7.35133e-09,56.5306,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28198,Q#1900 - >seq8547,superfamily,295487,470,529,7.35133e-09,56.5306,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28199,Q#1900 - >seq8547,non-specific,223780,79,195,2.8296999999999995e-07,52.2155,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28200,Q#1900 - >seq8547,non-specific,197307,79,196,2.52247e-06,49.2085,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28201,Q#1900 - >seq8547,specific,335306,100,198,1.86323e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28202,Q#1900 - >seq8547,non-specific,272954,79,208,0.00045547199999999995,42.3701,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28203,Q#1900 - >seq8547,non-specific,339261,96,136,0.00347635,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1M2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28204,Q#1900 - >seq8547,non-specific,197311,90,134,0.00484239,38.8121,cd09077,R1-I-EN,NC,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs6_sqmonkey.pars.frame1,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1M2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28205,Q#1901 - >seq8548,specific,197310,9,235,5.171579999999999e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28206,Q#1901 - >seq8548,superfamily,351117,9,235,5.171579999999999e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28207,Q#1901 - >seq8548,specific,238827,508,770,2.1982800000000005e-57,197.514,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28208,Q#1901 - >seq8548,superfamily,295487,508,770,2.1982800000000005e-57,197.514,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28209,Q#1901 - >seq8548,non-specific,197306,9,235,5.299629999999999e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28210,Q#1901 - >seq8548,specific,333820,514,770,3.2178499999999997e-28,112.38600000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28211,Q#1901 - >seq8548,superfamily,333820,514,770,3.2178499999999997e-28,112.38600000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28212,Q#1901 - >seq8548,specific,335306,10,228,1.6137899999999999e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28213,Q#1901 - >seq8548,non-specific,197320,9,208,1.42798e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28214,Q#1901 - >seq8548,non-specific,197307,9,235,7.14536e-18,84.2617,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28215,Q#1901 - >seq8548,non-specific,223780,9,228,1.3769999999999998e-17,83.8019,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28216,Q#1901 - >seq8548,non-specific,197321,7,235,6.070409999999999e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28217,Q#1901 - >seq8548,non-specific,273186,9,236,1.1744300000000002e-13,71.9264,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28218,Q#1901 - >seq8548,non-specific,272954,9,207,2.46661e-13,71.2601,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28219,Q#1901 - >seq8548,non-specific,197319,9,235,1.3906899999999998e-10,62.6793,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28220,Q#1901 - >seq8548,non-specific,238828,580,735,1.7407699999999998e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28221,Q#1901 - >seq8548,non-specific,275209,585,789,3.3994400000000004e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28222,Q#1901 - >seq8548,superfamily,275209,585,789,3.3994400000000004e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28223,Q#1901 - >seq8548,non-specific,197336,9,228,2.28173e-08,56.0815,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28224,Q#1901 - >seq8548,non-specific,236970,9,207,6.45479e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28225,Q#1901 - >seq8548,non-specific,197311,7,235,2.7645799999999996e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28226,Q#1901 - >seq8548,non-specific,238185,654,770,9.23882e-05,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28227,Q#1901 - >seq8548,non-specific,339261,108,231,0.000720195,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28228,Q#1901 - >seq8548,non-specific,197318,9,235,0.0043719,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,marg,CompleteHit
28229,Q#1902 - >seq8549,specific,238827,509,771,2.95032e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28230,Q#1902 - >seq8549,superfamily,295487,509,771,2.95032e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28231,Q#1902 - >seq8549,specific,197310,9,237,4.97848e-46,165.602,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28232,Q#1902 - >seq8549,superfamily,351117,9,237,4.97848e-46,165.602,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28233,Q#1902 - >seq8549,specific,333820,515,771,1.0128399999999998e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28234,Q#1902 - >seq8549,superfamily,333820,515,771,1.0128399999999998e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28235,Q#1902 - >seq8549,non-specific,197306,9,237,3.3810099999999995e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28236,Q#1902 - >seq8549,specific,335306,10,230,2.33393e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28237,Q#1902 - >seq8549,non-specific,197320,7,230,9.99418e-15,75.2441,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28238,Q#1902 - >seq8549,non-specific,197307,9,237,1.3939299999999999e-12,68.8537,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28239,Q#1902 - >seq8549,non-specific,238828,515,736,1.75447e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28240,Q#1902 - >seq8549,non-specific,223780,7,230,6.9489e-12,66.8531,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28241,Q#1902 - >seq8549,non-specific,197321,7,237,9.192889999999999e-10,60.6436,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28242,Q#1902 - >seq8549,non-specific,275209,466,736,1.3562000000000001e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28243,Q#1902 - >seq8549,superfamily,275209,466,736,1.3562000000000001e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28244,Q#1902 - >seq8549,non-specific,272954,7,208,4.095680000000001e-08,55.4669,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28245,Q#1902 - >seq8549,non-specific,273186,7,238,3.8915999999999997e-07,52.6664,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28246,Q#1902 - >seq8549,non-specific,197336,7,230,9.246649999999999e-06,48.3775,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28247,Q#1902 - >seq8549,non-specific,197319,7,237,1.43317e-05,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28248,Q#1902 - >seq8549,non-specific,238185,657,771,0.000239902,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28249,Q#1902 - >seq8549,non-specific,235175,307,463,0.000626444,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28250,Q#1902 - >seq8549,superfamily,235175,307,463,0.000626444,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28251,Q#1902 - >seq8549,non-specific,334125,218,410,0.00140538,42.5216,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
28252,Q#1902 - >seq8549,superfamily,334125,218,410,0.00140538,42.5216,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
28253,Q#1902 - >seq8549,non-specific,274009,306,500,0.00323863,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28254,Q#1902 - >seq8549,superfamily,274009,306,500,0.00323863,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28255,Q#1902 - >seq8549,specific,311990,1240,1258,0.00324906,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28256,Q#1902 - >seq8549,superfamily,311990,1240,1258,0.00324906,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs4_gibbon,marg,CompleteHit
28257,Q#1902 - >seq8549,non-specific,274475,256,427,0.00975073,40.052,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28258,Q#1902 - >seq8549,superfamily,274475,256,427,0.00975073,40.052,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28259,Q#1904 - >seq8551,specific,197310,9,235,2.2155399999999996e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28260,Q#1904 - >seq8551,superfamily,351117,9,235,2.2155399999999996e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28261,Q#1904 - >seq8551,non-specific,197306,9,235,8.112520000000001e-33,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28262,Q#1904 - >seq8551,specific,335306,10,228,1.14727e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28263,Q#1904 - >seq8551,non-specific,197320,9,208,7.34968e-19,86.8001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28264,Q#1904 - >seq8551,non-specific,197307,9,235,7.509789999999999e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28265,Q#1904 - >seq8551,non-specific,223780,9,228,7.5626000000000005e-19,86.8835,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28266,Q#1904 - >seq8551,non-specific,197321,7,235,8.85026e-15,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28267,Q#1904 - >seq8551,non-specific,273186,9,236,1.69916e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28268,Q#1904 - >seq8551,non-specific,272954,9,207,4.39349e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28269,Q#1904 - >seq8551,non-specific,197319,9,235,1.1065999999999998e-11,65.7609,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28270,Q#1904 - >seq8551,non-specific,238827,508,557,1.59748e-09,58.8418,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28271,Q#1904 - >seq8551,superfamily,295487,508,557,1.59748e-09,58.8418,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28272,Q#1904 - >seq8551,non-specific,197336,9,228,1.61962e-08,56.0815,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28273,Q#1904 - >seq8551,non-specific,236970,9,207,3.45686e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28274,Q#1904 - >seq8551,non-specific,197311,7,235,1.8115000000000001e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28275,Q#1904 - >seq8551,non-specific,339261,108,231,0.001837,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28276,Q#1904 - >seq8551,non-specific,197318,9,235,0.00474833,39.5871,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28277,Q#1905 - >seq8552,specific,238827,521,729,1.0220899999999997e-40,148.97899999999998,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28278,Q#1905 - >seq8552,superfamily,295487,521,729,1.0220899999999997e-40,148.97899999999998,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28279,Q#1905 - >seq8552,non-specific,333820,543,729,5.1950799999999994e-21,91.1997,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28280,Q#1905 - >seq8552,superfamily,333820,543,729,5.1950799999999994e-21,91.1997,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28281,Q#1905 - >seq8552,non-specific,238828,539,694,6.84326e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28282,Q#1905 - >seq8552,non-specific,275209,544,748,1.4060699999999999e-09,60.5492,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28283,Q#1905 - >seq8552,superfamily,275209,544,748,1.4060699999999999e-09,60.5492,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28284,Q#1905 - >seq8552,non-specific,238185,613,729,1.28075e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs5_gmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs5_gmonkey,pars,CompleteHit
28285,Q#1907 - >seq8554,specific,197310,9,236,5.418709999999999e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28286,Q#1907 - >seq8554,superfamily,351117,9,236,5.418709999999999e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28287,Q#1907 - >seq8554,specific,238827,524,768,1.33532e-51,180.95,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28288,Q#1907 - >seq8554,superfamily,295487,524,768,1.33532e-51,180.95,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28289,Q#1907 - >seq8554,non-specific,197306,9,236,4.4732199999999994e-30,119.508,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28290,Q#1907 - >seq8554,specific,333820,524,736,2.6724e-29,115.46700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28291,Q#1907 - >seq8554,superfamily,333820,524,736,2.6724e-29,115.46700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28292,Q#1907 - >seq8554,specific,335306,10,229,2.1659e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28293,Q#1907 - >seq8554,non-specific,197320,9,229,1.3468500000000001e-16,80.6369,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28294,Q#1907 - >seq8554,non-specific,197307,9,236,2.5947700000000003e-16,80.0245,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28295,Q#1907 - >seq8554,non-specific,223780,9,229,1.04805e-15,78.4091,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28296,Q#1907 - >seq8554,non-specific,197321,7,236,2.4381e-13,71.044,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28297,Q#1907 - >seq8554,non-specific,273186,9,237,9.06589e-12,66.5336,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28298,Q#1907 - >seq8554,non-specific,272954,9,236,4.71275e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28299,Q#1907 - >seq8554,non-specific,197319,9,236,9.81377e-11,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28300,Q#1907 - >seq8554,non-specific,238828,578,733,1.21137e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
28301,Q#1907 - >seq8554,non-specific,275209,583,733,2.9569599999999996e-06,50.534,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28302,Q#1907 - >seq8554,superfamily,275209,583,733,2.9569599999999996e-06,50.534,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28303,Q#1907 - >seq8554,non-specific,197336,9,229,3.7696600000000003e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28304,Q#1907 - >seq8554,non-specific,197311,7,146,7.552930000000001e-05,44.9753,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28305,Q#1907 - >seq8554,non-specific,339261,108,232,0.000348659,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28306,Q#1907 - >seq8554,non-specific,236970,9,207,0.00043796199999999997,43.3442,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28307,Q#1907 - >seq8554,non-specific,197318,9,236,0.00168088,41.5131,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs4_gibbon,marg,CompleteHit
28308,Q#1907 - >seq8554,non-specific,238185,652,712,0.00761989,36.9452,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28309,Q#1908 - >seq8555,non-specific,238827,637,716,3.10383e-09,57.6862,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28310,Q#1908 - >seq8555,superfamily,295487,637,716,3.10383e-09,57.6862,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28311,Q#1908 - >seq8555,non-specific,333820,644,695,0.0012476,40.3534,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28312,Q#1908 - >seq8555,superfamily,333820,644,695,0.0012476,40.3534,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs6_sqmonkey.pars.frame2,1909181135_L1M2.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M2,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28313,Q#1910 - >seq8557,specific,197310,9,236,1.41532e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28314,Q#1910 - >seq8557,superfamily,351117,9,236,1.41532e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28315,Q#1910 - >seq8557,specific,238827,509,770,1.9977e-62,211.766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28316,Q#1910 - >seq8557,superfamily,295487,509,770,1.9977e-62,211.766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28317,Q#1910 - >seq8557,non-specific,197306,9,236,8.40558e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28318,Q#1910 - >seq8557,specific,333820,515,770,2.02802e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28319,Q#1910 - >seq8557,superfamily,333820,515,770,2.02802e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28320,Q#1910 - >seq8557,non-specific,197320,7,229,5.118600000000001e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28321,Q#1910 - >seq8557,non-specific,223780,7,229,2.0555900000000002e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28322,Q#1910 - >seq8557,specific,335306,10,229,1.63171e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28323,Q#1910 - >seq8557,non-specific,197307,9,236,2.0580300000000002e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28324,Q#1910 - >seq8557,non-specific,197321,7,236,2.51664e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28325,Q#1910 - >seq8557,non-specific,272954,7,207,5.444919999999999e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28326,Q#1910 - >seq8557,non-specific,273186,7,237,1.64752e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28327,Q#1910 - >seq8557,non-specific,197319,7,236,1.1801299999999999e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28328,Q#1910 - >seq8557,non-specific,197336,7,229,1.24663e-11,66.0967,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28329,Q#1910 - >seq8557,non-specific,238828,515,735,1.70006e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28330,Q#1910 - >seq8557,non-specific,275209,466,735,9.16892e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,C-TerminusTruncated
28331,Q#1910 - >seq8557,superfamily,275209,466,735,9.16892e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,C-TerminusTruncated
28332,Q#1910 - >seq8557,non-specific,197311,7,236,1.1230100000000001e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28333,Q#1910 - >seq8557,non-specific,339261,108,232,8.73607e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28334,Q#1910 - >seq8557,non-specific,238185,656,770,0.000293488,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs0_human,marg,CompleteHit
28335,Q#1910 - >seq8557,non-specific,197318,9,236,0.000405233,43.4391,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,marg,CompleteHit
28336,Q#1910 - >seq8557,non-specific,334125,217,410,0.000412594,44.0624,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs0_human,marg,N-TerminusTruncated
28337,Q#1910 - >seq8557,superfamily,334125,217,410,0.000412594,44.0624,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs0_human,marg,N-TerminusTruncated
28338,Q#1910 - >seq8557,non-specific,223496,320,499,0.0009648839999999999,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M1,ORF2,hs0_human,marg,BothTerminiTruncated
28339,Q#1910 - >seq8557,superfamily,223496,320,499,0.0009648839999999999,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M1,ORF2,hs0_human,marg,BothTerminiTruncated
28340,Q#1910 - >seq8557,non-specific,235175,291,468,0.00242821,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs0_human,marg,BothTerminiTruncated
28341,Q#1910 - >seq8557,superfamily,235175,291,468,0.00242821,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs0_human.marg.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs0_human,marg,BothTerminiTruncated
28342,Q#1912 - >seq8559,specific,197310,9,236,4.7418499999999996e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28343,Q#1912 - >seq8559,superfamily,351117,9,236,4.7418499999999996e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28344,Q#1912 - >seq8559,non-specific,197306,9,236,3.9161699999999994e-36,136.842,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28345,Q#1912 - >seq8559,non-specific,197320,7,229,8.068489999999999e-24,101.823,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28346,Q#1912 - >seq8559,non-specific,223780,7,229,1.2842600000000001e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28347,Q#1912 - >seq8559,non-specific,197307,9,236,9.070549999999998e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28348,Q#1912 - >seq8559,specific,335306,10,229,2.7210400000000004e-20,90.7673,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28349,Q#1912 - >seq8559,non-specific,197321,7,236,1.34214e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28350,Q#1912 - >seq8559,non-specific,272954,7,207,3.0978e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28351,Q#1912 - >seq8559,non-specific,273186,7,237,2.25779e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28352,Q#1912 - >seq8559,non-specific,197319,7,236,3.1923899999999998e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28353,Q#1912 - >seq8559,non-specific,197336,7,229,1.9641e-11,65.3263,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28354,Q#1912 - >seq8559,non-specific,197311,7,236,1.21587e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28355,Q#1912 - >seq8559,non-specific,236970,9,207,3.5729400000000004e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28356,Q#1912 - >seq8559,non-specific,339261,108,232,2.476e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28357,Q#1912 - >seq8559,non-specific,197318,9,236,0.000383508,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,marg,CompleteHit
28358,Q#1912 - >seq8559,non-specific,197314,7,236,0.0005202830000000001,42.7159,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.marg.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs3_orang,marg,CompleteHit
28359,Q#1914 - >seq8561,specific,238827,473,735,4.7074199999999996e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28360,Q#1914 - >seq8561,superfamily,295487,473,735,4.7074199999999996e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28361,Q#1914 - >seq8561,specific,333820,479,735,2.01715e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28362,Q#1914 - >seq8561,superfamily,333820,479,735,2.01715e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28363,Q#1914 - >seq8561,non-specific,238828,479,700,1.33714e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28364,Q#1914 - >seq8561,non-specific,275209,430,825,1.14473e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28365,Q#1914 - >seq8561,superfamily,275209,430,825,1.14473e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28366,Q#1914 - >seq8561,non-specific,238185,619,735,0.000128386,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs3_orang.marg.frame1,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs3_orang,marg,CompleteHit
28367,Q#1915 - >seq8562,specific,197310,9,236,9.395659999999998e-63,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28368,Q#1915 - >seq8562,superfamily,351117,9,236,9.395659999999998e-63,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28369,Q#1915 - >seq8562,non-specific,197306,9,236,4.62687e-36,136.842,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28370,Q#1915 - >seq8562,non-specific,197320,7,229,7.78802e-24,101.823,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28371,Q#1915 - >seq8562,non-specific,223780,7,229,1.23936e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28372,Q#1915 - >seq8562,non-specific,197307,9,236,1.39444e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28373,Q#1915 - >seq8562,specific,335306,10,229,2.62942e-20,90.7673,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28374,Q#1915 - >seq8562,non-specific,197321,7,236,3.599049999999999e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28375,Q#1915 - >seq8562,non-specific,272954,7,207,1.58898e-17,83.2012,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28376,Q#1915 - >seq8562,non-specific,273186,7,237,2.1798599999999997e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28377,Q#1915 - >seq8562,non-specific,197319,7,236,3.3548499999999997e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28378,Q#1915 - >seq8562,non-specific,197336,7,229,1.89704e-11,65.3263,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28379,Q#1915 - >seq8562,non-specific,197311,7,236,7.8605e-08,53.8349,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28380,Q#1915 - >seq8562,non-specific,236970,9,207,1.5300799999999998e-06,50.663000000000004,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28381,Q#1915 - >seq8562,non-specific,339261,108,232,5.05214e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28382,Q#1915 - >seq8562,non-specific,197318,9,236,0.00031816799999999997,43.4391,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs3_orang,pars,CompleteHit
28383,Q#1915 - >seq8562,non-specific,197314,7,236,0.0005031780000000001,42.7159,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs3_orang.pars.frame3,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M1,ORF2,hs3_orang,pars,CompleteHit
28384,Q#1916 - >seq8563,specific,238827,492,754,2.01715e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28385,Q#1916 - >seq8563,superfamily,295487,492,754,2.01715e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28386,Q#1916 - >seq8563,specific,333820,498,754,8.68772e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28387,Q#1916 - >seq8563,superfamily,333820,498,754,8.68772e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28388,Q#1916 - >seq8563,non-specific,238828,498,719,1.3208599999999998e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28389,Q#1916 - >seq8563,non-specific,275209,449,719,1.9789300000000003e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,C-TerminusTruncated
28390,Q#1916 - >seq8563,superfamily,275209,449,719,1.9789300000000003e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,C-TerminusTruncated
28391,Q#1916 - >seq8563,non-specific,238185,638,754,7.28505e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs3_orang.pars.frame2,1909181135_L1M1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs3_orang,pars,CompleteHit
28392,Q#1918 - >seq8565,specific,197310,9,236,2.9481899999999997e-62,211.826,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28393,Q#1918 - >seq8565,superfamily,351117,9,236,2.9481899999999997e-62,211.826,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28394,Q#1918 - >seq8565,specific,238827,509,770,5.009599999999999e-62,210.61,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28395,Q#1918 - >seq8565,superfamily,295487,509,770,5.009599999999999e-62,210.61,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28396,Q#1918 - >seq8565,non-specific,197306,9,236,1.54462e-34,132.605,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28397,Q#1918 - >seq8565,specific,333820,515,770,2.9747199999999997e-30,118.164,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28398,Q#1918 - >seq8565,superfamily,333820,515,770,2.9747199999999997e-30,118.164,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28399,Q#1918 - >seq8565,non-specific,197320,7,229,1.6117200000000002e-23,101.053,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28400,Q#1918 - >seq8565,non-specific,223780,7,229,2.2653499999999997e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28401,Q#1918 - >seq8565,non-specific,197307,9,236,5.487190000000001e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28402,Q#1918 - >seq8565,specific,335306,10,229,7.22405e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28403,Q#1918 - >seq8565,non-specific,197321,7,236,1.0815599999999998e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28404,Q#1918 - >seq8565,non-specific,272954,7,207,1.3839399999999999e-16,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28405,Q#1918 - >seq8565,non-specific,273186,7,237,3.31326e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28406,Q#1918 - >seq8565,non-specific,197319,7,236,2.98049e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28407,Q#1918 - >seq8565,non-specific,197336,7,229,1.9605099999999997e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28408,Q#1918 - >seq8565,non-specific,238828,515,735,2.92186e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28409,Q#1918 - >seq8565,non-specific,197311,7,236,4.76903e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28410,Q#1918 - >seq8565,non-specific,275209,466,735,5.1254400000000005e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,C-TerminusTruncated
28411,Q#1918 - >seq8565,superfamily,275209,466,735,5.1254400000000005e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,C-TerminusTruncated
28412,Q#1918 - >seq8565,non-specific,339261,108,232,5.47655e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28413,Q#1918 - >seq8565,non-specific,238185,656,770,0.000231788,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28414,Q#1918 - >seq8565,non-specific,197318,9,236,0.000418546,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28415,Q#1918 - >seq8565,non-specific,197314,7,236,0.00151225,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs1_chimp,marg,CompleteHit
28416,Q#1918 - >seq8565,non-specific,235175,306,463,0.00423002,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs1_chimp,marg,BothTerminiTruncated
28417,Q#1918 - >seq8565,superfamily,235175,306,463,0.00423002,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs1_chimp,marg,BothTerminiTruncated
28418,Q#1918 - >seq8565,non-specific,223496,320,499,0.00792737,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M1,ORF2,hs1_chimp,marg,BothTerminiTruncated
28419,Q#1918 - >seq8565,superfamily,223496,320,499,0.00792737,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M1,ORF2,hs1_chimp,marg,BothTerminiTruncated
28420,Q#1918 - >seq8565,non-specific,274009,305,453,0.00902944,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs1_chimp,marg,C-TerminusTruncated
28421,Q#1918 - >seq8565,superfamily,274009,305,453,0.00902944,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs1_chimp.marg.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs1_chimp,marg,C-TerminusTruncated
28422,Q#1920 - >seq8567,specific,238827,448,691,2.1344699999999995e-59,202.90599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28423,Q#1920 - >seq8567,superfamily,295487,448,691,2.1344699999999995e-59,202.90599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28424,Q#1920 - >seq8567,specific,333820,454,678,5.774319999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28425,Q#1920 - >seq8567,superfamily,333820,454,678,5.774319999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28426,Q#1920 - >seq8567,non-specific,238828,454,675,6.72076e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28427,Q#1920 - >seq8567,non-specific,275209,525,675,3.9885599999999996e-07,53.2304,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28428,Q#1920 - >seq8567,superfamily,275209,525,675,3.9885599999999996e-07,53.2304,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28429,Q#1920 - >seq8567,non-specific,238185,596,679,0.00514674,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs4_gibbon.pars.frame1,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28430,Q#1923 - >seq8570,specific,238827,474,735,7.474759999999999e-63,212.922,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28431,Q#1923 - >seq8570,superfamily,295487,474,735,7.474759999999999e-63,212.922,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28432,Q#1923 - >seq8570,specific,333820,480,735,2.2479e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28433,Q#1923 - >seq8570,superfamily,333820,480,735,2.2479e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28434,Q#1923 - >seq8570,non-specific,238828,480,700,1.47972e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28435,Q#1923 - >seq8570,non-specific,275209,431,700,4.8078400000000004e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,C-TerminusTruncated
28436,Q#1923 - >seq8570,superfamily,275209,431,700,4.8078400000000004e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,C-TerminusTruncated
28437,Q#1923 - >seq8570,non-specific,238185,621,735,0.000150232,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28438,Q#1923 - >seq8570,non-specific,235175,271,428,0.00846332,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1M1,ORF2,hs1_chimp,pars,BothTerminiTruncated
28439,Q#1923 - >seq8570,superfamily,235175,271,428,0.00846332,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs1_chimp.pars.frame1,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1M1,ORF2,hs1_chimp,pars,BothTerminiTruncated
28440,Q#1924 - >seq8571,specific,238827,510,772,2.43217e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28441,Q#1924 - >seq8571,superfamily,295487,510,772,2.43217e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28442,Q#1924 - >seq8571,specific,197310,9,236,6.599529999999999e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28443,Q#1924 - >seq8571,superfamily,351117,9,236,6.599529999999999e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28444,Q#1924 - >seq8571,non-specific,197306,9,236,1.1393399999999999e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28445,Q#1924 - >seq8571,specific,333820,516,772,1.8759e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28446,Q#1924 - >seq8571,superfamily,333820,516,772,1.8759e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28447,Q#1924 - >seq8571,non-specific,197307,9,236,7.570419999999998e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28448,Q#1924 - >seq8571,non-specific,223780,9,238,2.3717300000000003e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28449,Q#1924 - >seq8571,non-specific,197320,8,236,2.2364e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28450,Q#1924 - >seq8571,non-specific,197321,7,236,2.76148e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28451,Q#1924 - >seq8571,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28452,Q#1924 - >seq8571,non-specific,273186,9,237,1.01467e-17,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28453,Q#1924 - >seq8571,non-specific,272954,9,236,2.79095e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28454,Q#1924 - >seq8571,non-specific,197319,8,236,6.699010000000001e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28455,Q#1924 - >seq8571,non-specific,197336,7,235,1.51595e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28456,Q#1924 - >seq8571,non-specific,238828,516,737,3.53632e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28457,Q#1924 - >seq8571,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28458,Q#1924 - >seq8571,non-specific,236970,9,238,3.13996e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28459,Q#1924 - >seq8571,non-specific,275209,467,800,1.98136e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28460,Q#1924 - >seq8571,superfamily,275209,467,800,1.98136e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28461,Q#1924 - >seq8571,non-specific,339261,108,232,1.51054e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28462,Q#1924 - >seq8571,non-specific,197317,139,229,8.0317e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,marg,N-TerminusTruncated
28463,Q#1924 - >seq8571,non-specific,197311,7,236,2.20123e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28464,Q#1924 - >seq8571,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28465,Q#1924 - >seq8571,non-specific,274009,305,453,0.000204323,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,marg,C-TerminusTruncated
28466,Q#1924 - >seq8571,superfamily,274009,305,453,0.000204323,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,marg,C-TerminusTruncated
28467,Q#1924 - >seq8571,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,marg,N-TerminusTruncated
28468,Q#1924 - >seq8571,specific,311990,1241,1259,0.00189836,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28469,Q#1924 - >seq8571,superfamily,311990,1241,1259,0.00189836,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28470,Q#1924 - >seq8571,non-specific,197314,7,236,0.00269581,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28471,Q#1924 - >seq8571,non-specific,239569,525,748,0.00364902,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1HS,ORF2,hs1_chimp,marg,CompleteHit
28472,Q#1924 - >seq8571,non-specific,235175,301,469,0.00452433,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,marg,BothTerminiTruncated
28473,Q#1924 - >seq8571,superfamily,235175,301,469,0.00452433,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,marg,BothTerminiTruncated
28474,Q#1924 - >seq8571,non-specific,293702,337,451,0.00890645,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1HS,ORF2,hs1_chimp,marg,C-TerminusTruncated
28475,Q#1924 - >seq8571,superfamily,293702,337,451,0.00890645,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs1_chimp.marg.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1HS,ORF2,hs1_chimp,marg,C-TerminusTruncated
28476,Q#1926 - >seq8573,non-specific,130141,277,387,0.00613043,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs1_chimp.marg.frame1,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1HS,ORF2,hs1_chimp,marg,N-TerminusTruncated
28477,Q#1926 - >seq8573,superfamily,130141,277,387,0.00613043,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs1_chimp.marg.frame1,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1HS,ORF2,hs1_chimp,marg,N-TerminusTruncated
28478,Q#1927 - >seq8574,specific,238827,510,772,1.9987e-66,223.322,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28479,Q#1927 - >seq8574,superfamily,295487,510,772,1.9987e-66,223.322,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28480,Q#1927 - >seq8574,specific,197310,9,236,5.357399999999999e-65,219.916,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28481,Q#1927 - >seq8574,superfamily,351117,9,236,5.357399999999999e-65,219.916,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28482,Q#1927 - >seq8574,non-specific,197306,9,236,1.2138199999999999e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28483,Q#1927 - >seq8574,specific,333820,516,772,1.6411599999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28484,Q#1927 - >seq8574,superfamily,333820,516,772,1.6411599999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28485,Q#1927 - >seq8574,non-specific,197307,9,236,8.32102e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28486,Q#1927 - >seq8574,non-specific,223780,9,238,2.5556699999999997e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28487,Q#1927 - >seq8574,non-specific,197320,8,236,2.62589e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28488,Q#1927 - >seq8574,non-specific,197321,7,236,2.78473e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28489,Q#1927 - >seq8574,specific,335306,10,229,1.67755e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28490,Q#1927 - >seq8574,non-specific,273186,9,237,1.1138399999999999e-17,83.8676,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28491,Q#1927 - >seq8574,non-specific,272954,9,236,3.15059e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28492,Q#1927 - >seq8574,non-specific,197319,8,236,6.44449e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28493,Q#1927 - >seq8574,non-specific,197336,7,235,1.6162299999999999e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28494,Q#1927 - >seq8574,non-specific,238828,516,737,3.43689e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28495,Q#1927 - >seq8574,non-specific,197322,9,236,2.70382e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28496,Q#1927 - >seq8574,non-specific,236970,9,238,2.9654000000000004e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28497,Q#1927 - >seq8574,non-specific,275209,467,800,1.97236e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28498,Q#1927 - >seq8574,superfamily,275209,467,800,1.97236e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28499,Q#1927 - >seq8574,non-specific,339261,108,232,1.4301900000000001e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28500,Q#1927 - >seq8574,non-specific,197317,139,229,7.80246e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,pars,N-TerminusTruncated
28501,Q#1927 - >seq8574,non-specific,197311,7,236,2.24343e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28502,Q#1927 - >seq8574,non-specific,238185,656,772,0.000174941,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28503,Q#1927 - >seq8574,non-specific,274009,305,453,0.000217504,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,pars,C-TerminusTruncated
28504,Q#1927 - >seq8574,superfamily,274009,305,453,0.000217504,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,pars,C-TerminusTruncated
28505,Q#1927 - >seq8574,non-specific,226098,138,239,0.000550723,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1HS,ORF2,hs1_chimp,pars,N-TerminusTruncated
28506,Q#1927 - >seq8574,non-specific,197314,7,236,0.00252856,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28507,Q#1927 - >seq8574,non-specific,239569,525,748,0.00339137,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1HS,ORF2,hs1_chimp,pars,CompleteHit
28508,Q#1927 - >seq8574,non-specific,235175,301,469,0.00446702,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,pars,BothTerminiTruncated
28509,Q#1927 - >seq8574,superfamily,235175,301,469,0.00446702,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1HS,ORF2,hs1_chimp,pars,BothTerminiTruncated
28510,Q#1927 - >seq8574,non-specific,293702,337,451,0.00850395,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1HS,ORF2,hs1_chimp,pars,C-TerminusTruncated
28511,Q#1927 - >seq8574,superfamily,293702,337,451,0.00850395,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1HS.ORF2.hs1_chimp.pars.frame3,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1HS,ORF2,hs1_chimp,pars,C-TerminusTruncated
28512,Q#1929 - >seq8576,non-specific,130141,277,387,0.00670326,40.1881,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs1_chimp.pars.frame1,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1HS,ORF2,hs1_chimp,pars,N-TerminusTruncated
28513,Q#1929 - >seq8576,superfamily,130141,277,387,0.00670326,40.1881,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1HS.ORF2.hs1_chimp.pars.frame1,1909181135_L1HS.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1HS,ORF2,hs1_chimp,pars,N-TerminusTruncated
28514,Q#1930 - >seq8577,specific,197310,9,236,2.8582899999999994e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28515,Q#1930 - >seq8577,superfamily,351117,9,236,2.8582899999999994e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28516,Q#1930 - >seq8577,non-specific,197306,9,236,5.478899999999999e-35,133.761,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28517,Q#1930 - >seq8577,non-specific,197320,7,229,1.02945e-23,101.43799999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28518,Q#1930 - >seq8577,non-specific,223780,7,229,1.6273700000000002e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28519,Q#1930 - >seq8577,non-specific,197307,9,236,2.4822e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28520,Q#1930 - >seq8577,specific,335306,10,229,6.520999999999999e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28521,Q#1930 - >seq8577,non-specific,197321,7,236,9.06954e-19,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28522,Q#1930 - >seq8577,non-specific,272954,7,207,2.9436100000000003e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28523,Q#1930 - >seq8577,non-specific,273186,7,237,7.825579999999999e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28524,Q#1930 - >seq8577,non-specific,197319,7,236,1.3179799999999998e-16,80.7837,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28525,Q#1930 - >seq8577,non-specific,197336,7,229,1.7668200000000001e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28526,Q#1930 - >seq8577,non-specific,197311,7,236,6.280790000000001e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28527,Q#1930 - >seq8577,non-specific,339261,108,232,2.30007e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28528,Q#1930 - >seq8577,non-specific,197318,9,236,0.00019242,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28529,Q#1930 - >seq8577,non-specific,197314,7,236,0.00136855,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs1_chimp.pars.frame3,1909181135_L1M1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M1,ORF2,hs1_chimp,pars,CompleteHit
28530,Q#1931 - >seq8578,specific,197310,9,238,8.61398e-43,155.972,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28531,Q#1931 - >seq8578,superfamily,351117,9,238,8.61398e-43,155.972,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28532,Q#1931 - >seq8578,specific,238827,558,775,1.1269299999999998e-41,152.445,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,CompleteHit
28533,Q#1931 - >seq8578,superfamily,295487,558,775,1.1269299999999998e-41,152.445,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,CompleteHit
28534,Q#1931 - >seq8578,non-specific,333820,557,775,2.53301e-22,95.4369,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,CompleteHit
28535,Q#1931 - >seq8578,superfamily,333820,557,775,2.53301e-22,95.4369,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,CompleteHit
28536,Q#1931 - >seq8578,non-specific,197306,9,238,1.04956e-18,86.7664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28537,Q#1931 - >seq8578,specific,335306,10,231,4.5700599999999995e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28538,Q#1931 - >seq8578,non-specific,238828,585,740,1.2620900000000001e-10,62.6036,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,N-TerminusTruncated
28539,Q#1931 - >seq8578,non-specific,197320,9,209,5.77753e-10,60.9918,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28540,Q#1931 - >seq8578,non-specific,197307,9,238,4.25793e-09,58.4533,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28541,Q#1931 - >seq8578,non-specific,223780,9,231,8.74387e-09,57.6083,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28542,Q#1931 - >seq8578,non-specific,275209,590,813,1.9388599999999997e-08,57.4676,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,N-TerminusTruncated
28543,Q#1931 - >seq8578,superfamily,275209,590,813,1.9388599999999997e-08,57.4676,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,N-TerminusTruncated
28544,Q#1931 - >seq8578,non-specific,197321,7,238,1.60284e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28545,Q#1931 - >seq8578,non-specific,272954,9,238,2.53827e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28546,Q#1931 - >seq8578,non-specific,273186,9,239,9.996060000000001e-06,48.4292,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28547,Q#1931 - >seq8578,non-specific,197319,9,238,5.81016e-05,46.1157,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,CompleteHit
28548,Q#1931 - >seq8578,non-specific,334125,219,414,0.000301218,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs0_human,marg,N-TerminusTruncated
28549,Q#1931 - >seq8578,superfamily,334125,219,414,0.000301218,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M2,ORF2,hs0_human,marg,N-TerminusTruncated
28550,Q#1931 - >seq8578,non-specific,235175,296,471,0.00040413300000000004,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs0_human,marg,BothTerminiTruncated
28551,Q#1931 - >seq8578,superfamily,235175,296,471,0.00040413300000000004,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M2,ORF2,hs0_human,marg,BothTerminiTruncated
28552,Q#1931 - >seq8578,non-specific,238185,659,775,0.00305578,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M2,ORF2,hs0_human,marg,CompleteHit
28553,Q#1931 - >seq8578,non-specific,197336,9,76,0.00409137,40.2883,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M2.ORF2.hs0_human.marg.frame3,1909181135_L1M2.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M2,ORF2,hs0_human,marg,C-TerminusTruncated
28554,Q#1932 - >seq8579,non-specific,235175,301,458,0.00114937,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28555,Q#1932 - >seq8579,superfamily,235175,301,458,0.00114937,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28556,Q#1932 - >seq8579,non-specific,334125,213,405,0.00268079,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
28557,Q#1932 - >seq8579,superfamily,334125,213,405,0.00268079,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
28558,Q#1932 - >seq8579,non-specific,274009,300,448,0.00554717,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28559,Q#1932 - >seq8579,superfamily,274009,300,448,0.00554717,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28560,Q#1932 - >seq8579,non-specific,274475,250,422,0.00686622,40.4372,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28561,Q#1932 - >seq8579,superfamily,274475,250,422,0.00686622,40.4372,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1M1.ORF2.hs4_gibbon.pars.frame2,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1M1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
28562,Q#1935 - >seq8582,specific,238827,508,769,2.0499699999999997e-62,211.766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28563,Q#1935 - >seq8582,superfamily,295487,508,769,2.0499699999999997e-62,211.766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28564,Q#1935 - >seq8582,specific,197310,9,235,1.4362099999999997e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28565,Q#1935 - >seq8582,superfamily,351117,9,235,1.4362099999999997e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28566,Q#1935 - >seq8582,non-specific,197306,9,235,6.0115199999999997e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28567,Q#1935 - >seq8582,specific,333820,514,769,2.2359e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28568,Q#1935 - >seq8582,superfamily,333820,514,769,2.2359e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28569,Q#1935 - >seq8582,non-specific,197320,7,228,1.0234499999999999e-22,98.7413,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28570,Q#1935 - >seq8582,non-specific,223780,7,228,6.51284e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28571,Q#1935 - >seq8582,specific,335306,10,228,1.7366699999999998e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28572,Q#1935 - >seq8582,non-specific,197307,9,235,3.48699e-18,85.4173,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28573,Q#1935 - >seq8582,non-specific,197321,7,235,1.00234e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28574,Q#1935 - >seq8582,non-specific,272954,7,206,1.5143000000000002e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28575,Q#1935 - >seq8582,non-specific,273186,7,236,2.23905e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28576,Q#1935 - >seq8582,non-specific,197319,7,235,8.216310000000001e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28577,Q#1935 - >seq8582,non-specific,197336,7,228,1.31577e-11,66.0967,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28578,Q#1935 - >seq8582,non-specific,238828,514,734,1.9015e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28579,Q#1935 - >seq8582,non-specific,275209,465,734,1.0146600000000001e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,C-TerminusTruncated
28580,Q#1935 - >seq8582,superfamily,275209,465,734,1.0146600000000001e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,C-TerminusTruncated
28581,Q#1935 - >seq8582,non-specific,197311,7,235,1.60277e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28582,Q#1935 - >seq8582,non-specific,339261,107,231,8.43043e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28583,Q#1935 - >seq8582,non-specific,238185,655,769,0.000272527,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs0_human,pars,CompleteHit
28584,Q#1935 - >seq8582,non-specific,334125,216,409,0.00046354199999999995,43.6772,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs0_human,pars,N-TerminusTruncated
28585,Q#1935 - >seq8582,superfamily,334125,216,409,0.00046354199999999995,43.6772,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs0_human,pars,N-TerminusTruncated
28586,Q#1935 - >seq8582,non-specific,223496,319,498,0.000993045,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1M1,ORF2,hs0_human,pars,BothTerminiTruncated
28587,Q#1935 - >seq8582,superfamily,223496,319,498,0.000993045,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1M1,ORF2,hs0_human,pars,BothTerminiTruncated
28588,Q#1935 - >seq8582,non-specific,197318,9,235,0.00221462,41.1279,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs0_human,pars,CompleteHit
28589,Q#1935 - >seq8582,non-specific,235175,290,467,0.00267517,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs0_human,pars,BothTerminiTruncated
28590,Q#1935 - >seq8582,superfamily,235175,290,467,0.00267517,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs0_human.pars.frame3,1909181135_L1M1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs0_human,pars,BothTerminiTruncated
28591,Q#1938 - >seq8585,specific,197310,9,236,2.6239099999999992e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28592,Q#1938 - >seq8585,superfamily,351117,9,236,2.6239099999999992e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28593,Q#1938 - >seq8585,specific,238827,510,768,9.97096e-47,166.69799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28594,Q#1938 - >seq8585,superfamily,295487,510,768,9.97096e-47,166.69799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28595,Q#1938 - >seq8585,non-specific,197306,9,236,3.4765999999999995e-35,134.531,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28596,Q#1938 - >seq8585,non-specific,197320,7,229,4.6645699999999995e-24,102.59299999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28597,Q#1938 - >seq8585,non-specific,223780,7,229,1.622e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28598,Q#1938 - >seq8585,non-specific,333820,516,768,4.166569999999999e-21,91.9701,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28599,Q#1938 - >seq8585,superfamily,333820,516,768,4.166569999999999e-21,91.9701,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28600,Q#1938 - >seq8585,specific,335306,10,229,1.77041e-20,91.1525,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28601,Q#1938 - >seq8585,non-specific,197307,9,236,2.2235200000000002e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28602,Q#1938 - >seq8585,non-specific,197321,7,236,9.458380000000001e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28603,Q#1938 - >seq8585,non-specific,273186,7,237,1.7264700000000003e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28604,Q#1938 - >seq8585,non-specific,272954,7,207,1.95786e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28605,Q#1938 - >seq8585,non-specific,197319,7,236,2.94732e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28606,Q#1938 - >seq8585,non-specific,197336,7,229,1.3992000000000003e-11,66.0967,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28607,Q#1938 - >seq8585,non-specific,197311,7,236,1.71782e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28608,Q#1938 - >seq8585,non-specific,236970,9,207,1.5523e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28609,Q#1938 - >seq8585,non-specific,339261,108,232,3.43039e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28610,Q#1938 - >seq8585,non-specific,238828,516,733,0.000145528,44.4993,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28611,Q#1938 - >seq8585,non-specific,197318,9,236,0.00018051400000000003,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28612,Q#1938 - >seq8585,non-specific,197314,7,236,0.000827087,42.3307,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs6_sqmonkey,marg,CompleteHit
28613,Q#1938 - >seq8585,non-specific,334125,217,411,0.000998199,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28614,Q#1938 - >seq8585,superfamily,334125,217,411,0.000998199,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
28615,Q#1938 - >seq8585,non-specific,235175,306,464,0.00237602,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28616,Q#1938 - >seq8585,superfamily,235175,306,464,0.00237602,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
28617,Q#1938 - >seq8585,non-specific,274009,305,458,0.00311058,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28618,Q#1938 - >seq8585,superfamily,274009,305,458,0.00311058,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs6_sqmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
28619,Q#1941 - >seq8588,specific,197310,9,236,1.33771e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28620,Q#1941 - >seq8588,superfamily,351117,9,236,1.33771e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28621,Q#1941 - >seq8588,specific,238827,510,768,4.78741e-47,167.85299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28622,Q#1941 - >seq8588,superfamily,295487,510,768,4.78741e-47,167.85299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28623,Q#1941 - >seq8588,non-specific,197306,9,236,4.2102199999999995e-35,134.14600000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28624,Q#1941 - >seq8588,non-specific,197320,7,229,4.52768e-24,102.59299999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28625,Q#1941 - >seq8588,non-specific,223780,7,229,5.53685e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28626,Q#1941 - >seq8588,non-specific,333820,516,768,3.3416900000000004e-21,92.3553,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28627,Q#1941 - >seq8588,superfamily,333820,516,768,3.3416900000000004e-21,92.3553,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28628,Q#1941 - >seq8588,non-specific,197307,9,236,1.04911e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28629,Q#1941 - >seq8588,specific,335306,10,229,1.7198900000000002e-20,91.1525,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28630,Q#1941 - >seq8588,non-specific,197321,7,236,3.81209e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28631,Q#1941 - >seq8588,non-specific,273186,7,237,8.663999999999999e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28632,Q#1941 - >seq8588,non-specific,272954,7,207,9.1987e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28633,Q#1941 - >seq8588,non-specific,197319,7,236,1.18162e-15,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28634,Q#1941 - >seq8588,non-specific,197336,7,229,1.35877e-11,66.0967,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28635,Q#1941 - >seq8588,non-specific,197311,7,236,1.6700199999999998e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28636,Q#1941 - >seq8588,non-specific,236970,9,207,1.50793e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28637,Q#1941 - >seq8588,non-specific,339261,108,232,2.8888400000000003e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28638,Q#1941 - >seq8588,non-specific,238828,516,733,0.00011156299999999999,44.8845,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28639,Q#1941 - >seq8588,non-specific,197318,9,236,0.00020643700000000002,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28640,Q#1941 - >seq8588,non-specific,197314,7,236,0.000803997,42.3307,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M1,ORF2,hs6_sqmonkey,pars,CompleteHit
28641,Q#1941 - >seq8588,non-specific,334125,217,411,0.000844668,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28642,Q#1941 - >seq8588,superfamily,334125,217,411,0.000844668,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
28643,Q#1941 - >seq8588,non-specific,235175,306,464,0.00174443,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28644,Q#1941 - >seq8588,superfamily,235175,306,464,0.00174443,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
28645,Q#1941 - >seq8588,non-specific,274009,305,458,0.00386116,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28646,Q#1941 - >seq8588,superfamily,274009,305,458,0.00386116,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs6_sqmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
28647,Q#1942 - >seq8589,specific,197310,9,228,2.33479e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28648,Q#1942 - >seq8589,superfamily,351117,9,228,2.33479e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28649,Q#1942 - >seq8589,non-specific,197306,9,211,5.1106300000000004e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28650,Q#1942 - >seq8589,non-specific,197320,7,208,1.1575599999999999e-23,101.43799999999999,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28651,Q#1942 - >seq8589,non-specific,223780,7,207,5.8627e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28652,Q#1942 - >seq8589,non-specific,197307,9,208,4.82141e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28653,Q#1942 - >seq8589,specific,335306,10,210,1.2820400000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28654,Q#1942 - >seq8589,non-specific,272954,7,207,1.83638e-18,86.2828,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28655,Q#1942 - >seq8589,non-specific,197321,7,207,2.0399599999999997e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28656,Q#1942 - >seq8589,non-specific,273186,7,208,1.96307e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28657,Q#1942 - >seq8589,non-specific,197319,7,218,4.11256e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28658,Q#1942 - >seq8589,non-specific,197336,7,204,3.07377e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28659,Q#1942 - >seq8589,non-specific,197311,7,204,7.51815e-08,53.8349,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,pars,CompleteHit
28660,Q#1942 - >seq8589,non-specific,339261,108,148,0.00156841,39.2427,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28661,Q#1942 - >seq8589,non-specific,197318,9,148,0.00233697,40.7427,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28662,Q#1944 - >seq8591,specific,197310,9,236,5.180439999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28663,Q#1944 - >seq8591,superfamily,351117,9,236,5.180439999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28664,Q#1944 - >seq8591,non-specific,197306,9,236,4.256859999999999e-34,131.064,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28665,Q#1944 - >seq8591,non-specific,197320,7,229,4.881689999999999e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28666,Q#1944 - >seq8591,non-specific,223780,7,229,9.763830000000001e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28667,Q#1944 - >seq8591,non-specific,197307,9,236,8.99182e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28668,Q#1944 - >seq8591,specific,335306,10,229,3.13686e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28669,Q#1944 - >seq8591,non-specific,197321,7,236,5.49839e-18,84.9112,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28670,Q#1944 - >seq8591,non-specific,272954,7,207,8.919510000000001e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28671,Q#1944 - >seq8591,non-specific,273186,7,237,3.4534800000000005e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28672,Q#1944 - >seq8591,non-specific,197319,7,236,5.4973e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28673,Q#1944 - >seq8591,non-specific,197336,7,229,8.27247e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28674,Q#1944 - >seq8591,non-specific,238827,509,547,2.9999499999999998e-09,58.4566,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28675,Q#1944 - >seq8591,superfamily,295487,509,547,2.9999499999999998e-09,58.4566,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28676,Q#1944 - >seq8591,non-specific,197311,7,236,5.17661e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28677,Q#1944 - >seq8591,non-specific,339261,108,232,4.7489e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28678,Q#1944 - >seq8591,non-specific,197314,7,236,0.00036327,43.4863,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28679,Q#1944 - >seq8591,non-specific,197318,9,236,0.000427708,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28680,Q#1944 - >seq8591,non-specific,223496,320,499,0.00140366,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28681,Q#1944 - >seq8591,superfamily,223496,320,499,0.00140366,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28682,Q#1944 - >seq8591,non-specific,334125,217,410,0.00255504,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28683,Q#1944 - >seq8591,superfamily,334125,217,410,0.00255504,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28684,Q#1944 - >seq8591,non-specific,235175,263,500,0.0026941,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28685,Q#1944 - >seq8591,superfamily,235175,263,500,0.0026941,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28686,Q#1944 - >seq8591,non-specific,274009,305,453,0.00300165,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28687,Q#1944 - >seq8591,superfamily,274009,305,453,0.00300165,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28688,Q#1944 - >seq8591,non-specific,333820,515,547,0.00501326,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28689,Q#1944 - >seq8591,superfamily,333820,515,547,0.00501326,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28690,Q#1946 - >seq8593,specific,238827,494,702,6.76447e-41,150.134,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28691,Q#1946 - >seq8593,superfamily,295487,494,702,6.76447e-41,150.134,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28692,Q#1946 - >seq8593,non-specific,333820,519,703,2.5760099999999997e-20,89.6589,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28693,Q#1946 - >seq8593,superfamily,333820,519,703,2.5760099999999997e-20,89.6589,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28694,Q#1946 - >seq8593,non-specific,238828,515,701,1.88741e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
28695,Q#1946 - >seq8593,non-specific,275209,520,670,3.2456499999999997e-07,53.6156,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28696,Q#1946 - >seq8593,superfamily,275209,520,670,3.2456499999999997e-07,53.6156,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28697,Q#1946 - >seq8593,non-specific,238185,589,703,1.2561400000000001e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.marg.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,marg,CompleteHit
28698,Q#1947 - >seq8594,specific,197310,9,236,5.542909999999998e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28699,Q#1947 - >seq8594,superfamily,351117,9,236,5.542909999999998e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28700,Q#1947 - >seq8594,non-specific,197306,9,236,6.01576e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28701,Q#1947 - >seq8594,non-specific,197320,7,229,5.36589e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28702,Q#1947 - >seq8594,non-specific,223780,7,229,8.90948e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28703,Q#1947 - >seq8594,specific,335306,10,229,3.0214199999999996e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28704,Q#1947 - >seq8594,non-specific,197307,9,236,1.00098e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28705,Q#1947 - >seq8594,non-specific,197321,7,236,3.81022e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28706,Q#1947 - >seq8594,non-specific,272954,7,207,6.324609999999999e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28707,Q#1947 - >seq8594,non-specific,273186,7,237,1.4842900000000001e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28708,Q#1947 - >seq8594,non-specific,197319,7,236,7.51252e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28709,Q#1947 - >seq8594,non-specific,197336,7,229,7.96368e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28710,Q#1947 - >seq8594,non-specific,238827,509,547,4.4877700000000005e-09,57.6862,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28711,Q#1947 - >seq8594,superfamily,295487,509,547,4.4877700000000005e-09,57.6862,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28712,Q#1947 - >seq8594,non-specific,197311,7,236,7.88875e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28713,Q#1947 - >seq8594,non-specific,339261,108,232,2.99798e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28714,Q#1947 - >seq8594,non-specific,197314,7,236,0.000350183,43.4863,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28715,Q#1947 - >seq8594,non-specific,197318,9,236,0.000624078,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28716,Q#1947 - >seq8594,non-specific,223496,320,499,0.00253188,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28717,Q#1947 - >seq8594,superfamily,223496,320,499,0.00253188,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28718,Q#1947 - >seq8594,non-specific,274009,305,453,0.00415927,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28719,Q#1947 - >seq8594,superfamily,274009,305,453,0.00415927,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28720,Q#1947 - >seq8594,non-specific,333820,515,547,0.00675158,38.8126,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28721,Q#1947 - >seq8594,superfamily,333820,515,547,0.00675158,38.8126,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28722,Q#1947 - >seq8594,non-specific,334125,217,410,0.00822628,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28723,Q#1947 - >seq8594,superfamily,334125,217,410,0.00822628,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1M1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28724,Q#1949 - >seq8596,specific,238827,494,644,1.2352099999999999e-27,111.61399999999999,cd01650,RT_nLTR_like,NC,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28725,Q#1949 - >seq8596,superfamily,295487,494,644,1.2352099999999999e-27,111.61399999999999,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28726,Q#1949 - >seq8596,non-specific,333820,519,652,1.9184099999999997e-14,72.325,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28727,Q#1949 - >seq8596,superfamily,333820,519,652,1.9184099999999997e-14,72.325,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28728,Q#1949 - >seq8596,non-specific,238828,515,644,1.8498e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
28729,Q#1949 - >seq8596,non-specific,275209,520,604,5.81872e-06,49.3784,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28730,Q#1949 - >seq8596,superfamily,275209,520,604,5.81872e-06,49.3784,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28731,Q#1949 - >seq8596,non-specific,238185,589,669,0.000552522,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs5_gmonkey.pars.frame1,1909181135_L1M1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1M1,ORF2,hs5_gmonkey,pars,CompleteHit
28732,Q#1950 - >seq8597,specific,238827,509,771,1.3550999999999996e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28733,Q#1950 - >seq8597,superfamily,295487,509,771,1.3550999999999996e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28734,Q#1950 - >seq8597,specific,197310,9,236,8.714229999999999e-63,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28735,Q#1950 - >seq8597,superfamily,351117,9,236,8.714229999999999e-63,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28736,Q#1950 - >seq8597,non-specific,197306,9,236,6.61338e-35,133.761,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28737,Q#1950 - >seq8597,specific,333820,515,771,3.2362099999999996e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28738,Q#1950 - >seq8597,superfamily,333820,515,771,3.2362099999999996e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28739,Q#1950 - >seq8597,non-specific,197320,7,229,6.260440000000001e-24,102.208,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28740,Q#1950 - >seq8597,non-specific,223780,7,229,1.7314400000000002e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28741,Q#1950 - >seq8597,specific,335306,10,229,1.4480000000000002e-20,91.5377,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28742,Q#1950 - >seq8597,non-specific,197307,9,236,5.79186e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28743,Q#1950 - >seq8597,non-specific,197321,7,236,1.90089e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28744,Q#1950 - >seq8597,non-specific,272954,7,207,6.93365e-17,81.6604,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28745,Q#1950 - >seq8597,non-specific,273186,7,237,2.97858e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28746,Q#1950 - >seq8597,non-specific,197319,7,236,3.58698e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28747,Q#1950 - >seq8597,non-specific,197336,7,229,1.69947e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28748,Q#1950 - >seq8597,non-specific,238828,515,736,2.29678e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28749,Q#1950 - >seq8597,non-specific,275209,466,736,2.09195e-08,57.4676,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28750,Q#1950 - >seq8597,superfamily,275209,466,736,2.09195e-08,57.4676,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28751,Q#1950 - >seq8597,non-specific,197311,7,236,4.53803e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28752,Q#1950 - >seq8597,non-specific,339261,108,232,1.34376e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28753,Q#1950 - >seq8597,non-specific,238185,657,771,0.000195895,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28754,Q#1950 - >seq8597,non-specific,197318,9,236,0.000406257,43.4391,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28755,Q#1950 - >seq8597,non-specific,197314,7,236,0.0008114460000000001,42.3307,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs4_gibbon,marg,CompleteHit
28756,Q#1950 - >seq8597,non-specific,235175,306,463,0.00400887,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28757,Q#1950 - >seq8597,superfamily,235175,306,463,0.00400887,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28758,Q#1950 - >seq8597,non-specific,334125,217,410,0.00927788,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
28759,Q#1950 - >seq8597,superfamily,334125,217,410,0.00927788,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1M1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
28760,Q#1955 - >seq8602,specific,238827,508,768,9.744769999999998e-59,200.21,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28761,Q#1955 - >seq8602,superfamily,295487,508,768,9.744769999999998e-59,200.21,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28762,Q#1955 - >seq8602,specific,197310,9,238,2.1591400000000001e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28763,Q#1955 - >seq8602,superfamily,351117,9,238,2.1591400000000001e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28764,Q#1955 - >seq8602,specific,333820,514,768,2.55373e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28765,Q#1955 - >seq8602,superfamily,333820,514,768,2.55373e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28766,Q#1955 - >seq8602,non-specific,197306,9,238,2.35049e-26,108.338,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28767,Q#1955 - >seq8602,non-specific,197320,7,223,1.09329e-17,83.3333,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28768,Q#1955 - >seq8602,non-specific,223780,7,227,1.7673099999999998e-16,79.9499,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28769,Q#1955 - >seq8602,non-specific,197307,9,231,2.14009e-15,76.5577,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28770,Q#1955 - >seq8602,specific,335306,10,231,5.99903e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28771,Q#1955 - >seq8602,non-specific,197321,7,231,1.88724e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28772,Q#1955 - >seq8602,non-specific,272954,7,209,2.1936299999999998e-10,62.0153,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28773,Q#1955 - >seq8602,non-specific,273186,7,239,8.45637e-10,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28774,Q#1955 - >seq8602,non-specific,238828,580,734,4.39457e-09,57.596000000000004,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,N-TerminusTruncated
28775,Q#1955 - >seq8602,non-specific,197319,7,238,1.82199e-07,53.0493,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28776,Q#1955 - >seq8602,non-specific,197336,7,196,0.000116485,44.5255,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28777,Q#1955 - >seq8602,non-specific,275209,465,734,0.00035278699999999997,43.6004,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,C-TerminusTruncated
28778,Q#1955 - >seq8602,superfamily,275209,465,734,0.00035278699999999997,43.6004,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,pars,C-TerminusTruncated
28779,Q#1955 - >seq8602,non-specific,197311,39,206,0.00044239999999999997,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28780,Q#1955 - >seq8602,non-specific,339261,110,233,0.00943251,36.9315,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs1_chimp.pars.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs1_chimp,pars,CompleteHit
28781,Q#1956 - >seq8603,specific,238827,507,769,2.1666799999999995e-62,211.766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28782,Q#1956 - >seq8603,superfamily,295487,507,769,2.1666799999999995e-62,211.766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28783,Q#1956 - >seq8603,specific,197310,9,236,7.309429999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28784,Q#1956 - >seq8603,superfamily,351117,9,236,7.309429999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28785,Q#1956 - >seq8603,non-specific,197306,9,236,8.451569999999999e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28786,Q#1956 - >seq8603,specific,333820,513,769,1.0555799999999999e-32,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28787,Q#1956 - >seq8603,superfamily,333820,513,769,1.0555799999999999e-32,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28788,Q#1956 - >seq8603,non-specific,223780,7,229,2.01043e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28789,Q#1956 - >seq8603,non-specific,197320,7,229,4.4026800000000004e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28790,Q#1956 - >seq8603,specific,335306,10,229,1.6398400000000001e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28791,Q#1956 - >seq8603,non-specific,197307,9,236,2.57456e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28792,Q#1956 - >seq8603,non-specific,197321,7,236,1.08921e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28793,Q#1956 - >seq8603,non-specific,197319,7,236,6.208600000000001e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28794,Q#1956 - >seq8603,non-specific,273186,7,237,1.2853200000000001e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28795,Q#1956 - >seq8603,non-specific,272954,7,207,1.61476e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28796,Q#1956 - >seq8603,non-specific,197336,7,229,2.38654e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28797,Q#1956 - >seq8603,non-specific,238828,513,734,3.7566599999999995e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28798,Q#1956 - >seq8603,non-specific,275209,451,734,3.8090699999999995e-09,59.7788,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,C-TerminusTruncated
28799,Q#1956 - >seq8603,superfamily,275209,451,734,3.8090699999999995e-09,59.7788,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,C-TerminusTruncated
28800,Q#1956 - >seq8603,non-specific,197311,30,236,1.95178e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28801,Q#1956 - >seq8603,non-specific,339261,108,232,2.82311e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28802,Q#1956 - >seq8603,non-specific,236970,9,207,4.65631e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,marg,CompleteHit
28803,Q#1956 - >seq8603,non-specific,238185,653,769,0.00157096,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,CompleteHit
28804,Q#1956 - >seq8603,specific,311990,1238,1256,0.00311932,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs0_human,marg,CompleteHit
28805,Q#1956 - >seq8603,superfamily,311990,1238,1256,0.00311932,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs0_human,marg,CompleteHit
28806,Q#1956 - >seq8603,specific,225881,480,714,0.0063595,40.2073,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,N-TerminusTruncated
28807,Q#1956 - >seq8603,superfamily,225881,480,714,0.0063595,40.2073,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.marg.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs0_human,marg,N-TerminusTruncated
28808,Q#1959 - >seq8606,specific,197310,9,236,1.2664699999999998e-61,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28809,Q#1959 - >seq8606,superfamily,351117,9,236,1.2664699999999998e-61,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28810,Q#1959 - >seq8606,non-specific,197306,9,236,9.16565e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28811,Q#1959 - >seq8606,non-specific,223780,7,229,9.85511e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28812,Q#1959 - >seq8606,non-specific,197320,7,229,1.29713e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28813,Q#1959 - >seq8606,non-specific,197307,9,236,4.77616e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28814,Q#1959 - >seq8606,specific,335306,10,229,1.5417199999999999e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28815,Q#1959 - >seq8606,non-specific,197321,7,236,6.20952e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28816,Q#1959 - >seq8606,non-specific,197319,7,236,9.051730000000001e-16,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28817,Q#1959 - >seq8606,non-specific,272954,7,207,2.95884e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28818,Q#1959 - >seq8606,non-specific,273186,7,237,3.62733e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28819,Q#1959 - >seq8606,non-specific,197336,7,229,1.44551e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28820,Q#1959 - >seq8606,non-specific,197311,30,236,1.2776e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28821,Q#1959 - >seq8606,non-specific,236970,9,207,1.28923e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs0_human,pars,CompleteHit
28822,Q#1959 - >seq8606,non-specific,339261,108,232,4.67344e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs0_human.pars.frame3,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28823,Q#1960 - >seq8607,specific,238827,496,756,1.9244099999999998e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28824,Q#1960 - >seq8607,superfamily,295487,496,756,1.9244099999999998e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28825,Q#1960 - >seq8607,specific,333820,502,757,8.177519999999998e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28826,Q#1960 - >seq8607,superfamily,333820,502,757,8.177519999999998e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28827,Q#1960 - >seq8607,non-specific,238828,502,723,2.0366099999999998e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28828,Q#1960 - >seq8607,non-specific,275209,441,723,3.8624099999999994e-08,56.6972,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,C-TerminusTruncated
28829,Q#1960 - >seq8607,superfamily,275209,441,723,3.8624099999999994e-08,56.6972,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,C-TerminusTruncated
28830,Q#1960 - >seq8607,non-specific,238185,642,757,0.00022245599999999997,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,CompleteHit
28831,Q#1960 - >seq8607,specific,225881,468,703,0.00251477,41.3629,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,N-TerminusTruncated
28832,Q#1960 - >seq8607,superfamily,225881,468,703,0.00251477,41.3629,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs0_human.pars.frame2,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA1,ORF2,hs0_human,pars,N-TerminusTruncated
28833,Q#1962 - >seq8609,specific,238827,507,769,1.2167899999999998e-62,212.53599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28834,Q#1962 - >seq8609,superfamily,295487,507,769,1.2167899999999998e-62,212.53599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28835,Q#1962 - >seq8609,specific,197310,9,236,1.6085099999999997e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28836,Q#1962 - >seq8609,superfamily,351117,9,236,1.6085099999999997e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28837,Q#1962 - >seq8609,non-specific,197306,9,236,8.260599999999999e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28838,Q#1962 - >seq8609,specific,333820,513,769,8.26285e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28839,Q#1962 - >seq8609,superfamily,333820,513,769,8.26285e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28840,Q#1962 - >seq8609,non-specific,197320,7,229,6.081480000000001e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28841,Q#1962 - >seq8609,non-specific,223780,7,229,8.44891e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28842,Q#1962 - >seq8609,non-specific,197307,9,236,3.56829e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28843,Q#1962 - >seq8609,specific,335306,10,229,4.535360000000001e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28844,Q#1962 - >seq8609,non-specific,197319,7,236,1.9725299999999998e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28845,Q#1962 - >seq8609,non-specific,273186,7,237,2.78783e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28846,Q#1962 - >seq8609,non-specific,197321,7,236,1.0852399999999999e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28847,Q#1962 - >seq8609,non-specific,272954,7,207,3.4167900000000004e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28848,Q#1962 - >seq8609,non-specific,197336,7,229,2.76078e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28849,Q#1962 - >seq8609,non-specific,238828,513,734,2.9859200000000003e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28850,Q#1962 - >seq8609,non-specific,275209,465,734,1.26208e-07,55.1564,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28851,Q#1962 - >seq8609,superfamily,275209,465,734,1.26208e-07,55.1564,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28852,Q#1962 - >seq8609,non-specific,197311,30,236,2.98596e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28853,Q#1962 - >seq8609,non-specific,339261,108,232,1.38843e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28854,Q#1962 - >seq8609,non-specific,236970,9,207,4.05516e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28855,Q#1962 - >seq8609,non-specific,197318,9,236,0.00010768899999999999,44.9799,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28856,Q#1962 - >seq8609,non-specific,235175,306,462,0.000436364,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28857,Q#1962 - >seq8609,superfamily,235175,306,462,0.000436364,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28858,Q#1962 - >seq8609,non-specific,238185,653,769,0.00116892,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28859,Q#1962 - >seq8609,non-specific,274009,305,456,0.00193953,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28860,Q#1962 - >seq8609,superfamily,274009,305,456,0.00193953,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
28861,Q#1962 - >seq8609,specific,311990,1234,1252,0.0029901,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28862,Q#1962 - >seq8609,superfamily,311990,1234,1252,0.0029901,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs5_gmonkey,marg,CompleteHit
28863,Q#1962 - >seq8609,non-specific,224117,305,498,0.00328685,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28864,Q#1962 - >seq8609,superfamily,224117,305,498,0.00328685,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28865,Q#1962 - >seq8609,non-specific,274475,255,426,0.00340354,41.5928,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28866,Q#1962 - >seq8609,superfamily,274475,255,426,0.00340354,41.5928,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
28867,Q#1964 - >seq8611,non-specific,197310,81,116,0.000343748,43.4941,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28868,Q#1964 - >seq8611,superfamily,351117,81,116,0.000343748,43.4941,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,pars,BothTerminiTruncated
28869,Q#1968 - >seq8615,specific,197310,9,236,9.203789999999998e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28870,Q#1968 - >seq8615,superfamily,351117,9,236,9.203789999999998e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28871,Q#1968 - >seq8615,specific,238827,508,770,2.9297299999999995e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28872,Q#1968 - >seq8615,superfamily,295487,508,770,2.9297299999999995e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28873,Q#1968 - >seq8615,non-specific,197306,9,236,3.92514e-34,131.45,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28874,Q#1968 - >seq8615,specific,333820,514,770,5.51299e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28875,Q#1968 - >seq8615,superfamily,333820,514,770,5.51299e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28876,Q#1968 - >seq8615,non-specific,223780,7,229,8.020169999999999e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28877,Q#1968 - >seq8615,non-specific,197320,7,229,5.6959499999999996e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28878,Q#1968 - >seq8615,specific,335306,10,229,4.39861e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28879,Q#1968 - >seq8615,non-specific,197307,9,236,1.15156e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28880,Q#1968 - >seq8615,non-specific,197319,7,236,4.4163699999999996e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28881,Q#1968 - >seq8615,non-specific,197321,7,236,1.2918100000000002e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28882,Q#1968 - >seq8615,non-specific,273186,7,237,1.82316e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28883,Q#1968 - >seq8615,non-specific,272954,7,207,2.81834e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28884,Q#1968 - >seq8615,non-specific,238828,514,735,2.1988599999999998e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28885,Q#1968 - >seq8615,non-specific,197336,7,229,6.917860000000001e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28886,Q#1968 - >seq8615,non-specific,275209,465,735,1.92276e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28887,Q#1968 - >seq8615,superfamily,275209,465,735,1.92276e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
28888,Q#1968 - >seq8615,non-specific,197311,30,236,2.2064500000000003e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28889,Q#1968 - >seq8615,non-specific,339261,108,232,2.24306e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28890,Q#1968 - >seq8615,non-specific,236970,9,207,5.4779799999999993e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28891,Q#1968 - >seq8615,non-specific,238185,656,770,0.000869042,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28892,Q#1968 - >seq8615,non-specific,223496,320,498,0.0023109000000000003,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28893,Q#1968 - >seq8615,superfamily,223496,320,498,0.0023109000000000003,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.marg.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28894,Q#1969 - >seq8616,specific,311990,1160,1178,0.000220764,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs4_gibbon.marg.frame2,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28895,Q#1969 - >seq8616,superfamily,311990,1160,1178,0.000220764,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs4_gibbon.marg.frame2,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA1,ORF2,hs4_gibbon,marg,CompleteHit
28896,Q#1971 - >seq8618,specific,197310,9,236,1.8788999999999996e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28897,Q#1971 - >seq8618,superfamily,351117,9,236,1.8788999999999996e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28898,Q#1971 - >seq8618,specific,238827,507,767,4.34613e-62,210.99599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28899,Q#1971 - >seq8618,superfamily,295487,507,767,4.34613e-62,210.99599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28900,Q#1971 - >seq8618,non-specific,197306,9,236,1.29619e-34,132.605,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28901,Q#1971 - >seq8618,specific,333820,513,768,2.23984e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28902,Q#1971 - >seq8618,superfamily,333820,513,768,2.23984e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28903,Q#1971 - >seq8618,non-specific,223780,7,229,5.18781e-23,99.5951,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28904,Q#1971 - >seq8618,non-specific,197320,7,229,2.07445e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28905,Q#1971 - >seq8618,non-specific,197307,9,236,1.18819e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28906,Q#1971 - >seq8618,specific,335306,10,229,4.3431599999999994e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28907,Q#1971 - >seq8618,non-specific,197319,7,236,3.58029e-17,82.3245,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28908,Q#1971 - >seq8618,non-specific,197321,7,236,1.15412e-16,81.0592,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28909,Q#1971 - >seq8618,non-specific,273186,7,237,3.56605e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28910,Q#1971 - >seq8618,non-specific,272954,7,207,8.269160000000002e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28911,Q#1971 - >seq8618,non-specific,238828,513,734,3.16984e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28912,Q#1971 - >seq8618,non-specific,197336,7,229,3.1794e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28913,Q#1971 - >seq8618,non-specific,275209,465,734,8.580629999999999e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28914,Q#1971 - >seq8618,superfamily,275209,465,734,8.580629999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
28915,Q#1971 - >seq8618,non-specific,197311,30,236,1.0828e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28916,Q#1971 - >seq8618,non-specific,339261,108,232,1.75748e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28917,Q#1971 - >seq8618,non-specific,236970,9,207,3.67698e-05,46.81100000000001,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28918,Q#1971 - >seq8618,non-specific,238185,655,768,0.0006732960000000001,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28919,Q#1971 - >seq8618,specific,311990,1215,1233,0.00171857,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28920,Q#1971 - >seq8618,superfamily,311990,1215,1233,0.00171857,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs4_gibbon,pars,CompleteHit
28921,Q#1971 - >seq8618,specific,225881,479,714,0.00312757,40.9777,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
28922,Q#1971 - >seq8618,superfamily,225881,479,714,0.00312757,40.9777,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
28923,Q#1974 - >seq8621,specific,197310,9,236,1.6064799999999996e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28924,Q#1974 - >seq8621,superfamily,351117,9,236,1.6064799999999996e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28925,Q#1974 - >seq8621,specific,238827,507,768,4.132119999999999e-61,208.299,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28926,Q#1974 - >seq8621,superfamily,295487,507,768,4.132119999999999e-61,208.299,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28927,Q#1974 - >seq8621,non-specific,197306,9,236,8.332689999999999e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28928,Q#1974 - >seq8621,specific,333820,513,768,1.18012e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28929,Q#1974 - >seq8621,superfamily,333820,513,768,1.18012e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28930,Q#1974 - >seq8621,non-specific,197320,7,229,6.01841e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28931,Q#1974 - >seq8621,non-specific,223780,7,229,8.282420000000001e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28932,Q#1974 - >seq8621,non-specific,197307,9,236,3.5313500000000004e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28933,Q#1974 - >seq8621,specific,335306,10,229,4.5313e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28934,Q#1974 - >seq8621,non-specific,197319,7,236,1.95223e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28935,Q#1974 - >seq8621,non-specific,273186,7,237,2.78528e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28936,Q#1974 - >seq8621,non-specific,197321,7,236,1.09451e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28937,Q#1974 - >seq8621,non-specific,272954,7,207,3.4136699999999997e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28938,Q#1974 - >seq8621,non-specific,197336,7,229,2.75827e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28939,Q#1974 - >seq8621,non-specific,238828,513,733,2.62172e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28940,Q#1974 - >seq8621,non-specific,275209,465,733,1.46982e-06,51.6896,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28941,Q#1974 - >seq8621,superfamily,275209,465,733,1.46982e-06,51.6896,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28942,Q#1974 - >seq8621,non-specific,197311,30,236,2.98335e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28943,Q#1974 - >seq8621,non-specific,339261,108,232,1.29641e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28944,Q#1974 - >seq8621,non-specific,236970,9,207,4.05155e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28945,Q#1974 - >seq8621,non-specific,197318,9,236,0.000109558,44.9799,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28946,Q#1974 - >seq8621,non-specific,238185,653,768,0.000270753,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28947,Q#1974 - >seq8621,non-specific,235175,306,462,0.000432285,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28948,Q#1974 - >seq8621,superfamily,235175,306,462,0.000432285,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28949,Q#1974 - >seq8621,non-specific,274009,305,456,0.00190528,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28950,Q#1974 - >seq8621,superfamily,274009,305,456,0.00190528,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
28951,Q#1974 - >seq8621,specific,311990,1233,1251,0.00295863,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28952,Q#1974 - >seq8621,superfamily,311990,1233,1251,0.00295863,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs5_gmonkey,pars,CompleteHit
28953,Q#1974 - >seq8621,non-specific,224117,305,498,0.00331177,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28954,Q#1974 - >seq8621,superfamily,224117,305,498,0.00331177,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28955,Q#1974 - >seq8621,non-specific,274475,255,426,0.00340049,41.5928,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28956,Q#1974 - >seq8621,superfamily,274475,255,426,0.00340049,41.5928,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1MA1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
28957,Q#1975 - >seq8622,specific,238827,508,770,4.784879999999999e-63,213.692,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28958,Q#1975 - >seq8622,superfamily,295487,508,770,4.784879999999999e-63,213.692,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28959,Q#1975 - >seq8622,specific,197310,9,236,1.1105899999999997e-61,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28960,Q#1975 - >seq8622,superfamily,351117,9,236,1.1105899999999997e-61,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28961,Q#1975 - >seq8622,non-specific,197306,9,236,8.81885e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28962,Q#1975 - >seq8622,specific,333820,514,770,3.4586e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28963,Q#1975 - >seq8622,superfamily,333820,514,770,3.4586e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28964,Q#1975 - >seq8622,non-specific,223780,7,229,3.87288e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28965,Q#1975 - >seq8622,non-specific,197320,7,229,2.91071e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28966,Q#1975 - >seq8622,specific,335306,10,229,4.41049e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28967,Q#1975 - >seq8622,non-specific,197307,9,236,1.2339899999999999e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28968,Q#1975 - >seq8622,non-specific,197319,7,236,4.775230000000001e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28969,Q#1975 - >seq8622,non-specific,197321,7,236,1.24751e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28970,Q#1975 - >seq8622,non-specific,273186,7,237,1.6177900000000002e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28971,Q#1975 - >seq8622,non-specific,272954,7,207,2.8261e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28972,Q#1975 - >seq8622,non-specific,238828,514,735,2.68718e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28973,Q#1975 - >seq8622,non-specific,197336,7,229,3.2294e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28974,Q#1975 - >seq8622,non-specific,275209,465,735,3.00678e-09,60.163999999999994,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,C-TerminusTruncated
28975,Q#1975 - >seq8622,superfamily,275209,465,735,3.00678e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,C-TerminusTruncated
28976,Q#1975 - >seq8622,non-specific,197311,30,236,1.7040000000000001e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28977,Q#1975 - >seq8622,non-specific,339261,108,232,2.4532600000000003e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28978,Q#1975 - >seq8622,non-specific,236970,9,207,5.5421800000000005e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28979,Q#1975 - >seq8622,non-specific,223496,320,498,0.000157763,45.9067,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28980,Q#1975 - >seq8622,superfamily,223496,320,498,0.000157763,45.9067,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28981,Q#1975 - >seq8622,non-specific,235175,306,462,0.000305054,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28982,Q#1975 - >seq8622,superfamily,235175,306,462,0.000305054,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28983,Q#1975 - >seq8622,non-specific,238185,654,770,0.000584234,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,CompleteHit
28984,Q#1975 - >seq8622,non-specific,274009,305,452,0.00166269,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,marg,C-TerminusTruncated
28985,Q#1975 - >seq8622,superfamily,274009,305,452,0.00166269,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,marg,C-TerminusTruncated
28986,Q#1975 - >seq8622,non-specific,274475,255,426,0.00320085,41.5928,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28987,Q#1975 - >seq8622,superfamily,274475,255,426,0.00320085,41.5928,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs3_orang,marg,BothTerminiTruncated
28988,Q#1975 - >seq8622,specific,225881,481,715,0.00828894,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,N-TerminusTruncated
28989,Q#1975 - >seq8622,superfamily,225881,481,715,0.00828894,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.marg.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs3_orang,marg,N-TerminusTruncated
28990,Q#1976 - >seq8623,specific,311990,1174,1192,0.000409124,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs1_chimp.pars.frame2,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
28991,Q#1976 - >seq8623,superfamily,311990,1174,1192,0.000409124,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs1_chimp.pars.frame2,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
28992,Q#1977 - >seq8624,non-specific,197310,81,116,0.00027494,43.4941,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28993,Q#1977 - >seq8624,superfamily,351117,81,116,0.00027494,43.4941,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,marg,BothTerminiTruncated
28994,Q#1978 - >seq8625,non-specific,197310,83,119,9.19235e-05,45.0349,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28995,Q#1978 - >seq8625,superfamily,351117,83,119,9.19235e-05,45.0349,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.marg.frame1,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
28996,Q#1979 - >seq8626,specific,238827,508,770,2.9383499999999996e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
28997,Q#1979 - >seq8626,superfamily,295487,508,770,2.9383499999999996e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
28998,Q#1979 - >seq8626,specific,197310,9,237,4.91732e-46,165.602,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
28999,Q#1979 - >seq8626,superfamily,351117,9,237,4.91732e-46,165.602,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29000,Q#1979 - >seq8626,specific,333820,514,770,1.0199999999999998e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29001,Q#1979 - >seq8626,superfamily,333820,514,770,1.0199999999999998e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29002,Q#1979 - >seq8626,non-specific,197306,9,237,3.50297e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29003,Q#1979 - >seq8626,specific,335306,10,230,2.3276999999999997e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29004,Q#1979 - >seq8626,non-specific,197320,7,230,1.02517e-14,75.2441,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29005,Q#1979 - >seq8626,non-specific,197307,9,237,1.39015e-12,68.8537,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29006,Q#1979 - >seq8626,non-specific,238828,514,735,1.78308e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29007,Q#1979 - >seq8626,non-specific,223780,7,230,6.92998e-12,66.8531,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29008,Q#1979 - >seq8626,non-specific,197321,7,237,9.08369e-10,60.6436,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29009,Q#1979 - >seq8626,non-specific,275209,465,735,1.49079e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29010,Q#1979 - >seq8626,superfamily,275209,465,735,1.49079e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29011,Q#1979 - >seq8626,non-specific,272954,7,208,4.237430000000001e-08,55.4669,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29012,Q#1979 - >seq8626,non-specific,273186,7,238,3.9527700000000005e-07,52.6664,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29013,Q#1979 - >seq8626,non-specific,197336,7,230,9.39099e-06,48.3775,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29014,Q#1979 - >seq8626,non-specific,197319,7,237,1.5092899999999999e-05,47.6565,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29015,Q#1979 - >seq8626,non-specific,238185,656,770,0.00024165900000000003,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29016,Q#1979 - >seq8626,non-specific,235175,292,448,0.00210018,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29017,Q#1979 - >seq8626,superfamily,235175,292,448,0.00210018,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29018,Q#1979 - >seq8626,specific,311990,1239,1257,0.0032415,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29019,Q#1979 - >seq8626,superfamily,311990,1239,1257,0.0032415,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA2,ORF2,hs4_gibbon,pars,CompleteHit
29020,Q#1979 - >seq8626,non-specific,235175,307,462,0.00580841,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs4_gibbon.pars.frame3,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29021,Q#1981 - >seq8628,non-specific,197310,83,119,9.17442e-05,45.0349,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29022,Q#1981 - >seq8628,superfamily,351117,83,119,9.17442e-05,45.0349,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs4_gibbon.pars.frame1,1909181135_L1MA2.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29023,Q#1982 - >seq8629,specific,238827,508,766,3.76493e-58,199.825,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29024,Q#1982 - >seq8629,superfamily,295487,508,766,3.76493e-58,199.825,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29025,Q#1982 - >seq8629,specific,197310,9,237,2.9448900000000005e-46,165.988,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29026,Q#1982 - >seq8629,superfamily,351117,9,237,2.9448900000000005e-46,165.988,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29027,Q#1982 - >seq8629,non-specific,333820,514,766,5.943550000000001e-26,105.837,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29028,Q#1982 - >seq8629,superfamily,333820,514,766,5.943550000000001e-26,105.837,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29029,Q#1982 - >seq8629,non-specific,197306,9,237,6.43866e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29030,Q#1982 - >seq8629,specific,335306,10,230,2.45432e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29031,Q#1982 - >seq8629,non-specific,197320,7,230,1.16099e-17,84.1037,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29032,Q#1982 - >seq8629,non-specific,223780,7,230,3.6953800000000005e-15,76.8683,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29033,Q#1982 - >seq8629,non-specific,197307,9,237,5.65364e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29034,Q#1982 - >seq8629,non-specific,197321,7,237,6.05128e-11,64.1104,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29035,Q#1982 - >seq8629,non-specific,272954,7,208,3.2221100000000003e-10,62.0153,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29036,Q#1982 - >seq8629,non-specific,273186,7,238,3.3371499999999997e-10,61.9112,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29037,Q#1982 - >seq8629,non-specific,197319,7,237,4.37984e-10,61.5237,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29038,Q#1982 - >seq8629,non-specific,197318,9,237,1.62845e-06,50.7579,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29039,Q#1982 - >seq8629,non-specific,197336,7,230,1.9451300000000002e-06,50.3035,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29040,Q#1982 - >seq8629,non-specific,238828,514,731,2.73337e-06,49.5068,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29041,Q#1982 - >seq8629,non-specific,334125,218,410,0.0013991,42.5216,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs3_orang,marg,N-TerminusTruncated
29042,Q#1982 - >seq8629,superfamily,334125,218,410,0.0013991,42.5216,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs3_orang,marg,N-TerminusTruncated
29043,Q#1982 - >seq8629,non-specific,197317,8,230,0.00141114,41.8188,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29044,Q#1982 - >seq8629,specific,311990,1235,1253,0.0030816999999999997,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29045,Q#1982 - >seq8629,superfamily,311990,1235,1253,0.0030816999999999997,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs3_orang,marg,CompleteHit
29046,Q#1982 - >seq8629,non-specific,274009,306,457,0.0040853,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs3_orang,marg,C-TerminusTruncated
29047,Q#1982 - >seq8629,superfamily,274009,306,457,0.0040853,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs3_orang.marg.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs3_orang,marg,C-TerminusTruncated
29048,Q#1984 - >seq8631,non-specific,197310,69,122,7.65581e-05,45.4201,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs3_orang.marg.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,marg,BothTerminiTruncated
29049,Q#1984 - >seq8631,superfamily,351117,69,122,7.65581e-05,45.4201,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.marg.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,marg,BothTerminiTruncated
29050,Q#1985 - >seq8632,non-specific,197310,9,85,2.83697e-20,90.8737,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29051,Q#1985 - >seq8632,superfamily,351117,9,85,2.83697e-20,90.8737,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29052,Q#1985 - >seq8632,non-specific,197306,9,108,2.9825000000000003e-10,61.7285,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29053,Q#1985 - >seq8632,non-specific,223780,7,82,1.2247399999999999e-08,57.2231,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29054,Q#1985 - >seq8632,non-specific,197321,7,80,1.90072e-06,50.2432,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29055,Q#1985 - >seq8632,non-specific,197320,7,76,1.91483e-06,50.5914,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29056,Q#1985 - >seq8632,non-specific,197307,9,80,3.36793e-06,49.5937,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29057,Q#1985 - >seq8632,specific,335306,10,87,4.448819999999999e-06,48.7806,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29058,Q#1985 - >seq8632,non-specific,272954,7,76,5.582909999999999e-06,48.9185,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29059,Q#1985 - >seq8632,non-specific,197336,7,76,1.1641e-05,47.9923,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29060,Q#1985 - >seq8632,non-specific,273186,7,76,7.63112e-05,45.3476,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29061,Q#1985 - >seq8632,non-specific,197319,7,43,0.00429059,39.9525,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs3_orang.pars.frame3,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29062,Q#1986 - >seq8633,specific,238827,509,771,1.2645399999999997e-65,221.011,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29063,Q#1986 - >seq8633,superfamily,295487,509,771,1.2645399999999997e-65,221.011,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29064,Q#1986 - >seq8633,specific,197310,9,236,5.573429999999999e-47,168.299,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29065,Q#1986 - >seq8633,superfamily,351117,9,236,5.573429999999999e-47,168.299,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29066,Q#1986 - >seq8633,specific,333820,515,771,1.89514e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29067,Q#1986 - >seq8633,superfamily,333820,515,771,1.89514e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29068,Q#1986 - >seq8633,non-specific,197306,9,236,3.21785e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29069,Q#1986 - >seq8633,non-specific,197307,9,236,2.3633999999999997e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29070,Q#1986 - >seq8633,non-specific,197320,7,229,5.163580000000001e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29071,Q#1986 - >seq8633,specific,335306,10,229,1.51877e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29072,Q#1986 - >seq8633,non-specific,223780,7,229,7.15743e-17,81.8759,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29073,Q#1986 - >seq8633,non-specific,272954,7,207,1.0520999999999999e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29074,Q#1986 - >seq8633,non-specific,238828,515,736,3.5512e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29075,Q#1986 - >seq8633,non-specific,273186,7,237,1.00915e-11,66.5336,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29076,Q#1986 - >seq8633,non-specific,197321,7,236,5.17845e-11,64.1104,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29077,Q#1986 - >seq8633,non-specific,197319,7,236,1.0522499999999999e-10,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29078,Q#1986 - >seq8633,non-specific,275209,466,736,2.0647599999999996e-08,57.4676,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29079,Q#1986 - >seq8633,superfamily,275209,466,736,2.0647599999999996e-08,57.4676,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29080,Q#1986 - >seq8633,non-specific,197336,7,229,5.69024e-07,52.2295,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29081,Q#1986 - >seq8633,non-specific,197318,9,236,1.3168e-05,47.6763,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29082,Q#1986 - >seq8633,non-specific,238185,655,771,6.08218e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29083,Q#1986 - >seq8633,non-specific,334125,217,410,0.000649764,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
29084,Q#1986 - >seq8633,superfamily,334125,217,410,0.000649764,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
29085,Q#1986 - >seq8633,non-specific,197314,7,236,0.00259053,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs1_chimp,pars,CompleteHit
29086,Q#1986 - >seq8633,specific,225881,420,679,0.00428846,40.5925,COG3344,YkfC,C,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29087,Q#1986 - >seq8633,superfamily,225881,420,679,0.00428846,40.5925,cl34590,YkfC superfamily,C, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29088,Q#1986 - >seq8633,non-specific,274009,305,500,0.00467652,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29089,Q#1986 - >seq8633,superfamily,274009,305,500,0.00467652,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
29090,Q#1988 - >seq8635,specific,238827,511,773,2.1722499999999998e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29091,Q#1988 - >seq8635,superfamily,295487,511,773,2.1722499999999998e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29092,Q#1988 - >seq8635,specific,197310,9,237,8.766760000000001e-48,170.61,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29093,Q#1988 - >seq8635,superfamily,351117,9,237,8.766760000000001e-48,170.61,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29094,Q#1988 - >seq8635,specific,333820,517,773,1.9242599999999997e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29095,Q#1988 - >seq8635,superfamily,333820,517,773,1.9242599999999997e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29096,Q#1988 - >seq8635,non-specific,197306,9,237,1.4548400000000001e-22,97.9372,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29097,Q#1988 - >seq8635,specific,335306,10,230,1.7999900000000003e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29098,Q#1988 - >seq8635,non-specific,197320,7,230,5.52898e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29099,Q#1988 - >seq8635,non-specific,197307,9,237,1.8023800000000003e-15,77.3281,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29100,Q#1988 - >seq8635,non-specific,223780,7,230,4.3538800000000005e-15,76.4831,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29101,Q#1988 - >seq8635,non-specific,197321,7,237,2.04919e-12,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29102,Q#1988 - >seq8635,non-specific,238828,517,738,3.20654e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29103,Q#1988 - >seq8635,non-specific,272954,7,208,8.13252e-11,63.5561,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29104,Q#1988 - >seq8635,non-specific,273186,7,238,3.1128500000000003e-10,61.9112,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29105,Q#1988 - >seq8635,non-specific,197319,7,237,3.62171e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29106,Q#1988 - >seq8635,non-specific,275209,588,811,3.9563300000000005e-08,56.6972,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29107,Q#1988 - >seq8635,superfamily,275209,588,811,3.9563300000000005e-08,56.6972,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29108,Q#1988 - >seq8635,non-specific,197336,7,230,3.20728e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29109,Q#1988 - >seq8635,non-specific,197318,9,237,2.9616900000000005e-06,49.9875,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29110,Q#1988 - >seq8635,non-specific,238185,657,773,0.000224081,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29111,Q#1988 - >seq8635,non-specific,334125,218,411,0.0002976,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29112,Q#1988 - >seq8635,superfamily,334125,218,411,0.0002976,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29113,Q#1988 - >seq8635,non-specific,197317,8,230,0.000547494,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29114,Q#1988 - >seq8635,non-specific,235175,309,464,0.000693539,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29115,Q#1988 - >seq8635,superfamily,235175,309,464,0.000693539,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29116,Q#1988 - >seq8635,non-specific,223496,321,501,0.00148942,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29117,Q#1988 - >seq8635,superfamily,223496,321,501,0.00148942,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29118,Q#1988 - >seq8635,non-specific,224117,307,502,0.00158366,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29119,Q#1988 - >seq8635,superfamily,224117,307,502,0.00158366,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29120,Q#1988 - >seq8635,non-specific,274009,306,502,0.00160542,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29121,Q#1988 - >seq8635,superfamily,274009,306,502,0.00160542,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29122,Q#1988 - >seq8635,non-specific,235175,292,489,0.0025161999999999997,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29123,Q#1988 - >seq8635,specific,311990,1242,1260,0.00324906,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29124,Q#1988 - >seq8635,superfamily,311990,1242,1260,0.00324906,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs2_gorilla,marg,CompleteHit
29125,Q#1988 - >seq8635,non-specific,274475,256,428,0.0067045,40.4372,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29126,Q#1988 - >seq8635,superfamily,274475,256,428,0.0067045,40.4372,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA2.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29127,Q#1990 - >seq8637,non-specific,197310,81,122,9.63872e-05,45.0349,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29128,Q#1990 - >seq8637,superfamily,351117,81,122,9.63872e-05,45.0349,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29129,Q#1990 - >seq8637,non-specific,197306,68,181,0.00127293,41.6981,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.marg.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29130,Q#1991 - >seq8638,specific,197310,9,237,8.9594e-47,167.528,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29131,Q#1991 - >seq8638,superfamily,351117,9,237,8.9594e-47,167.528,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29132,Q#1991 - >seq8638,non-specific,197306,9,237,8.94845e-23,98.3224,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29133,Q#1991 - >seq8638,specific,335306,10,230,1.70217e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29134,Q#1991 - >seq8638,non-specific,197320,7,230,2.2722599999999997e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29135,Q#1991 - >seq8638,non-specific,197307,9,237,6.22429e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29136,Q#1991 - >seq8638,non-specific,223780,7,230,2.01768e-16,80.3351,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29137,Q#1991 - >seq8638,non-specific,197321,7,237,1.4525e-13,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29138,Q#1991 - >seq8638,non-specific,272954,7,208,9.14447e-12,66.6377,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29139,Q#1991 - >seq8638,non-specific,197319,7,237,1.26457e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29140,Q#1991 - >seq8638,non-specific,273186,7,238,6.79711e-11,63.8372,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29141,Q#1991 - >seq8638,non-specific,197336,7,230,2.00941e-07,53.3851,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29142,Q#1991 - >seq8638,non-specific,197318,9,237,2.16981e-06,50.3727,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29143,Q#1991 - >seq8638,non-specific,197317,8,230,0.0005136240000000001,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29144,Q#1993 - >seq8640,specific,238827,474,719,6.268649999999999e-60,204.832,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29145,Q#1993 - >seq8640,superfamily,295487,474,719,6.268649999999999e-60,204.832,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29146,Q#1993 - >seq8640,specific,333820,471,719,1.7229199999999999e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29147,Q#1993 - >seq8640,superfamily,333820,471,719,1.7229199999999999e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29148,Q#1993 - >seq8640,non-specific,238828,471,684,2.63249e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29149,Q#1993 - >seq8640,non-specific,275209,534,757,3.9278400000000004e-08,56.6972,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
29150,Q#1993 - >seq8640,superfamily,275209,534,757,3.9278400000000004e-08,56.6972,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
29151,Q#1993 - >seq8640,non-specific,238185,603,719,8.16222e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29152,Q#1993 - >seq8640,non-specific,197310,81,122,0.000143051,44.6497,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29153,Q#1993 - >seq8640,superfamily,351117,81,122,0.000143051,44.6497,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29154,Q#1993 - >seq8640,non-specific,197306,68,181,0.00181598,41.3129,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
29155,Q#1993 - >seq8640,specific,311990,1188,1206,0.00188866,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29156,Q#1993 - >seq8640,superfamily,311990,1188,1206,0.00188866,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs2_gorilla.pars.frame1,1909181135_L1MA2.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs2_gorilla,pars,CompleteHit
29157,Q#1994 - >seq8641,specific,238827,509,771,2.0754e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29158,Q#1994 - >seq8641,superfamily,295487,509,771,2.0754e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29159,Q#1994 - >seq8641,specific,197310,9,236,5.59177e-47,168.299,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29160,Q#1994 - >seq8641,superfamily,351117,9,236,5.59177e-47,168.299,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29161,Q#1994 - >seq8641,specific,333820,515,771,1.8725599999999997e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29162,Q#1994 - >seq8641,superfamily,333820,515,771,1.8725599999999997e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29163,Q#1994 - >seq8641,non-specific,197306,9,236,5.0564599999999997e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29164,Q#1994 - >seq8641,non-specific,197307,9,236,2.0369e-18,86.1877,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29165,Q#1994 - >seq8641,non-specific,197320,7,229,1.2601500000000002e-17,83.7185,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29166,Q#1994 - >seq8641,specific,335306,10,229,1.5675300000000002e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29167,Q#1994 - >seq8641,non-specific,223780,7,229,1.4829700000000001e-15,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29168,Q#1994 - >seq8641,non-specific,272954,7,207,7.744449999999999e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29169,Q#1994 - >seq8641,non-specific,238828,515,736,1.90195e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29170,Q#1994 - >seq8641,non-specific,273186,7,237,4.83354e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29171,Q#1994 - >seq8641,non-specific,197321,7,236,2.40489e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29172,Q#1994 - >seq8641,non-specific,197319,7,236,1.05221e-09,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29173,Q#1994 - >seq8641,non-specific,275209,466,736,1.11387e-07,55.1564,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
29174,Q#1994 - >seq8641,superfamily,275209,466,736,1.11387e-07,55.1564,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
29175,Q#1994 - >seq8641,non-specific,197336,7,229,9.354219999999999e-07,51.4591,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29176,Q#1994 - >seq8641,non-specific,197318,9,236,2.47508e-05,46.9059,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29177,Q#1994 - >seq8641,non-specific,238185,655,771,0.000233368,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29178,Q#1994 - >seq8641,non-specific,334125,217,410,0.00222293,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
29179,Q#1994 - >seq8641,superfamily,334125,217,410,0.00222293,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
29180,Q#1994 - >seq8641,non-specific,197314,7,236,0.00267176,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29181,Q#1994 - >seq8641,specific,311990,1242,1260,0.00297939,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29182,Q#1994 - >seq8641,superfamily,311990,1242,1260,0.00297939,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA2,ORF2,hs1_chimp,marg,CompleteHit
29183,Q#1994 - >seq8641,non-specific,274009,305,500,0.00660028,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
29184,Q#1994 - >seq8641,superfamily,274009,305,500,0.00660028,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA2.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
29185,Q#1996 - >seq8643,specific,238827,495,753,3.20473e-58,199.825,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29186,Q#1996 - >seq8643,superfamily,295487,495,753,3.20473e-58,199.825,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29187,Q#1996 - >seq8643,specific,197310,69,224,4.2171600000000005e-34,131.32,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29188,Q#1996 - >seq8643,superfamily,351117,69,224,4.2171600000000005e-34,131.32,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29189,Q#1996 - >seq8643,non-specific,333820,501,753,6.21512e-26,105.837,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29190,Q#1996 - >seq8643,superfamily,333820,501,753,6.21512e-26,105.837,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29191,Q#1996 - >seq8643,non-specific,197306,75,224,3.04965e-17,82.5292,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29192,Q#1996 - >seq8643,non-specific,197320,71,217,9.93176e-13,69.4662,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29193,Q#1996 - >seq8643,non-specific,223780,71,217,1.6567999999999999e-07,53.7563,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29194,Q#1996 - >seq8643,non-specific,197307,94,224,1.90743e-07,53.4457,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29195,Q#1996 - >seq8643,non-specific,197319,94,224,2.6271999999999996e-07,53.0493,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29196,Q#1996 - >seq8643,specific,335306,100,217,1.20373e-06,50.7066,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29197,Q#1996 - >seq8643,non-specific,238828,501,718,2.5995999999999996e-06,49.891999999999996,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29198,Q#1996 - >seq8643,non-specific,273186,94,225,4.4731e-06,49.1996,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29199,Q#1996 - >seq8643,non-specific,339261,96,220,2.0604200000000002e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29200,Q#1996 - >seq8643,non-specific,197321,94,224,4.5376e-05,46.3912,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29201,Q#1996 - >seq8643,non-specific,272954,94,195,0.00139841,41.5997,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29202,Q#1996 - >seq8643,non-specific,197311,69,224,0.00149202,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29203,Q#1996 - >seq8643,non-specific,334125,205,397,0.00206965,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29204,Q#1996 - >seq8643,superfamily,334125,205,397,0.00206965,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_Chrom,L1MA2,ORF2,hs3_orang,pars,N-TerminusTruncated
29205,Q#1996 - >seq8643,specific,311990,1222,1240,0.0043342,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29206,Q#1996 - >seq8643,superfamily,311990,1222,1240,0.0043342,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA2,ORF2,hs3_orang,pars,CompleteHit
29207,Q#1996 - >seq8643,non-specific,274009,293,444,0.00799398,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29208,Q#1996 - >seq8643,superfamily,274009,293,444,0.00799398,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA2.ORF2.hs3_orang.pars.frame1,1909181135_L1MA2.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA2,ORF2,hs3_orang,pars,C-TerminusTruncated
29209,Q#1998 - >seq8645,specific,311990,1124,1142,0.00034270800000000005,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs0_human.pars.frame1,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA1,ORF2,hs0_human,pars,CompleteHit
29210,Q#1998 - >seq8645,superfamily,311990,1124,1142,0.00034270800000000005,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs0_human.pars.frame1,1909181135_L1MA1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA1,ORF2,hs0_human,pars,CompleteHit
29211,Q#1999 - >seq8646,specific,238827,508,770,5.019609999999999e-63,213.692,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29212,Q#1999 - >seq8646,superfamily,295487,508,770,5.019609999999999e-63,213.692,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29213,Q#1999 - >seq8646,specific,197310,9,236,8.473869999999998e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29214,Q#1999 - >seq8646,superfamily,351117,9,236,8.473869999999998e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29215,Q#1999 - >seq8646,non-specific,197306,9,236,6.10224e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29216,Q#1999 - >seq8646,specific,333820,514,770,2.8989999999999996e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29217,Q#1999 - >seq8646,superfamily,333820,514,770,2.8989999999999996e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29218,Q#1999 - >seq8646,non-specific,223780,7,229,2.22511e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29219,Q#1999 - >seq8646,non-specific,197320,7,229,2.0802800000000005e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29220,Q#1999 - >seq8646,specific,335306,10,229,4.35504e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29221,Q#1999 - >seq8646,non-specific,197307,9,236,7.368989999999999e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29222,Q#1999 - >seq8646,non-specific,197319,7,236,2.41432e-16,80.0133,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29223,Q#1999 - >seq8646,non-specific,197321,7,236,6.13606e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29224,Q#1999 - >seq8646,non-specific,273186,7,237,1.08596e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29225,Q#1999 - >seq8646,non-specific,272954,7,207,1.6950199999999999e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29226,Q#1999 - >seq8646,non-specific,238828,514,735,1.58024e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29227,Q#1999 - >seq8646,non-specific,197336,7,229,3.18823e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29228,Q#1999 - >seq8646,non-specific,275209,465,735,1.8038900000000003e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,C-TerminusTruncated
29229,Q#1999 - >seq8646,superfamily,275209,465,735,1.8038900000000003e-09,60.9344,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,C-TerminusTruncated
29230,Q#1999 - >seq8646,non-specific,197311,30,236,1.84763e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29231,Q#1999 - >seq8646,non-specific,339261,108,232,2.80341e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29232,Q#1999 - >seq8646,non-specific,236970,9,207,5.00323e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29233,Q#1999 - >seq8646,non-specific,235175,294,462,0.00020912,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29234,Q#1999 - >seq8646,superfamily,235175,294,462,0.00020912,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29235,Q#1999 - >seq8646,non-specific,223496,320,498,0.000235942,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29236,Q#1999 - >seq8646,superfamily,223496,320,498,0.000235942,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29237,Q#1999 - >seq8646,non-specific,238185,654,770,0.000539441,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29238,Q#1999 - >seq8646,non-specific,274009,305,452,0.0018169,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,pars,C-TerminusTruncated
29239,Q#1999 - >seq8646,superfamily,274009,305,452,0.0018169,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs3_orang,pars,C-TerminusTruncated
29240,Q#1999 - >seq8646,non-specific,274475,255,426,0.00411531,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29241,Q#1999 - >seq8646,superfamily,274475,255,426,0.00411531,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs3_orang,pars,BothTerminiTruncated
29242,Q#1999 - >seq8646,specific,225881,481,715,0.00603341,40.2073,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,N-TerminusTruncated
29243,Q#1999 - >seq8646,superfamily,225881,481,715,0.00603341,40.2073,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs3_orang.pars.frame3,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs3_orang,pars,N-TerminusTruncated
29244,Q#2001 - >seq8648,specific,238827,502,764,1.12838e-61,209.455,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29245,Q#2001 - >seq8648,superfamily,295487,502,764,1.12838e-61,209.455,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29246,Q#2001 - >seq8648,specific,197310,7,231,1.45251e-50,178.31400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29247,Q#2001 - >seq8648,superfamily,351117,7,231,1.45251e-50,178.31400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29248,Q#2001 - >seq8648,specific,333820,508,764,9.531880000000001e-32,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29249,Q#2001 - >seq8648,superfamily,333820,508,764,9.531880000000001e-32,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29250,Q#2001 - >seq8648,non-specific,197306,7,231,4.61725e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29251,Q#2001 - >seq8648,non-specific,197320,8,216,3.8514000000000005e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29252,Q#2001 - >seq8648,non-specific,223780,8,220,4.2130300000000006e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29253,Q#2001 - >seq8648,specific,335306,7,224,9.51328e-16,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29254,Q#2001 - >seq8648,non-specific,197307,8,224,5.337e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29255,Q#2001 - >seq8648,non-specific,273186,8,232,4.66062e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29256,Q#2001 - >seq8648,non-specific,197321,8,224,6.26734e-11,63.7252,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29257,Q#2001 - >seq8648,non-specific,238828,508,732,2.15485e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29258,Q#2001 - >seq8648,non-specific,272954,8,202,1.4247499999999999e-09,59.7041,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29259,Q#2001 - >seq8648,non-specific,197319,8,231,3.0480799999999997e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29260,Q#2001 - >seq8648,non-specific,275209,459,792,5.42189e-07,52.8452,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29261,Q#2001 - >seq8648,superfamily,275209,459,792,5.42189e-07,52.8452,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29262,Q#2001 - >seq8648,non-specific,197336,7,189,8.50625e-05,45.2959,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29263,Q#2001 - >seq8648,non-specific,238185,648,764,0.00105546,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29264,Q#2001 - >seq8648,non-specific,235175,318,456,0.00529352,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M4c,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29265,Q#2001 - >seq8648,superfamily,235175,318,456,0.00529352,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1M4c,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29266,Q#2001 - >seq8648,non-specific,339261,103,226,0.00824788,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs5_gmonkey.pars.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs5_gmonkey,pars,CompleteHit
29267,Q#2004 - >seq8651,specific,238827,508,742,3.220129999999999e-58,199.825,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29268,Q#2004 - >seq8651,superfamily,295487,508,742,3.220129999999999e-58,199.825,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29269,Q#2004 - >seq8651,specific,197310,9,236,1.0669499999999998e-57,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29270,Q#2004 - >seq8651,superfamily,351117,9,236,1.0669499999999998e-57,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29271,Q#2004 - >seq8651,specific,333820,514,738,6.23439e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29272,Q#2004 - >seq8651,superfamily,333820,514,738,6.23439e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29273,Q#2004 - >seq8651,non-specific,197306,9,236,2.21233e-28,114.88600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29274,Q#2004 - >seq8651,non-specific,223780,7,229,6.75542e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29275,Q#2004 - >seq8651,non-specific,197307,9,236,5.255119999999999e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29276,Q#2004 - >seq8651,non-specific,197320,7,229,5.59995e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29277,Q#2004 - >seq8651,specific,335306,10,229,9.58157e-14,71.5073,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29278,Q#2004 - >seq8651,non-specific,238828,514,738,4.88733e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29279,Q#2004 - >seq8651,non-specific,273186,7,237,6.86132e-12,66.9188,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29280,Q#2004 - >seq8651,non-specific,272954,7,236,9.61684e-12,66.2525,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29281,Q#2004 - >seq8651,non-specific,197321,7,236,2.45273e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29282,Q#2004 - >seq8651,non-specific,275209,465,737,2.42232e-09,60.163999999999994,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29283,Q#2004 - >seq8651,superfamily,275209,465,737,2.42232e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29284,Q#2004 - >seq8651,non-specific,197319,7,236,3.4697100000000004e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29285,Q#2004 - >seq8651,non-specific,197336,7,229,5.00033e-06,49.1479,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29286,Q#2004 - >seq8651,non-specific,197311,38,236,1.70095e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29287,Q#2004 - >seq8651,non-specific,339261,108,232,0.000504254,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29288,Q#2004 - >seq8651,non-specific,236970,9,229,0.00722665,39.4922,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29289,Q#2004 - >seq8651,non-specific,238185,654,735,0.00825464,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs4_gibbon.marg.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,marg,CompleteHit
29290,Q#2007 - >seq8654,specific,197310,9,236,1.0447500000000001e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29291,Q#2007 - >seq8654,superfamily,351117,9,236,1.0447500000000001e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29292,Q#2007 - >seq8654,specific,238827,508,770,2.4050099999999995e-58,199.825,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29293,Q#2007 - >seq8654,superfamily,295487,508,770,2.4050099999999995e-58,199.825,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29294,Q#2007 - >seq8654,specific,333820,514,738,1.2890999999999997e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29295,Q#2007 - >seq8654,superfamily,333820,514,738,1.2890999999999997e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29296,Q#2007 - >seq8654,non-specific,197306,9,236,1.19386e-28,115.271,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29297,Q#2007 - >seq8654,non-specific,223780,7,229,1.39741e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29298,Q#2007 - >seq8654,non-specific,197320,7,229,1.7735400000000003e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29299,Q#2007 - >seq8654,non-specific,197307,9,236,1.86358e-18,86.1877,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29300,Q#2007 - >seq8654,specific,335306,10,229,7.986360000000001e-14,71.8925,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29301,Q#2007 - >seq8654,non-specific,238828,514,738,4.1507299999999993e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29302,Q#2007 - >seq8654,non-specific,273186,7,237,2.66012e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29303,Q#2007 - >seq8654,non-specific,272954,7,236,4.17182e-12,67.4081,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29304,Q#2007 - >seq8654,non-specific,197321,7,236,1.1081200000000001e-10,62.9548,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29305,Q#2007 - >seq8654,non-specific,197319,7,236,1.08655e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29306,Q#2007 - >seq8654,non-specific,275209,465,737,2.14419e-09,60.5492,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29307,Q#2007 - >seq8654,superfamily,275209,465,737,2.14419e-09,60.5492,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29308,Q#2007 - >seq8654,non-specific,197311,38,236,3.2766e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29309,Q#2007 - >seq8654,non-specific,197336,7,229,4.18116e-06,49.1479,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29310,Q#2007 - >seq8654,non-specific,339261,108,232,0.00013398200000000002,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29311,Q#2007 - >seq8654,non-specific,236970,9,229,0.004525,39.8774,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs4_gibbon,pars,CompleteHit
29312,Q#2007 - >seq8654,non-specific,238185,654,731,0.00984276,36.56,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs4_gibbon.pars.frame3,1909181135_L1M4c.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29313,Q#2010 - >seq8657,specific,311990,1130,1148,0.000944541,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs3_orang.marg.frame1,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA1,ORF2,hs3_orang,marg,CompleteHit
29314,Q#2010 - >seq8657,superfamily,311990,1130,1148,0.000944541,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs3_orang.marg.frame1,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA1,ORF2,hs3_orang,marg,CompleteHit
29315,Q#2011 - >seq8658,specific,238827,512,773,9.399839999999998e-61,207.144,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29316,Q#2011 - >seq8658,superfamily,295487,512,773,9.399839999999998e-61,207.144,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29317,Q#2011 - >seq8658,specific,197310,9,238,6.80773e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29318,Q#2011 - >seq8658,superfamily,351117,9,238,6.80773e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29319,Q#2011 - >seq8658,specific,333820,518,773,5.52408e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29320,Q#2011 - >seq8658,superfamily,333820,518,773,5.52408e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29321,Q#2011 - >seq8658,non-specific,197306,9,238,1.92364e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29322,Q#2011 - >seq8658,non-specific,197320,7,223,8.77294e-18,84.1037,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29323,Q#2011 - >seq8658,non-specific,223780,7,227,1.59377e-16,80.7203,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29324,Q#2011 - >seq8658,non-specific,197307,9,231,3.16588e-15,76.5577,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29325,Q#2011 - >seq8658,specific,335306,10,231,8.22881e-13,68.811,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29326,Q#2011 - >seq8658,non-specific,272954,7,209,2.6114299999999996e-10,62.0153,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29327,Q#2011 - >seq8658,non-specific,197321,7,231,3.5372500000000004e-10,61.7992,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29328,Q#2011 - >seq8658,non-specific,273186,7,239,9.971189999999999e-10,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29329,Q#2011 - >seq8658,non-specific,238828,584,738,5.854520000000001e-09,57.596000000000004,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,N-TerminusTruncated
29330,Q#2011 - >seq8658,non-specific,197319,7,238,3.14851e-07,52.6641,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29331,Q#2011 - >seq8658,non-specific,197336,7,196,0.000162173,44.5255,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29332,Q#2011 - >seq8658,non-specific,197311,39,206,0.000389261,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29333,Q#2011 - >seq8658,non-specific,275209,589,797,0.000593301,43.2152,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,N-TerminusTruncated
29334,Q#2011 - >seq8658,superfamily,275209,589,797,0.000593301,43.2152,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs1_chimp,marg,N-TerminusTruncated
29335,Q#2011 - >seq8658,non-specific,339261,110,233,0.00988762,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs1_chimp.marg.frame3,1909181135_L1M4c.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs1_chimp,marg,CompleteHit
29336,Q#2014 - >seq8661,specific,238827,502,764,8.523569999999999e-61,207.144,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29337,Q#2014 - >seq8661,superfamily,295487,502,764,8.523569999999999e-61,207.144,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29338,Q#2014 - >seq8661,specific,197310,7,231,7.05448e-51,179.47,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29339,Q#2014 - >seq8661,superfamily,351117,7,231,7.05448e-51,179.47,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29340,Q#2014 - >seq8661,specific,333820,508,764,3.0573799999999995e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29341,Q#2014 - >seq8661,superfamily,333820,508,764,3.0573799999999995e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29342,Q#2014 - >seq8661,non-specific,197306,7,231,3.90963e-23,99.478,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29343,Q#2014 - >seq8661,non-specific,197320,8,216,5.01062e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29344,Q#2014 - >seq8661,non-specific,223780,8,220,5.84967e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29345,Q#2014 - >seq8661,specific,335306,7,224,1.08985e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29346,Q#2014 - >seq8661,non-specific,197307,8,224,7.68498e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29347,Q#2014 - >seq8661,non-specific,273186,8,232,4.8313e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29348,Q#2014 - >seq8661,non-specific,197321,8,224,8.50384e-11,63.7252,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29349,Q#2014 - >seq8661,non-specific,238828,508,732,3.5889099999999994e-10,61.0628,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29350,Q#2014 - >seq8661,non-specific,272954,8,202,1.33416e-09,60.0893,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29351,Q#2014 - >seq8661,non-specific,197319,8,231,4.16642e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29352,Q#2014 - >seq8661,non-specific,275209,459,792,6.58104e-07,52.8452,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29353,Q#2014 - >seq8661,superfamily,275209,459,792,6.58104e-07,52.8452,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29354,Q#2014 - >seq8661,non-specific,197336,7,189,9.72921e-05,45.2959,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29355,Q#2014 - >seq8661,non-specific,238185,648,764,0.00194377,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29356,Q#2014 - >seq8661,non-specific,235175,313,456,0.00450923,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M4c,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29357,Q#2014 - >seq8661,superfamily,235175,313,456,0.00450923,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M4c,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29358,Q#2014 - >seq8661,non-specific,339261,103,226,0.00873647,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs5_gmonkey.marg.frame3,1909181135_L1M4c.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs5_gmonkey,marg,CompleteHit
29359,Q#2017 - >seq8664,specific,311990,1130,1148,0.000944541,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs3_orang.pars.frame1,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29360,Q#2017 - >seq8664,superfamily,311990,1130,1148,0.000944541,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs3_orang.pars.frame1,1909181135_L1MA1.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA1,ORF2,hs3_orang,pars,CompleteHit
29361,Q#2018 - >seq8665,specific,197310,9,236,3.8956799999999995e-62,211.826,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29362,Q#2018 - >seq8665,superfamily,351117,9,236,3.8956799999999995e-62,211.826,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29363,Q#2018 - >seq8665,specific,238827,508,769,7.70833e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29364,Q#2018 - >seq8665,superfamily,295487,508,769,7.70833e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29365,Q#2018 - >seq8665,non-specific,197306,9,236,3.5607699999999997e-34,131.45,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29366,Q#2018 - >seq8665,specific,333820,514,769,8.618259999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29367,Q#2018 - >seq8665,superfamily,333820,514,769,8.618259999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29368,Q#2018 - >seq8665,non-specific,223780,7,229,8.087260000000002e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29369,Q#2018 - >seq8665,non-specific,197320,7,229,4.9339599999999996e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29370,Q#2018 - >seq8665,specific,335306,10,229,4.43426e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29371,Q#2018 - >seq8665,non-specific,197307,9,236,1.24079e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29372,Q#2018 - >seq8665,non-specific,197319,7,236,4.62389e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29373,Q#2018 - >seq8665,non-specific,197321,7,236,1.30248e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29374,Q#2018 - >seq8665,non-specific,273186,7,237,1.7703700000000002e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29375,Q#2018 - >seq8665,non-specific,272954,7,207,3.3027700000000002e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29376,Q#2018 - >seq8665,non-specific,238828,514,735,3.72144e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29377,Q#2018 - >seq8665,non-specific,197336,7,229,5.03319e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29378,Q#2018 - >seq8665,non-specific,275209,465,735,4.5490200000000005e-09,59.3936,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29379,Q#2018 - >seq8665,superfamily,275209,465,735,4.5490200000000005e-09,59.3936,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29380,Q#2018 - >seq8665,non-specific,197311,30,236,1.6812900000000003e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29381,Q#2018 - >seq8665,non-specific,339261,108,232,1.79156e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29382,Q#2018 - >seq8665,non-specific,236970,9,207,5.67272e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29383,Q#2018 - >seq8665,non-specific,238185,654,769,0.000974532,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29384,Q#2018 - >seq8665,non-specific,235175,306,462,0.00219309,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29385,Q#2018 - >seq8665,superfamily,235175,306,462,0.00219309,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29386,Q#2018 - >seq8665,non-specific,274009,305,452,0.00294572,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29387,Q#2018 - >seq8665,superfamily,274009,305,452,0.00294572,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
29388,Q#2018 - >seq8665,specific,311990,1238,1256,0.0033408,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29389,Q#2018 - >seq8665,superfamily,311990,1238,1256,0.0033408,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs2_gorilla,marg,CompleteHit
29390,Q#2018 - >seq8665,non-specific,274475,255,426,0.00398151,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29391,Q#2018 - >seq8665,superfamily,274475,255,426,0.00398151,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29392,Q#2018 - >seq8665,non-specific,223496,263,443,0.00576902,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29393,Q#2018 - >seq8665,superfamily,223496,263,443,0.00576902,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29394,Q#2018 - >seq8665,non-specific,223496,321,498,0.00689261,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
29395,Q#2018 - >seq8665,specific,225881,481,715,0.00744012,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29396,Q#2018 - >seq8665,superfamily,225881,481,715,0.00744012,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.marg.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
29397,Q#2021 - >seq8668,specific,197310,9,236,4.083649999999999e-62,211.826,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29398,Q#2021 - >seq8668,superfamily,351117,9,236,4.083649999999999e-62,211.826,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29399,Q#2021 - >seq8668,specific,238827,507,768,8.080819999999998e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29400,Q#2021 - >seq8668,superfamily,295487,507,768,8.080819999999998e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29401,Q#2021 - >seq8668,non-specific,197306,9,236,3.5918599999999995e-34,131.45,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29402,Q#2021 - >seq8668,specific,333820,513,768,9.575799999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29403,Q#2021 - >seq8668,superfamily,333820,513,768,9.575799999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29404,Q#2021 - >seq8668,non-specific,223780,7,229,8.0798e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29405,Q#2021 - >seq8668,non-specific,197320,7,229,4.9764600000000004e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29406,Q#2021 - >seq8668,specific,335306,10,229,4.4303e-20,90.3821,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29407,Q#2021 - >seq8668,non-specific,197307,9,236,1.2279599999999999e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29408,Q#2021 - >seq8668,non-specific,197319,7,236,4.40709e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29409,Q#2021 - >seq8668,non-specific,197321,7,236,1.3013e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29410,Q#2021 - >seq8668,non-specific,273186,7,237,1.7522000000000002e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29411,Q#2021 - >seq8668,non-specific,272954,7,207,3.2688899999999998e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29412,Q#2021 - >seq8668,non-specific,238828,513,734,3.6832800000000004e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29413,Q#2021 - >seq8668,non-specific,197336,7,229,4.98196e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29414,Q#2021 - >seq8668,non-specific,275209,465,734,1.27682e-07,55.1564,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
29415,Q#2021 - >seq8668,superfamily,275209,465,734,1.27682e-07,55.1564,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
29416,Q#2021 - >seq8668,non-specific,197311,30,236,1.6955700000000001e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29417,Q#2021 - >seq8668,non-specific,339261,108,232,1.79008e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29418,Q#2021 - >seq8668,non-specific,236970,9,207,5.667689999999999e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29419,Q#2021 - >seq8668,non-specific,238185,653,768,0.0009832719999999999,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29420,Q#2021 - >seq8668,non-specific,235175,306,462,0.00210018,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29421,Q#2021 - >seq8668,superfamily,235175,306,462,0.00210018,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29422,Q#2021 - >seq8668,non-specific,274009,305,498,0.00220777,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
29423,Q#2021 - >seq8668,superfamily,274009,305,498,0.00220777,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
29424,Q#2021 - >seq8668,specific,311990,1237,1255,0.00333821,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29425,Q#2021 - >seq8668,superfamily,311990,1237,1255,0.00333821,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs2_gorilla,pars,CompleteHit
29426,Q#2021 - >seq8668,non-specific,274475,255,426,0.00387763,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29427,Q#2021 - >seq8668,superfamily,274475,255,426,0.00387763,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29428,Q#2021 - >seq8668,non-specific,223496,263,443,0.005667,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29429,Q#2021 - >seq8668,superfamily,223496,263,443,0.005667,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs2_gorilla.pars.frame3,1909181135_L1MA1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
29430,Q#2025 - >seq8672,specific,238827,509,770,3.950699999999999e-62,210.99599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29431,Q#2025 - >seq8672,superfamily,295487,509,770,3.950699999999999e-62,210.99599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29432,Q#2025 - >seq8672,specific,197310,9,237,1.01962e-38,144.416,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29433,Q#2025 - >seq8672,superfamily,351117,9,237,1.01962e-38,144.416,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29434,Q#2025 - >seq8672,specific,333820,515,770,6.901719999999999e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29435,Q#2025 - >seq8672,superfamily,333820,515,770,6.901719999999999e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29436,Q#2025 - >seq8672,non-specific,197306,9,237,1.1708199999999998e-21,95.2408,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29437,Q#2025 - >seq8672,specific,335306,10,230,3.30936e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29438,Q#2025 - >seq8672,non-specific,197307,9,237,7.71257e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29439,Q#2025 - >seq8672,non-specific,197320,7,230,5.298800000000001e-13,70.2366,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29440,Q#2025 - >seq8672,non-specific,223780,7,230,1.2642e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29441,Q#2025 - >seq8672,non-specific,238828,515,736,3.6865599999999996e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29442,Q#2025 - >seq8672,non-specific,275209,466,736,6.26081e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29443,Q#2025 - >seq8672,superfamily,275209,466,736,6.26081e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29444,Q#2025 - >seq8672,non-specific,197319,7,237,3.42231e-08,55.7457,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29445,Q#2025 - >seq8672,non-specific,273186,7,238,3.86421e-08,55.748000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29446,Q#2025 - >seq8672,non-specific,272954,7,208,1.85434e-07,53.5409,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29447,Q#2025 - >seq8672,non-specific,197321,7,237,1.92793e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29448,Q#2025 - >seq8672,non-specific,197336,7,230,1.2227400000000001e-05,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29449,Q#2025 - >seq8672,non-specific,238185,655,770,0.000866982,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29450,Q#2025 - >seq8672,non-specific,334125,218,410,0.0011212,42.9068,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA1,ORF2,hs1_chimp,marg,N-TerminusTruncated
29451,Q#2025 - >seq8672,superfamily,334125,218,410,0.0011212,42.9068,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA1,ORF2,hs1_chimp,marg,N-TerminusTruncated
29452,Q#2025 - >seq8672,specific,311990,1238,1256,0.00269292,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29453,Q#2025 - >seq8672,superfamily,311990,1238,1256,0.00269292,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA1,ORF2,hs1_chimp,marg,CompleteHit
29454,Q#2025 - >seq8672,non-specific,274009,306,453,0.00363905,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29455,Q#2025 - >seq8672,superfamily,274009,306,453,0.00363905,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs1_chimp.marg.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29456,Q#2026 - >seq8673,non-specific,197310,36,119,8.26198e-09,57.3613,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29457,Q#2026 - >seq8673,superfamily,351117,36,119,8.26198e-09,57.3613,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29458,Q#2026 - >seq8673,non-specific,197306,36,119,0.00200033,40.9277,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.marg.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,marg,C-TerminusTruncated
29459,Q#2027 - >seq8674,specific,238827,508,769,4.051759999999999e-62,210.99599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29460,Q#2027 - >seq8674,superfamily,295487,508,769,4.051759999999999e-62,210.99599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29461,Q#2027 - >seq8674,specific,197310,9,237,1.01685e-38,144.416,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29462,Q#2027 - >seq8674,superfamily,351117,9,237,1.01685e-38,144.416,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29463,Q#2027 - >seq8674,specific,333820,514,769,7.72949e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29464,Q#2027 - >seq8674,superfamily,333820,514,769,7.72949e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29465,Q#2027 - >seq8674,non-specific,197306,9,237,1.2014900000000001e-21,95.2408,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29466,Q#2027 - >seq8674,specific,335306,10,230,3.3005100000000003e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29467,Q#2027 - >seq8674,non-specific,197307,9,237,7.69158e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29468,Q#2027 - >seq8674,non-specific,197320,7,230,5.334e-13,70.2366,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29469,Q#2027 - >seq8674,non-specific,223780,7,230,1.26074e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29470,Q#2027 - >seq8674,non-specific,238828,514,735,3.64225e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29471,Q#2027 - >seq8674,non-specific,275209,465,735,5.9196499999999995e-09,59.3936,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29472,Q#2027 - >seq8674,superfamily,275209,465,735,5.9196499999999995e-09,59.3936,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29473,Q#2027 - >seq8674,non-specific,197319,7,237,3.4131199999999994e-08,55.7457,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29474,Q#2027 - >seq8674,non-specific,273186,7,238,3.8893699999999994e-08,55.748000000000005,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29475,Q#2027 - >seq8674,non-specific,197321,7,237,1.92276e-07,53.71,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29476,Q#2027 - >seq8674,non-specific,272954,7,208,2.04516e-07,53.5409,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29477,Q#2027 - >seq8674,non-specific,197336,7,230,1.2305999999999999e-05,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29478,Q#2027 - >seq8674,non-specific,334125,218,409,0.00034604,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA1,ORF2,hs1_chimp,pars,N-TerminusTruncated
29479,Q#2027 - >seq8674,superfamily,334125,218,409,0.00034604,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA1,ORF2,hs1_chimp,pars,N-TerminusTruncated
29480,Q#2027 - >seq8674,non-specific,238185,654,769,0.000908043,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29481,Q#2027 - >seq8674,non-specific,274009,306,452,0.00119888,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29482,Q#2027 - >seq8674,superfamily,274009,306,452,0.00119888,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29483,Q#2027 - >seq8674,specific,311990,1236,1254,0.00282156,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29484,Q#2027 - >seq8674,superfamily,311990,1236,1254,0.00282156,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA1,ORF2,hs1_chimp,pars,CompleteHit
29485,Q#2027 - >seq8674,non-specific,274009,254,467,0.0032790999999999996,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA1,ORF2,hs1_chimp,pars,BothTerminiTruncated
29486,Q#2027 - >seq8674,non-specific,223496,322,462,0.00481561,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,BothTerminiTruncated
29487,Q#2027 - >seq8674,superfamily,223496,322,462,0.00481561,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA1.ORF2.hs1_chimp.pars.frame3,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA1,ORF2,hs1_chimp,pars,BothTerminiTruncated
29488,Q#2029 - >seq8676,non-specific,197310,36,119,8.391799999999999e-09,57.3613,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29489,Q#2029 - >seq8676,superfamily,351117,36,119,8.391799999999999e-09,57.3613,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29490,Q#2029 - >seq8676,non-specific,197306,36,119,0.00199454,40.9277,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA1.ORF2.hs1_chimp.pars.frame1,1909181135_L1MA1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA1,ORF2,hs1_chimp,pars,C-TerminusTruncated
29491,Q#2030 - >seq8677,specific,238827,503,763,9.142779999999998e-59,201.36599999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29492,Q#2030 - >seq8677,superfamily,295487,503,763,9.142779999999998e-59,201.36599999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29493,Q#2030 - >seq8677,specific,197310,2,229,5.4730399999999994e-58,199.885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29494,Q#2030 - >seq8677,superfamily,351117,2,229,5.4730399999999994e-58,199.885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29495,Q#2030 - >seq8677,specific,333820,509,732,7.0342499999999994e-31,120.09,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29496,Q#2030 - >seq8677,superfamily,333820,509,732,7.0342499999999994e-31,120.09,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29497,Q#2030 - >seq8677,non-specific,197306,2,229,7.231419999999998e-30,119.12299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29498,Q#2030 - >seq8677,non-specific,197320,2,222,1.68914e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29499,Q#2030 - >seq8677,non-specific,223780,2,222,1.1683900000000001e-18,86.8835,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29500,Q#2030 - >seq8677,specific,335306,3,222,1.9525000000000002e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29501,Q#2030 - >seq8677,non-specific,197307,2,222,5.77639e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29502,Q#2030 - >seq8677,non-specific,273186,2,230,6.47593e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29503,Q#2030 - >seq8677,non-specific,197321,1,222,3.5315099999999998e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29504,Q#2030 - >seq8677,non-specific,272954,2,200,1.4619e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29505,Q#2030 - >seq8677,non-specific,238828,509,729,1.0549899999999999e-09,59.9072,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29506,Q#2030 - >seq8677,non-specific,197319,2,229,1.4162199999999999e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29507,Q#2030 - >seq8677,non-specific,275209,460,787,2.39161e-07,54.0008,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29508,Q#2030 - >seq8677,superfamily,275209,460,787,2.39161e-07,54.0008,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29509,Q#2030 - >seq8677,non-specific,197311,21,197,3.22039e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29510,Q#2030 - >seq8677,non-specific,197336,2,222,0.000114613,44.9107,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29511,Q#2030 - >seq8677,non-specific,236970,2,222,0.000214412,44.1146,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,marg,CompleteHit
29512,Q#2030 - >seq8677,non-specific,238185,649,763,0.000555316,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29513,Q#2030 - >seq8677,non-specific,339261,101,224,0.000623635,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs0_human.marg.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs0_human,marg,CompleteHit
29514,Q#2033 - >seq8680,specific,238827,502,758,6.29158e-58,199.054,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29515,Q#2033 - >seq8680,superfamily,295487,502,758,6.29158e-58,199.054,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29516,Q#2033 - >seq8680,specific,197310,2,229,6.644909999999999e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29517,Q#2033 - >seq8680,superfamily,351117,2,229,6.644909999999999e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29518,Q#2033 - >seq8680,specific,333820,508,758,1.53091e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29519,Q#2033 - >seq8680,superfamily,333820,508,758,1.53091e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29520,Q#2033 - >seq8680,non-specific,197306,2,229,8.82871e-30,118.738,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29521,Q#2033 - >seq8680,non-specific,197320,2,222,1.3551200000000001e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29522,Q#2033 - >seq8680,non-specific,223780,2,222,1.15426e-18,86.8835,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29523,Q#2033 - >seq8680,specific,335306,3,222,1.87737e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29524,Q#2033 - >seq8680,non-specific,197307,2,222,4.95366e-18,85.0321,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29525,Q#2033 - >seq8680,non-specific,273186,2,230,6.459300000000001e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29526,Q#2033 - >seq8680,non-specific,197321,1,222,3.1789999999999997e-12,67.5772,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29527,Q#2033 - >seq8680,non-specific,272954,2,200,1.43122e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29528,Q#2033 - >seq8680,non-specific,238828,508,728,7.245850000000001e-10,60.2924,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29529,Q#2033 - >seq8680,non-specific,197319,2,229,1.2296400000000001e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29530,Q#2033 - >seq8680,non-specific,197311,21,197,3.5645999999999997e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29531,Q#2033 - >seq8680,non-specific,275209,459,728,1.50207e-05,48.2228,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,C-TerminusTruncated
29532,Q#2033 - >seq8680,superfamily,275209,459,728,1.50207e-05,48.2228,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,C-TerminusTruncated
29533,Q#2033 - >seq8680,non-specific,197336,2,222,0.000109274,44.9107,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29534,Q#2033 - >seq8680,non-specific,236970,2,222,0.000217624,44.1146,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M4c,ORF2,hs0_human,pars,CompleteHit
29535,Q#2033 - >seq8680,non-specific,339261,101,224,0.0007731789999999999,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs0_human,pars,CompleteHit
29536,Q#2033 - >seq8680,non-specific,238185,648,724,0.00852765,36.9452,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs0_human.pars.frame3,1909181135_L1M4c.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1M4c,ORF2,hs0_human,pars,C-TerminusTruncated
29537,Q#2035 - >seq8682,specific,238827,510,772,2.1923699999999996e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29538,Q#2035 - >seq8682,superfamily,295487,510,772,2.1923699999999996e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29539,Q#2035 - >seq8682,specific,197310,9,236,1.5096799999999997e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29540,Q#2035 - >seq8682,superfamily,351117,9,236,1.5096799999999997e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29541,Q#2035 - >seq8682,non-specific,197306,9,236,2.25697e-53,186.918,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29542,Q#2035 - >seq8682,specific,333820,516,772,3.1761499999999997e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29543,Q#2035 - >seq8682,superfamily,333820,516,772,3.1761499999999997e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29544,Q#2035 - >seq8682,non-specific,197307,9,236,1.02616e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29545,Q#2035 - >seq8682,non-specific,223780,9,238,6.09774e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29546,Q#2035 - >seq8682,non-specific,197320,8,221,9.82483e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29547,Q#2035 - >seq8682,specific,335306,10,229,1.07445e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29548,Q#2035 - >seq8682,non-specific,197321,7,236,2.02553e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29549,Q#2035 - >seq8682,non-specific,273186,9,237,2.4931999999999996e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29550,Q#2035 - >seq8682,non-specific,272954,9,236,4.2704900000000004e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29551,Q#2035 - >seq8682,non-specific,197319,8,236,2.11621e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29552,Q#2035 - >seq8682,non-specific,197336,7,235,4.17532e-14,73.4155,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29553,Q#2035 - >seq8682,non-specific,197322,9,236,3.32655e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29554,Q#2035 - >seq8682,non-specific,238828,516,737,1.46263e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29555,Q#2035 - >seq8682,non-specific,275209,467,800,4.71523e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29556,Q#2035 - >seq8682,superfamily,275209,467,800,4.71523e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29557,Q#2035 - >seq8682,non-specific,339261,108,232,1.22238e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29558,Q#2035 - >seq8682,non-specific,236970,9,238,9.30057e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29559,Q#2035 - >seq8682,non-specific,197311,7,236,1.46288e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29560,Q#2035 - >seq8682,non-specific,238185,656,772,0.00012607799999999998,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29561,Q#2035 - >seq8682,non-specific,197317,139,229,0.000141062,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
29562,Q#2035 - >seq8682,non-specific,226098,138,239,0.00057742,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
29563,Q#2035 - >seq8682,non-specific,274009,305,453,0.00134288,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29564,Q#2035 - >seq8682,superfamily,274009,305,453,0.00134288,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29565,Q#2035 - >seq8682,non-specific,235175,295,464,0.00146136,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
29566,Q#2035 - >seq8682,superfamily,235175,295,464,0.00146136,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
29567,Q#2035 - >seq8682,non-specific,197314,7,192,0.00190288,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29568,Q#2035 - >seq8682,non-specific,239569,525,748,0.00730718,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,marg,CompleteHit
29569,Q#2035 - >seq8682,non-specific,293702,337,451,0.00882372,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29570,Q#2035 - >seq8682,superfamily,293702,337,451,0.00882372,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs4_gibbon.marg.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
29571,Q#2040 - >seq8687,specific,238827,510,772,2.0433799999999998e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29572,Q#2040 - >seq8687,superfamily,295487,510,772,2.0433799999999998e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29573,Q#2040 - >seq8687,specific,197310,9,236,1.6001499999999997e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29574,Q#2040 - >seq8687,superfamily,351117,9,236,1.6001499999999997e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29575,Q#2040 - >seq8687,non-specific,197306,9,236,2.6346999999999994e-53,186.533,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29576,Q#2040 - >seq8687,specific,333820,516,772,2.84051e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29577,Q#2040 - >seq8687,superfamily,333820,516,772,2.84051e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29578,Q#2040 - >seq8687,non-specific,197307,9,236,9.99693e-25,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29579,Q#2040 - >seq8687,non-specific,223780,9,238,5.71748e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29580,Q#2040 - >seq8687,non-specific,197320,8,221,9.48095e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29581,Q#2040 - >seq8687,specific,335306,10,229,1.04746e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29582,Q#2040 - >seq8687,non-specific,197321,7,236,1.9180600000000002e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29583,Q#2040 - >seq8687,non-specific,273186,9,237,2.36092e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29584,Q#2040 - >seq8687,non-specific,272954,9,236,4.16084e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29585,Q#2040 - >seq8687,non-specific,197319,8,236,2.04281e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29586,Q#2040 - >seq8687,non-specific,197336,7,235,3.7043e-14,73.4155,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29587,Q#2040 - >seq8687,non-specific,197322,9,236,3.23924e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29588,Q#2040 - >seq8687,non-specific,238828,516,737,1.56629e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29589,Q#2040 - >seq8687,non-specific,275209,467,800,4.46866e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29590,Q#2040 - >seq8687,superfamily,275209,467,800,4.46866e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29591,Q#2040 - >seq8687,non-specific,339261,108,232,1.1939900000000001e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29592,Q#2040 - >seq8687,non-specific,236970,9,238,9.06392e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29593,Q#2040 - >seq8687,non-specific,197311,7,236,1.36175e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29594,Q#2040 - >seq8687,non-specific,238185,656,772,0.00011506899999999999,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29595,Q#2040 - >seq8687,non-specific,197317,139,229,0.00013032700000000001,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
29596,Q#2040 - >seq8687,non-specific,226098,138,239,0.000563169,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
29597,Q#2040 - >seq8687,non-specific,274009,305,453,0.00161697,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29598,Q#2040 - >seq8687,superfamily,274009,305,453,0.00161697,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29599,Q#2040 - >seq8687,non-specific,197314,7,192,0.00183964,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29600,Q#2040 - >seq8687,non-specific,235175,295,464,0.00199959,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29601,Q#2040 - >seq8687,superfamily,235175,295,464,0.00199959,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
29602,Q#2040 - >seq8687,non-specific,239569,525,748,0.00824709,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs4_gibbon,pars,CompleteHit
29603,Q#2040 - >seq8687,non-specific,293702,337,451,0.00890858,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29604,Q#2040 - >seq8687,superfamily,293702,337,451,0.00890858,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs4_gibbon.pars.frame3,1909181222_L1P2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
29605,Q#2043 - >seq8690,specific,238827,510,772,2.1185899999999998e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29606,Q#2043 - >seq8690,superfamily,295487,510,772,2.1185899999999998e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29607,Q#2043 - >seq8690,specific,197310,9,236,5.9673199999999985e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29608,Q#2043 - >seq8690,superfamily,351117,9,236,5.9673199999999985e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29609,Q#2043 - >seq8690,non-specific,197306,9,236,1.7661e-53,186.918,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29610,Q#2043 - >seq8690,specific,333820,516,772,4.3318699999999997e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29611,Q#2043 - >seq8690,superfamily,333820,516,772,4.3318699999999997e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29612,Q#2043 - >seq8690,non-specific,197307,9,236,1.2493200000000001e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29613,Q#2043 - >seq8690,non-specific,223780,9,238,6.30744e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29614,Q#2043 - >seq8690,non-specific,197320,8,221,1.35138e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29615,Q#2043 - >seq8690,specific,335306,10,229,6.720180000000001e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29616,Q#2043 - >seq8690,non-specific,197321,7,236,1.6537699999999999e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29617,Q#2043 - >seq8690,non-specific,273186,9,237,2.1546600000000002e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29618,Q#2043 - >seq8690,non-specific,272954,9,236,5.48456e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29619,Q#2043 - >seq8690,non-specific,197319,8,236,4.06554e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29620,Q#2043 - >seq8690,non-specific,197336,7,235,7.096000000000001e-14,72.6451,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29621,Q#2043 - >seq8690,non-specific,238828,516,737,2.4988e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29622,Q#2043 - >seq8690,non-specific,197322,9,236,8.34267e-11,64.2606,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29623,Q#2043 - >seq8690,non-specific,275209,467,800,1.44624e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29624,Q#2043 - >seq8690,superfamily,275209,467,800,1.44624e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29625,Q#2043 - >seq8690,non-specific,339261,108,232,3.08668e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29626,Q#2043 - >seq8690,non-specific,236970,9,238,1.39646e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29627,Q#2043 - >seq8690,non-specific,197311,7,236,2.33356e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29628,Q#2043 - >seq8690,non-specific,197317,139,229,0.000107175,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
29629,Q#2043 - >seq8690,non-specific,238185,656,772,0.000107489,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,pars,CompleteHit
29630,Q#2043 - >seq8690,non-specific,226098,138,239,0.0010753,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
29631,Q#2043 - >seq8690,non-specific,274009,305,453,0.00167087,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29632,Q#2043 - >seq8690,superfamily,274009,305,453,0.00167087,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29633,Q#2043 - >seq8690,non-specific,197314,7,192,0.00194726,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29634,Q#2043 - >seq8690,non-specific,235175,295,464,0.00837925,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29635,Q#2043 - >seq8690,superfamily,235175,295,464,0.00837925,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs5_gmonkey.pars.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29636,Q#2046 - >seq8693,specific,238827,510,772,1.5808599999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29637,Q#2046 - >seq8693,superfamily,295487,510,772,1.5808599999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29638,Q#2046 - >seq8693,specific,197310,9,236,3.238779999999999e-62,211.826,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29639,Q#2046 - >seq8693,superfamily,351117,9,236,3.238779999999999e-62,211.826,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29640,Q#2046 - >seq8693,non-specific,197306,9,236,1.5309499999999999e-53,187.304,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29641,Q#2046 - >seq8693,specific,333820,516,772,4.5325799999999994e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29642,Q#2046 - >seq8693,superfamily,333820,516,772,4.5325799999999994e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29643,Q#2046 - >seq8693,non-specific,197307,9,236,1.3504799999999999e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29644,Q#2046 - >seq8693,non-specific,223780,9,238,7.154070000000001e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29645,Q#2046 - >seq8693,non-specific,197320,8,221,1.4887299999999998e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29646,Q#2046 - >seq8693,specific,335306,10,229,7.1822e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29647,Q#2046 - >seq8693,non-specific,197321,7,236,2.04091e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29648,Q#2046 - >seq8693,non-specific,273186,9,237,2.56016e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29649,Q#2046 - >seq8693,non-specific,272954,9,236,5.548030000000001e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29650,Q#2046 - >seq8693,non-specific,197319,8,236,4.60213e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29651,Q#2046 - >seq8693,non-specific,197336,7,235,9.15821e-14,72.2599,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29652,Q#2046 - >seq8693,non-specific,238828,516,737,2.38503e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29653,Q#2046 - >seq8693,non-specific,197322,9,236,8.94249e-11,64.2606,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29654,Q#2046 - >seq8693,non-specific,275209,467,800,1.25329e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29655,Q#2046 - >seq8693,superfamily,275209,467,800,1.25329e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29656,Q#2046 - >seq8693,non-specific,339261,108,232,2.92122e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29657,Q#2046 - >seq8693,non-specific,236970,9,238,1.3883299999999999e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29658,Q#2046 - >seq8693,non-specific,197311,7,236,2.3101e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29659,Q#2046 - >seq8693,non-specific,197317,139,229,0.00011442700000000001,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
29660,Q#2046 - >seq8693,non-specific,238185,656,772,0.000125865,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs5_gmonkey,marg,CompleteHit
29661,Q#2046 - >seq8693,non-specific,274009,305,453,0.00103122,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29662,Q#2046 - >seq8693,superfamily,274009,305,453,0.00103122,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29663,Q#2046 - >seq8693,non-specific,226098,138,239,0.00114766,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
29664,Q#2046 - >seq8693,non-specific,197314,7,192,0.00202249,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29665,Q#2046 - >seq8693,non-specific,235175,295,464,0.00431851,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29666,Q#2046 - >seq8693,superfamily,235175,295,464,0.00431851,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29667,Q#2046 - >seq8693,non-specific,274008,157,500,0.00465259,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
29668,Q#2046 - >seq8693,superfamily,274008,157,500,0.00465259,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
29669,Q#2046 - >seq8693,non-specific,293702,337,451,0.00873155,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29670,Q#2046 - >seq8693,superfamily,293702,337,451,0.00873155,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs5_gmonkey.marg.frame3,1909181401_L1P2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29671,Q#2047 - >seq8694,specific,238827,502,754,2.4595499999999995e-60,205.988,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29672,Q#2047 - >seq8694,superfamily,295487,502,754,2.4595499999999995e-60,205.988,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29673,Q#2047 - >seq8694,specific,197310,3,229,2.3028199999999998e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29674,Q#2047 - >seq8694,superfamily,351117,3,229,2.3028199999999998e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29675,Q#2047 - >seq8694,non-specific,197306,3,229,7.89931e-31,121.82,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29676,Q#2047 - >seq8694,specific,333820,508,732,6.65546e-30,117.39299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29677,Q#2047 - >seq8694,superfamily,333820,508,732,6.65546e-30,117.39299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29678,Q#2047 - >seq8694,non-specific,197320,3,222,1.9036399999999998e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29679,Q#2047 - >seq8694,non-specific,223780,3,230,1.50562e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29680,Q#2047 - >seq8694,non-specific,197307,3,229,1.01407e-18,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29681,Q#2047 - >seq8694,non-specific,273186,3,230,1.15074e-17,83.8676,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29682,Q#2047 - >seq8694,specific,335306,4,222,4.96618e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29683,Q#2047 - >seq8694,non-specific,197321,1,229,8.424489999999999e-16,78.3628,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29684,Q#2047 - >seq8694,non-specific,272954,3,229,1.2623400000000001e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29685,Q#2047 - >seq8694,non-specific,197319,7,229,4.283869999999999e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29686,Q#2047 - >seq8694,non-specific,238828,508,729,2.55339e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29687,Q#2047 - >seq8694,non-specific,197336,3,187,6.006069999999999e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29688,Q#2047 - >seq8694,non-specific,236970,3,230,1.2153399999999998e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29689,Q#2047 - >seq8694,non-specific,275209,458,663,1.78178e-07,54.386,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
29690,Q#2047 - >seq8694,superfamily,275209,458,663,1.78178e-07,54.386,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
29691,Q#2047 - >seq8694,non-specific,197322,2,229,2.5641e-07,53.8602,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29692,Q#2047 - >seq8694,non-specific,197311,1,139,3.24988e-06,49.2125,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
29693,Q#2047 - >seq8694,non-specific,339261,101,225,5.2809700000000004e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29694,Q#2047 - >seq8694,non-specific,235175,284,461,0.000114374,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
29695,Q#2047 - >seq8694,superfamily,235175,284,461,0.000114374,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
29696,Q#2047 - >seq8694,specific,311990,1236,1253,0.000636504,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29697,Q#2047 - >seq8694,superfamily,311990,1236,1253,0.000636504,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs6_sqmonkey,marg,CompleteHit
29698,Q#2047 - >seq8694,specific,225881,475,672,0.0047981000000000005,40.5925,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
29699,Q#2047 - >seq8694,superfamily,225881,475,672,0.0047981000000000005,40.5925,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
29700,Q#2047 - >seq8694,non-specific,274009,300,450,0.00831098,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
29701,Q#2047 - >seq8694,superfamily,274009,300,450,0.00831098,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs6_sqmonkey.marg.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
29702,Q#2050 - >seq8697,specific,238827,502,755,4.764449999999999e-62,210.61,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29703,Q#2050 - >seq8697,superfamily,295487,502,755,4.764449999999999e-62,210.61,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29704,Q#2050 - >seq8697,specific,197310,3,229,9.332599999999998e-60,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29705,Q#2050 - >seq8697,superfamily,351117,3,229,9.332599999999998e-60,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29706,Q#2050 - >seq8697,non-specific,197306,3,229,4.8541099999999995e-31,122.59,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29707,Q#2050 - >seq8697,specific,333820,508,732,5.8150799999999995e-31,120.09,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29708,Q#2050 - >seq8697,superfamily,333820,508,732,5.8150799999999995e-31,120.09,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29709,Q#2050 - >seq8697,non-specific,197320,3,222,1.25507e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29710,Q#2050 - >seq8697,non-specific,223780,3,230,1.49685e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29711,Q#2050 - >seq8697,non-specific,197307,3,229,5.17861e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29712,Q#2050 - >seq8697,non-specific,273186,3,230,2.6631599999999997e-18,85.7936,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29713,Q#2050 - >seq8697,non-specific,197321,1,229,6.94112e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29714,Q#2050 - >seq8697,non-specific,272954,3,229,9.66335e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29715,Q#2050 - >seq8697,specific,335306,4,222,4.7488e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29716,Q#2050 - >seq8697,non-specific,197319,7,229,1.6616900000000002e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29717,Q#2050 - >seq8697,non-specific,238828,508,729,3.5827300000000004e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29718,Q#2050 - >seq8697,non-specific,197336,3,187,5.53163e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29719,Q#2050 - >seq8697,non-specific,236970,3,230,4.95688e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29720,Q#2050 - >seq8697,non-specific,275209,458,663,3.53245e-08,56.6972,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
29721,Q#2050 - >seq8697,superfamily,275209,458,663,3.53245e-08,56.6972,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
29722,Q#2050 - >seq8697,non-specific,197322,2,229,2.44921e-07,53.8602,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29723,Q#2050 - >seq8697,non-specific,197311,1,139,2.0840900000000002e-06,49.5977,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
29724,Q#2050 - >seq8697,non-specific,235175,284,461,1.22353e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29725,Q#2050 - >seq8697,superfamily,235175,284,461,1.22353e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29726,Q#2050 - >seq8697,non-specific,339261,101,225,7.45942e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29727,Q#2050 - >seq8697,specific,225881,475,672,0.00055881,43.2889,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29728,Q#2050 - >seq8697,superfamily,225881,475,672,0.00055881,43.2889,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29729,Q#2050 - >seq8697,non-specific,274009,300,450,0.0040056,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
29730,Q#2050 - >seq8697,superfamily,274009,300,450,0.0040056,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
29731,Q#2050 - >seq8697,non-specific,223496,301,492,0.00798737,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29732,Q#2050 - >seq8697,superfamily,223496,301,492,0.00798737,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF2.hs6_sqmonkey.pars.frame3,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB2,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
29733,Q#2051 - >seq8698,specific,311990,1185,1202,6.36889e-05,40.7332,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs6_sqmonkey.pars.frame2,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29734,Q#2051 - >seq8698,superfamily,311990,1185,1202,6.36889e-05,40.7332,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs6_sqmonkey.pars.frame2,1909181529_L1PB2.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs6_sqmonkey,pars,CompleteHit
29735,Q#2054 - >seq8701,specific,238827,500,763,1.2062099999999998e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29736,Q#2054 - >seq8701,superfamily,295487,500,763,1.2062099999999998e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29737,Q#2054 - >seq8701,specific,197310,25,229,4.45098e-50,176.773,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29738,Q#2054 - >seq8701,superfamily,351117,25,229,4.45098e-50,176.773,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29739,Q#2054 - >seq8701,specific,333820,506,763,3.67211e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29740,Q#2054 - >seq8701,superfamily,333820,506,763,3.67211e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29741,Q#2054 - >seq8701,non-specific,197306,26,229,3.57808e-30,119.89399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29742,Q#2054 - >seq8701,non-specific,197307,25,229,1.0440100000000002e-14,75.0169,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29743,Q#2054 - >seq8701,non-specific,273186,14,230,1.67468e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29744,Q#2054 - >seq8701,non-specific,238828,506,727,2.9268e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29745,Q#2054 - >seq8701,non-specific,197321,25,229,3.3037e-13,70.6588,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29746,Q#2054 - >seq8701,non-specific,197320,13,222,3.57442e-13,70.6218,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29747,Q#2054 - >seq8701,non-specific,223780,23,230,1.1600799999999998e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29748,Q#2054 - >seq8701,specific,335306,23,222,1.71677e-11,64.959,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29749,Q#2054 - >seq8701,non-specific,197319,15,229,5.19155e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29750,Q#2054 - >seq8701,non-specific,272954,17,229,5.67437e-10,60.8597,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29751,Q#2054 - >seq8701,non-specific,275209,453,791,9.81141e-10,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29752,Q#2054 - >seq8701,superfamily,275209,453,791,9.81141e-10,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29753,Q#2054 - >seq8701,non-specific,339261,101,225,3.15663e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29754,Q#2054 - >seq8701,non-specific,197322,27,229,3.63001e-06,50.0082,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29755,Q#2054 - >seq8701,non-specific,197311,28,229,9.90962e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29756,Q#2054 - >seq8701,non-specific,236970,25,230,4.9422700000000004e-05,46.0406,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29757,Q#2054 - >seq8701,non-specific,197336,20,187,0.000733435,42.2143,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29758,Q#2054 - >seq8701,non-specific,238185,646,731,0.00101542,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs5_gmonkey.marg.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs5_gmonkey,marg,CompleteHit
29759,Q#2055 - >seq8702,specific,238827,471,732,8.775679999999999e-65,217.929,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29760,Q#2055 - >seq8702,superfamily,295487,471,732,8.775679999999999e-65,217.929,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29761,Q#2055 - >seq8702,specific,333820,477,732,3.0226999999999998e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29762,Q#2055 - >seq8702,superfamily,333820,477,732,3.0226999999999998e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29763,Q#2055 - >seq8702,non-specific,238828,477,698,5.5595500000000007e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29764,Q#2055 - >seq8702,non-specific,275209,426,760,4.38922e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29765,Q#2055 - >seq8702,superfamily,275209,426,760,4.38922e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29766,Q#2055 - >seq8702,non-specific,238185,617,702,0.00025370599999999997,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29767,Q#2057 - >seq8704,specific,197310,25,230,4.27238e-52,182.551,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29768,Q#2057 - >seq8704,superfamily,351117,25,230,4.27238e-52,182.551,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29769,Q#2057 - >seq8704,non-specific,197306,25,230,3.7359599999999997e-31,122.59,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29770,Q#2057 - >seq8704,non-specific,197307,25,230,3.7073299999999995e-17,81.9505,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29771,Q#2057 - >seq8704,non-specific,197321,25,230,1.0920999999999999e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29772,Q#2057 - >seq8704,non-specific,223780,25,231,1.90944e-14,74.1719,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29773,Q#2057 - >seq8704,non-specific,197320,25,223,4.6974699999999994e-14,72.933,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29774,Q#2057 - >seq8704,non-specific,273186,14,231,2.32895e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29775,Q#2057 - >seq8704,non-specific,197319,25,230,1.0577899999999999e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29776,Q#2057 - >seq8704,specific,335306,25,223,1.15045e-11,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29777,Q#2057 - >seq8704,non-specific,272954,17,230,1.72223e-10,62.4005,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29778,Q#2057 - >seq8704,non-specific,339261,102,226,2.2522099999999998e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29779,Q#2057 - >seq8704,non-specific,236970,26,231,3.2023200000000004e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29780,Q#2057 - >seq8704,non-specific,197322,28,230,3.4089300000000005e-06,50.0082,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29781,Q#2057 - >seq8704,non-specific,197311,21,230,4.11748e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29782,Q#2057 - >seq8704,non-specific,197336,20,188,0.000133104,44.5255,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA15-16,ORF2,hs5_gmonkey,pars,CompleteHit
29783,Q#2057 - >seq8704,non-specific,235175,285,460,0.0008480489999999999,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15-16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29784,Q#2057 - >seq8704,superfamily,235175,285,460,0.0008480489999999999,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs5_gmonkey.pars.frame1,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA15-16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
29785,Q#2058 - >seq8705,non-specific,240274,256,516,0.0069015,40.3585,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1PA15-16.ORF2.hs5_gmonkey.marg.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29786,Q#2058 - >seq8705,superfamily,240274,256,516,0.0069015,40.3585,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1PA15-16.ORF2.hs5_gmonkey.marg.frame3,1909181529_L1PA15-16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15-16,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29787,Q#2059 - >seq8706,specific,197310,3,229,5.01519e-58,199.885,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29788,Q#2059 - >seq8706,superfamily,351117,3,229,5.01519e-58,199.885,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29789,Q#2059 - >seq8706,non-specific,197306,3,229,1.98431e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29790,Q#2059 - >seq8706,non-specific,197320,3,222,3.67584e-22,96.8153,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29791,Q#2059 - >seq8706,non-specific,223780,3,230,5.15526e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29792,Q#2059 - >seq8706,non-specific,197307,3,229,1.77337e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29793,Q#2059 - >seq8706,non-specific,273186,3,230,1.67738e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29794,Q#2059 - >seq8706,specific,335306,4,222,4.2859899999999995e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29795,Q#2059 - >seq8706,non-specific,197319,7,229,1.2785100000000001e-16,80.7837,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29796,Q#2059 - >seq8706,non-specific,272954,3,229,7.5157e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29797,Q#2059 - >seq8706,non-specific,197321,1,229,1.58121e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29798,Q#2059 - >seq8706,non-specific,197336,3,187,1.3042500000000001e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29799,Q#2059 - >seq8706,non-specific,197322,2,229,1.3574e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29800,Q#2059 - >seq8706,non-specific,236970,3,242,9.61663e-08,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29801,Q#2059 - >seq8706,non-specific,197311,24,229,3.71648e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29802,Q#2059 - >seq8706,non-specific,339261,101,225,0.000132964,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29803,Q#2059 - >seq8706,non-specific,235175,299,460,0.00545247,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29804,Q#2059 - >seq8706,superfamily,235175,299,460,0.00545247,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
29805,Q#2060 - >seq8707,specific,238827,473,737,1.4975699999999999e-64,217.929,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29806,Q#2060 - >seq8707,superfamily,295487,473,737,1.4975699999999999e-64,217.929,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29807,Q#2060 - >seq8707,specific,333820,479,702,1.21527e-34,130.875,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29808,Q#2060 - >seq8707,superfamily,333820,479,702,1.21527e-34,130.875,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29809,Q#2060 - >seq8707,non-specific,238828,479,699,1.2436799999999999e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29810,Q#2060 - >seq8707,non-specific,275209,429,699,3.2130400000000005e-10,62.8604,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29811,Q#2060 - >seq8707,superfamily,275209,429,699,3.2130400000000005e-10,62.8604,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29812,Q#2060 - >seq8707,non-specific,238185,618,695,0.00061911,40.0268,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
29813,Q#2060 - >seq8707,non-specific,239569,488,700,0.000935647,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs5_gmonkey.marg.frame2,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs5_gmonkey,marg,CompleteHit
29814,Q#2062 - >seq8709,specific,238827,506,758,4.4089899999999996e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29815,Q#2062 - >seq8709,superfamily,295487,506,758,4.4089899999999996e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29816,Q#2062 - >seq8709,specific,197310,3,229,6.624839999999999e-57,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29817,Q#2062 - >seq8709,superfamily,351117,3,229,6.624839999999999e-57,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29818,Q#2062 - >seq8709,specific,333820,512,735,4.3015899999999997e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29819,Q#2062 - >seq8709,superfamily,333820,512,735,4.3015899999999997e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29820,Q#2062 - >seq8709,non-specific,197306,3,229,1.1703199999999999e-32,126.82700000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29821,Q#2062 - >seq8709,non-specific,197320,3,222,3.2051400000000003e-22,96.8153,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29822,Q#2062 - >seq8709,non-specific,223780,3,230,4.49118e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29823,Q#2062 - >seq8709,non-specific,197307,3,229,2.0933199999999997e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29824,Q#2062 - >seq8709,non-specific,273186,3,230,1.46353e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29825,Q#2062 - >seq8709,specific,335306,4,222,3.75431e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29826,Q#2062 - >seq8709,non-specific,197319,7,229,5.33597e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29827,Q#2062 - >seq8709,non-specific,197321,1,229,2.8479299999999997e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29828,Q#2062 - >seq8709,non-specific,272954,3,229,3.18478e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29829,Q#2062 - >seq8709,non-specific,238828,512,732,1.19321e-14,74.1596,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29830,Q#2062 - >seq8709,non-specific,275209,462,732,8.58642e-11,64.4012,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29831,Q#2062 - >seq8709,superfamily,275209,462,732,8.58642e-11,64.4012,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29832,Q#2062 - >seq8709,non-specific,197336,3,187,1.1408e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29833,Q#2062 - >seq8709,non-specific,197322,2,229,1.1831399999999999e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29834,Q#2062 - >seq8709,non-specific,236970,3,182,6.27059e-07,51.8186,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29835,Q#2062 - >seq8709,non-specific,197311,24,229,3.2687400000000004e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29836,Q#2062 - >seq8709,non-specific,339261,101,225,0.000200485,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29837,Q#2062 - >seq8709,non-specific,239569,521,733,0.000548679,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29838,Q#2062 - >seq8709,non-specific,238185,651,728,0.000571682,40.0268,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
29839,Q#2062 - >seq8709,specific,225881,430,730,0.00373851,40.5925,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29840,Q#2062 - >seq8709,superfamily,225881,430,730,0.00373851,40.5925,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa1,ORF2,hs5_gmonkey,pars,CompleteHit
29841,Q#2067 - >seq8714,non-specific,335182,156,252,1.40243e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29842,Q#2067 - >seq8714,superfamily,335182,156,252,1.40243e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29843,Q#2067 - >seq8714,non-specific,335182,156,252,1.40243e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29844,Q#2067 - >seq8714,non-specific,340205,255,318,9.183910000000002e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29845,Q#2067 - >seq8714,superfamily,340205,255,318,9.183910000000002e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29846,Q#2067 - >seq8714,non-specific,340205,255,318,9.183910000000002e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29847,Q#2067 - >seq8714,non-specific,340204,111,153,1.14907e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29848,Q#2067 - >seq8714,superfamily,340204,111,153,1.14907e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29849,Q#2067 - >seq8714,non-specific,340204,111,153,1.14907e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,pars,CompleteHit
29850,Q#2067 - >seq8714,non-specific,274009,60,203,1.25775e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29851,Q#2067 - >seq8714,superfamily,274009,60,203,1.25775e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29852,Q#2067 - >seq8714,non-specific,274009,60,203,1.25775e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29853,Q#2067 - >seq8714,non-specific,274008,41,202,0.00011107100000000001,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29854,Q#2067 - >seq8714,superfamily,274008,41,202,0.00011107100000000001,43.8919,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29855,Q#2067 - >seq8714,non-specific,274008,41,202,0.00011107100000000001,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29856,Q#2067 - >seq8714,non-specific,235175,49,156,0.00017340900000000002,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29857,Q#2067 - >seq8714,superfamily,235175,49,156,0.00017340900000000002,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29858,Q#2067 - >seq8714,non-specific,235175,49,156,0.00017340900000000002,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29859,Q#2067 - >seq8714,non-specific,237177,42,149,0.000240011,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29860,Q#2067 - >seq8714,superfamily,237177,42,149,0.000240011,42.4578,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29861,Q#2067 - >seq8714,non-specific,237177,42,149,0.000240011,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29862,Q#2067 - >seq8714,non-specific,224117,28,177,0.00040360699999999995,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29863,Q#2067 - >seq8714,superfamily,224117,28,177,0.00040360699999999995,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29864,Q#2067 - >seq8714,non-specific,224117,28,177,0.00040360699999999995,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29865,Q#2067 - >seq8714,non-specific,336159,60,145,0.000610393,41.2009,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29866,Q#2067 - >seq8714,superfamily,336159,60,145,0.000610393,41.2009,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29867,Q#2067 - >seq8714,non-specific,336159,60,145,0.000610393,41.2009,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29868,Q#2067 - >seq8714,non-specific,235461,47,170,0.000691082,40.8218,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29869,Q#2067 - >seq8714,superfamily,235461,47,170,0.000691082,40.8218,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29870,Q#2067 - >seq8714,non-specific,235461,47,170,0.000691082,40.8218,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29871,Q#2067 - >seq8714,non-specific,223250,47,170,0.0009015830000000001,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29872,Q#2067 - >seq8714,superfamily,223250,47,170,0.0009015830000000001,40.6593,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29873,Q#2067 - >seq8714,non-specific,223250,47,170,0.0009015830000000001,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29874,Q#2067 - >seq8714,non-specific,337663,79,183,0.00168416,39.3303,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29875,Q#2067 - >seq8714,superfamily,337663,79,183,0.00168416,39.3303,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29876,Q#2067 - >seq8714,non-specific,337663,79,183,0.00168416,39.3303,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29877,Q#2067 - >seq8714,non-specific,275056,60,152,0.00191188,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29878,Q#2067 - >seq8714,superfamily,275056,60,152,0.00191188,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29879,Q#2067 - >seq8714,non-specific,275056,60,152,0.00191188,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
29880,Q#2067 - >seq8714,non-specific,274009,33,150,0.00344446,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29881,Q#2067 - >seq8714,superfamily,274009,33,150,0.00344446,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29882,Q#2067 - >seq8714,non-specific,274009,33,150,0.00344446,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29883,Q#2067 - >seq8714,non-specific,226400,79,149,0.00407522,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29884,Q#2067 - >seq8714,superfamily,226400,79,149,0.00407522,38.161,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29885,Q#2067 - >seq8714,non-specific,226400,79,149,0.00407522,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29886,Q#2067 - >seq8714,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29887,Q#2067 - >seq8714,superfamily,274386,27,147,0.00426967,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29888,Q#2067 - >seq8714,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29889,Q#2067 - >seq8714,non-specific,112704,2,148,0.00430423,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29890,Q#2067 - >seq8714,superfamily,112704,2,148,0.00430423,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29891,Q#2067 - >seq8714,non-specific,112704,2,148,0.00430423,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29892,Q#2067 - >seq8714,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29893,Q#2067 - >seq8714,superfamily,274008,45,150,0.00471737,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29894,Q#2067 - >seq8714,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
29895,Q#2067 - >seq8714,non-specific,310273,60,194,0.00491252,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29896,Q#2067 - >seq8714,superfamily,310273,60,194,0.00491252,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29897,Q#2067 - >seq8714,non-specific,310273,60,194,0.00491252,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29898,Q#2067 - >seq8714,non-specific,129694,80,146,0.00677157,38.1041,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29899,Q#2067 - >seq8714,superfamily,129694,80,146,0.00677157,38.1041,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29900,Q#2067 - >seq8714,non-specific,129694,80,146,0.00677157,38.1041,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.pars.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,pars,C-TerminusTruncated
29901,Q#2070 - >seq8717,non-specific,335182,156,252,1.40243e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29902,Q#2070 - >seq8717,superfamily,335182,156,252,1.40243e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29903,Q#2070 - >seq8717,non-specific,335182,156,252,1.40243e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29904,Q#2070 - >seq8717,non-specific,340205,255,318,9.183910000000002e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29905,Q#2070 - >seq8717,superfamily,340205,255,318,9.183910000000002e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29906,Q#2070 - >seq8717,non-specific,340205,255,318,9.183910000000002e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29907,Q#2070 - >seq8717,non-specific,340204,111,153,1.14907e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29908,Q#2070 - >seq8717,superfamily,340204,111,153,1.14907e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29909,Q#2070 - >seq8717,non-specific,340204,111,153,1.14907e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs5_gmonkey,marg,CompleteHit
29910,Q#2070 - >seq8717,non-specific,274009,60,203,1.25775e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29911,Q#2070 - >seq8717,superfamily,274009,60,203,1.25775e-05,46.5995,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29912,Q#2070 - >seq8717,non-specific,274009,60,203,1.25775e-05,46.5995,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29913,Q#2070 - >seq8717,non-specific,274008,41,202,0.00011107100000000001,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29914,Q#2070 - >seq8717,superfamily,274008,41,202,0.00011107100000000001,43.8919,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29915,Q#2070 - >seq8717,non-specific,274008,41,202,0.00011107100000000001,43.8919,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29916,Q#2070 - >seq8717,non-specific,235175,49,156,0.00017340900000000002,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29917,Q#2070 - >seq8717,superfamily,235175,49,156,0.00017340900000000002,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29918,Q#2070 - >seq8717,non-specific,235175,49,156,0.00017340900000000002,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29919,Q#2070 - >seq8717,non-specific,237177,42,149,0.000240011,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29920,Q#2070 - >seq8717,superfamily,237177,42,149,0.000240011,42.4578,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29921,Q#2070 - >seq8717,non-specific,237177,42,149,0.000240011,42.4578,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29922,Q#2070 - >seq8717,non-specific,224117,28,177,0.00040360699999999995,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29923,Q#2070 - >seq8717,superfamily,224117,28,177,0.00040360699999999995,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29924,Q#2070 - >seq8717,non-specific,224117,28,177,0.00040360699999999995,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29925,Q#2070 - >seq8717,non-specific,336159,60,145,0.000610393,41.2009,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29926,Q#2070 - >seq8717,superfamily,336159,60,145,0.000610393,41.2009,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29927,Q#2070 - >seq8717,non-specific,336159,60,145,0.000610393,41.2009,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29928,Q#2070 - >seq8717,non-specific,235461,47,170,0.000691082,40.8218,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29929,Q#2070 - >seq8717,superfamily,235461,47,170,0.000691082,40.8218,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29930,Q#2070 - >seq8717,non-specific,235461,47,170,0.000691082,40.8218,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29931,Q#2070 - >seq8717,non-specific,223250,47,170,0.0009015830000000001,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29932,Q#2070 - >seq8717,superfamily,223250,47,170,0.0009015830000000001,40.6593,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29933,Q#2070 - >seq8717,non-specific,223250,47,170,0.0009015830000000001,40.6593,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29934,Q#2070 - >seq8717,non-specific,337663,79,183,0.00168416,39.3303,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29935,Q#2070 - >seq8717,superfamily,337663,79,183,0.00168416,39.3303,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29936,Q#2070 - >seq8717,non-specific,337663,79,183,0.00168416,39.3303,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29937,Q#2070 - >seq8717,non-specific,275056,60,152,0.00191188,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29938,Q#2070 - >seq8717,superfamily,275056,60,152,0.00191188,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29939,Q#2070 - >seq8717,non-specific,275056,60,152,0.00191188,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
29940,Q#2070 - >seq8717,non-specific,274009,33,150,0.00344446,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29941,Q#2070 - >seq8717,superfamily,274009,33,150,0.00344446,38.8955,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29942,Q#2070 - >seq8717,non-specific,274009,33,150,0.00344446,38.8955,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29943,Q#2070 - >seq8717,non-specific,226400,79,149,0.00407522,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29944,Q#2070 - >seq8717,superfamily,226400,79,149,0.00407522,38.161,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29945,Q#2070 - >seq8717,non-specific,226400,79,149,0.00407522,38.161,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29946,Q#2070 - >seq8717,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29947,Q#2070 - >seq8717,superfamily,274386,27,147,0.00426967,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29948,Q#2070 - >seq8717,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29949,Q#2070 - >seq8717,non-specific,112704,2,148,0.00430423,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29950,Q#2070 - >seq8717,superfamily,112704,2,148,0.00430423,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29951,Q#2070 - >seq8717,non-specific,112704,2,148,0.00430423,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29952,Q#2070 - >seq8717,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29953,Q#2070 - >seq8717,superfamily,274008,45,150,0.00471737,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29954,Q#2070 - >seq8717,non-specific,274008,45,150,0.00471737,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
29955,Q#2070 - >seq8717,non-specific,310273,60,194,0.00491252,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29956,Q#2070 - >seq8717,superfamily,310273,60,194,0.00491252,38.573,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29957,Q#2070 - >seq8717,non-specific,310273,60,194,0.00491252,38.573,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29958,Q#2070 - >seq8717,non-specific,129694,80,146,0.00677157,38.1041,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29959,Q#2070 - >seq8717,superfamily,129694,80,146,0.00677157,38.1041,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29960,Q#2070 - >seq8717,non-specific,129694,80,146,0.00677157,38.1041,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs5_gmonkey.marg.frame3,1909181600_L1PBa1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
29961,Q#2071 - >seq8718,specific,197310,15,228,7.182979999999999e-41,150.58,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29962,Q#2071 - >seq8718,superfamily,351117,15,228,7.182979999999999e-41,150.58,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29963,Q#2071 - >seq8718,specific,238827,500,757,3.5324599999999995e-34,130.874,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29964,Q#2071 - >seq8718,superfamily,295487,500,757,3.5324599999999995e-34,130.874,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29965,Q#2071 - >seq8718,non-specific,197306,15,228,2.74602e-17,82.5292,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29966,Q#2071 - >seq8718,non-specific,333820,506,757,1.98342e-14,72.7102,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29967,Q#2071 - >seq8718,superfamily,333820,506,757,1.98342e-14,72.7102,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29968,Q#2071 - >seq8718,non-specific,197307,15,221,1.7036099999999998e-10,62.6905,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29969,Q#2071 - >seq8718,non-specific,223780,15,207,2.3488299999999994e-10,62.2307,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29970,Q#2071 - >seq8718,non-specific,197320,25,208,2.71135e-09,59.0658,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29971,Q#2071 - >seq8718,specific,335306,24,221,1.07664e-06,50.7066,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29972,Q#2071 - >seq8718,non-specific,197311,30,228,2.97577e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29973,Q#2071 - >seq8718,non-specific,197321,23,228,2.6829499999999998e-05,47.1616,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29974,Q#2071 - >seq8718,non-specific,273186,15,229,6.120520000000001e-05,45.7328,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29975,Q#2071 - >seq8718,non-specific,272954,24,207,0.00054031,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,CompleteHit
29976,Q#2071 - >seq8718,non-specific,197322,91,228,0.00056437,43.4598,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.pars.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,pars,N-TerminusTruncated
29977,Q#2074 - >seq8721,specific,197310,15,236,5.2439599999999994e-46,165.602,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29978,Q#2074 - >seq8721,superfamily,351117,15,236,5.2439599999999994e-46,165.602,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29979,Q#2074 - >seq8721,specific,238827,508,766,9.65978e-35,132.415,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29980,Q#2074 - >seq8721,superfamily,295487,508,766,9.65978e-35,132.415,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29981,Q#2074 - >seq8721,non-specific,197306,15,236,4.98885e-19,87.5368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29982,Q#2074 - >seq8721,non-specific,333820,514,766,3.3673400000000003e-14,71.9398,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29983,Q#2074 - >seq8721,superfamily,333820,514,766,3.3673400000000003e-14,71.9398,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29984,Q#2074 - >seq8721,non-specific,197307,15,229,2.40403e-12,68.0833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29985,Q#2074 - >seq8721,non-specific,223780,15,229,1.28655e-11,66.0827,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29986,Q#2074 - >seq8721,non-specific,197320,25,229,3.9416800000000003e-10,61.7622,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29987,Q#2074 - >seq8721,specific,335306,24,229,3.05798e-08,55.32899999999999,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29988,Q#2074 - >seq8721,non-specific,197321,23,236,1.61241e-06,50.6284,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29989,Q#2074 - >seq8721,non-specific,197322,91,236,2.8387599999999996e-06,50.3934,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
29990,Q#2074 - >seq8721,non-specific,273186,15,237,4.95651e-06,49.1996,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29991,Q#2074 - >seq8721,non-specific,197311,30,236,0.00015672600000000002,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29992,Q#2074 - >seq8721,non-specific,197319,21,236,0.000160638,44.5749,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29993,Q#2074 - >seq8721,non-specific,272954,24,207,0.000643007,42.7553,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29994,Q#2074 - >seq8721,non-specific,339261,108,232,0.00083743,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1ME1,ORF2,hs7_bushaby,marg,CompleteHit
29995,Q#2074 - >seq8721,non-specific,235175,306,460,0.00347821,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
29996,Q#2074 - >seq8721,superfamily,235175,306,460,0.00347821,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1ME1,ORF2,hs7_bushaby,marg,BothTerminiTruncated
29997,Q#2074 - >seq8721,non-specific,238828,562,737,0.00715588,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs7_bushaby.marg.frame3,1909181618_L1ME1.RM_HPGPNRMPCCSO_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs7_bushaby,marg,N-TerminusTruncated
29998,Q#2077 - >seq8724,non-specific,335182,156,252,1.4790899999999999e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
29999,Q#2077 - >seq8724,superfamily,335182,156,252,1.4790899999999999e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30000,Q#2077 - >seq8724,non-specific,335182,156,252,1.4790899999999999e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30001,Q#2077 - >seq8724,non-specific,340205,255,318,8.9945e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30002,Q#2077 - >seq8724,superfamily,340205,255,318,8.9945e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30003,Q#2077 - >seq8724,non-specific,340205,255,318,8.9945e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30004,Q#2077 - >seq8724,non-specific,340204,111,153,3.823680000000001e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30005,Q#2077 - >seq8724,superfamily,340204,111,153,3.823680000000001e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30006,Q#2077 - >seq8724,non-specific,340204,111,153,3.823680000000001e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,pars,CompleteHit
30007,Q#2077 - >seq8724,non-specific,274009,60,203,1.11201e-05,46.9847,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30008,Q#2077 - >seq8724,superfamily,274009,60,203,1.11201e-05,46.9847,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30009,Q#2077 - >seq8724,non-specific,274009,60,203,1.11201e-05,46.9847,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30010,Q#2077 - >seq8724,non-specific,235175,49,156,7.40003e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30011,Q#2077 - >seq8724,superfamily,235175,49,156,7.40003e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30012,Q#2077 - >seq8724,non-specific,235175,49,156,7.40003e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30013,Q#2077 - >seq8724,non-specific,237177,42,149,7.47879e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30014,Q#2077 - >seq8724,superfamily,237177,42,149,7.47879e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30015,Q#2077 - >seq8724,non-specific,237177,42,149,7.47879e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30016,Q#2077 - >seq8724,non-specific,274008,41,202,0.00012231,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30017,Q#2077 - >seq8724,superfamily,274008,41,202,0.00012231,43.5067,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30018,Q#2077 - >seq8724,non-specific,274008,41,202,0.00012231,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30019,Q#2077 - >seq8724,non-specific,224117,28,177,0.00025163700000000003,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30020,Q#2077 - >seq8724,superfamily,224117,28,177,0.00025163700000000003,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30021,Q#2077 - >seq8724,non-specific,224117,28,177,0.00025163700000000003,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30022,Q#2077 - >seq8724,non-specific,310273,60,194,0.0016429000000000003,39.7286,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30023,Q#2077 - >seq8724,superfamily,310273,60,194,0.0016429000000000003,39.7286,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30024,Q#2077 - >seq8724,non-specific,310273,60,194,0.0016429000000000003,39.7286,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30025,Q#2077 - >seq8724,non-specific,275056,60,152,0.00187685,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30026,Q#2077 - >seq8724,superfamily,275056,60,152,0.00187685,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30027,Q#2077 - >seq8724,non-specific,275056,60,152,0.00187685,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30028,Q#2077 - >seq8724,non-specific,223250,47,170,0.0023835,39.1185,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30029,Q#2077 - >seq8724,superfamily,223250,47,170,0.0023835,39.1185,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30030,Q#2077 - >seq8724,non-specific,223250,47,170,0.0023835,39.1185,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30031,Q#2077 - >seq8724,non-specific,129694,80,146,0.00266681,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30032,Q#2077 - >seq8724,superfamily,129694,80,146,0.00266681,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30033,Q#2077 - >seq8724,non-specific,129694,80,146,0.00266681,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30034,Q#2077 - >seq8724,non-specific,336159,60,145,0.00270914,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30035,Q#2077 - >seq8724,superfamily,336159,60,145,0.00270914,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30036,Q#2077 - >seq8724,non-specific,336159,60,145,0.00270914,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,pars,N-TerminusTruncated
30037,Q#2077 - >seq8724,non-specific,274008,45,150,0.00279587,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30038,Q#2077 - >seq8724,non-specific,274008,45,150,0.00279587,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30039,Q#2077 - >seq8724,non-specific,235175,60,144,0.00314469,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30040,Q#2077 - >seq8724,non-specific,235175,60,144,0.00314469,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30041,Q#2077 - >seq8724,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30042,Q#2077 - >seq8724,superfamily,274386,27,147,0.00426967,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30043,Q#2077 - >seq8724,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30044,Q#2077 - >seq8724,non-specific,235461,47,170,0.00454188,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30045,Q#2077 - >seq8724,superfamily,235461,47,170,0.00454188,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30046,Q#2077 - >seq8724,non-specific,235461,47,170,0.00454188,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30047,Q#2077 - >seq8724,non-specific,226400,79,149,0.00483528,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30048,Q#2077 - >seq8724,superfamily,226400,79,149,0.00483528,37.7758,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30049,Q#2077 - >seq8724,non-specific,226400,79,149,0.00483528,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30050,Q#2077 - >seq8724,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30051,Q#2077 - >seq8724,superfamily,337663,79,183,0.00497954,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30052,Q#2077 - >seq8724,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30053,Q#2077 - >seq8724,non-specific,112704,2,148,0.00742743,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30054,Q#2077 - >seq8724,superfamily,112704,2,148,0.00742743,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30055,Q#2077 - >seq8724,non-specific,112704,2,148,0.00742743,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30056,Q#2077 - >seq8724,non-specific,274008,60,145,0.00775138,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30057,Q#2077 - >seq8724,non-specific,274008,60,145,0.00775138,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30058,Q#2077 - >seq8724,non-specific,188306,43,150,0.00790726,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30059,Q#2077 - >seq8724,superfamily,188306,43,150,0.00790726,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30060,Q#2077 - >seq8724,non-specific,188306,43,150,0.00790726,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,pars,C-TerminusTruncated
30061,Q#2077 - >seq8724,non-specific,274009,33,150,0.00938265,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30062,Q#2077 - >seq8724,superfamily,274009,33,150,0.00938265,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30063,Q#2077 - >seq8724,non-specific,274009,33,150,0.00938265,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,pars,BothTerminiTruncated
30064,Q#2079 - >seq8726,non-specific,335182,156,252,1.4790899999999999e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30065,Q#2079 - >seq8726,superfamily,335182,156,252,1.4790899999999999e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30066,Q#2079 - >seq8726,non-specific,335182,156,252,1.4790899999999999e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30067,Q#2079 - >seq8726,non-specific,340205,255,318,8.9945e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30068,Q#2079 - >seq8726,superfamily,340205,255,318,8.9945e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30069,Q#2079 - >seq8726,non-specific,340205,255,318,8.9945e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30070,Q#2079 - >seq8726,non-specific,340204,111,153,3.823680000000001e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30071,Q#2079 - >seq8726,superfamily,340204,111,153,3.823680000000001e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30072,Q#2079 - >seq8726,non-specific,340204,111,153,3.823680000000001e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs4_gibbon,marg,CompleteHit
30073,Q#2079 - >seq8726,non-specific,274009,60,203,1.11201e-05,46.9847,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30074,Q#2079 - >seq8726,superfamily,274009,60,203,1.11201e-05,46.9847,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30075,Q#2079 - >seq8726,non-specific,274009,60,203,1.11201e-05,46.9847,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30076,Q#2079 - >seq8726,non-specific,235175,49,156,7.40003e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30077,Q#2079 - >seq8726,superfamily,235175,49,156,7.40003e-05,44.2844,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30078,Q#2079 - >seq8726,non-specific,235175,49,156,7.40003e-05,44.2844,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30079,Q#2079 - >seq8726,non-specific,237177,42,149,7.47879e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30080,Q#2079 - >seq8726,superfamily,237177,42,149,7.47879e-05,43.9986,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30081,Q#2079 - >seq8726,non-specific,237177,42,149,7.47879e-05,43.9986,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30082,Q#2079 - >seq8726,non-specific,274008,41,202,0.00012231,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30083,Q#2079 - >seq8726,superfamily,274008,41,202,0.00012231,43.5067,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30084,Q#2079 - >seq8726,non-specific,274008,41,202,0.00012231,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30085,Q#2079 - >seq8726,non-specific,224117,28,177,0.00025163700000000003,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30086,Q#2079 - >seq8726,superfamily,224117,28,177,0.00025163700000000003,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30087,Q#2079 - >seq8726,non-specific,224117,28,177,0.00025163700000000003,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30088,Q#2079 - >seq8726,non-specific,310273,60,194,0.0016429000000000003,39.7286,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30089,Q#2079 - >seq8726,superfamily,310273,60,194,0.0016429000000000003,39.7286,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30090,Q#2079 - >seq8726,non-specific,310273,60,194,0.0016429000000000003,39.7286,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30091,Q#2079 - >seq8726,non-specific,275056,60,152,0.00187685,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30092,Q#2079 - >seq8726,superfamily,275056,60,152,0.00187685,38.4505,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30093,Q#2079 - >seq8726,non-specific,275056,60,152,0.00187685,38.4505,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30094,Q#2079 - >seq8726,non-specific,223250,47,170,0.0023835,39.1185,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30095,Q#2079 - >seq8726,superfamily,223250,47,170,0.0023835,39.1185,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30096,Q#2079 - >seq8726,non-specific,223250,47,170,0.0023835,39.1185,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30097,Q#2079 - >seq8726,non-specific,129694,80,146,0.00266681,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30098,Q#2079 - >seq8726,superfamily,129694,80,146,0.00266681,39.2597,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30099,Q#2079 - >seq8726,non-specific,129694,80,146,0.00266681,39.2597,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30100,Q#2079 - >seq8726,non-specific,336159,60,145,0.00270914,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30101,Q#2079 - >seq8726,superfamily,336159,60,145,0.00270914,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30102,Q#2079 - >seq8726,non-specific,336159,60,145,0.00270914,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs4_gibbon,marg,N-TerminusTruncated
30103,Q#2079 - >seq8726,non-specific,274008,45,150,0.00279587,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30104,Q#2079 - >seq8726,non-specific,274008,45,150,0.00279587,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30105,Q#2079 - >seq8726,non-specific,235175,60,144,0.00314469,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30106,Q#2079 - >seq8726,non-specific,235175,60,144,0.00314469,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30107,Q#2079 - >seq8726,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30108,Q#2079 - >seq8726,superfamily,274386,27,147,0.00426967,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30109,Q#2079 - >seq8726,non-specific,274386,27,147,0.00426967,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30110,Q#2079 - >seq8726,non-specific,235461,47,170,0.00454188,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30111,Q#2079 - >seq8726,superfamily,235461,47,170,0.00454188,38.1254,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30112,Q#2079 - >seq8726,non-specific,235461,47,170,0.00454188,38.1254,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30113,Q#2079 - >seq8726,non-specific,226400,79,149,0.00483528,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30114,Q#2079 - >seq8726,superfamily,226400,79,149,0.00483528,37.7758,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30115,Q#2079 - >seq8726,non-specific,226400,79,149,0.00483528,37.7758,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30116,Q#2079 - >seq8726,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30117,Q#2079 - >seq8726,superfamily,337663,79,183,0.00497954,38.1747,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30118,Q#2079 - >seq8726,non-specific,337663,79,183,0.00497954,38.1747,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30119,Q#2079 - >seq8726,non-specific,112704,2,148,0.00742743,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30120,Q#2079 - >seq8726,superfamily,112704,2,148,0.00742743,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30121,Q#2079 - >seq8726,non-specific,112704,2,148,0.00742743,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30122,Q#2079 - >seq8726,non-specific,274008,60,145,0.00775138,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30123,Q#2079 - >seq8726,non-specific,274008,60,145,0.00775138,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30124,Q#2079 - >seq8726,non-specific,188306,43,150,0.00790726,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30125,Q#2079 - >seq8726,superfamily,188306,43,150,0.00790726,37.5978,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30126,Q#2079 - >seq8726,non-specific,188306,43,150,0.00790726,37.5978,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs4_gibbon,marg,C-TerminusTruncated
30127,Q#2079 - >seq8726,non-specific,274009,33,150,0.00938265,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30128,Q#2079 - >seq8726,superfamily,274009,33,150,0.00938265,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30129,Q#2079 - >seq8726,non-specific,274009,33,150,0.00938265,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs4_gibbon,marg,BothTerminiTruncated
30130,Q#2081 - >seq8728,specific,197310,34,223,8.18611e-40,147.498,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30131,Q#2081 - >seq8728,superfamily,351117,34,223,8.18611e-40,147.498,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30132,Q#2081 - >seq8728,non-specific,197306,50,223,6.93035e-20,89.848,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30133,Q#2081 - >seq8728,non-specific,197320,44,216,8.499469999999999e-13,69.4662,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30134,Q#2081 - >seq8728,non-specific,223780,37,224,3.87859e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30135,Q#2081 - >seq8728,non-specific,197307,44,223,4.05181e-11,64.2313,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30136,Q#2081 - >seq8728,non-specific,197319,40,223,3.80655e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30137,Q#2081 - >seq8728,non-specific,272954,50,223,1.7000800000000002e-07,53.5409,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30138,Q#2081 - >seq8728,specific,335306,17,216,1.29184e-06,50.3214,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30139,Q#2081 - >seq8728,non-specific,273186,42,224,1.7735e-06,50.3552,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30140,Q#2081 - >seq8728,non-specific,197321,56,223,3.97e-06,49.4728,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30141,Q#2081 - >seq8728,non-specific,339261,95,219,0.00202587,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs4_gibbon.pars.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30142,Q#2082 - >seq8729,specific,238827,455,716,1.5537299999999998e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30143,Q#2082 - >seq8729,superfamily,295487,455,716,1.5537299999999998e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30144,Q#2082 - >seq8729,specific,333820,461,685,1.7326299999999998e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30145,Q#2082 - >seq8729,superfamily,333820,461,685,1.7326299999999998e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30146,Q#2082 - >seq8729,non-specific,238828,461,682,2.18352e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30147,Q#2082 - >seq8729,non-specific,275209,407,669,1.20581e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30148,Q#2082 - >seq8729,superfamily,275209,407,669,1.20581e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30149,Q#2082 - >seq8729,non-specific,238185,601,678,0.00297983,38.1008,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30150,Q#2082 - >seq8729,non-specific,239569,470,683,0.00378277,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs4_gibbon.pars.frame2,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs4_gibbon,pars,CompleteHit
30151,Q#2083 - >seq8730,non-specific,197310,3,65,1.54152e-09,59.2873,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30152,Q#2083 - >seq8730,superfamily,351117,3,65,1.54152e-09,59.2873,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30153,Q#2083 - >seq8730,non-specific,197306,3,82,8.431510000000002e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30154,Q#2083 - >seq8730,specific,335306,4,67,3.66935e-05,46.0842,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30155,Q#2083 - >seq8730,non-specific,223780,3,37,4.97859e-05,46.0523,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30156,Q#2083 - >seq8730,non-specific,197321,1,68,0.000222985,44.08,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30157,Q#2083 - >seq8730,non-specific,273186,3,37,0.00149632,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30158,Q#2083 - >seq8730,non-specific,197307,3,68,0.0022069000000000004,40.7341,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30159,Q#2083 - >seq8730,non-specific,197336,3,68,0.00384061,40.2883,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30160,Q#2083 - >seq8730,non-specific,197320,3,37,0.00757869,39.4206,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.pars.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30161,Q#2084 - >seq8731,specific,197310,34,223,4.98614e-41,150.965,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30162,Q#2084 - >seq8731,superfamily,351117,34,223,4.98614e-41,150.965,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30163,Q#2084 - >seq8731,non-specific,197306,50,223,4.44769e-20,90.6184,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30164,Q#2084 - >seq8731,non-specific,197320,44,216,8.447020000000001e-13,69.4662,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30165,Q#2084 - >seq8731,non-specific,223780,37,224,3.85457e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30166,Q#2084 - >seq8731,non-specific,197307,44,223,2.04144e-11,65.3869,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30167,Q#2084 - >seq8731,non-specific,197319,40,223,3.17475e-09,58.8273,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30168,Q#2084 - >seq8731,non-specific,272954,50,223,1.04973e-07,54.3113,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30169,Q#2084 - >seq8731,specific,335306,17,216,1.28417e-06,50.3214,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30170,Q#2084 - >seq8731,non-specific,273186,42,224,1.7628e-06,50.3552,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30171,Q#2084 - >seq8731,non-specific,197321,56,223,4.01851e-06,49.4728,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30172,Q#2084 - >seq8731,non-specific,334125,199,395,9.420789999999999e-06,49.07,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PBa1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30173,Q#2084 - >seq8731,superfamily,334125,199,395,9.420789999999999e-06,49.07,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1PBa1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30174,Q#2084 - >seq8731,non-specific,235850,291,462,0.000177348,44.622,PRK06669,fliH,C,cl35503,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30175,Q#2084 - >seq8731,superfamily,235850,291,462,0.000177348,44.622,cl35503,fliH superfamily,C, - ,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30176,Q#2084 - >seq8731,non-specific,339261,95,219,0.0006027480000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30177,Q#2084 - >seq8731,non-specific,235175,277,428,0.000677845,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PBa1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
30178,Q#2084 - >seq8731,superfamily,235175,277,428,0.000677845,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PBa1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
30179,Q#2084 - >seq8731,non-specific,274009,293,441,0.00074525,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30180,Q#2084 - >seq8731,superfamily,274009,293,441,0.00074525,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30181,Q#2084 - >seq8731,non-specific,274009,280,419,0.00404894,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs4_gibbon.marg.frame1,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PBa1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
30182,Q#2086 - >seq8733,specific,238827,470,731,2.0055899999999996e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30183,Q#2086 - >seq8733,superfamily,295487,470,731,2.0055899999999996e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30184,Q#2086 - >seq8733,specific,333820,476,700,2.3388e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30185,Q#2086 - >seq8733,superfamily,333820,476,700,2.3388e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30186,Q#2086 - >seq8733,non-specific,238828,476,697,2.93216e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30187,Q#2086 - >seq8733,non-specific,197310,3,65,5.6328e-09,57.7465,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30188,Q#2086 - >seq8733,superfamily,351117,3,65,5.6328e-09,57.7465,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30189,Q#2086 - >seq8733,non-specific,275209,422,684,1.47319e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30190,Q#2086 - >seq8733,superfamily,275209,422,684,1.47319e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30191,Q#2086 - >seq8733,non-specific,197306,3,82,1.8866499999999998e-07,53.2541,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30192,Q#2086 - >seq8733,specific,335306,4,67,3.92446e-05,46.0842,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30193,Q#2086 - >seq8733,non-specific,223780,3,37,7.30412e-05,45.6671,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30194,Q#2086 - >seq8733,non-specific,197321,1,68,0.000630076,42.5392,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30195,Q#2086 - >seq8733,non-specific,273186,3,37,0.00205649,41.1104,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30196,Q#2086 - >seq8733,non-specific,238185,616,693,0.002621,38.1008,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30197,Q#2086 - >seq8733,non-specific,197336,3,68,0.00410765,40.2883,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30198,Q#2086 - >seq8733,non-specific,239569,485,698,0.00442503,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa1,ORF2,hs4_gibbon,marg,CompleteHit
30199,Q#2086 - >seq8733,non-specific,197320,3,37,0.00810456,39.4206,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30200,Q#2086 - >seq8733,non-specific,197307,3,68,0.00870465,39.1933,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs4_gibbon.marg.frame3,1909181618_L1PBa1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30201,Q#2089 - >seq8736,specific,238827,501,761,4.4329e-49,173.63099999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30202,Q#2089 - >seq8736,superfamily,295487,501,761,4.4329e-49,173.63099999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30203,Q#2089 - >seq8736,specific,197310,37,230,4.848669999999999e-39,145.187,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,CompleteHit
30204,Q#2089 - >seq8736,superfamily,351117,37,230,4.848669999999999e-39,145.187,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,marg,CompleteHit
30205,Q#2089 - >seq8736,non-specific,333820,512,761,6.95077e-25,102.756,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30206,Q#2089 - >seq8736,superfamily,333820,512,761,6.95077e-25,102.756,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30207,Q#2089 - >seq8736,non-specific,197306,57,230,4.6335900000000004e-15,75.9808,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30208,Q#2089 - >seq8736,non-specific,197320,48,223,3.4701999999999997e-13,70.6218,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,marg,CompleteHit
30209,Q#2089 - >seq8736,non-specific,223780,48,223,6.1883099999999995e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,marg,CompleteHit
30210,Q#2089 - >seq8736,non-specific,197307,100,223,1.29817e-08,56.9125,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30211,Q#2089 - >seq8736,non-specific,238828,576,761,3.23735e-08,55.2848,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30212,Q#2089 - >seq8736,specific,335306,50,223,8.36845e-08,54.1734,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30213,Q#2089 - >seq8736,non-specific,197319,100,230,8.47265e-08,54.5901,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30214,Q#2089 - >seq8736,non-specific,273186,100,231,1.9821799999999997e-06,50.3552,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30215,Q#2089 - >seq8736,non-specific,238185,646,761,6.560750000000001e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30216,Q#2089 - >seq8736,non-specific,339261,102,225,6.603889999999999e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB1,ORF2,hs0_human,marg,CompleteHit
30217,Q#2089 - >seq8736,non-specific,275209,577,783,1.1558099999999999e-05,48.9932,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30218,Q#2089 - >seq8736,superfamily,275209,577,783,1.1558099999999999e-05,48.9932,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30219,Q#2089 - >seq8736,non-specific,272954,100,201,0.000422469,43.5257,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30220,Q#2089 - >seq8736,non-specific,197321,100,223,0.00046200300000000006,43.3096,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30221,Q#2089 - >seq8736,non-specific,197311,100,198,0.00571099,39.1973,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs0_human.marg.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,marg,N-TerminusTruncated
30222,Q#2091 - >seq8738,non-specific,340205,165,229,2.05269e-29,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30223,Q#2091 - >seq8738,superfamily,340205,165,229,2.05269e-29,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30224,Q#2091 - >seq8738,non-specific,340205,165,229,2.05269e-29,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30225,Q#2091 - >seq8738,non-specific,335182,66,162,3.02402e-24,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30226,Q#2091 - >seq8738,superfamily,335182,66,162,3.02402e-24,92.3658,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30227,Q#2091 - >seq8738,non-specific,335182,66,162,3.02402e-24,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.pars.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,pars,CompleteHit
30228,Q#2094 - >seq8741,non-specific,340205,165,229,2.05269e-29,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30229,Q#2094 - >seq8741,superfamily,340205,165,229,2.05269e-29,104.726,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30230,Q#2094 - >seq8741,non-specific,340205,165,229,2.05269e-29,104.726,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30231,Q#2094 - >seq8741,non-specific,335182,66,162,3.02402e-24,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30232,Q#2094 - >seq8741,superfamily,335182,66,162,3.02402e-24,92.3658,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30233,Q#2094 - >seq8741,non-specific,335182,66,162,3.02402e-24,92.3658,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs2_gorilla.marg.frame3,1909181618_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs2_gorilla,marg,CompleteHit
30234,Q#2095 - >seq8742,non-specific,340205,187,251,3.26151e-28,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs3_orang.pars.frame1,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs3_orang,pars,CompleteHit
30235,Q#2095 - >seq8742,superfamily,340205,187,251,3.26151e-28,102.029,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs3_orang.pars.frame1,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs3_orang,pars,CompleteHit
30236,Q#2095 - >seq8742,non-specific,335182,97,184,1.8261e-22,88.1286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs3_orang.pars.frame1,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs3_orang,pars,CompleteHit
30237,Q#2095 - >seq8742,superfamily,335182,97,184,1.8261e-22,88.1286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs3_orang.pars.frame1,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1MA9,ORF1,hs3_orang,pars,CompleteHit
30238,Q#2096 - >seq8743,non-specific,197310,9,57,1.083e-08,56.9761,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs0_human.marg.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs0_human,marg,C-TerminusTruncated
30239,Q#2096 - >seq8743,superfamily,351117,9,57,1.083e-08,56.9761,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.marg.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,marg,C-TerminusTruncated
30240,Q#2096 - >seq8743,non-specific,197306,9,60,0.000523087,42.8537,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.marg.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,marg,C-TerminusTruncated
30241,Q#2096 - >seq8743,non-specific,223780,9,41,0.0034704000000000002,40.2743,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs0_human.marg.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs0_human,marg,C-TerminusTruncated
30242,Q#2100 - >seq8747,non-specific,340205,209,273,6.51364e-28,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs3_orang.marg.frame3,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs3_orang,marg,CompleteHit
30243,Q#2100 - >seq8747,superfamily,340205,209,273,6.51364e-28,102.029,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1MA9.ORF1.hs3_orang.marg.frame3,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs3_orang,marg,CompleteHit
30244,Q#2100 - >seq8747,non-specific,335182,119,206,3.6843900000000005e-22,88.1286,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs3_orang.marg.frame3,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs3_orang,marg,CompleteHit
30245,Q#2100 - >seq8747,superfamily,335182,119,206,3.6843900000000005e-22,88.1286,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1MA9.ORF1.hs3_orang.marg.frame3,1909181618_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1MA9,ORF1,hs3_orang,marg,CompleteHit
30246,Q#2102 - >seq8749,non-specific,197310,120,218,7.75909e-20,89.7181,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30247,Q#2102 - >seq8749,superfamily,351117,120,218,7.75909e-20,89.7181,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30248,Q#2102 - >seq8749,non-specific,197306,110,218,4.82411e-08,55.1801,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30249,Q#2102 - >seq8749,non-specific,197320,116,211,4.05029e-07,52.5174,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30250,Q#2102 - >seq8749,specific,335306,52,211,4.7368000000000004e-07,51.8622,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30251,Q#2102 - >seq8749,non-specific,223780,122,211,8.230589999999999e-07,51.4451,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30252,Q#2102 - >seq8749,non-specific,197307,112,211,1.1351600000000001e-06,51.1345,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30253,Q#2102 - >seq8749,non-specific,197319,112,218,1.1125e-05,48.0417,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30254,Q#2102 - >seq8749,non-specific,197321,120,211,0.00339498,40.6132,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30255,Q#2102 - >seq8749,non-specific,339261,88,213,0.00383431,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs0_human.pars.frame2,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30256,Q#2103 - >seq8750,specific,238827,466,725,4.31632e-49,173.63099999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30257,Q#2103 - >seq8750,superfamily,295487,466,725,4.31632e-49,173.63099999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30258,Q#2103 - >seq8750,non-specific,333820,477,725,4.43685e-25,103.52600000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30259,Q#2103 - >seq8750,superfamily,333820,477,725,4.43685e-25,103.52600000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30260,Q#2103 - >seq8750,non-specific,197310,4,124,2.0362000000000002e-22,97.42200000000001,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30261,Q#2103 - >seq8750,superfamily,351117,4,124,2.0362000000000002e-22,97.42200000000001,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30262,Q#2103 - >seq8750,non-specific,238828,541,725,3.21291e-08,55.2848,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30263,Q#2103 - >seq8750,non-specific,197306,4,125,9.07102e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30264,Q#2103 - >seq8750,non-specific,238185,611,725,1.24839e-06,47.7308,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,CompleteHit
30265,Q#2103 - >seq8750,non-specific,275209,542,744,1.28084e-05,48.608000000000004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30266,Q#2103 - >seq8750,superfamily,275209,542,744,1.28084e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs0_human,pars,N-TerminusTruncated
30267,Q#2103 - >seq8750,non-specific,223780,4,74,0.00017077,44.5115,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30268,Q#2103 - >seq8750,specific,335306,4,75,0.000326157,43.3878,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30269,Q#2103 - >seq8750,non-specific,197307,4,72,0.00424136,39.9637,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs0_human.pars.frame3,1909181618_L1MB1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs0_human,pars,C-TerminusTruncated
30270,Q#2107 - >seq8754,specific,238827,524,715,3.15719e-29,116.62200000000001,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30271,Q#2107 - >seq8754,superfamily,295487,524,715,3.15719e-29,116.62200000000001,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30272,Q#2107 - >seq8754,non-specific,333820,531,715,1.53708e-18,84.6513,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30273,Q#2107 - >seq8754,superfamily,333820,531,715,1.53708e-18,84.6513,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30274,Q#2107 - >seq8754,non-specific,238828,531,715,4.03873e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30275,Q#2107 - >seq8754,non-specific,275209,532,739,9.168519999999999e-07,52.0748,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30276,Q#2107 - >seq8754,superfamily,275209,532,739,9.168519999999999e-07,52.0748,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30277,Q#2107 - >seq8754,non-specific,238185,601,715,7.65921e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs1_chimp.marg.frame2,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30278,Q#2108 - >seq8755,specific,197310,9,234,4.11977e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30279,Q#2108 - >seq8755,superfamily,351117,9,234,4.11977e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30280,Q#2108 - >seq8755,non-specific,197306,9,234,1.6885099999999998e-29,117.96799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30281,Q#2108 - >seq8755,non-specific,197320,7,227,4.33447e-22,96.8153,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30282,Q#2108 - >seq8755,non-specific,223780,9,227,7.780710000000001e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30283,Q#2108 - >seq8755,non-specific,197307,9,227,2.93975e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30284,Q#2108 - >seq8755,specific,335306,10,227,3.28883e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30285,Q#2108 - >seq8755,non-specific,272954,7,205,2.42083e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30286,Q#2108 - >seq8755,non-specific,197319,7,234,5.64974e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30287,Q#2108 - >seq8755,non-specific,273186,7,235,1.41107e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30288,Q#2108 - >seq8755,non-specific,197321,7,227,7.18232e-14,72.5848,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30289,Q#2108 - >seq8755,non-specific,238827,498,553,2.10127e-12,67.7014,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
30290,Q#2108 - >seq8755,superfamily,295487,498,553,2.10127e-12,67.7014,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
30291,Q#2108 - >seq8755,non-specific,197336,7,227,3.08381e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30292,Q#2108 - >seq8755,non-specific,197311,38,202,8.921389999999998e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30293,Q#2108 - >seq8755,non-specific,236970,9,227,2.76051e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30294,Q#2108 - >seq8755,non-specific,339261,106,229,3.04806e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30295,Q#2108 - >seq8755,non-specific,197318,9,228,5.0023999999999994e-05,46.1355,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,marg,CompleteHit
30296,Q#2108 - >seq8755,non-specific,333820,504,557,8.30078e-05,44.5906,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
30297,Q#2108 - >seq8755,superfamily,333820,504,557,8.30078e-05,44.5906,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.marg.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
30298,Q#2112 - >seq8759,specific,197310,9,237,1.2205499999999999e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30299,Q#2112 - >seq8759,superfamily,351117,9,237,1.2205499999999999e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30300,Q#2112 - >seq8759,specific,238827,502,760,7.226749999999999e-47,167.468,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30301,Q#2112 - >seq8759,superfamily,295487,502,760,7.226749999999999e-47,167.468,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30302,Q#2112 - >seq8759,non-specific,197306,9,237,1.5064999999999998e-28,115.271,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30303,Q#2112 - >seq8759,non-specific,333820,508,760,2.46127e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30304,Q#2112 - >seq8759,superfamily,333820,508,760,2.46127e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30305,Q#2112 - >seq8759,non-specific,197320,7,230,4.259439999999999e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30306,Q#2112 - >seq8759,non-specific,223780,9,230,3.99581e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30307,Q#2112 - >seq8759,specific,335306,10,230,2.96435e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30308,Q#2112 - >seq8759,non-specific,197307,9,230,2.29533e-17,83.1061,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30309,Q#2112 - >seq8759,non-specific,273186,7,238,4.6248199999999994e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30310,Q#2112 - >seq8759,non-specific,272954,7,208,1.0283900000000001e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30311,Q#2112 - >seq8759,non-specific,197319,7,237,2.26717e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30312,Q#2112 - >seq8759,non-specific,197321,7,230,1.4962899999999999e-12,68.7328,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30313,Q#2112 - >seq8759,non-specific,238828,575,760,1.82909e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30314,Q#2112 - >seq8759,non-specific,275209,576,784,6.04884e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30315,Q#2112 - >seq8759,superfamily,275209,576,784,6.04884e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30316,Q#2112 - >seq8759,non-specific,197336,7,230,6.560120000000001e-07,51.8443,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30317,Q#2112 - >seq8759,non-specific,197311,38,205,7.78013e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30318,Q#2112 - >seq8759,non-specific,339261,109,232,4.7401e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30319,Q#2112 - >seq8759,non-specific,236970,9,230,7.32542e-05,45.6554,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30320,Q#2112 - >seq8759,non-specific,238185,645,760,0.000392114,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30321,Q#2112 - >seq8759,non-specific,197318,9,231,0.000477334,43.0539,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MB1.ORF2.hs1_chimp.pars.frame3,1909181622_L1MB1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MB1,ORF2,hs1_chimp,pars,CompleteHit
30322,Q#2113 - >seq8760,specific,238827,505,697,1.0117200000000001e-26,109.303,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30323,Q#2113 - >seq8760,superfamily,295487,505,697,1.0117200000000001e-26,109.303,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30324,Q#2113 - >seq8760,non-specific,333820,519,697,1.17561e-15,76.17699999999999,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30325,Q#2113 - >seq8760,superfamily,333820,519,697,1.17561e-15,76.17699999999999,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30326,Q#2113 - >seq8760,non-specific,238828,514,651,6.885160000000001e-10,60.2924,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30327,Q#2113 - >seq8760,non-specific,275209,515,719,0.00017606799999999998,45.1412,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30328,Q#2113 - >seq8760,superfamily,275209,515,719,0.00017606799999999998,45.1412,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30329,Q#2113 - >seq8760,non-specific,238185,584,697,0.00281831,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.pars.frame1,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30330,Q#2114 - >seq8761,specific,197310,18,221,9.30258e-36,135.942,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30331,Q#2114 - >seq8761,superfamily,351117,18,221,9.30258e-36,135.942,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30332,Q#2114 - >seq8761,non-specific,197306,16,227,1.2948e-13,71.7437,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30333,Q#2114 - >seq8761,non-specific,223780,17,220,2.80048e-10,62.2307,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30334,Q#2114 - >seq8761,non-specific,197320,19,220,9.03863e-10,60.6066,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30335,Q#2114 - >seq8761,specific,335306,12,220,2.1253299999999998e-08,55.7142,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30336,Q#2114 - >seq8761,non-specific,238827,494,533,1.46653e-07,53.449,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30337,Q#2114 - >seq8761,superfamily,295487,494,533,1.46653e-07,53.449,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30338,Q#2114 - >seq8761,non-specific,197307,16,220,1.57344e-07,53.8309,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30339,Q#2114 - >seq8761,non-specific,273186,100,228,5.46078e-06,49.1996,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30340,Q#2114 - >seq8761,non-specific,197321,16,220,1.0750799999999999e-05,47.931999999999995,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30341,Q#2114 - >seq8761,non-specific,272954,17,227,2.41502e-05,46.9925,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30342,Q#2114 - >seq8761,non-specific,274009,251,487,8.52608e-05,46.5995,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30343,Q#2114 - >seq8761,superfamily,274009,251,487,8.52608e-05,46.5995,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
30344,Q#2114 - >seq8761,non-specific,339261,100,221,0.0005356769999999999,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30345,Q#2114 - >seq8761,non-specific,313050,242,431,0.00105805,42.4814,pfam09755,DUF2046,N,cl25730,Uncharacterized conserved protein H4 (DUF2046); This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.,L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30346,Q#2114 - >seq8761,superfamily,313050,242,431,0.00105805,42.4814,cl25730,DUF2046 superfamily,N, - ,Uncharacterized conserved protein H4 (DUF2046); This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.,L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1MB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
30347,Q#2114 - >seq8761,non-specific,224259,208,453,0.00130333,41.9756,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30348,Q#2114 - >seq8761,superfamily,224259,208,453,0.00130333,41.9756,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs4_gibbon.pars.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs4_gibbon,pars,CompleteHit
30349,Q#2117 - >seq8764,specific,197310,18,221,4.321699999999999e-35,134.016,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30350,Q#2117 - >seq8764,superfamily,351117,18,221,4.321699999999999e-35,134.016,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30351,Q#2117 - >seq8764,non-specific,238827,495,579,1.34303e-13,71.1682,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30352,Q#2117 - >seq8764,superfamily,295487,495,579,1.34303e-13,71.1682,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30353,Q#2117 - >seq8764,non-specific,197306,16,227,2.6149899999999997e-13,70.9733,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30354,Q#2117 - >seq8764,non-specific,223780,17,220,2.77115e-10,62.2307,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30355,Q#2117 - >seq8764,non-specific,197320,19,220,7.78409e-10,60.6066,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30356,Q#2117 - >seq8764,specific,335306,12,220,2.26335e-08,55.7142,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30357,Q#2117 - >seq8764,non-specific,197307,16,220,2.0872199999999998e-07,53.4457,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30358,Q#2117 - >seq8764,non-specific,273186,100,228,7.840089999999999e-06,48.4292,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30359,Q#2117 - >seq8764,non-specific,197321,16,220,9.71601e-06,48.3172,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30360,Q#2117 - >seq8764,non-specific,272954,17,227,5.01457e-05,46.2221,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30361,Q#2117 - >seq8764,non-specific,274009,251,488,7.14841e-05,46.9847,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30362,Q#2117 - >seq8764,superfamily,274009,251,488,7.14841e-05,46.9847,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30363,Q#2117 - >seq8764,non-specific,333820,501,552,0.000178722,43.435,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30364,Q#2117 - >seq8764,superfamily,333820,501,552,0.000178722,43.435,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
30365,Q#2117 - >seq8764,non-specific,224259,208,454,0.0008015089999999999,42.746,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30366,Q#2117 - >seq8764,superfamily,224259,208,454,0.0008015089999999999,42.746,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30367,Q#2117 - >seq8764,non-specific,339261,100,221,0.00108906,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs4_gibbon.marg.frame2,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30368,Q#2118 - >seq8765,non-specific,238827,497,689,3.6049300000000004e-26,107.762,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30369,Q#2118 - >seq8765,superfamily,295487,497,689,3.6049300000000004e-26,107.762,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30370,Q#2118 - >seq8765,non-specific,333820,511,689,1.4025499999999999e-15,75.7918,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30371,Q#2118 - >seq8765,superfamily,333820,511,689,1.4025499999999999e-15,75.7918,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30372,Q#2118 - >seq8765,non-specific,238828,506,643,5.46861e-10,60.6776,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30373,Q#2118 - >seq8765,non-specific,275209,507,713,4.809559999999999e-06,49.7636,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30374,Q#2118 - >seq8765,superfamily,275209,507,713,4.809559999999999e-06,49.7636,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
30375,Q#2118 - >seq8765,non-specific,238185,576,689,0.00434626,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs4_gibbon.marg.frame3,1909181623_L1MB3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MB3,ORF2,hs4_gibbon,marg,CompleteHit
30376,Q#2120 - >seq8767,specific,238827,496,751,8.091359999999999e-47,167.083,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30377,Q#2120 - >seq8767,superfamily,295487,496,751,8.091359999999999e-47,167.083,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30378,Q#2120 - >seq8767,specific,197310,21,223,2.26068e-41,152.12,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30379,Q#2120 - >seq8767,superfamily,351117,21,223,2.26068e-41,152.12,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30380,Q#2120 - >seq8767,non-specific,333820,502,751,1.98761e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30381,Q#2120 - >seq8767,superfamily,333820,502,751,1.98761e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30382,Q#2120 - >seq8767,non-specific,197306,22,223,1.0801199999999999e-13,72.1289,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30383,Q#2120 - >seq8767,specific,335306,21,216,5.801949999999999e-13,69.5814,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30384,Q#2120 - >seq8767,non-specific,197320,21,216,1.09171e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30385,Q#2120 - >seq8767,non-specific,223780,21,216,1.5690100000000001e-09,59.9195,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30386,Q#2120 - >seq8767,non-specific,238828,571,751,2.4348899999999996e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,N-TerminusTruncated
30387,Q#2120 - >seq8767,non-specific,197321,16,216,1.64928e-06,50.6284,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30388,Q#2120 - >seq8767,non-specific,197307,17,216,3.38079e-06,49.5937,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30389,Q#2120 - >seq8767,non-specific,275209,572,777,8.96915e-06,48.9932,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,N-TerminusTruncated
30390,Q#2120 - >seq8767,superfamily,275209,572,777,8.96915e-06,48.9932,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,N-TerminusTruncated
30391,Q#2120 - >seq8767,non-specific,339261,98,218,1.82014e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30392,Q#2120 - >seq8767,non-specific,272954,21,194,0.000347592,43.5257,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30393,Q#2120 - >seq8767,non-specific,197311,26,223,0.0003965,42.6641,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30394,Q#2120 - >seq8767,non-specific,197322,97,216,0.00114832,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,N-TerminusTruncated
30395,Q#2120 - >seq8767,non-specific,273186,21,224,0.00137154,41.8808,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,pars,CompleteHit
30396,Q#2120 - >seq8767,non-specific,238185,641,751,0.00295161,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MB3,ORF2,hs0_human,pars,CompleteHit
30397,Q#2120 - >seq8767,non-specific,224259,249,455,0.00562002,40.0496,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs0_human,pars,CompleteHit
30398,Q#2120 - >seq8767,superfamily,224259,249,455,0.00562002,40.0496,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs0_human.pars.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MB3,ORF2,hs0_human,pars,CompleteHit
30399,Q#2123 - >seq8770,specific,238827,504,756,4.46096e-37,138.963,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,CompleteHit
30400,Q#2123 - >seq8770,superfamily,295487,504,756,4.46096e-37,138.963,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,CompleteHit
30401,Q#2123 - >seq8770,specific,197310,41,231,1.95266e-34,132.09,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,marg,CompleteHit
30402,Q#2123 - >seq8770,superfamily,351117,41,231,1.95266e-34,132.09,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,marg,CompleteHit
30403,Q#2123 - >seq8770,non-specific,333820,510,726,2.1561199999999997e-25,104.29700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,CompleteHit
30404,Q#2123 - >seq8770,superfamily,333820,510,726,2.1561199999999997e-25,104.29700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,CompleteHit
30405,Q#2123 - >seq8770,non-specific,197306,46,231,2.34943e-10,62.1137,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,marg,CompleteHit
30406,Q#2123 - >seq8770,specific,335306,53,224,1.1237e-08,56.8698,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30407,Q#2123 - >seq8770,non-specific,238828,577,714,1.1778999999999999e-08,56.8256,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30408,Q#2123 - >seq8770,non-specific,197320,106,224,1.79013e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30409,Q#2123 - >seq8770,non-specific,223780,50,224,6.083650000000001e-07,52.2155,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,marg,CompleteHit
30410,Q#2123 - >seq8770,non-specific,275209,578,792,3.38964e-06,50.534,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30411,Q#2123 - >seq8770,superfamily,275209,578,792,3.38964e-06,50.534,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30412,Q#2123 - >seq8770,non-specific,339261,106,226,2.2959200000000002e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1MB3,ORF2,hs0_human,marg,CompleteHit
30413,Q#2123 - >seq8770,non-specific,273186,105,232,0.000306569,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30414,Q#2123 - >seq8770,non-specific,197321,107,224,0.0009329280000000001,42.153999999999996,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30415,Q#2123 - >seq8770,non-specific,197322,105,224,0.00114832,42.3042,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30416,Q#2123 - >seq8770,non-specific,197307,50,224,0.00281652,40.7341,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MB3,ORF2,hs0_human,marg,CompleteHit
30417,Q#2123 - >seq8770,non-specific,272954,105,202,0.00306584,40.4441,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MB3,ORF2,hs0_human,marg,N-TerminusTruncated
30418,Q#2123 - >seq8770,non-specific,224259,257,463,0.00911461,39.2792,COG1340,COG1340, - ,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs0_human,marg,CompleteHit
30419,Q#2123 - >seq8770,superfamily,224259,257,463,0.00911461,39.2792,cl34231,COG1340 superfamily, - , - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MB3.ORF2.hs0_human.marg.frame2,1909181625_L1MB3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MB3,ORF2,hs0_human,marg,CompleteHit
30420,Q#2125 - >seq8772,specific,197310,3,230,4.82336e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30421,Q#2125 - >seq8772,superfamily,351117,3,230,4.82336e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30422,Q#2125 - >seq8772,non-specific,197306,3,230,1.60645e-33,129.524,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30423,Q#2125 - >seq8772,non-specific,223780,3,231,8.443939999999998e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30424,Q#2125 - >seq8772,non-specific,197320,3,200,2.80814e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30425,Q#2125 - >seq8772,non-specific,197307,3,230,3.92569e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30426,Q#2125 - >seq8772,specific,335306,4,223,5.0798000000000005e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30427,Q#2125 - >seq8772,non-specific,197319,7,230,1.45897e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30428,Q#2125 - >seq8772,non-specific,273186,3,231,5.14124e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30429,Q#2125 - >seq8772,non-specific,272954,3,230,8.33539e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30430,Q#2125 - >seq8772,non-specific,197321,1,230,1.2734999999999999e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30431,Q#2125 - >seq8772,non-specific,197336,3,188,1.42618e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30432,Q#2125 - >seq8772,non-specific,197322,2,230,2.0340700000000004e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30433,Q#2125 - >seq8772,non-specific,236970,3,183,3.19464e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30434,Q#2125 - >seq8772,non-specific,197311,24,230,3.5474300000000005e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30435,Q#2125 - >seq8772,non-specific,334125,206,403,2.7724099999999998e-05,47.5292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs3_orang,marg,N-TerminusTruncated
30436,Q#2125 - >seq8772,superfamily,334125,206,403,2.7724099999999998e-05,47.5292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs3_orang,marg,N-TerminusTruncated
30437,Q#2125 - >seq8772,non-specific,274009,301,449,0.000487011,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30438,Q#2125 - >seq8772,superfamily,274009,301,449,0.000487011,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30439,Q#2125 - >seq8772,non-specific,235175,285,436,0.000494043,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,marg,BothTerminiTruncated
30440,Q#2125 - >seq8772,superfamily,235175,285,436,0.000494043,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,marg,BothTerminiTruncated
30441,Q#2125 - >seq8772,non-specific,339261,102,226,0.000606115,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30442,Q#2125 - >seq8772,non-specific,338310,984,1046,0.00136724,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,marg,BothTerminiTruncated
30443,Q#2125 - >seq8772,superfamily,338310,984,1046,0.00136724,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,marg,BothTerminiTruncated
30444,Q#2125 - >seq8772,non-specific,274009,288,427,0.00262363,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,marg,BothTerminiTruncated
30445,Q#2125 - >seq8772,non-specific,235850,299,470,0.00339235,40.3848,PRK06669,fliH,C,cl35503,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30446,Q#2125 - >seq8772,superfamily,235850,299,470,0.00339235,40.3848,cl35503,fliH superfamily,C, - ,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs3_orang.marg.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30447,Q#2126 - >seq8773,non-specific,130009,400,685,0.0049513000000000005,40.7366,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs3_orang.marg.frame1,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30448,Q#2126 - >seq8773,superfamily,130009,400,685,0.0049513000000000005,40.7366,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs3_orang.marg.frame1,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30449,Q#2127 - >seq8774,specific,238827,468,730,1.17127e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30450,Q#2127 - >seq8774,superfamily,295487,468,730,1.17127e-68,229.485,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30451,Q#2127 - >seq8774,non-specific,238827,468,730,1.17127e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30452,Q#2127 - >seq8774,specific,333820,474,730,3.5433400000000002e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30453,Q#2127 - >seq8774,superfamily,333820,474,730,3.5433400000000002e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30454,Q#2127 - >seq8774,non-specific,333820,474,730,3.5433400000000002e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30455,Q#2127 - >seq8774,non-specific,238828,474,695,3.82889e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30456,Q#2127 - >seq8774,non-specific,238828,474,695,3.82889e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30457,Q#2127 - >seq8774,non-specific,275209,424,682,1.35945e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30458,Q#2127 - >seq8774,superfamily,275209,424,682,1.35945e-09,60.9344,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30459,Q#2127 - >seq8774,non-specific,275209,424,682,1.35945e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,C-TerminusTruncated
30460,Q#2127 - >seq8774,non-specific,238185,614,728,2.72966e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30461,Q#2127 - >seq8774,non-specific,238185,614,728,2.72966e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30462,Q#2127 - >seq8774,non-specific,239569,483,696,0.0033542000000000003,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30463,Q#2127 - >seq8774,non-specific,239569,483,696,0.0033542000000000003,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs3_orang.marg.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,marg,CompleteHit
30464,Q#2128 - >seq8775,specific,238827,468,730,1.17127e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30465,Q#2128 - >seq8775,superfamily,295487,468,730,1.17127e-68,229.485,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30466,Q#2128 - >seq8775,non-specific,238827,468,730,1.17127e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30467,Q#2128 - >seq8775,specific,333820,474,730,3.5433400000000002e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30468,Q#2128 - >seq8775,superfamily,333820,474,730,3.5433400000000002e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30469,Q#2128 - >seq8775,non-specific,333820,474,730,3.5433400000000002e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30470,Q#2128 - >seq8775,non-specific,238828,474,695,3.82889e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30471,Q#2128 - >seq8775,non-specific,238828,474,695,3.82889e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30472,Q#2128 - >seq8775,non-specific,275209,424,682,1.35945e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30473,Q#2128 - >seq8775,superfamily,275209,424,682,1.35945e-09,60.9344,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30474,Q#2128 - >seq8775,non-specific,275209,424,682,1.35945e-09,60.9344,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30475,Q#2128 - >seq8775,non-specific,238185,614,728,2.72966e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30476,Q#2128 - >seq8775,non-specific,238185,614,728,2.72966e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30477,Q#2128 - >seq8775,non-specific,239569,483,696,0.0033542000000000003,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30478,Q#2128 - >seq8775,non-specific,239569,483,696,0.0033542000000000003,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa1.ORF2.hs3_orang.pars.frame2,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30479,Q#2129 - >seq8776,non-specific,130009,400,685,0.0049513000000000005,40.7366,TIGR00934,2a38euk,C,cl30043,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs3_orang.pars.frame1,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30480,Q#2129 - >seq8776,superfamily,130009,400,685,0.0049513000000000005,40.7366,cl30043,2a38euk superfamily,C, - ,"potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]",L1PBa1.ORF2.hs3_orang.pars.frame1,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30481,Q#2130 - >seq8777,specific,197310,3,230,4.82336e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30482,Q#2130 - >seq8777,superfamily,351117,3,230,4.82336e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30483,Q#2130 - >seq8777,non-specific,197306,3,230,1.60645e-33,129.524,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30484,Q#2130 - >seq8777,non-specific,223780,3,231,8.443939999999998e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30485,Q#2130 - >seq8777,non-specific,197320,3,200,2.80814e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30486,Q#2130 - >seq8777,non-specific,197307,3,230,3.92569e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30487,Q#2130 - >seq8777,specific,335306,4,223,5.0798000000000005e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30488,Q#2130 - >seq8777,non-specific,197319,7,230,1.45897e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30489,Q#2130 - >seq8777,non-specific,273186,3,231,5.14124e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30490,Q#2130 - >seq8777,non-specific,272954,3,230,8.33539e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30491,Q#2130 - >seq8777,non-specific,197321,1,230,1.2734999999999999e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30492,Q#2130 - >seq8777,non-specific,197336,3,188,1.42618e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30493,Q#2130 - >seq8777,non-specific,197322,2,230,2.0340700000000004e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30494,Q#2130 - >seq8777,non-specific,236970,3,183,3.19464e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30495,Q#2130 - >seq8777,non-specific,197311,24,230,3.5474300000000005e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30496,Q#2130 - >seq8777,non-specific,334125,206,403,2.7724099999999998e-05,47.5292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs3_orang,pars,N-TerminusTruncated
30497,Q#2130 - >seq8777,superfamily,334125,206,403,2.7724099999999998e-05,47.5292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa1,ORF2,hs3_orang,pars,N-TerminusTruncated
30498,Q#2130 - >seq8777,non-specific,274009,301,449,0.000487011,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30499,Q#2130 - >seq8777,superfamily,274009,301,449,0.000487011,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30500,Q#2130 - >seq8777,non-specific,235175,285,436,0.000494043,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,pars,BothTerminiTruncated
30501,Q#2130 - >seq8777,superfamily,235175,285,436,0.000494043,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,pars,BothTerminiTruncated
30502,Q#2130 - >seq8777,non-specific,339261,102,226,0.000606115,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa1,ORF2,hs3_orang,pars,CompleteHit
30503,Q#2130 - >seq8777,non-specific,338310,984,1046,0.00136724,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,pars,BothTerminiTruncated
30504,Q#2130 - >seq8777,superfamily,338310,984,1046,0.00136724,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,pars,BothTerminiTruncated
30505,Q#2130 - >seq8777,non-specific,274009,288,427,0.00262363,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF2,hs3_orang,pars,BothTerminiTruncated
30506,Q#2130 - >seq8777,non-specific,235850,299,470,0.00339235,40.3848,PRK06669,fliH,C,cl35503,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30507,Q#2130 - >seq8777,superfamily,235850,299,470,0.00339235,40.3848,cl35503,fliH superfamily,C, - ,flagellar assembly protein H; Validated,L1PBa1.ORF2.hs3_orang.pars.frame3,1909181629_L1PBa1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF2,hs3_orang,pars,C-TerminusTruncated
30508,Q#2133 - >seq8780,specific,197310,9,232,1.289e-34,132.475,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30509,Q#2133 - >seq8780,superfamily,351117,9,232,1.289e-34,132.475,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30510,Q#2133 - >seq8780,non-specific,197306,9,232,2.04091e-15,77.1364,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30511,Q#2133 - >seq8780,specific,335306,10,225,1.0703799999999999e-08,56.8698,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30512,Q#2133 - >seq8780,non-specific,223780,9,221,1.24186e-07,54.1415,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30513,Q#2133 - >seq8780,non-specific,197307,9,232,6.588379999999999e-07,51.9049,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30514,Q#2133 - >seq8780,non-specific,197320,9,217,3.4941e-06,49.4358,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30515,Q#2133 - >seq8780,non-specific,272954,9,203,0.000168801,44.2961,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30516,Q#2133 - >seq8780,non-specific,197319,9,232,0.00021271200000000002,44.1897,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30517,Q#2133 - >seq8780,non-specific,273186,9,233,0.000375876,43.4216,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,pars,CompleteHit
30518,Q#2133 - >seq8780,non-specific,234767,480,839,0.00151489,42.9028,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MD1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
30519,Q#2133 - >seq8780,superfamily,234767,480,839,0.00151489,42.9028,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MD1.ORF2.hs2_gorilla.pars.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MD1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
30520,Q#2134 - >seq8781,non-specific,234767,665,949,0.00161223,42.5176,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1MD1.ORF2.hs2_gorilla.marg.frame1,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
30521,Q#2134 - >seq8781,superfamily,234767,665,949,0.00161223,42.5176,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1MD1.ORF2.hs2_gorilla.marg.frame1,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_Chrom,L1MD1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
30522,Q#2134 - >seq8781,non-specific,238827,462,671,0.00431611,39.967,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs2_gorilla.marg.frame1,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30523,Q#2134 - >seq8781,superfamily,295487,462,671,0.00431611,39.967,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs2_gorilla.marg.frame1,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30524,Q#2136 - >seq8783,specific,197310,9,233,6.644299999999999e-37,139.024,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30525,Q#2136 - >seq8783,superfamily,351117,9,233,6.644299999999999e-37,139.024,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30526,Q#2136 - >seq8783,non-specific,197306,9,233,3.7676e-16,79.0624,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30527,Q#2136 - >seq8783,specific,335306,10,226,2.5746900000000003e-08,55.7142,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30528,Q#2136 - >seq8783,non-specific,223780,9,222,4.4646999999999996e-08,55.2971,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30529,Q#2136 - >seq8783,non-specific,197307,9,233,4.7018e-07,52.2901,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30530,Q#2136 - >seq8783,non-specific,197320,9,218,2.68616e-06,49.821000000000005,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30531,Q#2136 - >seq8783,non-specific,272954,9,204,0.000483588,43.1405,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30532,Q#2136 - >seq8783,non-specific,197319,9,233,0.00396606,40.3377,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs2_gorilla.marg.frame3,1909181630_L1MD1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs2_gorilla,marg,CompleteHit
30533,Q#2137 - >seq8784,specific,197310,9,232,2.99138e-37,140.179,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30534,Q#2137 - >seq8784,superfamily,351117,9,232,2.99138e-37,140.179,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30535,Q#2137 - >seq8784,non-specific,197306,9,232,4.16203e-17,82.14399999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30536,Q#2137 - >seq8784,non-specific,197320,9,203,2.94109e-08,55.9842,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30537,Q#2137 - >seq8784,non-specific,238827,550,748,6.150299999999999e-08,54.6046,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs0_human,marg,N-TerminusTruncated
30538,Q#2137 - >seq8784,superfamily,295487,550,748,6.150299999999999e-08,54.6046,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs0_human,marg,N-TerminusTruncated
30539,Q#2137 - >seq8784,non-specific,223780,9,203,1.14987e-06,51.0599,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30540,Q#2137 - >seq8784,specific,335306,10,225,1.61605e-06,50.3214,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30541,Q#2137 - >seq8784,non-specific,197321,7,232,3.8143200000000004e-05,46.3912,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30542,Q#2137 - >seq8784,non-specific,197307,9,232,5.23672e-05,46.1269,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,marg,CompleteHit
30543,Q#2137 - >seq8784,non-specific,197322,102,225,0.00259909,41.1486,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs0_human,marg,N-TerminusTruncated
30544,Q#2137 - >seq8784,non-specific,333820,561,711,0.00421563,39.583,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs0_human,marg,N-TerminusTruncated
30545,Q#2137 - >seq8784,superfamily,333820,561,711,0.00421563,39.583,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs0_human.marg.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs0_human,marg,N-TerminusTruncated
30546,Q#2142 - >seq8789,specific,197310,1,222,1.59026e-33,129.394,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs0_human,pars,CompleteHit
30547,Q#2142 - >seq8789,superfamily,351117,1,222,1.59026e-33,129.394,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,pars,CompleteHit
30548,Q#2142 - >seq8789,non-specific,197306,1,222,3.37931e-15,76.366,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,pars,CompleteHit
30549,Q#2142 - >seq8789,non-specific,238827,540,738,1.83486e-08,56.1454,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30550,Q#2142 - >seq8789,superfamily,295487,540,738,1.83486e-08,56.1454,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30551,Q#2142 - >seq8789,non-specific,197320,49,193,4.51256e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30552,Q#2142 - >seq8789,non-specific,223780,49,193,1.74048e-05,47.5931,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,pars,CompleteHit
30553,Q#2142 - >seq8789,specific,335306,49,215,2.69033e-05,46.4694,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30554,Q#2142 - >seq8789,non-specific,333820,551,701,0.00201546,40.3534,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30555,Q#2142 - >seq8789,superfamily,333820,551,701,0.00201546,40.3534,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30556,Q#2142 - >seq8789,non-specific,197307,93,222,0.00255484,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs0_human.pars.frame3,1909181645_L1MD1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs0_human,pars,N-TerminusTruncated
30557,Q#2143 - >seq8790,specific,197310,11,235,1.81827e-35,135.172,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30558,Q#2143 - >seq8790,superfamily,351117,11,235,1.81827e-35,135.172,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30559,Q#2143 - >seq8790,specific,238827,527,725,6.736839999999999e-31,121.244,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30560,Q#2143 - >seq8790,superfamily,295487,527,725,6.736839999999999e-31,121.244,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30561,Q#2143 - >seq8790,non-specific,197306,11,235,2.9605799999999996e-18,85.2256,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30562,Q#2143 - >seq8790,non-specific,333820,527,725,1.22205e-16,79.2586,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30563,Q#2143 - >seq8790,superfamily,333820,527,725,1.22205e-16,79.2586,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30564,Q#2143 - >seq8790,non-specific,238828,551,718,2.46227e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30565,Q#2143 - >seq8790,specific,335306,11,228,2.34092e-09,58.7958,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30566,Q#2143 - >seq8790,non-specific,223780,52,228,2.99561e-08,56.0675,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30567,Q#2143 - >seq8790,non-specific,197320,61,207,1.9112700000000001e-07,53.673,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
30568,Q#2143 - >seq8790,non-specific,197307,61,235,9.273980000000001e-07,51.5197,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
30569,Q#2143 - >seq8790,non-specific,275209,586,718,5.36073e-06,49.7636,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
30570,Q#2143 - >seq8790,superfamily,275209,586,718,5.36073e-06,49.7636,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,marg,BothTerminiTruncated
30571,Q#2143 - >seq8790,non-specific,272954,11,206,4.1142299999999994e-05,46.6073,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30572,Q#2143 - >seq8790,non-specific,197322,90,235,4.18611e-05,46.9266,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
30573,Q#2143 - >seq8790,non-specific,339261,107,231,0.000107751,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1ME1,ORF2,hs8_ctshrew,marg,CompleteHit
30574,Q#2143 - >seq8790,non-specific,273186,61,236,0.00028053,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
30575,Q#2143 - >seq8790,non-specific,197319,90,235,0.00028742599999999997,43.8045,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME1.ORF2.hs8_ctshrew.marg.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,marg,N-TerminusTruncated
30576,Q#2145 - >seq8792,specific,238827,496,692,1.39815e-31,123.17,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,CompleteHit
30577,Q#2145 - >seq8792,superfamily,295487,496,692,1.39815e-31,123.17,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,CompleteHit
30578,Q#2145 - >seq8792,non-specific,333820,496,692,1.40667e-16,78.8734,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,CompleteHit
30579,Q#2145 - >seq8792,superfamily,333820,496,692,1.40667e-16,78.8734,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,CompleteHit
30580,Q#2145 - >seq8792,non-specific,238828,519,685,9.63768e-13,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,CompleteHit
30581,Q#2145 - >seq8792,non-specific,197310,130,205,1.99012e-12,68.1469,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1ME1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
30582,Q#2145 - >seq8792,superfamily,351117,130,205,1.99012e-12,68.1469,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
30583,Q#2145 - >seq8792,non-specific,275209,550,634,2.25134e-05,47.8376,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
30584,Q#2145 - >seq8792,superfamily,275209,550,634,2.25134e-05,47.8376,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1ME1,ORF2,hs8_ctshrew,pars,BothTerminiTruncated
30585,Q#2145 - >seq8792,non-specific,197320,139,178,0.00678701,39.4206,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs8_ctshrew.pars.frame2,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,N-TerminusTruncated
30586,Q#2146 - >seq8793,non-specific,197310,3,124,1.39187e-12,68.5321,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30587,Q#2146 - >seq8793,superfamily,351117,3,124,1.39187e-12,68.5321,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30588,Q#2146 - >seq8793,non-specific,197306,3,138,0.000101266,44.7797,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30589,Q#2146 - >seq8793,non-specific,272954,3,127,0.0007133080000000001,42.3701,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30590,Q#2146 - >seq8793,non-specific,223780,3,120,0.000806199,42.2003,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30591,Q#2146 - >seq8793,non-specific,197307,3,127,0.00209853,41.1193,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs8_ctshrew.pars.frame3,1909181646_L1ME1.RM_HPGPNRMPCCSOT_1708181205.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs8_ctshrew,pars,C-TerminusTruncated
30592,Q#2149 - >seq8796,specific,197310,5,234,7.0736e-50,176.388,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30593,Q#2149 - >seq8796,superfamily,351117,5,234,7.0736e-50,176.388,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30594,Q#2149 - >seq8796,non-specific,197306,5,234,2.6498e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30595,Q#2149 - >seq8796,non-specific,197307,5,234,5.738060000000001e-14,72.7057,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30596,Q#2149 - >seq8796,non-specific,197320,3,227,7.65906e-13,69.4662,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30597,Q#2149 - >seq8796,non-specific,223780,5,227,6.39942e-12,66.8531,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30598,Q#2149 - >seq8796,specific,335306,6,227,6.712060000000001e-10,60.3366,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30599,Q#2149 - >seq8796,non-specific,197319,5,234,5.74516e-08,54.9753,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30600,Q#2149 - >seq8796,non-specific,272954,5,234,6.3719e-08,54.6965,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30601,Q#2149 - >seq8796,non-specific,273186,5,235,2.2938600000000001e-07,53.0516,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30602,Q#2149 - >seq8796,non-specific,197321,5,234,1.43029e-06,50.6284,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30603,Q#2149 - >seq8796,non-specific,339261,106,230,0.00882594,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA8.ORF2.hs5_gmonkey.marg.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30604,Q#2151 - >seq8798,specific,238827,484,747,2.7724799999999996e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30605,Q#2151 - >seq8798,superfamily,295487,484,747,2.7724799999999996e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30606,Q#2151 - >seq8798,specific,333820,490,747,2.39377e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30607,Q#2151 - >seq8798,superfamily,333820,490,747,2.39377e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30608,Q#2151 - >seq8798,non-specific,238828,556,721,3.91542e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
30609,Q#2151 - >seq8798,non-specific,275209,441,775,6.70454e-08,55.9268,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30610,Q#2151 - >seq8798,superfamily,275209,441,775,6.70454e-08,55.9268,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30611,Q#2151 - >seq8798,non-specific,274009,284,432,0.000863368,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
30612,Q#2151 - >seq8798,superfamily,274009,284,432,0.000863368,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
30613,Q#2151 - >seq8798,non-specific,224117,215,424,0.00146328,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
30614,Q#2151 - >seq8798,superfamily,224117,215,424,0.00146328,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
30615,Q#2151 - >seq8798,non-specific,238185,630,747,0.0015488,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs5_gmonkey,marg,CompleteHit
30616,Q#2151 - >seq8798,non-specific,224117,237,475,0.00198402,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
30617,Q#2151 - >seq8798,non-specific,235175,218,443,0.00236468,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
30618,Q#2151 - >seq8798,superfamily,235175,218,443,0.00236468,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
30619,Q#2151 - >seq8798,non-specific,313357,328,438,0.00463119,39.5572,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
30620,Q#2151 - >seq8798,superfamily,321788,328,438,0.00463119,39.5572,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1MA8.ORF2.hs5_gmonkey.marg.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
30621,Q#2152 - >seq8799,specific,197310,1,224,4.83233e-44,159.82399999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30622,Q#2152 - >seq8799,superfamily,351117,1,224,4.83233e-44,159.82399999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30623,Q#2152 - >seq8799,non-specific,197306,1,224,3.98248e-19,87.92200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30624,Q#2152 - >seq8799,non-specific,197320,94,217,1.00457e-09,60.2214,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30625,Q#2152 - >seq8799,non-specific,197307,1,224,1.32689e-09,59.9941,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30626,Q#2152 - >seq8799,specific,335306,44,217,2.751e-07,52.6326,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30627,Q#2152 - >seq8799,non-specific,223780,1,217,4.96139e-07,52.2155,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30628,Q#2152 - >seq8799,non-specific,197319,45,224,5.4472900000000005e-06,49.1973,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30629,Q#2152 - >seq8799,non-specific,273186,95,225,0.00206321,41.1104,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30630,Q#2152 - >seq8799,non-specific,272954,1,224,0.00300154,40.4441,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs5_gmonkey.pars.frame2,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30631,Q#2153 - >seq8800,specific,238827,463,726,4.599449999999999e-61,207.91400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30632,Q#2153 - >seq8800,superfamily,295487,463,726,4.599449999999999e-61,207.91400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30633,Q#2153 - >seq8800,specific,333820,469,726,2.7200100000000002e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30634,Q#2153 - >seq8800,superfamily,333820,469,726,2.7200100000000002e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30635,Q#2153 - >seq8800,non-specific,238828,535,700,3.18855e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30636,Q#2153 - >seq8800,non-specific,275209,421,754,3.19207e-07,53.6156,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30637,Q#2153 - >seq8800,superfamily,275209,421,754,3.19207e-07,53.6156,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30638,Q#2153 - >seq8800,non-specific,274009,263,412,8.353299999999999e-05,46.9847,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
30639,Q#2153 - >seq8800,superfamily,274009,263,412,8.353299999999999e-05,46.9847,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
30640,Q#2153 - >seq8800,non-specific,235175,222,423,0.000123477,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
30641,Q#2153 - >seq8800,superfamily,235175,222,423,0.000123477,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
30642,Q#2153 - >seq8800,non-specific,224117,175,421,0.000187197,45.8608,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30643,Q#2153 - >seq8800,superfamily,224117,175,421,0.000187197,45.8608,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30644,Q#2153 - >seq8800,non-specific,238185,609,726,0.00185216,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30645,Q#2153 - >seq8800,non-specific,313357,308,418,0.00595627,39.172,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30646,Q#2153 - >seq8800,superfamily,321788,308,418,0.00595627,39.172,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30647,Q#2153 - >seq8800,non-specific,214019,219,375,0.00713541,38.5246,cd12926,iSH2_PIK3R2, - ,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30648,Q#2153 - >seq8800,superfamily,355389,219,375,0.00713541,38.5246,cl25402,iSH2_PI3K_IA_R superfamily, - , - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA8,ORF2,hs5_gmonkey,pars,CompleteHit
30649,Q#2153 - >seq8800,non-specific,224117,219,418,0.00841873,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MA8.ORF2.hs5_gmonkey.pars.frame3,1909181650_L1MA8.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
30650,Q#2157 - >seq8804,specific,238827,501,763,2.2727099999999997e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30651,Q#2157 - >seq8804,superfamily,295487,501,763,2.2727099999999997e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30652,Q#2157 - >seq8804,specific,197310,3,231,4.472569999999999e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30653,Q#2157 - >seq8804,superfamily,351117,3,231,4.472569999999999e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30654,Q#2157 - >seq8804,specific,333820,507,763,6.19552e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30655,Q#2157 - >seq8804,superfamily,333820,507,763,6.19552e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30656,Q#2157 - >seq8804,non-specific,197306,3,231,8.93903e-30,118.738,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30657,Q#2157 - >seq8804,non-specific,197320,1,216,3.3120500000000005e-17,82.5629,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30658,Q#2157 - >seq8804,non-specific,223780,1,220,1.2563799999999997e-16,81.1055,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30659,Q#2157 - >seq8804,non-specific,197307,3,231,5.2452599999999996e-15,76.1725,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30660,Q#2157 - >seq8804,specific,335306,4,224,1.56783e-11,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30661,Q#2157 - >seq8804,non-specific,197321,1,231,1.66175e-11,65.6512,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30662,Q#2157 - >seq8804,non-specific,272954,1,202,1.73185e-11,65.8673,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30663,Q#2157 - >seq8804,non-specific,273186,1,232,2.0428e-11,65.378,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30664,Q#2157 - >seq8804,non-specific,238828,507,728,7.88333e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30665,Q#2157 - >seq8804,non-specific,197319,1,231,1.7823900000000001e-10,62.6793,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30666,Q#2157 - >seq8804,non-specific,275209,458,787,5.85785e-08,55.9268,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30667,Q#2157 - >seq8804,superfamily,275209,458,787,5.85785e-08,55.9268,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30668,Q#2157 - >seq8804,non-specific,197336,1,189,3.7460599999999998e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30669,Q#2157 - >seq8804,non-specific,197311,1,199,3.31812e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,marg,CompleteHit
30670,Q#2157 - >seq8804,non-specific,238185,647,763,8.19056e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30671,Q#2157 - >seq8804,specific,311990,1229,1247,0.004225199999999999,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA7,ORF2,hs0_human,marg,CompleteHit
30672,Q#2157 - >seq8804,superfamily,311990,1229,1247,0.004225199999999999,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA7,ORF2,hs0_human,marg,CompleteHit
30673,Q#2157 - >seq8804,non-specific,339261,103,227,0.00908851,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs0_human.marg.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA7,ORF2,hs0_human,marg,CompleteHit
30674,Q#2159 - >seq8806,specific,238827,470,732,4.498079999999999e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30675,Q#2159 - >seq8806,superfamily,295487,470,732,4.498079999999999e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30676,Q#2159 - >seq8806,specific,333820,476,732,3.06532e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30677,Q#2159 - >seq8806,superfamily,333820,476,732,3.06532e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30678,Q#2159 - >seq8806,non-specific,238828,476,697,3.11145e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30679,Q#2159 - >seq8806,non-specific,275209,547,756,1.06966e-06,52.0748,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,N-TerminusTruncated
30680,Q#2159 - >seq8806,superfamily,275209,547,756,1.06966e-06,52.0748,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,N-TerminusTruncated
30681,Q#2159 - >seq8806,non-specific,238185,616,732,5.35192e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA7,ORF2,hs0_human,pars,CompleteHit
30682,Q#2159 - >seq8806,specific,311990,1198,1216,0.00450257,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs0_human,pars,CompleteHit
30683,Q#2159 - >seq8806,superfamily,311990,1198,1216,0.00450257,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs0_human,pars,CompleteHit
30684,Q#2159 - >seq8806,non-specific,223496,284,471,0.00883344,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA7,ORF2,hs0_human,pars,BothTerminiTruncated
30685,Q#2159 - >seq8806,superfamily,223496,284,471,0.00883344,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA7.ORF2.hs0_human.pars.frame1,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MA7,ORF2,hs0_human,pars,BothTerminiTruncated
30686,Q#2160 - >seq8807,specific,197310,10,238,1.85421e-56,195.263,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30687,Q#2160 - >seq8807,superfamily,351117,10,238,1.85421e-56,195.263,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30688,Q#2160 - >seq8807,non-specific,197306,10,238,5.85984e-30,119.12299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30689,Q#2160 - >seq8807,non-specific,223780,8,227,5.1416099999999994e-18,84.9575,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30690,Q#2160 - >seq8807,non-specific,197320,8,223,1.2384300000000001e-17,83.7185,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30691,Q#2160 - >seq8807,non-specific,197307,10,238,1.93888e-16,80.0245,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30692,Q#2160 - >seq8807,non-specific,197321,8,238,8.002359999999999e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30693,Q#2160 - >seq8807,non-specific,272954,8,209,2.1852099999999997e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30694,Q#2160 - >seq8807,non-specific,273186,8,239,2.88357e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30695,Q#2160 - >seq8807,non-specific,197319,8,238,3.92203e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30696,Q#2160 - >seq8807,specific,335306,11,231,1.46802e-11,65.3442,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30697,Q#2160 - >seq8807,non-specific,197336,8,196,3.4127300000000004e-06,49.5331,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30698,Q#2160 - >seq8807,non-specific,197311,8,206,4.7651499999999996e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs0_human.pars.frame3,1909181655_L1MA7.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs0_human,pars,CompleteHit
30699,Q#2163 - >seq8810,non-specific,335182,155,251,3.5362499999999997e-34,120.485,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30700,Q#2163 - >seq8810,superfamily,335182,155,251,3.5362499999999997e-34,120.485,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30701,Q#2163 - >seq8810,non-specific,335182,155,251,3.5362499999999997e-34,120.485,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30702,Q#2163 - >seq8810,non-specific,340205,254,317,4.1353000000000005e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30703,Q#2163 - >seq8810,superfamily,340205,254,317,4.1353000000000005e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30704,Q#2163 - >seq8810,non-specific,340205,254,317,4.1353000000000005e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30705,Q#2163 - >seq8810,non-specific,340204,111,153,2.72942e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30706,Q#2163 - >seq8810,superfamily,340204,111,153,2.72942e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30707,Q#2163 - >seq8810,non-specific,340204,111,153,2.72942e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,pars,CompleteHit
30708,Q#2163 - >seq8810,non-specific,274009,60,202,3.7481500000000004e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30709,Q#2163 - >seq8810,superfamily,274009,60,202,3.7481500000000004e-05,45.0587,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30710,Q#2163 - >seq8810,non-specific,274009,60,202,3.7481500000000004e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30711,Q#2163 - >seq8810,non-specific,237177,41,149,6.283430000000001e-05,44.3838,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30712,Q#2163 - >seq8810,superfamily,237177,41,149,6.283430000000001e-05,44.3838,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30713,Q#2163 - >seq8810,non-specific,237177,41,149,6.283430000000001e-05,44.3838,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30714,Q#2163 - >seq8810,non-specific,235175,49,155,0.00019318,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30715,Q#2163 - >seq8810,superfamily,235175,49,155,0.00019318,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30716,Q#2163 - >seq8810,non-specific,235175,49,155,0.00019318,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30717,Q#2163 - >seq8810,non-specific,274008,53,149,0.00131259,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30718,Q#2163 - >seq8810,superfamily,274008,53,149,0.00131259,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30719,Q#2163 - >seq8810,non-specific,274008,53,149,0.00131259,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30720,Q#2163 - >seq8810,non-specific,129694,80,146,0.00232708,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30721,Q#2163 - >seq8810,superfamily,129694,80,146,0.00232708,39.6449,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30722,Q#2163 - >seq8810,non-specific,129694,80,146,0.00232708,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30723,Q#2163 - >seq8810,non-specific,235461,47,169,0.00232933,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30724,Q#2163 - >seq8810,superfamily,235461,47,169,0.00232933,39.281,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30725,Q#2163 - >seq8810,non-specific,235461,47,169,0.00232933,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30726,Q#2163 - >seq8810,non-specific,275056,64,152,0.0028585,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30727,Q#2163 - >seq8810,superfamily,275056,64,152,0.0028585,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30728,Q#2163 - >seq8810,non-specific,275056,64,152,0.0028585,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30729,Q#2163 - >seq8810,non-specific,224117,28,155,0.00326423,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30730,Q#2163 - >seq8810,superfamily,224117,28,155,0.00326423,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30731,Q#2163 - >seq8810,non-specific,224117,28,155,0.00326423,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30732,Q#2163 - >seq8810,non-specific,223250,47,150,0.00349673,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30733,Q#2163 - >seq8810,superfamily,223250,47,150,0.00349673,38.7333,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30734,Q#2163 - >seq8810,non-specific,223250,47,150,0.00349673,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30735,Q#2163 - >seq8810,non-specific,112704,2,148,0.00350695,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30736,Q#2163 - >seq8810,superfamily,112704,2,148,0.00350695,38.0707,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30737,Q#2163 - >seq8810,non-specific,112704,2,148,0.00350695,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30738,Q#2163 - >seq8810,non-specific,336159,60,145,0.00389219,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30739,Q#2163 - >seq8810,superfamily,336159,60,145,0.00389219,38.8897,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30740,Q#2163 - >seq8810,non-specific,336159,60,145,0.00389219,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,pars,N-TerminusTruncated
30741,Q#2163 - >seq8810,non-specific,235175,41,144,0.00501274,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30742,Q#2163 - >seq8810,non-specific,235175,41,144,0.00501274,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30743,Q#2163 - >seq8810,non-specific,337663,79,147,0.00581309,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30744,Q#2163 - >seq8810,superfamily,337663,79,147,0.00581309,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30745,Q#2163 - >seq8810,non-specific,337663,79,147,0.00581309,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30746,Q#2163 - >seq8810,non-specific,274008,45,150,0.00620096,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30747,Q#2163 - >seq8810,non-specific,274008,45,150,0.00620096,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30748,Q#2163 - >seq8810,non-specific,223671,70,161,0.00623901,37.6897,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30749,Q#2163 - >seq8810,superfamily,320984,70,161,0.00623901,37.6897,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30750,Q#2163 - >seq8810,non-specific,223671,70,161,0.00623901,37.6897,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30751,Q#2163 - >seq8810,non-specific,274386,11,147,0.00636519,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30752,Q#2163 - >seq8810,superfamily,274386,11,147,0.00636519,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30753,Q#2163 - >seq8810,non-specific,274386,11,147,0.00636519,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30754,Q#2163 - >seq8810,non-specific,222878,57,150,0.006721300000000001,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30755,Q#2163 - >seq8810,superfamily,222878,57,150,0.006721300000000001,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30756,Q#2163 - >seq8810,non-specific,222878,57,150,0.006721300000000001,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30757,Q#2163 - >seq8810,non-specific,224117,49,201,0.00794156,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30758,Q#2163 - >seq8810,non-specific,224117,49,201,0.00794156,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,pars,BothTerminiTruncated
30759,Q#2163 - >seq8810,non-specific,188306,41,150,0.00988485,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30760,Q#2163 - >seq8810,superfamily,188306,41,150,0.00988485,37.2126,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30761,Q#2163 - >seq8810,non-specific,188306,41,150,0.00988485,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.pars.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,pars,C-TerminusTruncated
30762,Q#2166 - >seq8813,non-specific,335182,155,251,3.5362499999999997e-34,120.485,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30763,Q#2166 - >seq8813,superfamily,335182,155,251,3.5362499999999997e-34,120.485,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30764,Q#2166 - >seq8813,non-specific,335182,155,251,3.5362499999999997e-34,120.485,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30765,Q#2166 - >seq8813,non-specific,340205,254,317,4.1353000000000005e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30766,Q#2166 - >seq8813,superfamily,340205,254,317,4.1353000000000005e-23,90.4732,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30767,Q#2166 - >seq8813,non-specific,340205,254,317,4.1353000000000005e-23,90.4732,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30768,Q#2166 - >seq8813,non-specific,340204,111,153,2.72942e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30769,Q#2166 - >seq8813,superfamily,340204,111,153,2.72942e-06,43.5504,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30770,Q#2166 - >seq8813,non-specific,340204,111,153,2.72942e-06,43.5504,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs0_human,marg,CompleteHit
30771,Q#2166 - >seq8813,non-specific,274009,60,202,3.7481500000000004e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30772,Q#2166 - >seq8813,superfamily,274009,60,202,3.7481500000000004e-05,45.0587,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30773,Q#2166 - >seq8813,non-specific,274009,60,202,3.7481500000000004e-05,45.0587,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30774,Q#2166 - >seq8813,non-specific,237177,41,149,6.283430000000001e-05,44.3838,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30775,Q#2166 - >seq8813,superfamily,237177,41,149,6.283430000000001e-05,44.3838,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30776,Q#2166 - >seq8813,non-specific,237177,41,149,6.283430000000001e-05,44.3838,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30777,Q#2166 - >seq8813,non-specific,235175,49,155,0.00019318,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30778,Q#2166 - >seq8813,superfamily,235175,49,155,0.00019318,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30779,Q#2166 - >seq8813,non-specific,235175,49,155,0.00019318,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30780,Q#2166 - >seq8813,non-specific,274008,53,149,0.00131259,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30781,Q#2166 - >seq8813,superfamily,274008,53,149,0.00131259,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30782,Q#2166 - >seq8813,non-specific,274008,53,149,0.00131259,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30783,Q#2166 - >seq8813,non-specific,129694,80,146,0.00232708,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30784,Q#2166 - >seq8813,superfamily,129694,80,146,0.00232708,39.6449,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30785,Q#2166 - >seq8813,non-specific,129694,80,146,0.00232708,39.6449,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30786,Q#2166 - >seq8813,non-specific,235461,47,169,0.00232933,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30787,Q#2166 - >seq8813,superfamily,235461,47,169,0.00232933,39.281,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30788,Q#2166 - >seq8813,non-specific,235461,47,169,0.00232933,39.281,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30789,Q#2166 - >seq8813,non-specific,275056,64,152,0.0028585,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30790,Q#2166 - >seq8813,superfamily,275056,64,152,0.0028585,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30791,Q#2166 - >seq8813,non-specific,275056,64,152,0.0028585,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30792,Q#2166 - >seq8813,non-specific,224117,28,155,0.00326423,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30793,Q#2166 - >seq8813,superfamily,224117,28,155,0.00326423,38.9272,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30794,Q#2166 - >seq8813,non-specific,224117,28,155,0.00326423,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30795,Q#2166 - >seq8813,non-specific,223250,47,150,0.00349673,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30796,Q#2166 - >seq8813,superfamily,223250,47,150,0.00349673,38.7333,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30797,Q#2166 - >seq8813,non-specific,223250,47,150,0.00349673,38.7333,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30798,Q#2166 - >seq8813,non-specific,112704,2,148,0.00350695,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30799,Q#2166 - >seq8813,superfamily,112704,2,148,0.00350695,38.0707,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30800,Q#2166 - >seq8813,non-specific,112704,2,148,0.00350695,38.0707,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30801,Q#2166 - >seq8813,non-specific,336159,60,145,0.00389219,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30802,Q#2166 - >seq8813,superfamily,336159,60,145,0.00389219,38.8897,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30803,Q#2166 - >seq8813,non-specific,336159,60,145,0.00389219,38.8897,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs0_human,marg,N-TerminusTruncated
30804,Q#2166 - >seq8813,non-specific,235175,41,144,0.00501274,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30805,Q#2166 - >seq8813,non-specific,235175,41,144,0.00501274,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30806,Q#2166 - >seq8813,non-specific,337663,79,147,0.00581309,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30807,Q#2166 - >seq8813,superfamily,337663,79,147,0.00581309,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30808,Q#2166 - >seq8813,non-specific,337663,79,147,0.00581309,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30809,Q#2166 - >seq8813,non-specific,274008,45,150,0.00620096,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30810,Q#2166 - >seq8813,non-specific,274008,45,150,0.00620096,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30811,Q#2166 - >seq8813,non-specific,223671,70,161,0.00623901,37.6897,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30812,Q#2166 - >seq8813,superfamily,320984,70,161,0.00623901,37.6897,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30813,Q#2166 - >seq8813,non-specific,223671,70,161,0.00623901,37.6897,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30814,Q#2166 - >seq8813,non-specific,274386,11,147,0.00636519,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30815,Q#2166 - >seq8813,superfamily,274386,11,147,0.00636519,38.1086,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30816,Q#2166 - >seq8813,non-specific,274386,11,147,0.00636519,38.1086,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30817,Q#2166 - >seq8813,non-specific,222878,57,150,0.006721300000000001,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30818,Q#2166 - >seq8813,superfamily,222878,57,150,0.006721300000000001,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30819,Q#2166 - >seq8813,non-specific,222878,57,150,0.006721300000000001,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30820,Q#2166 - >seq8813,non-specific,224117,49,201,0.00794156,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30821,Q#2166 - >seq8813,non-specific,224117,49,201,0.00794156,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs0_human,marg,BothTerminiTruncated
30822,Q#2166 - >seq8813,non-specific,188306,41,150,0.00988485,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30823,Q#2166 - >seq8813,superfamily,188306,41,150,0.00988485,37.2126,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30824,Q#2166 - >seq8813,non-specific,188306,41,150,0.00988485,37.2126,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PBa1.ORF1.hs0_human.marg.frame3,1909181657_L1PBa1.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa1,ORF1,hs0_human,marg,C-TerminusTruncated
30825,Q#2169 - >seq8816,specific,197310,2,228,1.2582e-39,147.113,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30826,Q#2169 - >seq8816,superfamily,351117,2,228,1.2582e-39,147.113,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30827,Q#2169 - >seq8816,non-specific,197306,2,228,1.4473e-17,83.2996,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30828,Q#2169 - >seq8816,non-specific,238827,524,730,2.53939e-13,70.3978,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30829,Q#2169 - >seq8816,superfamily,295487,524,730,2.53939e-13,70.3978,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30830,Q#2169 - >seq8816,non-specific,197320,55,213,9.93199e-07,51.3618,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30831,Q#2169 - >seq8816,non-specific,223780,55,217,1.58288e-05,47.5931,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30832,Q#2169 - >seq8816,specific,335306,3,221,8.40503e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30833,Q#2169 - >seq8816,non-specific,197322,84,228,0.00156988,41.919,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30834,Q#2169 - >seq8816,non-specific,273186,2,229,0.00185152,41.4956,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30835,Q#2169 - >seq8816,non-specific,197319,84,228,0.00732721,39.5673,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,marg,N-TerminusTruncated
30836,Q#2169 - >seq8816,non-specific,333820,524,724,0.00801613,38.8126,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30837,Q#2169 - >seq8816,superfamily,333820,524,724,0.00801613,38.8126,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30838,Q#2169 - >seq8816,non-specific,339261,101,224,0.00832988,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30839,Q#2169 - >seq8816,non-specific,197321,2,228,0.00975626,39.0724,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.marg.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,marg,CompleteHit
30840,Q#2171 - >seq8818,non-specific,238827,482,687,1.3291199999999998e-13,71.1682,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MD1.ORF2.hs1_chimp.pars.frame1,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30841,Q#2171 - >seq8818,superfamily,295487,482,687,1.3291199999999998e-13,71.1682,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MD1.ORF2.hs1_chimp.pars.frame1,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30842,Q#2171 - >seq8818,non-specific,333820,482,682,0.00702157,38.8126,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs1_chimp.pars.frame1,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30843,Q#2171 - >seq8818,superfamily,333820,482,682,0.00702157,38.8126,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MD1.ORF2.hs1_chimp.pars.frame1,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30844,Q#2172 - >seq8819,specific,197310,2,228,7.99847e-40,147.498,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30845,Q#2172 - >seq8819,superfamily,351117,2,228,7.99847e-40,147.498,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30846,Q#2172 - >seq8819,non-specific,197306,2,228,2.3645100000000004e-17,82.5292,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30847,Q#2172 - >seq8819,non-specific,197320,55,213,4.9018e-07,52.1322,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30848,Q#2172 - >seq8819,non-specific,223780,55,217,6.50188e-06,48.7487,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30849,Q#2172 - >seq8819,specific,335306,3,221,7.731989999999999e-05,45.3138,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30850,Q#2172 - >seq8819,non-specific,197322,84,228,0.00144219,41.919,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30851,Q#2172 - >seq8819,non-specific,273186,2,229,0.00263912,40.7252,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30852,Q#2172 - >seq8819,non-specific,197319,84,228,0.00529693,39.9525,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,pars,N-TerminusTruncated
30853,Q#2172 - >seq8819,non-specific,197321,2,228,0.00905634,39.0724,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MD1.ORF2.hs1_chimp.pars.frame3,1909181659_L1MD1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MD1,ORF2,hs1_chimp,pars,CompleteHit
30854,Q#2175 - >seq8822,non-specific,335182,156,252,1.5934899999999997e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30855,Q#2175 - >seq8822,superfamily,335182,156,252,1.5934899999999997e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30856,Q#2175 - >seq8822,non-specific,335182,156,252,1.5934899999999997e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30857,Q#2175 - >seq8822,non-specific,340205,255,318,1.15496e-23,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30858,Q#2175 - >seq8822,superfamily,340205,255,318,1.15496e-23,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30859,Q#2175 - >seq8822,non-specific,340205,255,318,1.15496e-23,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30860,Q#2175 - >seq8822,non-specific,274009,60,203,1.94247e-06,49.2959,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30861,Q#2175 - >seq8822,superfamily,274009,60,203,1.94247e-06,49.2959,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30862,Q#2175 - >seq8822,non-specific,274009,60,203,1.94247e-06,49.2959,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30863,Q#2175 - >seq8822,non-specific,340204,111,153,1.35798e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30864,Q#2175 - >seq8822,superfamily,340204,111,153,1.35798e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30865,Q#2175 - >seq8822,non-specific,340204,111,153,1.35798e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,pars,CompleteHit
30866,Q#2175 - >seq8822,non-specific,274008,41,202,0.00015225700000000002,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30867,Q#2175 - >seq8822,superfamily,274008,41,202,0.00015225700000000002,43.5067,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30868,Q#2175 - >seq8822,non-specific,274008,41,202,0.00015225700000000002,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30869,Q#2175 - >seq8822,non-specific,235175,49,156,0.00019606900000000002,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30870,Q#2175 - >seq8822,superfamily,235175,49,156,0.00019606900000000002,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30871,Q#2175 - >seq8822,non-specific,235175,49,156,0.00019606900000000002,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30872,Q#2175 - >seq8822,non-specific,224117,28,177,0.000286936,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30873,Q#2175 - >seq8822,superfamily,224117,28,177,0.000286936,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30874,Q#2175 - >seq8822,non-specific,224117,28,177,0.000286936,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30875,Q#2175 - >seq8822,non-specific,235461,47,170,0.000290126,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30876,Q#2175 - >seq8822,superfamily,235461,47,170,0.000290126,41.9774,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30877,Q#2175 - >seq8822,non-specific,235461,47,170,0.000290126,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30878,Q#2175 - >seq8822,non-specific,223250,47,170,0.00032296,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30879,Q#2175 - >seq8822,superfamily,223250,47,170,0.00032296,41.8149,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30880,Q#2175 - >seq8822,non-specific,223250,47,170,0.00032296,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30881,Q#2175 - >seq8822,non-specific,313406,73,214,0.000525351,41.5614,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30882,Q#2175 - >seq8822,superfamily,313406,73,214,0.000525351,41.5614,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30883,Q#2175 - >seq8822,non-specific,313406,73,214,0.000525351,41.5614,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30884,Q#2175 - >seq8822,non-specific,237177,42,149,0.000530898,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30885,Q#2175 - >seq8822,superfamily,237177,42,149,0.000530898,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30886,Q#2175 - >seq8822,non-specific,237177,42,149,0.000530898,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30887,Q#2175 - >seq8822,non-specific,337663,79,183,0.00133644,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30888,Q#2175 - >seq8822,superfamily,337663,79,183,0.00133644,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30889,Q#2175 - >seq8822,non-specific,337663,79,183,0.00133644,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30890,Q#2175 - >seq8822,non-specific,336159,60,145,0.0029313000000000004,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30891,Q#2175 - >seq8822,superfamily,336159,60,145,0.0029313000000000004,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30892,Q#2175 - >seq8822,non-specific,336159,60,145,0.0029313000000000004,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30893,Q#2175 - >seq8822,non-specific,274008,45,150,0.00329971,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30894,Q#2175 - >seq8822,non-specific,274008,45,150,0.00329971,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30895,Q#2175 - >seq8822,non-specific,275056,60,152,0.00342199,37.6801,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30896,Q#2175 - >seq8822,superfamily,275056,60,152,0.00342199,37.6801,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30897,Q#2175 - >seq8822,non-specific,275056,60,152,0.00342199,37.6801,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30898,Q#2175 - >seq8822,non-specific,274386,27,147,0.00454081,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30899,Q#2175 - >seq8822,superfamily,274386,27,147,0.00454081,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30900,Q#2175 - >seq8822,non-specific,274386,27,147,0.00454081,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30901,Q#2175 - >seq8822,non-specific,112704,2,148,0.0046292,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30902,Q#2175 - >seq8822,superfamily,112704,2,148,0.0046292,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30903,Q#2175 - >seq8822,non-specific,112704,2,148,0.0046292,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30904,Q#2175 - >seq8822,non-specific,206779,64,132,0.00637438,37.2164,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30905,Q#2175 - >seq8822,superfamily,357649,64,132,0.00637438,37.2164,cl30773,MCP_signal superfamily,N, - ,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30906,Q#2175 - >seq8822,non-specific,206779,64,132,0.00637438,37.2164,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30907,Q#2175 - >seq8822,non-specific,226400,79,149,0.00674503,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30908,Q#2175 - >seq8822,superfamily,226400,79,149,0.00674503,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30909,Q#2175 - >seq8822,non-specific,226400,79,149,0.00674503,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,pars,C-TerminusTruncated
30910,Q#2175 - >seq8822,non-specific,274091,65,150,0.00704017,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30911,Q#2175 - >seq8822,superfamily,274091,65,150,0.00704017,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30912,Q#2175 - >seq8822,non-specific,274091,65,150,0.00704017,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,pars,N-TerminusTruncated
30913,Q#2175 - >seq8822,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30914,Q#2175 - >seq8822,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.pars.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,pars,BothTerminiTruncated
30915,Q#2178 - >seq8825,non-specific,335182,156,252,1.5934899999999997e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30916,Q#2178 - >seq8825,superfamily,335182,156,252,1.5934899999999997e-34,121.641,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30917,Q#2178 - >seq8825,non-specific,335182,156,252,1.5934899999999997e-34,121.641,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30918,Q#2178 - >seq8825,non-specific,340205,255,318,1.15496e-23,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30919,Q#2178 - >seq8825,superfamily,340205,255,318,1.15496e-23,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30920,Q#2178 - >seq8825,non-specific,340205,255,318,1.15496e-23,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30921,Q#2178 - >seq8825,non-specific,274009,60,203,1.94247e-06,49.2959,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30922,Q#2178 - >seq8825,superfamily,274009,60,203,1.94247e-06,49.2959,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30923,Q#2178 - >seq8825,non-specific,274009,60,203,1.94247e-06,49.2959,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30924,Q#2178 - >seq8825,non-specific,340204,111,153,1.35798e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30925,Q#2178 - >seq8825,superfamily,340204,111,153,1.35798e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30926,Q#2178 - >seq8825,non-specific,340204,111,153,1.35798e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa1,ORF1,hs1_chimp,marg,CompleteHit
30927,Q#2178 - >seq8825,non-specific,274008,41,202,0.00015225700000000002,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30928,Q#2178 - >seq8825,superfamily,274008,41,202,0.00015225700000000002,43.5067,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30929,Q#2178 - >seq8825,non-specific,274008,41,202,0.00015225700000000002,43.5067,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30930,Q#2178 - >seq8825,non-specific,235175,49,156,0.00019606900000000002,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30931,Q#2178 - >seq8825,superfamily,235175,49,156,0.00019606900000000002,42.7436,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30932,Q#2178 - >seq8825,non-specific,235175,49,156,0.00019606900000000002,42.7436,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30933,Q#2178 - >seq8825,non-specific,224117,28,177,0.000286936,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30934,Q#2178 - >seq8825,superfamily,224117,28,177,0.000286936,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30935,Q#2178 - >seq8825,non-specific,224117,28,177,0.000286936,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30936,Q#2178 - >seq8825,non-specific,235461,47,170,0.000290126,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30937,Q#2178 - >seq8825,superfamily,235461,47,170,0.000290126,41.9774,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30938,Q#2178 - >seq8825,non-specific,235461,47,170,0.000290126,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30939,Q#2178 - >seq8825,non-specific,223250,47,170,0.00032296,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30940,Q#2178 - >seq8825,superfamily,223250,47,170,0.00032296,41.8149,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30941,Q#2178 - >seq8825,non-specific,223250,47,170,0.00032296,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30942,Q#2178 - >seq8825,non-specific,313406,73,214,0.000525351,41.5614,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30943,Q#2178 - >seq8825,superfamily,313406,73,214,0.000525351,41.5614,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30944,Q#2178 - >seq8825,non-specific,313406,73,214,0.000525351,41.5614,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30945,Q#2178 - >seq8825,non-specific,237177,42,149,0.000530898,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30946,Q#2178 - >seq8825,superfamily,237177,42,149,0.000530898,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30947,Q#2178 - >seq8825,non-specific,237177,42,149,0.000530898,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30948,Q#2178 - >seq8825,non-specific,337663,79,183,0.00133644,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30949,Q#2178 - >seq8825,superfamily,337663,79,183,0.00133644,39.7155,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30950,Q#2178 - >seq8825,non-specific,337663,79,183,0.00133644,39.7155,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30951,Q#2178 - >seq8825,non-specific,336159,60,145,0.0029313000000000004,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30952,Q#2178 - >seq8825,superfamily,336159,60,145,0.0029313000000000004,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30953,Q#2178 - >seq8825,non-specific,336159,60,145,0.0029313000000000004,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30954,Q#2178 - >seq8825,non-specific,274008,45,150,0.00329971,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30955,Q#2178 - >seq8825,non-specific,274008,45,150,0.00329971,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30956,Q#2178 - >seq8825,non-specific,275056,60,152,0.00342199,37.6801,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30957,Q#2178 - >seq8825,superfamily,275056,60,152,0.00342199,37.6801,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30958,Q#2178 - >seq8825,non-specific,275056,60,152,0.00342199,37.6801,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30959,Q#2178 - >seq8825,non-specific,274386,27,147,0.00454081,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30960,Q#2178 - >seq8825,superfamily,274386,27,147,0.00454081,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30961,Q#2178 - >seq8825,non-specific,274386,27,147,0.00454081,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30962,Q#2178 - >seq8825,non-specific,112704,2,148,0.0046292,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30963,Q#2178 - >seq8825,superfamily,112704,2,148,0.0046292,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30964,Q#2178 - >seq8825,non-specific,112704,2,148,0.0046292,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30965,Q#2178 - >seq8825,non-specific,206779,64,132,0.00637438,37.2164,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30966,Q#2178 - >seq8825,superfamily,357649,64,132,0.00637438,37.2164,cl30773,MCP_signal superfamily,N, - ,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30967,Q#2178 - >seq8825,non-specific,206779,64,132,0.00637438,37.2164,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30968,Q#2178 - >seq8825,non-specific,226400,79,149,0.00674503,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30969,Q#2178 - >seq8825,superfamily,226400,79,149,0.00674503,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30970,Q#2178 - >seq8825,non-specific,226400,79,149,0.00674503,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa1,ORF1,hs1_chimp,marg,C-TerminusTruncated
30971,Q#2178 - >seq8825,non-specific,274091,65,150,0.00704017,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30972,Q#2178 - >seq8825,superfamily,274091,65,150,0.00704017,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30973,Q#2178 - >seq8825,non-specific,274091,65,150,0.00704017,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PBa1,ORF1,hs1_chimp,marg,N-TerminusTruncated
30974,Q#2178 - >seq8825,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30975,Q#2178 - >seq8825,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa1.ORF1.hs1_chimp.marg.frame3,1909181700_L1PBa1.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa1,ORF1,hs1_chimp,marg,BothTerminiTruncated
30976,Q#2179 - >seq8826,specific,238827,510,773,1.9744199999999996e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30977,Q#2179 - >seq8826,superfamily,295487,510,773,1.9744199999999996e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30978,Q#2179 - >seq8826,specific,197310,9,237,1.0334899999999999e-57,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30979,Q#2179 - >seq8826,superfamily,351117,9,237,1.0334899999999999e-57,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30980,Q#2179 - >seq8826,specific,333820,516,773,4.824359999999999e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30981,Q#2179 - >seq8826,superfamily,333820,516,773,4.824359999999999e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30982,Q#2179 - >seq8826,non-specific,197306,9,237,2.51148e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30983,Q#2179 - >seq8826,non-specific,223780,7,230,4.89039e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30984,Q#2179 - >seq8826,non-specific,197320,7,230,1.6818e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30985,Q#2179 - >seq8826,non-specific,197307,9,230,6.78739e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30986,Q#2179 - >seq8826,non-specific,197321,7,230,7.370000000000001e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30987,Q#2179 - >seq8826,specific,335306,10,230,4.23084e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30988,Q#2179 - >seq8826,non-specific,272954,7,208,5.63649e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30989,Q#2179 - >seq8826,non-specific,197319,7,237,5.822789999999999e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30990,Q#2179 - >seq8826,non-specific,273186,7,238,2.41095e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30991,Q#2179 - >seq8826,non-specific,238828,516,737,4.27063e-09,57.9812,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30992,Q#2179 - >seq8826,non-specific,197336,7,230,2.01268e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30993,Q#2179 - >seq8826,non-specific,275209,467,797,1.6445599999999998e-06,51.6896,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30994,Q#2179 - >seq8826,superfamily,275209,467,797,1.6445599999999998e-06,51.6896,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30995,Q#2179 - >seq8826,non-specific,197311,7,205,0.00127688,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30996,Q#2179 - >seq8826,non-specific,226098,125,238,0.00263298,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,marg,N-TerminusTruncated
30997,Q#2179 - >seq8826,non-specific,339261,109,232,0.00922246,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs1_chimp.marg.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30998,Q#2181 - >seq8828,specific,311990,1118,1136,0.000283077,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs1_chimp.marg.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
30999,Q#2181 - >seq8828,superfamily,311990,1118,1136,0.000283077,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs1_chimp.marg.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA7,ORF2,hs1_chimp,marg,CompleteHit
31000,Q#2182 - >seq8829,specific,238827,509,772,2.1909199999999997e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31001,Q#2182 - >seq8829,superfamily,295487,509,772,2.1909199999999997e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31002,Q#2182 - >seq8829,specific,197310,9,237,1.0616299999999998e-57,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31003,Q#2182 - >seq8829,superfamily,351117,9,237,1.0616299999999998e-57,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31004,Q#2182 - >seq8829,specific,333820,515,772,5.103169999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31005,Q#2182 - >seq8829,superfamily,333820,515,772,5.103169999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31006,Q#2182 - >seq8829,non-specific,197306,9,237,2.41255e-30,120.664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31007,Q#2182 - >seq8829,non-specific,223780,7,230,4.70026e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31008,Q#2182 - >seq8829,non-specific,197320,7,230,1.6317399999999999e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31009,Q#2182 - >seq8829,non-specific,197307,9,230,6.77495e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31010,Q#2182 - >seq8829,non-specific,197321,7,230,7.35651e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31011,Q#2182 - >seq8829,specific,335306,10,230,4.22327e-14,72.6629,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31012,Q#2182 - >seq8829,non-specific,272954,7,208,5.470219999999999e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31013,Q#2182 - >seq8829,non-specific,197319,7,237,5.59876e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31014,Q#2182 - >seq8829,non-specific,273186,7,238,2.34013e-12,68.4596,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31015,Q#2182 - >seq8829,non-specific,238828,515,736,4.30298e-09,57.9812,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31016,Q#2182 - >seq8829,non-specific,197336,7,230,2.0090499999999997e-08,56.4667,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31017,Q#2182 - >seq8829,non-specific,275209,467,791,7.27593e-05,46.2968,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31018,Q#2182 - >seq8829,superfamily,275209,467,791,7.27593e-05,46.2968,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31019,Q#2182 - >seq8829,non-specific,197311,7,205,0.00127467,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31020,Q#2182 - >seq8829,non-specific,226098,125,238,0.00262835,40.8468,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA7,ORF2,hs1_chimp,pars,N-TerminusTruncated
31021,Q#2182 - >seq8829,non-specific,339261,109,232,0.00920714,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA7.ORF2.hs1_chimp.pars.frame3,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31022,Q#2183 - >seq8830,specific,311990,1116,1134,0.00027984,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs1_chimp.pars.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31023,Q#2183 - >seq8830,superfamily,311990,1116,1134,0.00027984,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA7.ORF2.hs1_chimp.pars.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA7,ORF2,hs1_chimp,pars,CompleteHit
31024,Q#2183 - >seq8830,non-specific,340095,241,463,0.00754983,40.196,pfam17380,DUF5401,N,cl38662,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA7.ORF2.hs1_chimp.pars.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA7,ORF2,hs1_chimp,pars,N-TerminusTruncated
31025,Q#2183 - >seq8830,superfamily,340095,241,463,0.00754983,40.196,cl38662,DUF5401 superfamily,N, - ,Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.,L1MA7.ORF2.hs1_chimp.pars.frame1,1909181707_L1MA7.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA7,ORF2,hs1_chimp,pars,N-TerminusTruncated
31026,Q#2185 - >seq8832,non-specific,240274,200,505,0.0040298,41.1289,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MC1.ORF2.hs6_sqmonkey.pars.frame1,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31027,Q#2185 - >seq8832,superfamily,240274,200,505,0.0040298,41.1289,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MC1.ORF2.hs6_sqmonkey.pars.frame1,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MC1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31028,Q#2186 - >seq8833,specific,238827,512,772,3.16539e-42,153.986,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31029,Q#2186 - >seq8833,superfamily,295487,512,772,3.16539e-42,153.986,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31030,Q#2186 - >seq8833,specific,197310,9,242,1.42381e-40,149.809,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31031,Q#2186 - >seq8833,superfamily,351117,9,242,1.42381e-40,149.809,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31032,Q#2186 - >seq8833,non-specific,333820,518,750,1.9586300000000002e-22,95.8221,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31033,Q#2186 - >seq8833,superfamily,333820,518,750,1.9586300000000002e-22,95.8221,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31034,Q#2186 - >seq8833,non-specific,197306,9,242,3.67219e-16,79.0624,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31035,Q#2186 - >seq8833,non-specific,238828,518,750,1.05546e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31036,Q#2186 - >seq8833,non-specific,223780,9,235,5.86981e-11,64.1567,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31037,Q#2186 - >seq8833,non-specific,197320,113,227,1.87584e-09,59.451,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31038,Q#2186 - >seq8833,non-specific,275209,587,810,3.55052e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31039,Q#2186 - >seq8833,superfamily,275209,587,810,3.55052e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31040,Q#2186 - >seq8833,non-specific,339261,115,238,2.20708e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31041,Q#2186 - >seq8833,non-specific,335306,10,235,6.535519999999999e-07,51.477,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31042,Q#2186 - >seq8833,non-specific,273186,113,243,6.79399e-07,51.896,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31043,Q#2186 - >seq8833,non-specific,197307,98,242,2.35325e-06,50.3641,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31044,Q#2186 - >seq8833,non-specific,272954,9,242,3.11181e-05,46.9925,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,CompleteHit
31045,Q#2186 - >seq8833,non-specific,197322,114,242,4.95773e-05,46.5414,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31046,Q#2186 - >seq8833,non-specific,274009,309,452,0.00108669,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31047,Q#2186 - >seq8833,superfamily,274009,309,452,0.00108669,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MC1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31048,Q#2186 - >seq8833,non-specific,197311,80,242,0.00166577,41.1233,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs6_sqmonkey.pars.frame2,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31049,Q#2190 - >seq8837,specific,197310,9,237,1.0219799999999998e-47,170.225,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31050,Q#2190 - >seq8837,superfamily,351117,9,237,1.0219799999999998e-47,170.225,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31051,Q#2190 - >seq8837,specific,238827,511,772,4.57618e-44,159.379,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31052,Q#2190 - >seq8837,superfamily,295487,511,772,4.57618e-44,159.379,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31053,Q#2190 - >seq8837,non-specific,333820,517,750,4.88202e-24,100.445,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31054,Q#2190 - >seq8837,superfamily,333820,517,750,4.88202e-24,100.445,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31055,Q#2190 - >seq8837,non-specific,197306,9,237,1.6979899999999999e-19,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31056,Q#2190 - >seq8837,non-specific,238828,517,750,1.16871e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31057,Q#2190 - >seq8837,non-specific,223780,9,230,2.64245e-11,65.3123,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31058,Q#2190 - >seq8837,non-specific,197320,9,222,1.11295e-10,63.303000000000004,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31059,Q#2190 - >seq8837,non-specific,275209,587,810,3.42733e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31060,Q#2190 - >seq8837,superfamily,275209,587,810,3.42733e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31061,Q#2190 - >seq8837,non-specific,197307,9,237,4.07705e-08,55.3717,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31062,Q#2190 - >seq8837,non-specific,273186,9,238,1.0224500000000001e-07,54.2072,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31063,Q#2190 - >seq8837,specific,335306,10,230,1.38645e-07,53.403,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31064,Q#2190 - >seq8837,non-specific,339261,109,233,4.74912e-07,49.6431,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31065,Q#2190 - >seq8837,non-specific,197322,108,237,6.57943e-06,49.2378,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31066,Q#2190 - >seq8837,non-specific,272954,9,237,9.0732e-06,48.5333,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs6_sqmonkey,marg,CompleteHit
31067,Q#2190 - >seq8837,non-specific,224117,73,432,0.00109067,43.1644,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31068,Q#2190 - >seq8837,superfamily,224117,73,432,0.00109067,43.1644,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1MC1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31069,Q#2190 - >seq8837,non-specific,274009,308,451,0.0017308,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
31070,Q#2190 - >seq8837,superfamily,274009,308,451,0.0017308,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs6_sqmonkey.marg.frame3,1909181708_L1MC1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
31071,Q#2192 - >seq8839,specific,238827,520,762,6.42611e-46,164.386,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31072,Q#2192 - >seq8839,superfamily,295487,520,762,6.42611e-46,164.386,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31073,Q#2192 - >seq8839,specific,197310,40,231,5.161069999999999e-33,127.853,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31074,Q#2192 - >seq8839,superfamily,351117,40,231,5.161069999999999e-33,127.853,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31075,Q#2192 - >seq8839,non-specific,333820,520,762,1.6899600000000002e-24,101.6,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31076,Q#2192 - >seq8839,superfamily,333820,520,762,1.6899600000000002e-24,101.6,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31077,Q#2192 - >seq8839,non-specific,197306,46,231,1.9254e-11,65.1953,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31078,Q#2192 - >seq8839,non-specific,197320,53,216,3.0791799999999997e-09,59.0658,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31079,Q#2192 - >seq8839,non-specific,223780,49,220,2.1899199999999997e-08,56.4527,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31080,Q#2192 - >seq8839,non-specific,197307,49,224,6.80893e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31081,Q#2192 - >seq8839,non-specific,238828,572,727,5.49168e-07,51.818000000000005,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31082,Q#2192 - >seq8839,non-specific,339261,103,226,7.574980000000001e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MB3,ORF2,hs3_orang,marg,CompleteHit
31083,Q#2192 - >seq8839,non-specific,197322,101,224,1.83615e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31084,Q#2192 - >seq8839,non-specific,335306,52,224,2.42236e-05,46.8546,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31085,Q#2192 - >seq8839,non-specific,275209,577,790,0.000361482,43.9856,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31086,Q#2192 - >seq8839,superfamily,275209,577,790,0.000361482,43.9856,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31087,Q#2192 - >seq8839,non-specific,272954,62,202,0.00103775,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31088,Q#2192 - >seq8839,non-specific,273186,58,203,0.00142047,41.8808,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31089,Q#2192 - >seq8839,non-specific,197319,101,231,0.00155168,41.4933,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31090,Q#2192 - >seq8839,non-specific,197311,101,199,0.00434764,39.5825,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs3_orang.marg.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,marg,N-TerminusTruncated
31091,Q#2196 - >seq8843,specific,238827,519,760,7.07399e-49,172.861,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31092,Q#2196 - >seq8843,superfamily,295487,519,760,7.07399e-49,172.861,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31093,Q#2196 - >seq8843,specific,197310,40,231,6.0299699999999995e-33,127.853,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31094,Q#2196 - >seq8843,superfamily,351117,40,231,6.0299699999999995e-33,127.853,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31095,Q#2196 - >seq8843,non-specific,333820,519,760,9.495869999999999e-26,105.45200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31096,Q#2196 - >seq8843,superfamily,333820,519,760,9.495869999999999e-26,105.45200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31097,Q#2196 - >seq8843,non-specific,197306,46,231,3.10497e-11,64.8101,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31098,Q#2196 - >seq8843,non-specific,197320,53,216,2.9980699999999998e-09,59.0658,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31099,Q#2196 - >seq8843,non-specific,223780,49,220,1.68009e-08,56.8379,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31100,Q#2196 - >seq8843,non-specific,197307,49,224,5.7774199999999996e-08,54.9865,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31101,Q#2196 - >seq8843,non-specific,238828,571,725,1.87876e-07,52.9736,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31102,Q#2196 - >seq8843,non-specific,275209,576,784,2.45174e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31103,Q#2196 - >seq8843,superfamily,275209,576,784,2.45174e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31104,Q#2196 - >seq8843,non-specific,339261,103,226,1.71561e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MB3,ORF2,hs3_orang,pars,CompleteHit
31105,Q#2196 - >seq8843,non-specific,197322,101,224,1.78778e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31106,Q#2196 - >seq8843,non-specific,335306,52,224,2.36048e-05,46.8546,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31107,Q#2196 - >seq8843,non-specific,272954,62,202,0.00122042,41.9849,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31108,Q#2196 - >seq8843,non-specific,197319,101,231,0.00148511,41.4933,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31109,Q#2196 - >seq8843,non-specific,273186,58,203,0.00174677,41.4956,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31110,Q#2196 - >seq8843,non-specific,197311,101,199,0.00523115,39.5825,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MB3.ORF2.hs3_orang.pars.frame1,1909181711_L1MB3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MB3,ORF2,hs3_orang,pars,N-TerminusTruncated
31111,Q#2197 - >seq8844,specific,238827,497,759,1.6560399999999998e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31112,Q#2197 - >seq8844,superfamily,295487,497,759,1.6560399999999998e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31113,Q#2197 - >seq8844,specific,197310,38,230,1.02422e-43,158.66899999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31114,Q#2197 - >seq8844,superfamily,351117,38,230,1.02422e-43,158.66899999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31115,Q#2197 - >seq8844,specific,333820,503,759,1.4175499999999998e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31116,Q#2197 - >seq8844,superfamily,333820,503,759,1.4175499999999998e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31117,Q#2197 - >seq8844,non-specific,197306,36,230,1.56322e-18,85.99600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31118,Q#2197 - >seq8844,non-specific,197320,43,223,4.55593e-13,70.2366,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31119,Q#2197 - >seq8844,non-specific,223780,44,223,6.31054e-12,67.2383,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31120,Q#2197 - >seq8844,non-specific,238828,503,724,9.006989999999999e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31121,Q#2197 - >seq8844,non-specific,197307,44,230,1.2505200000000001e-10,63.0757,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31122,Q#2197 - >seq8844,non-specific,275209,454,778,2.02099e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31123,Q#2197 - >seq8844,superfamily,275209,454,778,2.02099e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31124,Q#2197 - >seq8844,specific,335306,48,223,1.0090799999999999e-07,53.7882,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31125,Q#2197 - >seq8844,non-specific,197319,98,230,7.42167e-07,51.8937,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31126,Q#2197 - >seq8844,non-specific,273186,98,231,7.89633e-06,48.8144,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31127,Q#2197 - >seq8844,non-specific,197321,36,230,2.40025e-05,47.1616,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31128,Q#2197 - >seq8844,non-specific,272954,55,230,4.82743e-05,46.2221,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31129,Q#2197 - >seq8844,non-specific,339261,100,226,5.00054e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31130,Q#2197 - >seq8844,non-specific,197322,83,230,8.693629999999999e-05,45.771,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31131,Q#2197 - >seq8844,non-specific,238185,643,759,0.00019544900000000002,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31132,Q#2197 - >seq8844,non-specific,197311,64,230,0.00260188,40.3529,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31133,Q#2197 - >seq8844,specific,225881,470,667,0.00674554,39.8221,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
31134,Q#2197 - >seq8844,superfamily,225881,470,667,0.00674554,39.8221,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.pars.frame1,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
31135,Q#2199 - >seq8846,non-specific,197310,9,51,1.2779000000000001e-09,59.6725,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31136,Q#2199 - >seq8846,superfamily,351117,9,51,1.2779000000000001e-09,59.6725,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31137,Q#2199 - >seq8846,non-specific,197306,9,54,9.152850000000001e-08,54.4097,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31138,Q#2199 - >seq8846,non-specific,223780,7,43,1.7667000000000002e-05,47.5931,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31139,Q#2199 - >seq8846,non-specific,197321,7,43,2.7469e-05,46.7764,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31140,Q#2199 - >seq8846,non-specific,272954,7,72,5.6741000000000004e-05,45.8369,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31141,Q#2199 - >seq8846,specific,311990,1168,1186,0.000262034,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31142,Q#2199 - >seq8846,superfamily,311990,1168,1186,0.000262034,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA4,ORF2,hs6_sqmonkey,pars,CompleteHit
31143,Q#2199 - >seq8846,non-specific,197307,9,43,0.000337987,43.4305,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31144,Q#2199 - >seq8846,non-specific,273186,7,43,0.00035630300000000003,43.4216,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31145,Q#2199 - >seq8846,specific,335306,10,74,0.00216497,40.6914,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31146,Q#2199 - >seq8846,non-specific,197320,7,43,0.00288927,40.5762,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31147,Q#2199 - >seq8846,non-specific,197319,7,43,0.00429635,39.9525,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31148,Q#2199 - >seq8846,non-specific,197336,7,43,0.00784358,39.1327,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs6_sqmonkey.pars.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31149,Q#2201 - >seq8848,specific,311990,1171,1189,0.000313306,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs6_sqmonkey.marg.frame2,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31150,Q#2201 - >seq8848,superfamily,311990,1171,1189,0.000313306,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs6_sqmonkey.marg.frame2,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31151,Q#2202 - >seq8849,specific,238827,510,772,1.6007999999999997e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31152,Q#2202 - >seq8849,superfamily,295487,510,772,1.6007999999999997e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31153,Q#2202 - >seq8849,specific,197310,9,236,6.87262e-63,213.752,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31154,Q#2202 - >seq8849,superfamily,351117,9,236,6.87262e-63,213.752,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31155,Q#2202 - >seq8849,non-specific,197306,9,236,8.97341e-34,130.29399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31156,Q#2202 - >seq8849,specific,333820,516,772,1.0537e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31157,Q#2202 - >seq8849,superfamily,333820,516,772,1.0537e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31158,Q#2202 - >seq8849,non-specific,197320,7,229,1.8638999999999998e-22,97.9709,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31159,Q#2202 - >seq8849,non-specific,223780,7,229,1.9514800000000001e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31160,Q#2202 - >seq8849,non-specific,197307,9,236,1.19344e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31161,Q#2202 - >seq8849,specific,335306,10,229,2.3075400000000004e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31162,Q#2202 - >seq8849,non-specific,197321,7,236,5.933390000000001e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31163,Q#2202 - >seq8849,non-specific,272954,7,236,1.26276e-16,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31164,Q#2202 - >seq8849,non-specific,273186,7,237,9.01172e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31165,Q#2202 - >seq8849,non-specific,197319,7,236,1.5918200000000002e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31166,Q#2202 - >seq8849,non-specific,238828,516,737,9.03602e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31167,Q#2202 - >seq8849,non-specific,275209,467,791,1.5273599999999998e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31168,Q#2202 - >seq8849,superfamily,275209,467,791,1.5273599999999998e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31169,Q#2202 - >seq8849,non-specific,197322,8,236,1.76919e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31170,Q#2202 - >seq8849,non-specific,236970,9,229,3.22004e-07,52.9742,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31171,Q#2202 - >seq8849,non-specific,197336,7,194,1.22784e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31172,Q#2202 - >seq8849,non-specific,197311,7,236,5.70905e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31173,Q#2202 - >seq8849,non-specific,238185,656,772,0.00019202599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31174,Q#2202 - >seq8849,non-specific,339261,108,232,0.00040041,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs6_sqmonkey,marg,CompleteHit
31175,Q#2202 - >seq8849,specific,225881,483,680,0.00535049,40.2073,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
31176,Q#2202 - >seq8849,superfamily,225881,483,680,0.00535049,40.2073,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs6_sqmonkey.marg.frame3,1909181715_L1MA4.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
31177,Q#2203 - >seq8850,non-specific,238827,463,480,0.00596302,39.1966,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs3_orang.marg.frame1,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs3_orang,marg,C-TerminusTruncated
31178,Q#2203 - >seq8850,superfamily,295487,463,480,0.00596302,39.1966,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.marg.frame1,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA6,ORF2,hs3_orang,marg,C-TerminusTruncated
31179,Q#2204 - >seq8851,specific,197310,9,235,2.7264599999999994e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31180,Q#2204 - >seq8851,superfamily,351117,9,235,2.7264599999999994e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31181,Q#2204 - >seq8851,specific,238827,555,766,1.0185700000000001e-41,152.445,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31182,Q#2204 - >seq8851,superfamily,295487,555,766,1.0185700000000001e-41,152.445,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31183,Q#2204 - >seq8851,non-specific,197306,9,235,3.97553e-29,116.81200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31184,Q#2204 - >seq8851,non-specific,333820,580,766,1.0377e-21,93.8961,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31185,Q#2204 - >seq8851,superfamily,333820,580,766,1.0377e-21,93.8961,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31186,Q#2204 - >seq8851,non-specific,223780,7,228,4.3297e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31187,Q#2204 - >seq8851,non-specific,197307,9,235,9.8915e-18,83.8765,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31188,Q#2204 - >seq8851,non-specific,197320,7,228,1.0146000000000001e-17,84.1037,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31189,Q#2204 - >seq8851,specific,335306,10,228,1.39523e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31190,Q#2204 - >seq8851,non-specific,273186,7,236,2.61279e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31191,Q#2204 - >seq8851,non-specific,197321,7,235,2.45232e-12,68.3476,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31192,Q#2204 - >seq8851,non-specific,197319,7,235,6.544980000000001e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31193,Q#2204 - >seq8851,non-specific,272954,7,235,2.45916e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31194,Q#2204 - >seq8851,non-specific,238828,576,766,4.23107e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31195,Q#2204 - >seq8851,non-specific,275209,581,785,2.42113e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31196,Q#2204 - >seq8851,superfamily,275209,581,785,2.42113e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,N-TerminusTruncated
31197,Q#2204 - >seq8851,non-specific,197336,7,228,2.76715e-06,49.9183,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31198,Q#2204 - >seq8851,non-specific,238185,650,766,2.14938e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31199,Q#2204 - >seq8851,non-specific,197311,25,235,5.3078800000000004e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31200,Q#2204 - >seq8851,non-specific,197318,9,235,0.000856465,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31201,Q#2204 - >seq8851,non-specific,339261,107,231,0.00754881,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA6.ORF2.hs3_orang.marg.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA6,ORF2,hs3_orang,marg,CompleteHit
31202,Q#2206 - >seq8853,specific,197310,9,235,3.4936499999999995e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31203,Q#2206 - >seq8853,superfamily,351117,9,235,3.4936499999999995e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31204,Q#2206 - >seq8853,specific,238827,555,766,1.2927299999999998e-41,152.06,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31205,Q#2206 - >seq8853,superfamily,295487,555,766,1.2927299999999998e-41,152.06,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31206,Q#2206 - >seq8853,non-specific,197306,9,235,3.8154299999999996e-29,116.81200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31207,Q#2206 - >seq8853,non-specific,333820,580,766,1.2189600000000001e-21,93.5109,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31208,Q#2206 - >seq8853,superfamily,333820,580,766,1.2189600000000001e-21,93.5109,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31209,Q#2206 - >seq8853,non-specific,223780,7,228,4.1183e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31210,Q#2206 - >seq8853,non-specific,197320,7,228,9.74254e-18,84.1037,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31211,Q#2206 - >seq8853,non-specific,197307,9,235,1.13668e-17,83.8765,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31212,Q#2206 - >seq8853,specific,335306,10,228,1.39145e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31213,Q#2206 - >seq8853,non-specific,273186,7,236,2.39518e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31214,Q#2206 - >seq8853,non-specific,197321,7,235,2.6598200000000003e-12,67.9624,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31215,Q#2206 - >seq8853,non-specific,197319,7,235,6.6498e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31216,Q#2206 - >seq8853,non-specific,272954,7,235,2.4753000000000002e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31217,Q#2206 - >seq8853,non-specific,238828,576,766,5.33612e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31218,Q#2206 - >seq8853,non-specific,197336,7,228,2.75967e-06,49.9183,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31219,Q#2206 - >seq8853,non-specific,275209,581,785,2.95438e-06,50.534,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31220,Q#2206 - >seq8853,superfamily,275209,581,785,2.95438e-06,50.534,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,N-TerminusTruncated
31221,Q#2206 - >seq8853,non-specific,238185,650,766,2.0822600000000003e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31222,Q#2206 - >seq8853,non-specific,197311,25,235,4.7812399999999996e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31223,Q#2206 - >seq8853,non-specific,197318,9,235,0.000809293,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31224,Q#2206 - >seq8853,non-specific,339261,107,231,0.00664304,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA6.ORF2.hs3_orang.pars.frame3,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA6,ORF2,hs3_orang,pars,CompleteHit
31225,Q#2208 - >seq8855,non-specific,238827,463,480,0.005786100000000001,39.1966,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs3_orang.pars.frame1,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA6,ORF2,hs3_orang,pars,C-TerminusTruncated
31226,Q#2208 - >seq8855,superfamily,295487,463,480,0.005786100000000001,39.1966,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs3_orang.pars.frame1,1909181717_L1MA6.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA6,ORF2,hs3_orang,pars,C-TerminusTruncated
31227,Q#2211 - >seq8858,specific,238827,510,772,2.2416899999999998e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31228,Q#2211 - >seq8858,superfamily,295487,510,772,2.2416899999999998e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31229,Q#2211 - >seq8858,specific,197310,9,236,6.986049999999999e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31230,Q#2211 - >seq8858,superfamily,351117,9,236,6.986049999999999e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31231,Q#2211 - >seq8858,non-specific,197306,9,236,6.50352e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31232,Q#2211 - >seq8858,specific,333820,516,772,2.5420799999999997e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31233,Q#2211 - >seq8858,superfamily,333820,516,772,2.5420799999999997e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31234,Q#2211 - >seq8858,non-specific,197307,9,236,3.49737e-24,102.751,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31235,Q#2211 - >seq8858,non-specific,223780,9,238,1.79118e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31236,Q#2211 - >seq8858,non-specific,197320,8,229,5.53945e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31237,Q#2211 - >seq8858,non-specific,197321,7,236,1.85005e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31238,Q#2211 - >seq8858,specific,335306,10,229,2.2411900000000003e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31239,Q#2211 - >seq8858,non-specific,273186,9,237,3.5890500000000005e-17,82.3268,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31240,Q#2211 - >seq8858,non-specific,272954,9,236,3.06104e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31241,Q#2211 - >seq8858,non-specific,197336,7,229,8.096530000000001e-14,72.6451,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31242,Q#2211 - >seq8858,non-specific,197319,8,236,3.54241e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31243,Q#2211 - >seq8858,non-specific,197322,9,236,5.32231e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31244,Q#2211 - >seq8858,non-specific,238828,516,737,5.64166e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31245,Q#2211 - >seq8858,non-specific,339261,108,232,2.18932e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31246,Q#2211 - >seq8858,non-specific,236970,9,238,6.1452200000000004e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31247,Q#2211 - >seq8858,non-specific,275209,467,800,2.49795e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31248,Q#2211 - >seq8858,superfamily,275209,467,800,2.49795e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31249,Q#2211 - >seq8858,non-specific,197311,7,236,2.05806e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31250,Q#2211 - >seq8858,non-specific,238185,656,772,0.000118925,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31251,Q#2211 - >seq8858,non-specific,197317,23,229,0.00050952,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31252,Q#2211 - >seq8858,non-specific,224117,263,467,0.00176766,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31253,Q#2211 - >seq8858,superfamily,224117,263,467,0.00176766,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31254,Q#2211 - >seq8858,non-specific,274009,306,456,0.00247093,41.9771,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31255,Q#2211 - >seq8858,superfamily,274009,306,456,0.00247093,41.9771,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
31256,Q#2211 - >seq8858,non-specific,197314,7,192,0.00333664,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
31257,Q#2211 - >seq8858,specific,311990,1240,1258,0.00440248,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31258,Q#2211 - >seq8858,superfamily,311990,1240,1258,0.00440248,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31259,Q#2211 - >seq8858,non-specific,197318,9,236,0.00552749,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs6_sqmonkey.pars.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,pars,CompleteHit
31260,Q#2214 - >seq8861,specific,238827,511,773,2.1009499999999995e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31261,Q#2214 - >seq8861,superfamily,295487,511,773,2.1009499999999995e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31262,Q#2214 - >seq8861,specific,197310,9,236,6.671899999999999e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31263,Q#2214 - >seq8861,superfamily,351117,9,236,6.671899999999999e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31264,Q#2214 - >seq8861,non-specific,197306,9,236,6.1492200000000005e-49,174.207,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31265,Q#2214 - >seq8861,specific,333820,517,773,2.4031e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31266,Q#2214 - >seq8861,superfamily,333820,517,773,2.4031e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31267,Q#2214 - >seq8861,non-specific,197307,9,236,3.2776000000000003e-24,103.13600000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31268,Q#2214 - >seq8861,non-specific,223780,9,238,1.76072e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31269,Q#2214 - >seq8861,non-specific,197320,8,229,5.39376e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31270,Q#2214 - >seq8861,non-specific,197321,7,236,1.71832e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31271,Q#2214 - >seq8861,specific,335306,10,229,2.24518e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31272,Q#2214 - >seq8861,non-specific,273186,9,237,3.59559e-17,82.3268,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31273,Q#2214 - >seq8861,non-specific,272954,9,236,3.12493e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31274,Q#2214 - >seq8861,non-specific,197336,7,229,8.111219999999999e-14,72.6451,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31275,Q#2214 - >seq8861,non-specific,197319,8,236,3.32381e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31276,Q#2214 - >seq8861,non-specific,238828,517,738,5.14392e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31277,Q#2214 - >seq8861,non-specific,197322,9,236,5.3322300000000006e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31278,Q#2214 - >seq8861,non-specific,339261,108,232,2.19294e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31279,Q#2214 - >seq8861,non-specific,236970,9,238,6.044579999999999e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31280,Q#2214 - >seq8861,non-specific,275209,468,801,2.3942999999999998e-08,57.4676,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31281,Q#2214 - >seq8861,superfamily,275209,468,801,2.3942999999999998e-08,57.4676,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31282,Q#2214 - >seq8861,non-specific,197311,7,236,2.06164e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31283,Q#2214 - >seq8861,non-specific,235175,263,470,1.5032000000000001e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
31284,Q#2214 - >seq8861,superfamily,235175,263,470,1.5032000000000001e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
31285,Q#2214 - >seq8861,non-specific,238185,657,773,0.000120285,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31286,Q#2214 - >seq8861,non-specific,224117,263,468,0.000285077,45.0904,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31287,Q#2214 - >seq8861,superfamily,224117,263,468,0.000285077,45.0904,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31288,Q#2214 - >seq8861,non-specific,197317,23,229,0.000510412,42.9744,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31289,Q#2214 - >seq8861,non-specific,274009,306,457,0.00130188,43.1327,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31290,Q#2214 - >seq8861,superfamily,274009,306,457,0.00130188,43.1327,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
31291,Q#2214 - >seq8861,non-specific,197314,7,192,0.00334244,40.4047,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
31292,Q#2214 - >seq8861,specific,311990,1241,1259,0.00440931,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31293,Q#2214 - >seq8861,superfamily,311990,1241,1259,0.00440931,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31294,Q#2214 - >seq8861,non-specific,197318,9,236,0.00548773,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs6_sqmonkey.marg.frame3,1909181723_L1PA11.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs6_sqmonkey,marg,CompleteHit
31295,Q#2221 - >seq8868,non-specific,238827,199,348,1.62047e-06,49.597,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs2_gorilla.marg.frame3,1909181731_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31296,Q#2221 - >seq8868,superfamily,295487,199,348,1.62047e-06,49.597,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs2_gorilla.marg.frame3,1909181731_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31297,Q#2223 - >seq8870,non-specific,238827,199,360,9.558889999999999e-05,44.2042,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs2_gorilla.pars.frame3,1909181731_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
31298,Q#2223 - >seq8870,superfamily,295487,199,360,9.558889999999999e-05,44.2042,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs2_gorilla.pars.frame3,1909181731_L1MC3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
31299,Q#2227 - >seq8874,specific,197310,9,236,4.3817499999999996e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31300,Q#2227 - >seq8874,superfamily,351117,9,236,4.3817499999999996e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31301,Q#2227 - >seq8874,specific,238827,526,768,1.51734e-53,186.343,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31302,Q#2227 - >seq8874,superfamily,295487,526,768,1.51734e-53,186.343,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31303,Q#2227 - >seq8874,non-specific,197306,9,236,1.5501099999999999e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31304,Q#2227 - >seq8874,specific,333820,526,738,1.8562e-29,115.853,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31305,Q#2227 - >seq8874,superfamily,333820,526,738,1.8562e-29,115.853,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31306,Q#2227 - >seq8874,non-specific,197320,7,229,1.1206199999999999e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31307,Q#2227 - >seq8874,non-specific,223780,7,229,3.72087e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31308,Q#2227 - >seq8874,non-specific,197307,9,236,3.075e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31309,Q#2227 - >seq8874,specific,335306,10,229,3.74151e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31310,Q#2227 - >seq8874,non-specific,197321,7,236,1.47728e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31311,Q#2227 - >seq8874,non-specific,272954,7,236,9.54014e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31312,Q#2227 - >seq8874,non-specific,197319,7,236,1.44517e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31313,Q#2227 - >seq8874,non-specific,273186,7,237,5.0989699999999996e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31314,Q#2227 - >seq8874,non-specific,197336,7,229,4.72337e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31315,Q#2227 - >seq8874,non-specific,238828,580,735,7.17457e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31316,Q#2227 - >seq8874,non-specific,236970,9,229,6.60175e-06,49.1222,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31317,Q#2227 - >seq8874,non-specific,197311,37,236,0.0005717809999999999,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31318,Q#2227 - >seq8874,non-specific,275209,585,792,0.00141792,42.0596,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31319,Q#2227 - >seq8874,superfamily,275209,585,792,0.00141792,42.0596,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31320,Q#2227 - >seq8874,non-specific,235175,307,468,0.00199489,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31321,Q#2227 - >seq8874,superfamily,235175,307,468,0.00199489,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs4_gibbon.marg.frame2,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31322,Q#2229 - >seq8876,specific,197310,9,236,8.04191e-64,216.449,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31323,Q#2229 - >seq8876,superfamily,351117,9,236,8.04191e-64,216.449,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31324,Q#2229 - >seq8876,specific,238827,526,761,3.3586300000000007e-54,188.269,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31325,Q#2229 - >seq8876,superfamily,295487,526,761,3.3586300000000007e-54,188.269,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31326,Q#2229 - >seq8876,non-specific,197306,9,236,3.37739e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31327,Q#2229 - >seq8876,specific,333820,526,738,3.97945e-30,117.779,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31328,Q#2229 - >seq8876,superfamily,333820,526,738,3.97945e-30,117.779,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31329,Q#2229 - >seq8876,non-specific,223780,7,229,3.2211800000000002e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31330,Q#2229 - >seq8876,non-specific,197320,7,229,6.71541e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31331,Q#2229 - >seq8876,non-specific,197307,9,236,4.231739999999999e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31332,Q#2229 - >seq8876,specific,335306,10,229,3.5763e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31333,Q#2229 - >seq8876,non-specific,197321,7,236,3.45853e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31334,Q#2229 - >seq8876,non-specific,197319,7,236,1.20873e-15,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31335,Q#2229 - >seq8876,non-specific,272954,7,236,1.57183e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31336,Q#2229 - >seq8876,non-specific,273186,7,237,1.1813899999999999e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31337,Q#2229 - >seq8876,non-specific,238828,580,735,2.23865e-09,58.7516,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
31338,Q#2229 - >seq8876,non-specific,197336,7,229,4.513390000000001e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31339,Q#2229 - >seq8876,non-specific,236970,9,229,3.23536e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31340,Q#2229 - >seq8876,non-specific,197311,37,236,0.00018789400000000003,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs4_gibbon,pars,CompleteHit
31341,Q#2229 - >seq8876,non-specific,235175,307,468,0.000270957,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31342,Q#2229 - >seq8876,superfamily,235175,307,468,0.000270957,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31343,Q#2229 - >seq8876,non-specific,275209,585,735,0.00134376,42.0596,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31344,Q#2229 - >seq8876,superfamily,275209,585,735,0.00134376,42.0596,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31345,Q#2229 - >seq8876,non-specific,274009,305,499,0.00539035,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31346,Q#2229 - >seq8876,superfamily,274009,305,499,0.00539035,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA8.ORF2.hs4_gibbon.pars.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31347,Q#2232 - >seq8879,specific,311990,1109,1127,0.00191208,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs4_gibbon.marg.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31348,Q#2232 - >seq8879,superfamily,311990,1109,1127,0.00191208,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs4_gibbon.marg.frame3,1909181731_L1MA8.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs4_gibbon,marg,CompleteHit
31349,Q#2235 - >seq8882,non-specific,238827,365,577,1.47347e-19,88.5022,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs0_human,pars,CompleteHit
31350,Q#2235 - >seq8882,superfamily,295487,365,577,1.47347e-19,88.5022,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs0_human,pars,CompleteHit
31351,Q#2235 - >seq8882,non-specific,333820,369,577,1.67051e-12,66.9322,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs0_human,pars,CompleteHit
31352,Q#2235 - >seq8882,superfamily,333820,369,577,1.67051e-12,66.9322,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs0_human,pars,CompleteHit
31353,Q#2235 - >seq8882,non-specific,238828,424,577,1.31379e-06,50.6624,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs0_human,pars,N-TerminusTruncated
31354,Q#2235 - >seq8882,non-specific,197310,32,144,0.000640149,42.3385,cd09076,L1-EN,NC,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC3,ORF2,hs0_human,pars,BothTerminiTruncated
31355,Q#2235 - >seq8882,superfamily,351117,32,144,0.000640149,42.3385,cl00490,EEP superfamily,NC, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs0_human.pars.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs0_human,pars,BothTerminiTruncated
31356,Q#2238 - >seq8885,non-specific,238827,612,836,3.25247e-22,96.5914,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs0_human,marg,CompleteHit
31357,Q#2238 - >seq8885,superfamily,295487,612,836,3.25247e-22,96.5914,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs0_human,marg,CompleteHit
31358,Q#2238 - >seq8885,non-specific,197310,154,348,5.3485199999999996e-15,75.8509,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC3,ORF2,hs0_human,marg,CompleteHit
31359,Q#2238 - >seq8885,superfamily,351117,154,348,5.3485199999999996e-15,75.8509,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs0_human,marg,CompleteHit
31360,Q#2238 - >seq8885,non-specific,333820,628,836,5.90592e-14,71.5546,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs0_human,marg,CompleteHit
31361,Q#2238 - >seq8885,superfamily,333820,628,836,5.90592e-14,71.5546,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs0_human,marg,CompleteHit
31362,Q#2238 - >seq8885,non-specific,238828,684,836,3.7562400000000004e-06,49.5068,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC3,ORF2,hs0_human,marg,N-TerminusTruncated
31363,Q#2238 - >seq8885,non-specific,197306,194,348,0.00299532,40.9277,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs0_human.marg.frame3,1909181735_L1MC3.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC3,ORF2,hs0_human,marg,CompleteHit
31364,Q#2240 - >seq8887,specific,238827,501,763,5.6533299999999996e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31365,Q#2240 - >seq8887,superfamily,295487,501,763,5.6533299999999996e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31366,Q#2240 - >seq8887,specific,197310,9,229,2.48492e-46,166.373,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31367,Q#2240 - >seq8887,superfamily,351117,9,229,2.48492e-46,166.373,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31368,Q#2240 - >seq8887,specific,333820,507,731,1.9242999999999997e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31369,Q#2240 - >seq8887,superfamily,333820,507,731,1.9242999999999997e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31370,Q#2240 - >seq8887,non-specific,197306,9,229,6.999449999999999e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31371,Q#2240 - >seq8887,non-specific,197307,9,229,1.02255e-12,69.2389,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31372,Q#2240 - >seq8887,non-specific,223780,7,222,1.36231e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31373,Q#2240 - >seq8887,non-specific,197320,7,222,1.65673e-12,68.6958,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31374,Q#2240 - >seq8887,non-specific,238828,507,728,1.36493e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31375,Q#2240 - >seq8887,non-specific,197321,7,229,2.5135799999999995e-09,59.1028,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31376,Q#2240 - >seq8887,non-specific,275209,458,782,2.9935300000000005e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31377,Q#2240 - >seq8887,superfamily,275209,458,782,2.9935300000000005e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31378,Q#2240 - >seq8887,specific,335306,10,222,6.97657e-09,57.255,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31379,Q#2240 - >seq8887,non-specific,197319,7,229,8.0708e-09,57.6717,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31380,Q#2240 - >seq8887,non-specific,272954,7,229,1.15818e-05,48.1481,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31381,Q#2240 - >seq8887,non-specific,339261,101,225,4.1279600000000004e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31382,Q#2240 - >seq8887,non-specific,238185,647,763,0.00487905,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs3_orang.marg.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31383,Q#2241 - >seq8888,specific,311990,1103,1120,0.00673992,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs3_orang.marg.frame1,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31384,Q#2241 - >seq8888,superfamily,311990,1103,1120,0.00673992,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs3_orang.marg.frame1,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA5,ORF2,hs3_orang,marg,CompleteHit
31385,Q#2243 - >seq8890,specific,311990,1102,1119,0.00721235,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs3_orang.pars.frame1,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31386,Q#2243 - >seq8890,superfamily,311990,1102,1119,0.00721235,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs3_orang.pars.frame1,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31387,Q#2244 - >seq8891,specific,238827,503,765,5.7641799999999994e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31388,Q#2244 - >seq8891,superfamily,295487,503,765,5.7641799999999994e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31389,Q#2244 - >seq8891,specific,197310,9,229,2.48492e-46,166.373,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31390,Q#2244 - >seq8891,superfamily,351117,9,229,2.48492e-46,166.373,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31391,Q#2244 - >seq8891,specific,333820,509,733,1.9242999999999997e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31392,Q#2244 - >seq8891,superfamily,333820,509,733,1.9242999999999997e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31393,Q#2244 - >seq8891,non-specific,197306,9,229,7.202980000000001e-25,104.486,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31394,Q#2244 - >seq8891,non-specific,197307,9,229,1.03215e-12,69.2389,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31395,Q#2244 - >seq8891,non-specific,223780,7,222,1.45406e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31396,Q#2244 - >seq8891,non-specific,197320,7,222,1.65673e-12,68.6958,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31397,Q#2244 - >seq8891,non-specific,238828,509,730,1.36493e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31398,Q#2244 - >seq8891,non-specific,197321,7,229,2.5135799999999995e-09,59.1028,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31399,Q#2244 - >seq8891,non-specific,275209,460,784,2.91482e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31400,Q#2244 - >seq8891,superfamily,275209,460,784,2.91482e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31401,Q#2244 - >seq8891,specific,335306,10,222,6.97657e-09,57.255,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31402,Q#2244 - >seq8891,non-specific,197319,7,229,8.37388e-09,57.6717,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31403,Q#2244 - >seq8891,non-specific,272954,7,229,1.1793599999999998e-05,48.1481,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31404,Q#2244 - >seq8891,non-specific,339261,101,225,4.08822e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31405,Q#2244 - >seq8891,non-specific,238185,649,765,0.00492681,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs3_orang.pars.frame3,1909181736_L1MA5.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs3_orang,pars,CompleteHit
31406,Q#2245 - >seq8892,specific,197310,41,228,4.494169999999999e-35,134.016,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,pars,CompleteHit
31407,Q#2245 - >seq8892,superfamily,351117,41,228,4.494169999999999e-35,134.016,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,pars,CompleteHit
31408,Q#2245 - >seq8892,non-specific,197306,32,228,3.3716800000000003e-16,79.4476,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,pars,CompleteHit
31409,Q#2245 - >seq8892,non-specific,197320,98,221,2.51622e-10,62.1474,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31410,Q#2245 - >seq8892,non-specific,197307,98,228,7.27123e-08,54.6013,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31411,Q#2245 - >seq8892,specific,335306,58,221,1.46223e-06,50.3214,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31412,Q#2245 - >seq8892,non-specific,223780,98,221,4.16932e-06,49.5191,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31413,Q#2245 - >seq8892,non-specific,197319,98,228,3.73843e-05,46.5009,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31414,Q#2245 - >seq8892,non-specific,272954,98,228,0.000467696,43.1405,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,pars,N-TerminusTruncated
31415,Q#2245 - >seq8892,non-specific,339261,100,224,0.0004994040000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31416,Q#2245 - >seq8892,non-specific,197311,54,228,0.00436549,39.5825,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs0_human.pars.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,pars,CompleteHit
31417,Q#2247 - >seq8894,specific,238827,482,739,1.9917999999999997e-60,205.988,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31418,Q#2247 - >seq8894,superfamily,295487,482,739,1.9917999999999997e-60,205.988,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31419,Q#2247 - >seq8894,specific,333820,488,709,2.4032499999999996e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31420,Q#2247 - >seq8894,superfamily,333820,488,709,2.4032499999999996e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31421,Q#2247 - >seq8894,non-specific,238828,488,706,6.45278e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31422,Q#2247 - >seq8894,non-specific,275209,439,758,1.17762e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31423,Q#2247 - >seq8894,superfamily,275209,439,758,1.17762e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31424,Q#2247 - >seq8894,specific,311990,1190,1208,0.00632988,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5,ORF2,hs0_human,pars,CompleteHit
31425,Q#2247 - >seq8894,superfamily,311990,1190,1208,0.00632988,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA5,ORF2,hs0_human,pars,CompleteHit
31426,Q#2247 - >seq8894,non-specific,238185,625,710,0.00831105,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs0_human.pars.frame3,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs0_human,pars,CompleteHit
31427,Q#2248 - >seq8895,specific,197310,41,228,3.82916e-34,131.32,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,marg,CompleteHit
31428,Q#2248 - >seq8895,superfamily,351117,41,228,3.82916e-34,131.32,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,marg,CompleteHit
31429,Q#2248 - >seq8895,non-specific,197306,32,228,6.10929e-16,78.6772,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,marg,CompleteHit
31430,Q#2248 - >seq8895,non-specific,197320,98,221,2.51376e-10,62.1474,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31431,Q#2248 - >seq8895,non-specific,197307,98,228,7.81772e-08,54.6013,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31432,Q#2248 - >seq8895,specific,335306,58,221,1.46084e-06,50.3214,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31433,Q#2248 - >seq8895,non-specific,223780,98,221,4.16529e-06,49.5191,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31434,Q#2248 - >seq8895,non-specific,197319,98,228,4.1255500000000005e-05,46.5009,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31435,Q#2248 - >seq8895,non-specific,272954,98,228,0.00071878,42.3701,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31436,Q#2248 - >seq8895,non-specific,339261,100,224,0.00350615,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31437,Q#2248 - >seq8895,non-specific,197311,54,228,0.00500314,39.5825,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,marg,CompleteHit
31438,Q#2248 - >seq8895,non-specific,197321,98,228,0.00920137,39.0724,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs0_human.marg.frame1,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA5,ORF2,hs0_human,marg,N-TerminusTruncated
31439,Q#2249 - >seq8896,specific,238827,467,725,6.300329999999998e-61,207.52900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31440,Q#2249 - >seq8896,superfamily,295487,467,725,6.300329999999998e-61,207.52900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31441,Q#2249 - >seq8896,specific,333820,473,725,7.502209999999999e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31442,Q#2249 - >seq8896,superfamily,333820,473,725,7.502209999999999e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31443,Q#2249 - >seq8896,non-specific,238828,473,691,4.6813699999999995e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31444,Q#2249 - >seq8896,non-specific,275209,424,763,6.135830000000001e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31445,Q#2249 - >seq8896,superfamily,275209,424,763,6.135830000000001e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31446,Q#2249 - >seq8896,non-specific,238185,610,725,0.00276506,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs0_human,marg,CompleteHit
31447,Q#2249 - >seq8896,specific,311990,1180,1198,0.00733905,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5,ORF2,hs0_human,marg,CompleteHit
31448,Q#2249 - >seq8896,superfamily,311990,1180,1198,0.00733905,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs0_human.marg.frame2,1909181737_L1MA5.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA5,ORF2,hs0_human,marg,CompleteHit
31449,Q#2253 - >seq8900,non-specific,197310,61,206,0.00011481200000000001,45.0349,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC3.ORF2.hs1_chimp.marg.frame2,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MC3,ORF2,hs1_chimp,marg,CompleteHit
31450,Q#2253 - >seq8900,superfamily,351117,61,206,0.00011481200000000001,45.0349,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC3.ORF2.hs1_chimp.marg.frame2,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MC3,ORF2,hs1_chimp,marg,CompleteHit
31451,Q#2254 - >seq8901,non-specific,238827,460,667,5.2190900000000005e-12,66.5458,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs1_chimp.marg.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,marg,CompleteHit
31452,Q#2254 - >seq8901,superfamily,295487,460,667,5.2190900000000005e-12,66.5458,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs1_chimp.marg.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,marg,CompleteHit
31453,Q#2254 - >seq8901,non-specific,333820,465,635,2.32064e-08,54.99100000000001,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs1_chimp.marg.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,marg,C-TerminusTruncated
31454,Q#2254 - >seq8901,superfamily,333820,465,635,2.32064e-08,54.99100000000001,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs1_chimp.marg.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,marg,C-TerminusTruncated
31455,Q#2254 - >seq8901,non-specific,238828,512,635,0.00881551,39.1065,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs1_chimp.marg.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,marg,N-TerminusTruncated
31456,Q#2256 - >seq8903,non-specific,238827,386,560,4.68153e-20,89.6578,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs1_chimp.pars.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,pars,C-TerminusTruncated
31457,Q#2256 - >seq8903,superfamily,295487,386,560,4.68153e-20,89.6578,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs1_chimp.pars.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,pars,C-TerminusTruncated
31458,Q#2256 - >seq8903,non-specific,333820,391,544,1.02846e-12,67.3174,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs1_chimp.pars.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,pars,C-TerminusTruncated
31459,Q#2256 - >seq8903,superfamily,333820,391,544,1.02846e-12,67.3174,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs1_chimp.pars.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,pars,C-TerminusTruncated
31460,Q#2256 - >seq8903,non-specific,238828,446,535,4.1537099999999996e-06,48.7364,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs1_chimp.pars.frame1,1909181742_L1MC3.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC3,ORF2,hs1_chimp,pars,BothTerminiTruncated
31461,Q#2258 - >seq8905,specific,238827,498,760,3.1977999999999996e-61,208.68400000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,CompleteHit
31462,Q#2258 - >seq8905,superfamily,295487,498,760,3.1977999999999996e-61,208.68400000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,CompleteHit
31463,Q#2258 - >seq8905,specific,333820,504,760,1.2021099999999999e-30,119.319,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,CompleteHit
31464,Q#2258 - >seq8905,superfamily,333820,504,760,1.2021099999999999e-30,119.319,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,CompleteHit
31465,Q#2258 - >seq8905,non-specific,197310,106,228,5.0312800000000004e-23,98.9628,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31466,Q#2258 - >seq8905,superfamily,351117,106,228,5.0312800000000004e-23,98.9628,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31467,Q#2258 - >seq8905,non-specific,197306,105,228,8.59747e-10,60.5729,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31468,Q#2258 - >seq8905,non-specific,238828,570,760,5.25217e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31469,Q#2258 - >seq8905,non-specific,275209,575,779,8.50769e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31470,Q#2258 - >seq8905,superfamily,275209,575,779,8.50769e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31471,Q#2258 - >seq8905,non-specific,197320,106,221,9.13927e-06,48.2802,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31472,Q#2258 - >seq8905,non-specific,238185,644,760,7.17554e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA6,ORF2,hs0_human,marg,CompleteHit
31473,Q#2258 - >seq8905,specific,335306,58,221,0.00011891799999999999,44.9286,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31474,Q#2258 - >seq8905,non-specific,223780,127,221,0.000316577,43.7411,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31475,Q#2258 - >seq8905,non-specific,197307,115,228,0.0006681660000000001,42.6601,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31476,Q#2258 - >seq8905,non-specific,273186,169,229,0.00145435,41.8808,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31477,Q#2258 - >seq8905,non-specific,197321,166,228,0.00766979,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame2,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA6,ORF2,hs0_human,marg,N-TerminusTruncated
31478,Q#2259 - >seq8906,specific,238827,496,759,6.67243e-60,204.832,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31479,Q#2259 - >seq8906,superfamily,295487,496,759,6.67243e-60,204.832,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31480,Q#2259 - >seq8906,specific,333820,502,759,8.47906e-30,117.008,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31481,Q#2259 - >seq8906,superfamily,333820,502,759,8.47906e-30,117.008,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31482,Q#2259 - >seq8906,non-specific,197310,105,226,1.3317e-21,95.1109,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31483,Q#2259 - >seq8906,superfamily,351117,105,226,1.3317e-21,95.1109,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31484,Q#2259 - >seq8906,non-specific,197306,104,226,1.5125399999999998e-10,62.4989,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31485,Q#2259 - >seq8906,non-specific,238828,502,759,4.5366599999999995e-09,57.9812,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31486,Q#2259 - >seq8906,non-specific,275209,574,778,9.05678e-06,49.3784,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31487,Q#2259 - >seq8906,superfamily,275209,574,778,9.05678e-06,49.3784,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31488,Q#2259 - >seq8906,specific,335306,57,219,4.9951800000000005e-05,45.699,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31489,Q#2259 - >seq8906,non-specific,238185,643,759,6.05037e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs0_human,pars,CompleteHit
31490,Q#2259 - >seq8906,non-specific,197320,105,219,6.2389e-05,45.968999999999994,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31491,Q#2259 - >seq8906,non-specific,223780,126,219,0.00288408,40.6595,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31492,Q#2259 - >seq8906,non-specific,197307,114,226,0.00480738,39.9637,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.pars.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,pars,N-TerminusTruncated
31493,Q#2261 - >seq8908,non-specific,197310,9,113,6.295219999999999e-24,101.65899999999999,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31494,Q#2261 - >seq8908,superfamily,351117,9,113,6.295219999999999e-24,101.65899999999999,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31495,Q#2261 - >seq8908,non-specific,197306,9,122,4.40662e-14,72.8993,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31496,Q#2261 - >seq8908,non-specific,223780,7,113,5.39397e-05,46.0523,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31497,Q#2261 - >seq8908,non-specific,197321,7,80,0.00017622599999999998,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31498,Q#2261 - >seq8908,non-specific,272954,7,76,0.000562368,42.7553,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31499,Q#2261 - >seq8908,specific,335306,10,134,0.00110499,41.847,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31500,Q#2261 - >seq8908,non-specific,197307,9,43,0.00283181,40.7341,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31501,Q#2261 - >seq8908,non-specific,197320,7,43,0.00443101,40.191,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31502,Q#2261 - >seq8908,non-specific,273186,7,43,0.00868357,39.1844,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs0_human.pars.frame1,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA6,ORF2,hs0_human,pars,C-TerminusTruncated
31503,Q#2262 - >seq8909,non-specific,197310,9,113,6.120099999999999e-24,101.65899999999999,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31504,Q#2262 - >seq8909,superfamily,351117,9,113,6.120099999999999e-24,101.65899999999999,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31505,Q#2262 - >seq8909,non-specific,197306,9,122,5.2229199999999994e-14,72.8993,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31506,Q#2262 - >seq8909,non-specific,223780,7,113,5.9064600000000004e-05,46.0523,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31507,Q#2262 - >seq8909,non-specific,197321,7,80,0.000181179,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31508,Q#2262 - >seq8909,non-specific,272954,7,76,0.00056783,42.7553,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31509,Q#2262 - >seq8909,specific,335306,10,134,0.00111557,41.847,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31510,Q#2262 - >seq8909,non-specific,197307,9,43,0.00291078,40.7341,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31511,Q#2262 - >seq8909,non-specific,197320,7,43,0.00447377,40.191,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31512,Q#2262 - >seq8909,non-specific,273186,7,43,0.00876713,39.1844,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs0_human.marg.frame3,1909181742_L1MA6.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs0_human,marg,C-TerminusTruncated
31513,Q#2263 - >seq8910,specific,238827,500,761,1.8853799999999995e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31514,Q#2263 - >seq8910,superfamily,295487,500,761,1.8853799999999995e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31515,Q#2263 - >seq8910,specific,333820,506,761,8.36209e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31516,Q#2263 - >seq8910,superfamily,333820,506,761,8.36209e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31517,Q#2263 - >seq8910,specific,197310,25,228,1.6840599999999997e-33,129.394,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31518,Q#2263 - >seq8910,superfamily,351117,25,228,1.6840599999999997e-33,129.394,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31519,Q#2263 - >seq8910,non-specific,197306,24,228,6.990860000000001e-15,75.5956,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31520,Q#2263 - >seq8910,non-specific,238828,506,727,2.54533e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31521,Q#2263 - >seq8910,non-specific,275209,457,799,8.110579999999999e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31522,Q#2263 - >seq8910,superfamily,275209,457,799,8.110579999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31523,Q#2263 - >seq8910,specific,335306,55,221,7.175920000000001e-07,51.477,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,marg,N-TerminusTruncated
31524,Q#2263 - >seq8910,non-specific,197320,106,201,0.000115759,45.1986,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5,ORF2,hs1_chimp,marg,N-TerminusTruncated
31525,Q#2263 - >seq8910,non-specific,197307,84,228,0.00242576,41.1193,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs1_chimp.marg.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA5,ORF2,hs1_chimp,marg,N-TerminusTruncated
31526,Q#2264 - >seq8911,specific,311990,1121,1139,0.00411544,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs1_chimp.marg.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31527,Q#2264 - >seq8911,superfamily,311990,1121,1139,0.00411544,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs1_chimp.marg.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA5,ORF2,hs1_chimp,marg,CompleteHit
31528,Q#2266 - >seq8913,specific,238827,482,702,2.93072e-43,156.68200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31529,Q#2266 - >seq8913,superfamily,295487,482,702,2.93072e-43,156.68200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31530,Q#2266 - >seq8913,non-specific,333820,487,702,1.5761700000000003e-22,95.8221,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31531,Q#2266 - >seq8913,superfamily,333820,487,702,1.5761700000000003e-22,95.8221,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31532,Q#2266 - >seq8913,non-specific,238828,513,668,5.39983e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,N-TerminusTruncated
31533,Q#2266 - >seq8913,non-specific,275209,518,740,1.84995e-06,51.3044,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,N-TerminusTruncated
31534,Q#2266 - >seq8913,superfamily,275209,518,740,1.84995e-06,51.3044,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,N-TerminusTruncated
31535,Q#2266 - >seq8913,non-specific,238185,587,702,0.00946559,36.56,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs1_chimp.pars.frame1,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31536,Q#2267 - >seq8914,specific,311990,1131,1149,0.00178853,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs1_chimp.pars.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31537,Q#2267 - >seq8914,superfamily,311990,1131,1149,0.00178853,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA5.ORF2.hs1_chimp.pars.frame2,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31538,Q#2268 - >seq8915,specific,197310,9,231,1.73879e-35,135.172,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31539,Q#2268 - >seq8915,superfamily,351117,9,231,1.73879e-35,135.172,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31540,Q#2268 - >seq8915,non-specific,197306,9,231,1.81112e-16,80.218,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31541,Q#2268 - >seq8915,non-specific,238827,503,541,3.9959800000000003e-10,60.7678,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs1_chimp,pars,C-TerminusTruncated
31542,Q#2268 - >seq8915,superfamily,295487,503,541,3.9959800000000003e-10,60.7678,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs1_chimp,pars,C-TerminusTruncated
31543,Q#2268 - >seq8915,specific,335306,10,224,3.4573999999999997e-07,52.2474,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31544,Q#2268 - >seq8915,non-specific,197307,9,231,7.61104e-05,45.3565,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs1_chimp,pars,CompleteHit
31545,Q#2268 - >seq8915,non-specific,197320,109,204,0.00011172,45.1986,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA5,ORF2,hs1_chimp,pars,N-TerminusTruncated
31546,Q#2268 - >seq8915,non-specific,333820,509,557,0.000499725,42.2794,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs1_chimp,pars,C-TerminusTruncated
31547,Q#2268 - >seq8915,superfamily,333820,509,557,0.000499725,42.2794,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA5.ORF2.hs1_chimp.pars.frame3,1909181751_L1MA5.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA5,ORF2,hs1_chimp,pars,C-TerminusTruncated
31548,Q#2269 - >seq8916,specific,197310,9,236,1.3316599999999997e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31549,Q#2269 - >seq8916,superfamily,351117,9,236,1.3316599999999997e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31550,Q#2269 - >seq8916,specific,238827,510,760,3.917999999999999e-43,156.297,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31551,Q#2269 - >seq8916,superfamily,295487,510,760,3.917999999999999e-43,156.297,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31552,Q#2269 - >seq8916,non-specific,197306,9,236,3.17754e-39,146.08700000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31553,Q#2269 - >seq8916,non-specific,333820,549,743,1.04122e-21,93.5109,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31554,Q#2269 - >seq8916,superfamily,333820,549,743,1.04122e-21,93.5109,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31555,Q#2269 - >seq8916,non-specific,223780,9,237,1.5613499999999999e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31556,Q#2269 - >seq8916,non-specific,197307,9,236,1.78837e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31557,Q#2269 - >seq8916,non-specific,197320,9,229,8.44503e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31558,Q#2269 - >seq8916,non-specific,197321,7,236,3.06813e-19,88.37799999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31559,Q#2269 - >seq8916,specific,335306,10,229,3.5560800000000004e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31560,Q#2269 - >seq8916,non-specific,273186,9,237,4.14196e-17,82.3268,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31561,Q#2269 - >seq8916,non-specific,197319,13,236,4.15199e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31562,Q#2269 - >seq8916,non-specific,272954,9,207,5.904470000000001e-13,70.1045,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31563,Q#2269 - >seq8916,non-specific,238828,561,734,5.2506699999999995e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,N-TerminusTruncated
31564,Q#2269 - >seq8916,non-specific,197322,8,236,1.3400399999999999e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31565,Q#2269 - >seq8916,non-specific,236970,9,237,5.26026e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31566,Q#2269 - >seq8916,non-specific,197336,9,194,4.477469999999999e-08,55.3111,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31567,Q#2269 - >seq8916,non-specific,275209,584,734,2.05757e-06,51.3044,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,BothTerminiTruncated
31568,Q#2269 - >seq8916,superfamily,275209,584,734,2.05757e-06,51.3044,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,BothTerminiTruncated
31569,Q#2269 - >seq8916,non-specific,339261,108,232,6.891860000000001e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31570,Q#2269 - >seq8916,non-specific,197311,7,236,2.5329099999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31571,Q#2269 - >seq8916,non-specific,238185,653,738,0.00066271,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs1_chimp.marg.frame3,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs1_chimp,marg,CompleteHit
31572,Q#2271 - >seq8918,specific,197310,9,236,8.132639999999999e-61,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31573,Q#2271 - >seq8918,superfamily,351117,9,236,8.132639999999999e-61,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31574,Q#2271 - >seq8918,specific,238827,510,759,4.87545e-42,153.216,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31575,Q#2271 - >seq8918,superfamily,295487,510,759,4.87545e-42,153.216,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31576,Q#2271 - >seq8918,non-specific,197306,9,236,2.7052899999999997e-39,146.08700000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31577,Q#2271 - >seq8918,non-specific,223780,9,237,1.59264e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31578,Q#2271 - >seq8918,non-specific,197307,9,236,1.67589e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31579,Q#2271 - >seq8918,non-specific,333820,549,742,1.7063900000000002e-20,90.0441,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31580,Q#2271 - >seq8918,superfamily,333820,549,742,1.7063900000000002e-20,90.0441,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31581,Q#2271 - >seq8918,non-specific,197320,9,229,7.91324e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31582,Q#2271 - >seq8918,non-specific,197321,7,236,2.42445e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31583,Q#2271 - >seq8918,specific,335306,10,229,3.3382300000000005e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31584,Q#2271 - >seq8918,non-specific,273186,9,237,3.88187e-17,82.3268,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31585,Q#2271 - >seq8918,non-specific,197319,13,236,3.47832e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31586,Q#2271 - >seq8918,non-specific,272954,9,207,5.433659999999999e-13,70.1045,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31587,Q#2271 - >seq8918,non-specific,238828,561,719,8.346499999999999e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,N-TerminusTruncated
31588,Q#2271 - >seq8918,non-specific,197322,8,236,1.25478e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31589,Q#2271 - >seq8918,non-specific,236970,9,237,5.07061e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31590,Q#2271 - >seq8918,non-specific,197336,9,194,4.2022199999999995e-08,55.3111,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31591,Q#2271 - >seq8918,non-specific,339261,108,232,6.4398699999999996e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31592,Q#2271 - >seq8918,non-specific,275209,584,718,1.06644e-05,48.608000000000004,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,BothTerminiTruncated
31593,Q#2271 - >seq8918,superfamily,275209,584,718,1.06644e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,BothTerminiTruncated
31594,Q#2271 - >seq8918,non-specific,197311,7,236,2.5659699999999998e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31595,Q#2271 - >seq8918,non-specific,238185,653,737,0.000432123,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs1_chimp.pars.frame2,1909181752_L1PA15-16.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs1_chimp,pars,CompleteHit
31596,Q#2277 - >seq8924,specific,238827,522,767,5.76441e-57,196.358,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31597,Q#2277 - >seq8924,superfamily,295487,522,767,5.76441e-57,196.358,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31598,Q#2277 - >seq8924,specific,197310,9,232,7.1532099999999985e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31599,Q#2277 - >seq8924,superfamily,351117,9,232,7.1532099999999985e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31600,Q#2277 - >seq8924,specific,333820,522,767,8.190250000000001e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31601,Q#2277 - >seq8924,superfamily,333820,522,767,8.190250000000001e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31602,Q#2277 - >seq8924,non-specific,197306,9,232,2.9191e-27,111.419,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31603,Q#2277 - >seq8924,non-specific,197307,9,232,1.5107099999999998e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31604,Q#2277 - >seq8924,non-specific,223780,7,225,1.64895e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31605,Q#2277 - >seq8924,non-specific,197320,7,225,1.06683e-19,89.8817,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31606,Q#2277 - >seq8924,specific,335306,10,225,2.0607399999999997e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31607,Q#2277 - >seq8924,non-specific,197321,7,232,7.013679999999999e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31608,Q#2277 - >seq8924,non-specific,197319,7,232,2.31344e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31609,Q#2277 - >seq8924,non-specific,273186,7,233,6.03869e-13,70.0004,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31610,Q#2277 - >seq8924,non-specific,272954,7,232,1.59904e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31611,Q#2277 - >seq8924,non-specific,238828,576,731,8.28745e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
31612,Q#2277 - >seq8924,non-specific,275209,581,791,3.84024e-06,50.534,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
31613,Q#2277 - >seq8924,superfamily,275209,581,791,3.84024e-06,50.534,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
31614,Q#2277 - >seq8924,non-specific,197336,7,225,1.52031e-05,47.6071,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31615,Q#2277 - >seq8924,non-specific,197318,9,232,0.000134316,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31616,Q#2277 - >seq8924,non-specific,238185,650,767,0.000642876,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,pars,CompleteHit
31617,Q#2277 - >seq8924,non-specific,223496,296,494,0.000841504,43.5955,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA6,ORF2,hs2_gorilla,pars,BothTerminiTruncated
31618,Q#2277 - >seq8924,superfamily,223496,296,494,0.000841504,43.5955,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.pars.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA6,ORF2,hs2_gorilla,pars,BothTerminiTruncated
31619,Q#2280 - >seq8927,specific,197310,9,236,4.140889999999999e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31620,Q#2280 - >seq8927,superfamily,351117,9,236,4.140889999999999e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31621,Q#2280 - >seq8927,specific,238827,526,771,6.607069999999999e-57,195.97299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31622,Q#2280 - >seq8927,superfamily,295487,526,771,6.607069999999999e-57,195.97299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31623,Q#2280 - >seq8927,specific,333820,526,771,9.88204e-32,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31624,Q#2280 - >seq8927,superfamily,333820,526,771,9.88204e-32,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31625,Q#2280 - >seq8927,non-specific,197306,9,236,1.9946e-28,114.88600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31626,Q#2280 - >seq8927,non-specific,223780,7,229,3.86414e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31627,Q#2280 - >seq8927,non-specific,197307,9,236,4.87114e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31628,Q#2280 - >seq8927,non-specific,197320,7,229,2.10713e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31629,Q#2280 - >seq8927,specific,335306,10,229,2.8600099999999995e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31630,Q#2280 - >seq8927,non-specific,197321,7,236,1.60049e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31631,Q#2280 - >seq8927,non-specific,197319,7,236,2.2045899999999998e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31632,Q#2280 - >seq8927,non-specific,273186,7,237,4.38933e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31633,Q#2280 - >seq8927,non-specific,272954,7,236,4.5262e-13,70.4897,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31634,Q#2280 - >seq8927,non-specific,238828,580,735,8.74469e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
31635,Q#2280 - >seq8927,non-specific,197336,7,229,3.3045e-06,49.9183,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31636,Q#2280 - >seq8927,non-specific,275209,585,795,4.1664e-06,50.1488,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
31637,Q#2280 - >seq8927,superfamily,275209,585,795,4.1664e-06,50.1488,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
31638,Q#2280 - >seq8927,non-specific,238185,654,771,0.000655952,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31639,Q#2280 - >seq8927,non-specific,223496,300,498,0.000809666,43.5955,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,BothTerminiTruncated
31640,Q#2280 - >seq8927,superfamily,223496,300,498,0.000809666,43.5955,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA6,ORF2,hs2_gorilla,marg,BothTerminiTruncated
31641,Q#2280 - >seq8927,non-specific,197311,7,236,0.0008400269999999999,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31642,Q#2280 - >seq8927,non-specific,197318,9,236,0.0009496410000000001,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs2_gorilla.marg.frame3,1909181752_L1MA6.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs2_gorilla,marg,CompleteHit
31643,Q#2282 - >seq8929,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31644,Q#2282 - >seq8929,superfamily,335182,154,251,3.9370899999999993e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31645,Q#2282 - >seq8929,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31646,Q#2282 - >seq8929,non-specific,340205,254,318,7.170599999999999e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31647,Q#2282 - >seq8929,superfamily,340205,254,318,7.170599999999999e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31648,Q#2282 - >seq8929,non-specific,340205,254,318,7.170599999999999e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31649,Q#2282 - >seq8929,non-specific,340204,109,151,2.73223e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31650,Q#2282 - >seq8929,superfamily,340204,109,151,2.73223e-13,63.1956,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31651,Q#2282 - >seq8929,non-specific,340204,109,151,2.73223e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,marg,CompleteHit
31652,Q#2282 - >seq8929,non-specific,224117,42,236,0.00119264,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31653,Q#2282 - >seq8929,superfamily,224117,42,236,0.00119264,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31654,Q#2282 - >seq8929,non-specific,224117,42,236,0.00119264,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31655,Q#2282 - >seq8929,non-specific,335623,52,146,0.00135265,39.8502,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31656,Q#2282 - >seq8929,superfamily,335623,52,146,0.00135265,39.8502,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31657,Q#2282 - >seq8929,non-specific,335623,52,146,0.00135265,39.8502,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31658,Q#2282 - >seq8929,non-specific,235175,52,140,0.00146822,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31659,Q#2282 - >seq8929,superfamily,235175,52,140,0.00146822,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31660,Q#2282 - >seq8929,non-specific,235175,52,140,0.00146822,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31661,Q#2282 - >seq8929,non-specific,273690,53,194,0.00251897,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31662,Q#2282 - >seq8929,superfamily,355611,53,194,0.00251897,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31663,Q#2282 - >seq8929,non-specific,273690,53,194,0.00251897,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,marg,C-TerminusTruncated
31664,Q#2282 - >seq8929,non-specific,274008,39,209,0.00296608,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31665,Q#2282 - >seq8929,superfamily,274008,39,209,0.00296608,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31666,Q#2282 - >seq8929,non-specific,274008,39,209,0.00296608,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31667,Q#2282 - >seq8929,non-specific,274008,38,161,0.0038174999999999997,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31668,Q#2282 - >seq8929,non-specific,274008,38,161,0.0038174999999999997,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31669,Q#2282 - >seq8929,non-specific,274009,49,148,0.00849122,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31670,Q#2282 - >seq8929,superfamily,274009,49,148,0.00849122,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31671,Q#2282 - >seq8929,non-specific,274009,49,148,0.00849122,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31672,Q#2282 - >seq8929,non-specific,235316,51,172,0.009247100000000001,37.6293,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31673,Q#2282 - >seq8929,superfamily,235316,51,172,0.009247100000000001,37.6293,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31674,Q#2282 - >seq8929,non-specific,235316,51,172,0.009247100000000001,37.6293,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.marg.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
31675,Q#2286 - >seq8933,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31676,Q#2286 - >seq8933,superfamily,335182,154,251,3.9370899999999993e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31677,Q#2286 - >seq8933,non-specific,335182,154,251,3.9370899999999993e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31678,Q#2286 - >seq8933,non-specific,340205,254,318,7.170599999999999e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31679,Q#2286 - >seq8933,superfamily,340205,254,318,7.170599999999999e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31680,Q#2286 - >seq8933,non-specific,340205,254,318,7.170599999999999e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31681,Q#2286 - >seq8933,non-specific,340204,109,151,2.73223e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31682,Q#2286 - >seq8933,superfamily,340204,109,151,2.73223e-13,63.1956,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31683,Q#2286 - >seq8933,non-specific,340204,109,151,2.73223e-13,63.1956,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs2_gorilla,pars,CompleteHit
31684,Q#2286 - >seq8933,non-specific,224117,42,236,0.00119264,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31685,Q#2286 - >seq8933,superfamily,224117,42,236,0.00119264,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31686,Q#2286 - >seq8933,non-specific,224117,42,236,0.00119264,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31687,Q#2286 - >seq8933,non-specific,335623,52,146,0.00135265,39.8502,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31688,Q#2286 - >seq8933,superfamily,335623,52,146,0.00135265,39.8502,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31689,Q#2286 - >seq8933,non-specific,335623,52,146,0.00135265,39.8502,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31690,Q#2286 - >seq8933,non-specific,235175,52,140,0.00146822,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31691,Q#2286 - >seq8933,superfamily,235175,52,140,0.00146822,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31692,Q#2286 - >seq8933,non-specific,235175,52,140,0.00146822,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31693,Q#2286 - >seq8933,non-specific,273690,53,194,0.00251897,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31694,Q#2286 - >seq8933,superfamily,355611,53,194,0.00251897,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31695,Q#2286 - >seq8933,non-specific,273690,53,194,0.00251897,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs2_gorilla,pars,C-TerminusTruncated
31696,Q#2286 - >seq8933,non-specific,274008,39,209,0.00296608,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31697,Q#2286 - >seq8933,superfamily,274008,39,209,0.00296608,39.2695,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31698,Q#2286 - >seq8933,non-specific,274008,39,209,0.00296608,39.2695,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31699,Q#2286 - >seq8933,non-specific,274008,38,161,0.0038174999999999997,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31700,Q#2286 - >seq8933,non-specific,274008,38,161,0.0038174999999999997,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31701,Q#2286 - >seq8933,non-specific,274009,49,148,0.00849122,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31702,Q#2286 - >seq8933,superfamily,274009,49,148,0.00849122,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31703,Q#2286 - >seq8933,non-specific,274009,49,148,0.00849122,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31704,Q#2286 - >seq8933,non-specific,235316,51,172,0.009247100000000001,37.6293,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31705,Q#2286 - >seq8933,superfamily,235316,51,172,0.009247100000000001,37.6293,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31706,Q#2286 - >seq8933,non-specific,235316,51,172,0.009247100000000001,37.6293,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs2_gorilla.pars.frame3,1909181754_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
31707,Q#2287 - >seq8934,specific,197310,8,235,1.3986599999999997e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31708,Q#2287 - >seq8934,superfamily,351117,8,235,1.3986599999999997e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31709,Q#2287 - >seq8934,specific,238827,507,766,3.4955e-58,199.825,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31710,Q#2287 - >seq8934,superfamily,295487,507,766,3.4955e-58,199.825,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31711,Q#2287 - >seq8934,non-specific,197306,8,235,9.37392e-39,144.93200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31712,Q#2287 - >seq8934,non-specific,333820,513,766,3.30932e-26,106.60799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31713,Q#2287 - >seq8934,superfamily,333820,513,766,3.30932e-26,106.60799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31714,Q#2287 - >seq8934,non-specific,197307,8,235,3.73789e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31715,Q#2287 - >seq8934,non-specific,223780,8,236,4.80956e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31716,Q#2287 - >seq8934,non-specific,197320,8,228,2.0098799999999998e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31717,Q#2287 - >seq8934,non-specific,197321,6,235,1.2889600000000001e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31718,Q#2287 - >seq8934,specific,335306,9,228,4.704380000000001e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31719,Q#2287 - >seq8934,non-specific,273186,8,236,1.88552e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31720,Q#2287 - >seq8934,non-specific,197319,12,235,1.23901e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31721,Q#2287 - >seq8934,non-specific,272954,8,206,5.26076e-13,70.1045,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31722,Q#2287 - >seq8934,non-specific,238828,513,731,7.90095e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31723,Q#2287 - >seq8934,non-specific,197322,7,235,7.121189999999999e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31724,Q#2287 - >seq8934,non-specific,197336,8,193,8.29365e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31725,Q#2287 - >seq8934,non-specific,236970,8,236,1.49021e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31726,Q#2287 - >seq8934,non-specific,339261,107,231,8.73609e-07,48.8727,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31727,Q#2287 - >seq8934,non-specific,275209,583,799,1.07619e-06,52.0748,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,N-TerminusTruncated
31728,Q#2287 - >seq8934,superfamily,275209,583,799,1.07619e-06,52.0748,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs2_gorilla,marg,N-TerminusTruncated
31729,Q#2287 - >seq8934,non-specific,197311,6,235,8.57529e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,marg,CompleteHit
31730,Q#2287 - >seq8934,non-specific,274009,306,456,0.0010151,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31731,Q#2287 - >seq8934,superfamily,274009,306,456,0.0010151,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31732,Q#2287 - >seq8934,non-specific,235175,290,467,0.00143535,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs2_gorilla,marg,BothTerminiTruncated
31733,Q#2287 - >seq8934,superfamily,235175,290,467,0.00143535,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs2_gorilla,marg,BothTerminiTruncated
31734,Q#2287 - >seq8934,non-specific,274009,262,476,0.00584262,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs2_gorilla.marg.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs2_gorilla,marg,BothTerminiTruncated
31735,Q#2288 - >seq8935,non-specific,240274,258,547,0.00157695,42.6697,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1PA15-16.ORF2.hs2_gorilla.marg.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA15-16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31736,Q#2288 - >seq8935,superfamily,240274,258,547,0.00157695,42.6697,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1PA15-16.ORF2.hs2_gorilla.marg.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA15-16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
31737,Q#2290 - >seq8937,specific,197310,3,230,1.1140799999999998e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31738,Q#2290 - >seq8937,superfamily,351117,3,230,1.1140799999999998e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31739,Q#2290 - >seq8937,non-specific,197306,3,230,5.01283e-40,148.398,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31740,Q#2290 - >seq8937,non-specific,197307,3,230,2.7192000000000004e-22,97.3585,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31741,Q#2290 - >seq8937,non-specific,223780,3,231,1.55849e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31742,Q#2290 - >seq8937,non-specific,197320,3,223,1.69877e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31743,Q#2290 - >seq8937,non-specific,197321,1,230,2.0981099999999998e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31744,Q#2290 - >seq8937,specific,335306,4,223,3.995e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31745,Q#2290 - >seq8937,non-specific,273186,3,231,6.438769999999999e-18,84.63799999999999,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31746,Q#2290 - >seq8937,non-specific,197319,7,230,1.28285e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31747,Q#2290 - >seq8937,non-specific,272954,3,230,7.18295e-14,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31748,Q#2290 - >seq8937,non-specific,197322,2,230,6.007080000000001e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31749,Q#2290 - >seq8937,non-specific,236970,3,231,2.73522e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31750,Q#2290 - >seq8937,non-specific,197336,3,188,7.035600000000001e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31751,Q#2290 - >seq8937,non-specific,339261,102,226,3.88852e-07,49.6431,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31752,Q#2290 - >seq8937,non-specific,197311,1,230,7.3172800000000005e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs2_gorilla.pars.frame3,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31753,Q#2291 - >seq8938,specific,238827,474,725,1.5882899999999998e-59,203.292,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31754,Q#2291 - >seq8938,superfamily,295487,474,725,1.5882899999999998e-59,203.292,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31755,Q#2291 - >seq8938,specific,333820,480,710,1.9514299999999998e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31756,Q#2291 - >seq8938,superfamily,333820,480,710,1.9514299999999998e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31757,Q#2291 - >seq8938,non-specific,238828,480,701,7.24556e-15,74.93,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31758,Q#2291 - >seq8938,non-specific,275209,432,701,3.72102e-07,53.2304,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
31759,Q#2291 - >seq8938,superfamily,275209,432,701,3.72102e-07,53.2304,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
31760,Q#2291 - >seq8938,non-specific,238185,620,705,0.0006820519999999999,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs2_gorilla.pars.frame2,1909181755_L1PA15-16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs2_gorilla,pars,CompleteHit
31761,Q#2292 - >seq8939,specific,197310,5,230,1.47623e-45,164.062,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31762,Q#2292 - >seq8939,superfamily,351117,5,230,1.47623e-45,164.062,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31763,Q#2292 - >seq8939,specific,238827,503,766,5.47814e-41,150.519,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31764,Q#2292 - >seq8939,superfamily,295487,503,766,5.47814e-41,150.519,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31765,Q#2292 - >seq8939,non-specific,197306,5,230,6.79867e-22,96.0112,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31766,Q#2292 - >seq8939,non-specific,333820,509,744,5.15033e-21,91.5849,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31767,Q#2292 - >seq8939,superfamily,333820,509,744,5.15033e-21,91.5849,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31768,Q#2292 - >seq8939,non-specific,223780,5,223,3.85902e-12,67.6235,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31769,Q#2292 - >seq8939,non-specific,197307,5,230,4.50966e-12,67.3129,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31770,Q#2292 - >seq8939,specific,335306,8,223,2.16298e-11,64.959,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31771,Q#2292 - >seq8939,non-specific,238828,576,701,1.5376500000000002e-09,59.522,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
31772,Q#2292 - >seq8939,non-specific,197320,9,215,1.96095e-08,56.3694,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31773,Q#2292 - >seq8939,non-specific,273186,5,231,2.9586700000000002e-08,56.1332,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31774,Q#2292 - >seq8939,non-specific,339261,102,226,7.79818e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31775,Q#2292 - >seq8939,non-specific,275209,581,665,1.1478399999999998e-05,48.9932,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
31776,Q#2292 - >seq8939,superfamily,275209,581,665,1.1478399999999998e-05,48.9932,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
31777,Q#2292 - >seq8939,non-specific,197322,101,230,1.71056e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
31778,Q#2292 - >seq8939,non-specific,272954,5,230,1.80339e-05,47.3777,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31779,Q#2292 - >seq8939,non-specific,197321,3,230,3.41888e-05,46.7764,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,marg,CompleteHit
31780,Q#2292 - >seq8939,non-specific,274009,300,443,0.00222519,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
31781,Q#2292 - >seq8939,superfamily,274009,300,443,0.00222519,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs5_gmonkey.marg.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
31782,Q#2298 - >seq8945,specific,238827,494,760,8.591400000000002e-57,195.588,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31783,Q#2298 - >seq8945,superfamily,295487,494,760,8.591400000000002e-57,195.588,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31784,Q#2298 - >seq8945,specific,197310,3,222,1.5230399999999998e-55,192.952,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31785,Q#2298 - >seq8945,superfamily,351117,3,222,1.5230399999999998e-55,192.952,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31786,Q#2298 - >seq8945,specific,333820,511,723,3.6966e-31,120.86,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31787,Q#2298 - >seq8945,superfamily,333820,511,723,3.6966e-31,120.86,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31788,Q#2298 - >seq8945,non-specific,197306,3,222,6.85169e-27,110.649,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31789,Q#2298 - >seq8945,non-specific,223780,1,215,5.19398e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31790,Q#2298 - >seq8945,non-specific,197320,1,215,2.17477e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31791,Q#2298 - >seq8945,non-specific,197307,3,222,5.09203e-18,85.0321,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31792,Q#2298 - >seq8945,specific,335306,4,215,5.60478e-17,81.1373,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31793,Q#2298 - >seq8945,non-specific,197321,1,222,9.48899e-15,75.2812,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31794,Q#2298 - >seq8945,non-specific,197319,1,222,2.2609699999999998e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31795,Q#2298 - >seq8945,non-specific,273186,1,223,1.14166e-12,69.23,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31796,Q#2298 - >seq8945,non-specific,272954,1,222,1.52872e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31797,Q#2298 - >seq8945,non-specific,238828,565,720,2.00971e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,N-TerminusTruncated
31798,Q#2298 - >seq8945,non-specific,197336,1,70,2.2686100000000003e-05,47.2219,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
31799,Q#2298 - >seq8945,non-specific,275209,570,720,7.74153e-05,46.2968,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
31800,Q#2298 - >seq8945,superfamily,275209,570,720,7.74153e-05,46.2968,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
31801,Q#2298 - >seq8945,non-specific,197318,3,222,0.00021523,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31802,Q#2298 - >seq8945,non-specific,197311,31,222,0.00107143,41.5085,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,marg,CompleteHit
31803,Q#2298 - >seq8945,non-specific,238185,639,699,0.00209061,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
31804,Q#2298 - >seq8945,non-specific,223496,306,486,0.00233268,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
31805,Q#2298 - >seq8945,superfamily,223496,306,486,0.00233268,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.marg.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
31806,Q#2301 - >seq8948,specific,238827,497,763,1.0168099999999999e-56,195.588,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31807,Q#2301 - >seq8948,superfamily,295487,497,763,1.0168099999999999e-56,195.588,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31808,Q#2301 - >seq8948,specific,197310,9,225,5.80813e-52,182.551,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31809,Q#2301 - >seq8948,superfamily,351117,9,225,5.80813e-52,182.551,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31810,Q#2301 - >seq8948,specific,333820,514,726,4.00356e-31,120.86,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31811,Q#2301 - >seq8948,superfamily,333820,514,726,4.00356e-31,120.86,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31812,Q#2301 - >seq8948,non-specific,197306,9,225,1.4957700000000002e-24,103.715,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31813,Q#2301 - >seq8948,non-specific,223780,7,218,2.0969699999999997e-17,83.4167,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31814,Q#2301 - >seq8948,non-specific,197320,7,218,4.7785100000000003e-17,82.1777,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31815,Q#2301 - >seq8948,non-specific,197307,9,225,6.857669999999999e-16,78.8689,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31816,Q#2301 - >seq8948,specific,335306,10,218,1.724e-14,73.8185,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31817,Q#2301 - >seq8948,non-specific,197321,7,225,1.17606e-13,72.1996,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31818,Q#2301 - >seq8948,non-specific,197319,7,225,1.74203e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31819,Q#2301 - >seq8948,non-specific,273186,7,226,1.85883e-11,65.7632,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31820,Q#2301 - >seq8948,non-specific,238828,568,723,2.11288e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
31821,Q#2301 - >seq8948,non-specific,272954,7,225,6.937649999999999e-10,60.8597,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31822,Q#2301 - >seq8948,non-specific,275209,573,723,7.439850000000001e-05,46.2968,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
31823,Q#2301 - >seq8948,superfamily,275209,573,723,7.439850000000001e-05,46.2968,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
31824,Q#2301 - >seq8948,non-specific,197311,37,225,0.00033082300000000005,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31825,Q#2301 - >seq8948,non-specific,197336,7,218,0.00039374699999999996,43.3699,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31826,Q#2301 - >seq8948,non-specific,197318,9,225,0.0008125239999999999,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA6,ORF2,hs1_chimp,pars,CompleteHit
31827,Q#2301 - >seq8948,non-specific,238185,642,702,0.00211466,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
31828,Q#2301 - >seq8948,non-specific,223496,309,489,0.00242306,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
31829,Q#2301 - >seq8948,superfamily,223496,309,489,0.00242306,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
31830,Q#2301 - >seq8948,non-specific,197322,130,225,0.00722742,39.993,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA6.ORF2.hs1_chimp.pars.frame3,1909181755_L1MA6.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
31831,Q#2304 - >seq8951,specific,197310,32,228,1.26884e-42,155.58700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31832,Q#2304 - >seq8951,superfamily,351117,32,228,1.26884e-42,155.58700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31833,Q#2304 - >seq8951,specific,238827,501,764,3.99234e-41,150.905,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31834,Q#2304 - >seq8951,superfamily,295487,501,764,3.99234e-41,150.905,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31835,Q#2304 - >seq8951,non-specific,333820,507,742,5.73543e-21,91.5849,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31836,Q#2304 - >seq8951,superfamily,333820,507,742,5.73543e-21,91.5849,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31837,Q#2304 - >seq8951,non-specific,197306,8,228,6.19976e-18,84.4552,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31838,Q#2304 - >seq8951,non-specific,223780,64,221,3.27536e-10,61.8455,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
31839,Q#2304 - >seq8951,non-specific,238828,574,699,1.59908e-09,59.1368,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
31840,Q#2304 - >seq8951,non-specific,197320,64,213,1.87623e-08,56.7546,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
31841,Q#2304 - >seq8951,specific,335306,41,221,5.42443e-08,54.9438,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31842,Q#2304 - >seq8951,non-specific,197307,49,228,9.35753e-07,51.5197,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31843,Q#2304 - >seq8951,non-specific,273186,98,229,1.8162299999999998e-06,50.7404,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
31844,Q#2304 - >seq8951,non-specific,339261,100,224,6.252080000000001e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs5_gmonkey,pars,CompleteHit
31845,Q#2304 - >seq8951,non-specific,275209,579,663,1.19094e-05,48.9932,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
31846,Q#2304 - >seq8951,superfamily,275209,579,663,1.19094e-05,48.9932,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
31847,Q#2304 - >seq8951,non-specific,197322,99,228,1.71367e-05,48.0822,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
31848,Q#2304 - >seq8951,non-specific,272954,83,228,0.000676085,42.7553,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
31849,Q#2304 - >seq8951,non-specific,274009,298,441,0.00221046,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
31850,Q#2304 - >seq8951,superfamily,274009,298,441,0.00221046,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs5_gmonkey.pars.frame3,1909181755_L1MC1.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
31851,Q#2305 - >seq8952,specific,238827,508,770,1.5904799999999997e-62,212.15099999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31852,Q#2305 - >seq8952,superfamily,295487,508,770,1.5904799999999997e-62,212.15099999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31853,Q#2305 - >seq8952,specific,197310,9,235,1.21425e-56,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31854,Q#2305 - >seq8952,superfamily,351117,9,235,1.21425e-56,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31855,Q#2305 - >seq8952,specific,333820,514,770,4.3386e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31856,Q#2305 - >seq8952,superfamily,333820,514,770,4.3386e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31857,Q#2305 - >seq8952,non-specific,197306,9,235,3.31178e-31,122.975,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31858,Q#2305 - >seq8952,non-specific,197320,7,228,3.9090899999999996e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31859,Q#2305 - >seq8952,non-specific,223780,7,228,8.52735e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31860,Q#2305 - >seq8952,specific,335306,10,228,1.75179e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31861,Q#2305 - >seq8952,non-specific,197307,9,228,4.06931e-17,82.3357,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31862,Q#2305 - >seq8952,non-specific,197321,7,228,1.53077e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31863,Q#2305 - >seq8952,non-specific,273186,7,236,1.1844200000000001e-12,69.23,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31864,Q#2305 - >seq8952,non-specific,272954,7,206,2.0982900000000003e-12,68.5637,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31865,Q#2305 - >seq8952,non-specific,238828,514,738,3.30195e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31866,Q#2305 - >seq8952,non-specific,197319,7,235,3.86488e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31867,Q#2305 - >seq8952,non-specific,275209,465,737,2.06861e-06,51.3044,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
31868,Q#2305 - >seq8952,superfamily,275209,465,737,2.06861e-06,51.3044,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
31869,Q#2305 - >seq8952,non-specific,197336,7,228,2.22713e-05,47.2219,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs5_gmonkey,marg,CompleteHit
31870,Q#2305 - >seq8952,non-specific,223496,307,500,0.00111891,43.2103,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA9,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
31871,Q#2305 - >seq8952,superfamily,223496,307,500,0.00111891,43.2103,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.marg.frame3,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA9,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
31872,Q#2309 - >seq8956,specific,238827,511,770,9.457289999999998e-59,201.36599999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31873,Q#2309 - >seq8956,superfamily,295487,511,770,9.457289999999998e-59,201.36599999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31874,Q#2309 - >seq8956,specific,197310,13,239,1.7596099999999997e-56,195.648,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31875,Q#2309 - >seq8956,superfamily,351117,13,239,1.7596099999999997e-56,195.648,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31876,Q#2309 - >seq8956,specific,333820,517,741,4.25678e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31877,Q#2309 - >seq8956,superfamily,333820,517,741,4.25678e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31878,Q#2309 - >seq8956,non-specific,197306,13,239,3.84067e-31,122.975,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31879,Q#2309 - >seq8956,non-specific,197320,11,232,4.19423e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31880,Q#2309 - >seq8956,non-specific,223780,11,232,8.89192e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31881,Q#2309 - >seq8956,specific,335306,14,232,1.74268e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31882,Q#2309 - >seq8956,non-specific,197307,13,232,4.08612e-17,82.3357,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31883,Q#2309 - >seq8956,non-specific,197321,11,232,1.49433e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31884,Q#2309 - >seq8956,non-specific,273186,11,240,1.25774e-12,69.23,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31885,Q#2309 - >seq8956,non-specific,272954,11,210,1.9012799999999998e-12,68.5637,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31886,Q#2309 - >seq8956,non-specific,238828,517,741,3.16369e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31887,Q#2309 - >seq8956,non-specific,197319,11,239,4.02752e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31888,Q#2309 - >seq8956,non-specific,275209,468,740,2.03959e-06,51.3044,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
31889,Q#2309 - >seq8956,superfamily,275209,468,740,2.03959e-06,51.3044,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
31890,Q#2309 - >seq8956,non-specific,197336,11,232,2.21565e-05,47.2219,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA9,ORF2,hs5_gmonkey,pars,CompleteHit
31891,Q#2309 - >seq8956,non-specific,223496,311,503,0.0008705119999999999,43.5955,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1MA9,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
31892,Q#2309 - >seq8956,superfamily,223496,311,503,0.0008705119999999999,43.5955,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs5_gmonkey.pars.frame2,1909181800_L1MA9.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1MA9,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
31893,Q#2315 - >seq8962,specific,238827,507,769,1.5599299999999997e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31894,Q#2315 - >seq8962,superfamily,295487,507,769,1.5599299999999997e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31895,Q#2315 - >seq8962,non-specific,238827,507,769,1.5599299999999997e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31896,Q#2315 - >seq8962,specific,197310,9,235,7.526519999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31897,Q#2315 - >seq8962,superfamily,351117,9,235,7.526519999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31898,Q#2315 - >seq8962,non-specific,197310,9,235,7.526519999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31899,Q#2315 - >seq8962,specific,333820,513,769,5.6104e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31900,Q#2315 - >seq8962,superfamily,333820,513,769,5.6104e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31901,Q#2315 - >seq8962,non-specific,333820,513,769,5.6104e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31902,Q#2315 - >seq8962,non-specific,197306,9,235,2.23302e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31903,Q#2315 - >seq8962,non-specific,197306,9,235,2.23302e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31904,Q#2315 - >seq8962,non-specific,197320,9,206,1.04436e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31905,Q#2315 - >seq8962,non-specific,197320,9,206,1.04436e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31906,Q#2315 - >seq8962,non-specific,197307,9,235,5.43689e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31907,Q#2315 - >seq8962,non-specific,197307,9,235,5.43689e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31908,Q#2315 - >seq8962,non-specific,223780,9,236,2.14228e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31909,Q#2315 - >seq8962,non-specific,223780,9,236,2.14228e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31910,Q#2315 - >seq8962,specific,335306,10,228,4.61559e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31911,Q#2315 - >seq8962,non-specific,335306,10,228,4.61559e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31912,Q#2315 - >seq8962,non-specific,197321,7,235,1.28327e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31913,Q#2315 - >seq8962,non-specific,197321,7,235,1.28327e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31914,Q#2315 - >seq8962,non-specific,272954,9,207,3.26298e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31915,Q#2315 - >seq8962,non-specific,272954,9,207,3.26298e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31916,Q#2315 - >seq8962,non-specific,273186,9,236,6.69569e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31917,Q#2315 - >seq8962,non-specific,273186,9,236,6.69569e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31918,Q#2315 - >seq8962,non-specific,197319,13,235,4.1846e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31919,Q#2315 - >seq8962,non-specific,197319,13,235,4.1846e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31920,Q#2315 - >seq8962,non-specific,238828,513,734,1.28688e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31921,Q#2315 - >seq8962,non-specific,238828,513,734,1.28688e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31922,Q#2315 - >seq8962,non-specific,197336,9,194,1.0987899999999999e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31923,Q#2315 - >seq8962,non-specific,197336,9,194,1.0987899999999999e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31924,Q#2315 - >seq8962,non-specific,236970,9,194,2.98874e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31925,Q#2315 - >seq8962,non-specific,236970,9,194,2.98874e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31926,Q#2315 - >seq8962,non-specific,275209,467,793,6.11709e-06,49.7636,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31927,Q#2315 - >seq8962,superfamily,275209,467,793,6.11709e-06,49.7636,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31928,Q#2315 - >seq8962,non-specific,275209,467,793,6.11709e-06,49.7636,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31929,Q#2315 - >seq8962,non-specific,197311,7,146,6.30943e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31930,Q#2315 - >seq8962,non-specific,197311,7,146,6.30943e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31931,Q#2315 - >seq8962,non-specific,197322,8,235,2.2733e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31932,Q#2315 - >seq8962,non-specific,197322,8,235,2.2733e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31933,Q#2315 - >seq8962,non-specific,197314,7,192,2.63327e-05,46.9531,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31934,Q#2315 - >seq8962,non-specific,197314,7,192,2.63327e-05,46.9531,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31935,Q#2315 - >seq8962,non-specific,238185,653,767,0.00010358700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31936,Q#2315 - >seq8962,non-specific,238185,653,767,0.00010358700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31937,Q#2315 - >seq8962,non-specific,235175,290,447,0.000133604,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31938,Q#2315 - >seq8962,superfamily,235175,290,447,0.000133604,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31939,Q#2315 - >seq8962,non-specific,235175,290,447,0.000133604,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31940,Q#2315 - >seq8962,specific,311990,1237,1255,0.000710562,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31941,Q#2315 - >seq8962,superfamily,311990,1237,1255,0.000710562,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31942,Q#2315 - >seq8962,non-specific,311990,1237,1255,0.000710562,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,marg,CompleteHit
31943,Q#2315 - >seq8962,non-specific,274009,299,432,0.00268411,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31944,Q#2315 - >seq8962,superfamily,274009,299,432,0.00268411,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31945,Q#2315 - >seq8962,non-specific,274009,299,432,0.00268411,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31946,Q#2315 - >seq8962,non-specific,274009,310,455,0.00438297,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31947,Q#2315 - >seq8962,non-specific,274009,310,455,0.00438297,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,marg,BothTerminiTruncated
31948,Q#2315 - >seq8962,non-specific,334125,213,409,0.00684565,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31949,Q#2315 - >seq8962,superfamily,334125,213,409,0.00684565,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31950,Q#2315 - >seq8962,non-specific,334125,213,409,0.00684565,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
31951,Q#2315 - >seq8962,non-specific,339261,108,148,0.00688028,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31952,Q#2315 - >seq8962,non-specific,339261,108,148,0.00688028,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs4_gibbon.marg.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
31953,Q#2316 - >seq8963,specific,238827,507,769,1.5599299999999997e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31954,Q#2316 - >seq8963,superfamily,295487,507,769,1.5599299999999997e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31955,Q#2316 - >seq8963,non-specific,238827,507,769,1.5599299999999997e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31956,Q#2316 - >seq8963,specific,197310,9,235,7.526519999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31957,Q#2316 - >seq8963,superfamily,351117,9,235,7.526519999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31958,Q#2316 - >seq8963,non-specific,197310,9,235,7.526519999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31959,Q#2316 - >seq8963,specific,333820,513,769,5.6104e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31960,Q#2316 - >seq8963,superfamily,333820,513,769,5.6104e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31961,Q#2316 - >seq8963,non-specific,333820,513,769,5.6104e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31962,Q#2316 - >seq8963,non-specific,197306,9,235,2.23302e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31963,Q#2316 - >seq8963,non-specific,197306,9,235,2.23302e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31964,Q#2316 - >seq8963,non-specific,197320,9,206,1.04436e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31965,Q#2316 - >seq8963,non-specific,197320,9,206,1.04436e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31966,Q#2316 - >seq8963,non-specific,197307,9,235,5.43689e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31967,Q#2316 - >seq8963,non-specific,197307,9,235,5.43689e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31968,Q#2316 - >seq8963,non-specific,223780,9,236,2.14228e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31969,Q#2316 - >seq8963,non-specific,223780,9,236,2.14228e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31970,Q#2316 - >seq8963,specific,335306,10,228,4.61559e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31971,Q#2316 - >seq8963,non-specific,335306,10,228,4.61559e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31972,Q#2316 - >seq8963,non-specific,197321,7,235,1.28327e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31973,Q#2316 - >seq8963,non-specific,197321,7,235,1.28327e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31974,Q#2316 - >seq8963,non-specific,272954,9,207,3.26298e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31975,Q#2316 - >seq8963,non-specific,272954,9,207,3.26298e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31976,Q#2316 - >seq8963,non-specific,273186,9,236,6.69569e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31977,Q#2316 - >seq8963,non-specific,273186,9,236,6.69569e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31978,Q#2316 - >seq8963,non-specific,197319,13,235,4.1846e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31979,Q#2316 - >seq8963,non-specific,197319,13,235,4.1846e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31980,Q#2316 - >seq8963,non-specific,238828,513,734,1.28688e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31981,Q#2316 - >seq8963,non-specific,238828,513,734,1.28688e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31982,Q#2316 - >seq8963,non-specific,197336,9,194,1.0987899999999999e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31983,Q#2316 - >seq8963,non-specific,197336,9,194,1.0987899999999999e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31984,Q#2316 - >seq8963,non-specific,236970,9,194,2.98874e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31985,Q#2316 - >seq8963,non-specific,236970,9,194,2.98874e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31986,Q#2316 - >seq8963,non-specific,275209,467,793,6.11709e-06,49.7636,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31987,Q#2316 - >seq8963,superfamily,275209,467,793,6.11709e-06,49.7636,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31988,Q#2316 - >seq8963,non-specific,275209,467,793,6.11709e-06,49.7636,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31989,Q#2316 - >seq8963,non-specific,197311,7,146,6.30943e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31990,Q#2316 - >seq8963,non-specific,197311,7,146,6.30943e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31991,Q#2316 - >seq8963,non-specific,197322,8,235,2.2733e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31992,Q#2316 - >seq8963,non-specific,197322,8,235,2.2733e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31993,Q#2316 - >seq8963,non-specific,197314,7,192,2.63327e-05,46.9531,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31994,Q#2316 - >seq8963,non-specific,197314,7,192,2.63327e-05,46.9531,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
31995,Q#2316 - >seq8963,non-specific,238185,653,767,0.00010358700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31996,Q#2316 - >seq8963,non-specific,238185,653,767,0.00010358700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
31997,Q#2316 - >seq8963,non-specific,235175,290,447,0.000133604,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31998,Q#2316 - >seq8963,superfamily,235175,290,447,0.000133604,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
31999,Q#2316 - >seq8963,non-specific,235175,290,447,0.000133604,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32000,Q#2316 - >seq8963,specific,311990,1237,1255,0.000710562,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
32001,Q#2316 - >seq8963,superfamily,311990,1237,1255,0.000710562,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
32002,Q#2316 - >seq8963,non-specific,311990,1237,1255,0.000710562,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs4_gibbon,pars,CompleteHit
32003,Q#2316 - >seq8963,non-specific,274009,299,432,0.00268411,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32004,Q#2316 - >seq8963,superfamily,274009,299,432,0.00268411,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32005,Q#2316 - >seq8963,non-specific,274009,299,432,0.00268411,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32006,Q#2316 - >seq8963,non-specific,274009,310,455,0.00438297,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32007,Q#2316 - >seq8963,non-specific,274009,310,455,0.00438297,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32008,Q#2316 - >seq8963,non-specific,334125,213,409,0.00684565,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32009,Q#2316 - >seq8963,superfamily,334125,213,409,0.00684565,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32010,Q#2316 - >seq8963,non-specific,334125,213,409,0.00684565,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32011,Q#2316 - >seq8963,non-specific,339261,108,148,0.00688028,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32012,Q#2316 - >seq8963,non-specific,339261,108,148,0.00688028,37.7019,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs4_gibbon.pars.frame3,1909181906_L1PB3.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32013,Q#2317 - >seq8964,specific,311990,1103,1121,0.00231394,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs3_orang.marg.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32014,Q#2317 - >seq8964,superfamily,311990,1103,1121,0.00231394,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs3_orang.marg.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32015,Q#2318 - >seq8965,specific,197310,7,152,1.45889e-32,126.697,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32016,Q#2318 - >seq8965,superfamily,351117,7,152,1.45889e-32,126.697,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32017,Q#2318 - >seq8965,non-specific,197306,7,156,3.49356e-19,87.92200000000001,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32018,Q#2318 - >seq8965,specific,335306,8,161,7.53766e-10,60.3366,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32019,Q#2318 - >seq8965,non-specific,223780,7,143,7.703760000000002e-10,60.6899,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32020,Q#2318 - >seq8965,non-specific,197307,7,162,6.5717e-09,57.6829,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32021,Q#2318 - >seq8965,non-specific,197320,5,143,1.2059799999999998e-07,54.0582,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32022,Q#2318 - >seq8965,non-specific,272954,5,150,1.01203e-06,51.2297,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32023,Q#2318 - >seq8965,non-specific,197321,5,143,6.44559e-06,48.7024,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32024,Q#2318 - >seq8965,non-specific,197319,5,144,8.724649999999999e-05,45.3453,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32025,Q#2318 - >seq8965,non-specific,273186,5,144,0.000686859,42.6512,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32026,Q#2318 - >seq8965,non-specific,197311,34,143,0.00182444,40.7381,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs3_orang.pars.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,pars,C-TerminusTruncated
32027,Q#2320 - >seq8967,specific,197310,9,236,3.9007399999999995e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32028,Q#2320 - >seq8967,superfamily,351117,9,236,3.9007399999999995e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32029,Q#2320 - >seq8967,specific,238827,524,760,1.3816199999999996e-49,175.172,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32030,Q#2320 - >seq8967,superfamily,295487,524,760,1.3816199999999996e-49,175.172,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32031,Q#2320 - >seq8967,non-specific,197306,9,236,9.2836e-29,116.042,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32032,Q#2320 - >seq8967,non-specific,333820,524,735,4.75358e-28,112.001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32033,Q#2320 - >seq8967,superfamily,333820,524,735,4.75358e-28,112.001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32034,Q#2320 - >seq8967,non-specific,197320,7,229,5.16312e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32035,Q#2320 - >seq8967,non-specific,223780,9,229,8.63981e-17,81.4907,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32036,Q#2320 - >seq8967,specific,335306,10,229,3.03843e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32037,Q#2320 - >seq8967,non-specific,197307,9,229,9.77433e-15,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32038,Q#2320 - >seq8967,non-specific,197321,7,229,1.65269e-10,62.5696,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32039,Q#2320 - >seq8967,non-specific,272954,7,207,6.17174e-10,61.2449,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32040,Q#2320 - >seq8967,non-specific,197319,7,236,4.03767e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32041,Q#2320 - >seq8967,non-specific,238828,577,732,6.97909e-09,57.596000000000004,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,N-TerminusTruncated
32042,Q#2320 - >seq8967,non-specific,273186,7,237,1.213e-08,57.2888,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32043,Q#2320 - >seq8967,non-specific,275209,582,788,2.15442e-05,47.8376,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,N-TerminusTruncated
32044,Q#2320 - >seq8967,superfamily,275209,582,788,2.15442e-05,47.8376,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1MA8,ORF2,hs3_orang,marg,N-TerminusTruncated
32045,Q#2320 - >seq8967,non-specific,235175,310,465,0.000429604,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs3_orang,marg,BothTerminiTruncated
32046,Q#2320 - >seq8967,superfamily,235175,310,465,0.000429604,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1MA8,ORF2,hs3_orang,marg,BothTerminiTruncated
32047,Q#2320 - >seq8967,non-specific,197336,7,229,0.00162992,41.4439,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,CompleteHit
32048,Q#2320 - >seq8967,non-specific,197311,37,146,0.00222831,40.7381,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs3_orang.marg.frame2,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1MA8,ORF2,hs3_orang,marg,C-TerminusTruncated
32049,Q#2321 - >seq8968,specific,311990,1101,1119,0.00286561,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs1_chimp.pars.frame1,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32050,Q#2321 - >seq8968,superfamily,311990,1101,1119,0.00286561,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs1_chimp.pars.frame1,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32051,Q#2322 - >seq8969,specific,197310,2,229,2.5145799999999997e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32052,Q#2322 - >seq8969,superfamily,351117,2,229,2.5145799999999997e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32053,Q#2322 - >seq8969,specific,238827,519,757,1.8655599999999998e-50,177.483,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32054,Q#2322 - >seq8969,superfamily,295487,519,757,1.8655599999999998e-50,177.483,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32055,Q#2322 - >seq8969,non-specific,197306,2,229,1.94412e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32056,Q#2322 - >seq8969,non-specific,333820,519,731,1.82817e-27,110.075,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32057,Q#2322 - >seq8969,superfamily,333820,519,731,1.82817e-27,110.075,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32058,Q#2322 - >seq8969,non-specific,197320,2,222,2.92471e-23,100.28200000000001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32059,Q#2322 - >seq8969,non-specific,223780,2,222,8.486390000000001e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32060,Q#2322 - >seq8969,non-specific,197307,2,222,1.16366e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32061,Q#2322 - >seq8969,specific,335306,3,222,1.14795e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32062,Q#2322 - >seq8969,non-specific,197321,1,222,7.7516e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32063,Q#2322 - >seq8969,non-specific,272954,2,200,1.39786e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32064,Q#2322 - >seq8969,non-specific,197319,2,229,1.70523e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32065,Q#2322 - >seq8969,non-specific,273186,2,230,6.302819999999999e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32066,Q#2322 - >seq8969,non-specific,197336,2,222,1.23384e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32067,Q#2322 - >seq8969,non-specific,238828,573,728,7.92348e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,N-TerminusTruncated
32068,Q#2322 - >seq8969,non-specific,236970,2,222,2.3000599999999998e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32069,Q#2322 - >seq8969,non-specific,197318,2,223,0.000571742,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,pars,CompleteHit
32070,Q#2322 - >seq8969,non-specific,197311,30,139,0.00104597,41.5085,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
32071,Q#2322 - >seq8969,non-specific,275209,578,728,0.00223921,41.6744,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
32072,Q#2322 - >seq8969,superfamily,275209,578,728,0.00223921,41.6744,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs1_chimp.pars.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
32073,Q#2323 - >seq8970,specific,311990,1108,1126,0.00288308,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs1_chimp.marg.frame1,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32074,Q#2323 - >seq8970,superfamily,311990,1108,1126,0.00288308,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs1_chimp.marg.frame1,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32075,Q#2325 - >seq8972,specific,197310,9,236,2.3358999999999998e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32076,Q#2325 - >seq8972,superfamily,351117,9,236,2.3358999999999998e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32077,Q#2325 - >seq8972,specific,238827,527,765,1.7941400000000003e-50,177.483,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32078,Q#2325 - >seq8972,superfamily,295487,527,765,1.7941400000000003e-50,177.483,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32079,Q#2325 - >seq8972,non-specific,197306,9,236,2.0785400000000002e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32080,Q#2325 - >seq8972,non-specific,333820,527,739,1.82672e-27,110.46,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32081,Q#2325 - >seq8972,superfamily,333820,527,739,1.82672e-27,110.46,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32082,Q#2325 - >seq8972,non-specific,197320,7,229,1.96054e-23,100.667,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32083,Q#2325 - >seq8972,non-specific,223780,7,229,4.70817e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32084,Q#2325 - >seq8972,non-specific,197307,9,229,1.18575e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32085,Q#2325 - >seq8972,specific,335306,10,229,1.15843e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32086,Q#2325 - >seq8972,non-specific,197321,7,229,3.0162100000000004e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32087,Q#2325 - >seq8972,non-specific,272954,7,207,8.40953e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32088,Q#2325 - >seq8972,non-specific,197319,7,236,1.0076600000000001e-14,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32089,Q#2325 - >seq8972,non-specific,273186,7,237,4.84767e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32090,Q#2325 - >seq8972,non-specific,197336,7,229,1.1564300000000001e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32091,Q#2325 - >seq8972,non-specific,238828,581,736,7.21589e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,N-TerminusTruncated
32092,Q#2325 - >seq8972,non-specific,236970,9,229,2.1213400000000003e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32093,Q#2325 - >seq8972,non-specific,197318,9,230,0.000582076,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs1_chimp,marg,CompleteHit
32094,Q#2325 - >seq8972,non-specific,197311,37,146,0.00111499,41.5085,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
32095,Q#2325 - >seq8972,non-specific,275209,586,736,0.00208948,41.6744,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
32096,Q#2325 - >seq8972,superfamily,275209,586,736,0.00208948,41.6744,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs1_chimp.marg.frame3,1909181906_L1MA8.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
32097,Q#2326 - >seq8973,non-specific,197310,151,223,7.091640000000001e-13,69.3025,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32098,Q#2326 - >seq8973,superfamily,351117,151,223,7.091640000000001e-13,69.3025,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32099,Q#2326 - >seq8973,non-specific,197320,161,216,0.000158889,44.4282,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32100,Q#2326 - >seq8973,non-specific,223780,164,216,0.00144643,41.4299,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32101,Q#2326 - >seq8973,non-specific,197307,164,216,0.00232336,40.7341,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32102,Q#2326 - >seq8973,non-specific,197321,161,216,0.0061339,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs3_orang.pars.frame1,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32103,Q#2327 - >seq8974,specific,238827,476,713,3.57593e-50,176.713,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32104,Q#2327 - >seq8974,superfamily,295487,476,713,3.57593e-50,176.713,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32105,Q#2327 - >seq8974,non-specific,333820,476,687,1.06211e-27,110.845,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32106,Q#2327 - >seq8974,superfamily,333820,476,687,1.06211e-27,110.845,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32107,Q#2327 - >seq8974,non-specific,238828,529,684,4.17963e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32108,Q#2327 - >seq8974,non-specific,275209,534,741,1.24645e-05,48.608000000000004,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32109,Q#2327 - >seq8974,superfamily,275209,534,741,1.24645e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs3_orang,pars,N-TerminusTruncated
32110,Q#2327 - >seq8974,specific,311990,1159,1177,0.00449894,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32111,Q#2327 - >seq8974,superfamily,311990,1159,1177,0.00449894,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs3_orang.pars.frame3,1909181906_L1MA8.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA8,ORF2,hs3_orang,pars,CompleteHit
32112,Q#2330 - >seq8977,specific,238827,510,772,1.2445099999999999e-64,218.31400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32113,Q#2330 - >seq8977,superfamily,295487,510,772,1.2445099999999999e-64,218.31400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32114,Q#2330 - >seq8977,specific,197310,9,236,9.147769999999998e-60,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32115,Q#2330 - >seq8977,superfamily,351117,9,236,9.147769999999998e-60,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32116,Q#2330 - >seq8977,non-specific,197306,9,236,1.0563899999999999e-43,159.184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32117,Q#2330 - >seq8977,specific,333820,516,772,6.75546e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32118,Q#2330 - >seq8977,superfamily,333820,516,772,6.75546e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32119,Q#2330 - >seq8977,non-specific,197307,9,236,1.17464e-23,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32120,Q#2330 - >seq8977,non-specific,223780,9,237,5.55489e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32121,Q#2330 - >seq8977,non-specific,197320,9,229,3.11972e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32122,Q#2330 - >seq8977,specific,335306,10,229,2.3581e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32123,Q#2330 - >seq8977,non-specific,197321,7,236,1.44889e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32124,Q#2330 - >seq8977,non-specific,273186,9,237,1.06272e-13,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32125,Q#2330 - >seq8977,non-specific,272954,9,236,1.04352e-12,69.3341,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32126,Q#2330 - >seq8977,non-specific,197319,13,236,7.73218e-12,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32127,Q#2330 - >seq8977,non-specific,238828,582,737,4.86471e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32128,Q#2330 - >seq8977,non-specific,197322,8,236,1.57273e-10,63.4902,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32129,Q#2330 - >seq8977,non-specific,197336,9,194,2.62432e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32130,Q#2330 - >seq8977,non-specific,275209,467,800,4.4009999999999995e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32131,Q#2330 - >seq8977,superfamily,275209,467,800,4.4009999999999995e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32132,Q#2330 - >seq8977,non-specific,236970,9,237,1.8706799999999998e-06,50.663000000000004,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32133,Q#2330 - >seq8977,non-specific,339261,108,232,1.3584200000000001e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32134,Q#2330 - >seq8977,non-specific,238185,656,772,1.71372e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32135,Q#2330 - >seq8977,non-specific,197311,30,236,9.943459999999998e-05,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32136,Q#2330 - >seq8977,non-specific,235175,294,469,0.00091001,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32137,Q#2330 - >seq8977,superfamily,235175,294,469,0.00091001,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32138,Q#2330 - >seq8977,non-specific,224117,266,391,0.00319586,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32139,Q#2330 - >seq8977,superfamily,224117,266,391,0.00319586,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs2_gorilla.marg.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32140,Q#2332 - >seq8979,non-specific,335182,154,251,4.15487e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32141,Q#2332 - >seq8979,superfamily,335182,154,251,4.15487e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32142,Q#2332 - >seq8979,non-specific,335182,154,251,4.15487e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32143,Q#2332 - >seq8979,non-specific,340205,254,318,7.324460000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32144,Q#2332 - >seq8979,superfamily,340205,254,318,7.324460000000001e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32145,Q#2332 - >seq8979,non-specific,340205,254,318,7.324460000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,pars,CompleteHit
32146,Q#2332 - >seq8979,non-specific,340204,109,151,2.21669e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,pars,CompleteHit
32147,Q#2332 - >seq8979,superfamily,340204,109,151,2.21669e-13,63.5808,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,pars,CompleteHit
32148,Q#2332 - >seq8979,non-specific,340204,109,151,2.21669e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,pars,CompleteHit
32149,Q#2332 - >seq8979,non-specific,235175,52,140,0.00058687,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32150,Q#2332 - >seq8979,superfamily,235175,52,140,0.00058687,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32151,Q#2332 - >seq8979,non-specific,235175,52,140,0.00058687,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32152,Q#2332 - >seq8979,non-specific,335623,52,146,0.00074987,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32153,Q#2332 - >seq8979,superfamily,335623,52,146,0.00074987,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32154,Q#2332 - >seq8979,non-specific,335623,52,146,0.00074987,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32155,Q#2332 - >seq8979,non-specific,273690,53,194,0.00222565,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32156,Q#2332 - >seq8979,superfamily,355611,53,194,0.00222565,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32157,Q#2332 - >seq8979,non-specific,273690,53,194,0.00222565,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32158,Q#2332 - >seq8979,non-specific,235316,51,172,0.00273989,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32159,Q#2332 - >seq8979,superfamily,235316,51,172,0.00273989,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32160,Q#2332 - >seq8979,non-specific,235316,51,172,0.00273989,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32161,Q#2332 - >seq8979,non-specific,274008,38,161,0.00594892,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32162,Q#2332 - >seq8979,superfamily,274008,38,161,0.00594892,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32163,Q#2332 - >seq8979,non-specific,274008,38,161,0.00594892,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32164,Q#2332 - >seq8979,non-specific,274008,39,209,0.00671904,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32165,Q#2332 - >seq8979,non-specific,274008,39,209,0.00671904,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,BothTerminiTruncated
32166,Q#2332 - >seq8979,non-specific,235175,30,154,0.00790014,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32167,Q#2332 - >seq8979,non-specific,235175,30,154,0.00790014,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.pars.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,pars,C-TerminusTruncated
32168,Q#2335 - >seq8982,non-specific,335182,154,251,4.15487e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32169,Q#2335 - >seq8982,superfamily,335182,154,251,4.15487e-48,157.079,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32170,Q#2335 - >seq8982,non-specific,335182,154,251,4.15487e-48,157.079,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32171,Q#2335 - >seq8982,non-specific,340205,254,318,7.324460000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32172,Q#2335 - >seq8982,superfamily,340205,254,318,7.324460000000001e-34,118.978,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32173,Q#2335 - >seq8982,non-specific,340205,254,318,7.324460000000001e-34,118.978,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA3,ORF1,hs0_human,marg,CompleteHit
32174,Q#2335 - >seq8982,non-specific,340204,109,151,2.21669e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,marg,CompleteHit
32175,Q#2335 - >seq8982,superfamily,340204,109,151,2.21669e-13,63.5808,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,marg,CompleteHit
32176,Q#2335 - >seq8982,non-specific,340204,109,151,2.21669e-13,63.5808,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA3,ORF1,hs0_human,marg,CompleteHit
32177,Q#2335 - >seq8982,non-specific,235175,52,140,0.00058687,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32178,Q#2335 - >seq8982,superfamily,235175,52,140,0.00058687,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32179,Q#2335 - >seq8982,non-specific,235175,52,140,0.00058687,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32180,Q#2335 - >seq8982,non-specific,335623,52,146,0.00074987,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32181,Q#2335 - >seq8982,superfamily,335623,52,146,0.00074987,40.6206,cl25896,APG6 superfamily,C, - ,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32182,Q#2335 - >seq8982,non-specific,335623,52,146,0.00074987,40.6206,pfam04111,APG6,C,cl25896,"Autophagy protein Apg6; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32183,Q#2335 - >seq8982,non-specific,273690,53,194,0.00222565,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32184,Q#2335 - >seq8982,superfamily,355611,53,194,0.00222565,39.2513,cl27082,Phage_capsid superfamily,C, - ,Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32185,Q#2335 - >seq8982,non-specific,273690,53,194,0.00222565,39.2513,TIGR01554,major_cap_HK97,C,cl27082,"phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Viral,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32186,Q#2335 - >seq8982,non-specific,235316,51,172,0.00273989,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32187,Q#2335 - >seq8982,superfamily,235316,51,172,0.00273989,39.5553,cl35272,mukB superfamily,NC, - ,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32188,Q#2335 - >seq8982,non-specific,235316,51,172,0.00273989,39.5553,PRK04863,mukB,NC,cl35272,cell division protein MukB; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32189,Q#2335 - >seq8982,non-specific,274008,38,161,0.00594892,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32190,Q#2335 - >seq8982,superfamily,274008,38,161,0.00594892,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32191,Q#2335 - >seq8982,non-specific,274008,38,161,0.00594892,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32192,Q#2335 - >seq8982,non-specific,274008,39,209,0.00671904,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32193,Q#2335 - >seq8982,non-specific,274008,39,209,0.00671904,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,BothTerminiTruncated
32194,Q#2335 - >seq8982,non-specific,235175,30,154,0.00790014,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32195,Q#2335 - >seq8982,non-specific,235175,30,154,0.00790014,37.736,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF1.hs0_human.marg.frame3,1909181907_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF1,hs0_human,marg,C-TerminusTruncated
32196,Q#2340 - >seq8987,non-specific,335182,156,252,1.66279e-34,121.256,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32197,Q#2340 - >seq8987,superfamily,335182,156,252,1.66279e-34,121.256,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32198,Q#2340 - >seq8987,non-specific,340205,255,318,9.280099999999998e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32199,Q#2340 - >seq8987,superfamily,340205,255,318,9.280099999999998e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32200,Q#2340 - >seq8987,non-specific,274009,60,203,4.94675e-06,48.1403,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32201,Q#2340 - >seq8987,superfamily,274009,60,203,4.94675e-06,48.1403,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32202,Q#2340 - >seq8987,non-specific,340204,111,153,1.11569e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32203,Q#2340 - >seq8987,superfamily,340204,111,153,1.11569e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs6_sqmonkey,marg,CompleteHit
32204,Q#2340 - >seq8987,non-specific,274008,41,202,0.000178254,43.1215,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32205,Q#2340 - >seq8987,superfamily,274008,41,202,0.000178254,43.1215,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32206,Q#2340 - >seq8987,non-specific,235175,49,156,0.00018601599999999998,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32207,Q#2340 - >seq8987,superfamily,235175,49,156,0.00018601599999999998,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32208,Q#2340 - >seq8987,non-specific,224117,28,177,0.000279501,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32209,Q#2340 - >seq8987,superfamily,224117,28,177,0.000279501,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32210,Q#2340 - >seq8987,non-specific,235461,47,170,0.000311441,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32211,Q#2340 - >seq8987,superfamily,235461,47,170,0.000311441,41.9774,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32212,Q#2340 - >seq8987,non-specific,223250,47,170,0.000337583,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32213,Q#2340 - >seq8987,superfamily,223250,47,170,0.000337583,41.8149,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32214,Q#2340 - >seq8987,non-specific,237177,42,149,0.000564691,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32215,Q#2340 - >seq8987,superfamily,237177,42,149,0.000564691,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32216,Q#2340 - >seq8987,non-specific,337663,79,183,0.00109886,40.1007,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32217,Q#2340 - >seq8987,superfamily,337663,79,183,0.00109886,40.1007,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32218,Q#2340 - >seq8987,non-specific,313406,73,214,0.00162861,40.0206,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32219,Q#2340 - >seq8987,superfamily,313406,73,214,0.00162861,40.0206,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32220,Q#2340 - >seq8987,non-specific,336159,60,145,0.00280572,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32221,Q#2340 - >seq8987,superfamily,336159,60,145,0.00280572,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32222,Q#2340 - >seq8987,non-specific,275056,60,152,0.00320779,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32223,Q#2340 - >seq8987,superfamily,275056,60,152,0.00320779,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32224,Q#2340 - >seq8987,non-specific,274008,45,150,0.00335776,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32225,Q#2340 - >seq8987,non-specific,112704,2,148,0.00415039,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32226,Q#2340 - >seq8987,superfamily,112704,2,148,0.00415039,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32227,Q#2340 - >seq8987,non-specific,274386,27,147,0.00438384,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32228,Q#2340 - >seq8987,superfamily,274386,27,147,0.00438384,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32229,Q#2340 - >seq8987,non-specific,206779,64,132,0.00643337,36.8312,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32230,Q#2340 - >seq8987,superfamily,357649,64,132,0.00643337,36.8312,cl30773,MCP_signal superfamily,N, - ,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32231,Q#2340 - >seq8987,non-specific,226400,79,149,0.00650669,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32232,Q#2340 - >seq8987,superfamily,226400,79,149,0.00650669,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32233,Q#2340 - >seq8987,non-specific,274091,65,150,0.00716468,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32234,Q#2340 - >seq8987,superfamily,274091,65,150,0.00716468,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
32235,Q#2340 - >seq8987,non-specific,310273,60,194,0.00761019,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32236,Q#2340 - >seq8987,superfamily,310273,60,194,0.00761019,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32237,Q#2340 - >seq8987,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
32238,Q#2340 - >seq8987,non-specific,129694,80,146,0.00967456,37.7189,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32239,Q#2340 - >seq8987,superfamily,129694,80,146,0.00967456,37.7189,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs6_sqmonkey.marg.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
32240,Q#2341 - >seq8988,specific,311990,1167,1185,0.00016894299999999998,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs2_gorilla.marg.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32241,Q#2341 - >seq8988,superfamily,311990,1167,1185,0.00016894299999999998,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs2_gorilla.marg.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs2_gorilla,marg,CompleteHit
32242,Q#2343 - >seq8990,non-specific,335182,157,252,5.1596e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32243,Q#2343 - >seq8990,superfamily,335182,157,252,5.1596e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32244,Q#2343 - >seq8990,non-specific,335182,157,252,5.1596e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32245,Q#2343 - >seq8990,non-specific,340205,255,318,1.2976799999999999e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32246,Q#2343 - >seq8990,superfamily,340205,255,318,1.2976799999999999e-27,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32247,Q#2343 - >seq8990,non-specific,340205,255,318,1.2976799999999999e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32248,Q#2343 - >seq8990,non-specific,340204,111,153,8.84453e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32249,Q#2343 - >seq8990,superfamily,340204,111,153,8.84453e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32250,Q#2343 - >seq8990,non-specific,340204,111,153,8.84453e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,pars,CompleteHit
32251,Q#2343 - >seq8990,non-specific,274008,28,149,0.000245597,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32252,Q#2343 - >seq8990,superfamily,274008,28,149,0.000245597,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32253,Q#2343 - >seq8990,non-specific,274008,28,149,0.000245597,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32254,Q#2343 - >seq8990,non-specific,336852,64,125,0.000854242,38.3348,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32255,Q#2343 - >seq8990,superfamily,336852,64,125,0.000854242,38.3348,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32256,Q#2343 - >seq8990,non-specific,336852,64,125,0.000854242,38.3348,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32257,Q#2343 - >seq8990,non-specific,224117,32,155,0.00125358,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32258,Q#2343 - >seq8990,superfamily,224117,32,155,0.00125358,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32259,Q#2343 - >seq8990,non-specific,224117,32,155,0.00125358,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32260,Q#2343 - >seq8990,non-specific,223571,61,122,0.00154389,39.8903,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32261,Q#2343 - >seq8990,superfamily,223571,61,122,0.00154389,39.8903,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32262,Q#2343 - >seq8990,non-specific,223571,61,122,0.00154389,39.8903,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32263,Q#2343 - >seq8990,non-specific,197874,49,162,0.00188908,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32264,Q#2343 - >seq8990,superfamily,197874,49,162,0.00188908,39.2305,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32265,Q#2343 - >seq8990,non-specific,197874,49,162,0.00188908,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32266,Q#2343 - >seq8990,non-specific,237177,42,150,0.00193373,39.3762,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32267,Q#2343 - >seq8990,superfamily,237177,42,150,0.00193373,39.3762,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32268,Q#2343 - >seq8990,non-specific,237177,42,150,0.00193373,39.3762,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32269,Q#2343 - >seq8990,non-specific,112704,2,121,0.00272973,38.4559,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32270,Q#2343 - >seq8990,superfamily,112704,2,121,0.00272973,38.4559,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32271,Q#2343 - >seq8990,non-specific,112704,2,121,0.00272973,38.4559,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32272,Q#2343 - >seq8990,non-specific,188306,64,150,0.00284652,39.1386,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32273,Q#2343 - >seq8990,superfamily,188306,64,150,0.00284652,39.1386,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32274,Q#2343 - >seq8990,non-specific,188306,64,150,0.00284652,39.1386,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,C-TerminusTruncated
32275,Q#2343 - >seq8990,non-specific,224117,43,150,0.0034506,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32276,Q#2343 - >seq8990,non-specific,224117,43,150,0.0034506,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32277,Q#2343 - >seq8990,non-specific,274009,33,150,0.00504383,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32278,Q#2343 - >seq8990,superfamily,274009,33,150,0.00504383,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32279,Q#2343 - >seq8990,non-specific,274009,33,150,0.00504383,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32280,Q#2343 - >seq8990,non-specific,274009,32,155,0.00517749,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32281,Q#2343 - >seq8990,non-specific,274009,32,155,0.00517749,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,N-TerminusTruncated
32282,Q#2343 - >seq8990,non-specific,222878,54,150,0.00628761,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32283,Q#2343 - >seq8990,superfamily,222878,54,150,0.00628761,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32284,Q#2343 - >seq8990,non-specific,222878,54,150,0.00628761,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32285,Q#2343 - >seq8990,non-specific,274009,33,150,0.00690306,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32286,Q#2343 - >seq8990,non-specific,274009,33,150,0.00690306,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32287,Q#2343 - >seq8990,non-specific,224117,49,150,0.00776261,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32288,Q#2343 - >seq8990,non-specific,224117,49,150,0.00776261,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32289,Q#2343 - >seq8990,non-specific,274008,32,144,0.00889289,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32290,Q#2343 - >seq8990,non-specific,274008,32,144,0.00889289,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32291,Q#2343 - >seq8990,non-specific,311007,65,150,0.00989625,37.3841,pfam06785,UPF0242,NC,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32292,Q#2343 - >seq8990,superfamily,311007,65,150,0.00989625,37.3841,cl26473,UPF0242 superfamily,NC, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32293,Q#2343 - >seq8990,non-specific,311007,65,150,0.00989625,37.3841,pfam06785,UPF0242,NC,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.pars.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,pars,BothTerminiTruncated
32294,Q#2346 - >seq8993,non-specific,335182,157,252,5.1596e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32295,Q#2346 - >seq8993,superfamily,335182,157,252,5.1596e-30,109.7,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32296,Q#2346 - >seq8993,non-specific,335182,157,252,5.1596e-30,109.7,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32297,Q#2346 - >seq8993,non-specific,340205,255,318,1.2976799999999999e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32298,Q#2346 - >seq8993,superfamily,340205,255,318,1.2976799999999999e-27,102.414,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32299,Q#2346 - >seq8993,non-specific,340205,255,318,1.2976799999999999e-27,102.414,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32300,Q#2346 - >seq8993,non-specific,340204,111,153,8.84453e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32301,Q#2346 - >seq8993,superfamily,340204,111,153,8.84453e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32302,Q#2346 - >seq8993,non-specific,340204,111,153,8.84453e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs1_chimp,marg,CompleteHit
32303,Q#2346 - >seq8993,non-specific,274008,28,149,0.000245597,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32304,Q#2346 - >seq8993,superfamily,274008,28,149,0.000245597,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32305,Q#2346 - >seq8993,non-specific,274008,28,149,0.000245597,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32306,Q#2346 - >seq8993,non-specific,336852,64,125,0.000854242,38.3348,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32307,Q#2346 - >seq8993,superfamily,336852,64,125,0.000854242,38.3348,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32308,Q#2346 - >seq8993,non-specific,336852,64,125,0.000854242,38.3348,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32309,Q#2346 - >seq8993,non-specific,224117,32,155,0.00125358,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32310,Q#2346 - >seq8993,superfamily,224117,32,155,0.00125358,40.468,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32311,Q#2346 - >seq8993,non-specific,224117,32,155,0.00125358,40.468,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32312,Q#2346 - >seq8993,non-specific,223571,61,122,0.00154389,39.8903,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32313,Q#2346 - >seq8993,superfamily,223571,61,122,0.00154389,39.8903,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32314,Q#2346 - >seq8993,non-specific,223571,61,122,0.00154389,39.8903,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32315,Q#2346 - >seq8993,non-specific,197874,49,162,0.00188908,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32316,Q#2346 - >seq8993,superfamily,197874,49,162,0.00188908,39.2305,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32317,Q#2346 - >seq8993,non-specific,197874,49,162,0.00188908,39.2305,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32318,Q#2346 - >seq8993,non-specific,237177,42,150,0.00193373,39.3762,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32319,Q#2346 - >seq8993,superfamily,237177,42,150,0.00193373,39.3762,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32320,Q#2346 - >seq8993,non-specific,237177,42,150,0.00193373,39.3762,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32321,Q#2346 - >seq8993,non-specific,112704,2,121,0.00272973,38.4559,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32322,Q#2346 - >seq8993,superfamily,112704,2,121,0.00272973,38.4559,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32323,Q#2346 - >seq8993,non-specific,112704,2,121,0.00272973,38.4559,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32324,Q#2346 - >seq8993,non-specific,188306,64,150,0.00284652,39.1386,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32325,Q#2346 - >seq8993,superfamily,188306,64,150,0.00284652,39.1386,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32326,Q#2346 - >seq8993,non-specific,188306,64,150,0.00284652,39.1386,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,C-TerminusTruncated
32327,Q#2346 - >seq8993,non-specific,224117,43,150,0.0034506,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32328,Q#2346 - >seq8993,non-specific,224117,43,150,0.0034506,38.9272,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32329,Q#2346 - >seq8993,non-specific,274009,33,150,0.00504383,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32330,Q#2346 - >seq8993,superfamily,274009,33,150,0.00504383,38.5103,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32331,Q#2346 - >seq8993,non-specific,274009,33,150,0.00504383,38.5103,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32332,Q#2346 - >seq8993,non-specific,274009,32,155,0.00517749,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32333,Q#2346 - >seq8993,non-specific,274009,32,155,0.00517749,38.5103,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,N-TerminusTruncated
32334,Q#2346 - >seq8993,non-specific,222878,54,150,0.00628761,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32335,Q#2346 - >seq8993,superfamily,222878,54,150,0.00628761,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32336,Q#2346 - >seq8993,non-specific,222878,54,150,0.00628761,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32337,Q#2346 - >seq8993,non-specific,274009,33,150,0.00690306,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32338,Q#2346 - >seq8993,non-specific,274009,33,150,0.00690306,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32339,Q#2346 - >seq8993,non-specific,224117,49,150,0.00776261,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32340,Q#2346 - >seq8993,non-specific,224117,49,150,0.00776261,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32341,Q#2346 - >seq8993,non-specific,274008,32,144,0.00889289,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32342,Q#2346 - >seq8993,non-specific,274008,32,144,0.00889289,37.7287,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32343,Q#2346 - >seq8993,non-specific,311007,65,150,0.00989625,37.3841,pfam06785,UPF0242,NC,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32344,Q#2346 - >seq8993,superfamily,311007,65,150,0.00989625,37.3841,cl26473,UPF0242 superfamily,NC, - ,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32345,Q#2346 - >seq8993,non-specific,311007,65,150,0.00989625,37.3841,pfam06785,UPF0242,NC,cl26473,Uncharacterized protein family (UPF0242); Uncharacterized protein family (UPF0242).  ,L1PB2.ORF1.hs1_chimp.marg.frame3,1909181907_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs1_chimp,marg,BothTerminiTruncated
32346,Q#2347 - >seq8994,non-specific,335182,156,252,1.66279e-34,121.256,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32347,Q#2347 - >seq8994,superfamily,335182,156,252,1.66279e-34,121.256,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32348,Q#2347 - >seq8994,non-specific,340205,255,318,9.280099999999998e-24,92.014,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32349,Q#2347 - >seq8994,superfamily,340205,255,318,9.280099999999998e-24,92.014,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32350,Q#2347 - >seq8994,non-specific,274009,60,203,4.94675e-06,48.1403,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32351,Q#2347 - >seq8994,superfamily,274009,60,203,4.94675e-06,48.1403,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32352,Q#2347 - >seq8994,non-specific,340204,111,153,1.11569e-05,41.6244,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32353,Q#2347 - >seq8994,superfamily,340204,111,153,1.11569e-05,41.6244,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs6_sqmonkey,pars,CompleteHit
32354,Q#2347 - >seq8994,non-specific,274008,41,202,0.000178254,43.1215,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32355,Q#2347 - >seq8994,superfamily,274008,41,202,0.000178254,43.1215,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32356,Q#2347 - >seq8994,non-specific,235175,49,156,0.00018601599999999998,43.1288,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32357,Q#2347 - >seq8994,superfamily,235175,49,156,0.00018601599999999998,43.1288,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32358,Q#2347 - >seq8994,non-specific,224117,28,177,0.000279501,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32359,Q#2347 - >seq8994,superfamily,224117,28,177,0.000279501,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32360,Q#2347 - >seq8994,non-specific,235461,47,170,0.000311441,41.9774,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32361,Q#2347 - >seq8994,superfamily,235461,47,170,0.000311441,41.9774,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32362,Q#2347 - >seq8994,non-specific,223250,47,170,0.000337583,41.8149,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32363,Q#2347 - >seq8994,superfamily,223250,47,170,0.000337583,41.8149,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32364,Q#2347 - >seq8994,non-specific,237177,42,149,0.000564691,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32365,Q#2347 - >seq8994,superfamily,237177,42,149,0.000564691,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32366,Q#2347 - >seq8994,non-specific,337663,79,183,0.00109886,40.1007,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32367,Q#2347 - >seq8994,superfamily,337663,79,183,0.00109886,40.1007,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32368,Q#2347 - >seq8994,non-specific,313406,73,214,0.00162861,40.0206,pfam10168,Nup88,N,cl25737,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32369,Q#2347 - >seq8994,superfamily,313406,73,214,0.00162861,40.0206,cl25737,Nup88 superfamily,N, - ,"Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumor cells.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32370,Q#2347 - >seq8994,non-specific,336159,60,145,0.00280572,39.2749,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32371,Q#2347 - >seq8994,superfamily,336159,60,145,0.00280572,39.2749,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32372,Q#2347 - >seq8994,non-specific,275056,60,152,0.00320779,38.0653,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32373,Q#2347 - >seq8994,superfamily,275056,60,152,0.00320779,38.0653,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32374,Q#2347 - >seq8994,non-specific,274008,45,150,0.00335776,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32375,Q#2347 - >seq8994,non-specific,112704,2,148,0.00415039,37.6855,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32376,Q#2347 - >seq8994,superfamily,112704,2,148,0.00415039,37.6855,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32377,Q#2347 - >seq8994,non-specific,274386,27,147,0.00438384,38.4938,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32378,Q#2347 - >seq8994,superfamily,274386,27,147,0.00438384,38.4938,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32379,Q#2347 - >seq8994,non-specific,206779,64,132,0.00643337,36.8312,cd11386,MCP_signal,N,cl30773,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32380,Q#2347 - >seq8994,superfamily,357649,64,132,0.00643337,36.8312,cl30773,MCP_signal superfamily,N, - ,"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32381,Q#2347 - >seq8994,non-specific,226400,79,149,0.00650669,37.3906,COG3883,CwlO1,C,cl25603,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32382,Q#2347 - >seq8994,superfamily,226400,79,149,0.00650669,37.3906,cl25603,CwlO1 superfamily,C, - ,Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO  [Function unknown]; Uncharacterized protein conserved in bacteria [Function unknown].,L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32383,Q#2347 - >seq8994,non-specific,274091,65,150,0.00716468,37.6754,TIGR02350,prok_dnaK,N,cl37092,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32384,Q#2347 - >seq8994,superfamily,274091,65,150,0.00716468,37.6754,cl37092,prok_dnaK superfamily,N, - ,"chaperone protein DnaK; Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
32385,Q#2347 - >seq8994,non-specific,310273,60,194,0.00761019,37.8026,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32386,Q#2347 - >seq8994,superfamily,310273,60,194,0.00761019,37.8026,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32387,Q#2347 - >seq8994,non-specific,274009,33,150,0.00906144,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
32388,Q#2347 - >seq8994,non-specific,129694,80,146,0.00967456,37.7189,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32389,Q#2347 - >seq8994,superfamily,129694,80,146,0.00967456,37.7189,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs6_sqmonkey.pars.frame3,1909181907_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
32390,Q#2350 - >seq8997,specific,238827,483,745,2.4577e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32391,Q#2350 - >seq8997,superfamily,295487,483,745,2.4577e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32392,Q#2350 - >seq8997,specific,333820,489,745,4.1525199999999995e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32393,Q#2350 - >seq8997,superfamily,333820,489,745,4.1525199999999995e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32394,Q#2350 - >seq8997,non-specific,238828,555,742,1.49038e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32395,Q#2350 - >seq8997,non-specific,275209,440,769,2.7734200000000003e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32396,Q#2350 - >seq8997,superfamily,275209,440,769,2.7734200000000003e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32397,Q#2350 - >seq8997,non-specific,238185,629,745,4.06736e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs2_gorilla.pars.frame2,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32398,Q#2351 - >seq8998,specific,197310,9,236,7.039039999999999e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32399,Q#2351 - >seq8998,superfamily,351117,9,236,7.039039999999999e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32400,Q#2351 - >seq8998,non-specific,197306,9,236,2.98619e-45,163.421,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32401,Q#2351 - >seq8998,non-specific,197307,9,236,1.79817e-25,106.603,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32402,Q#2351 - >seq8998,non-specific,223780,9,237,6.76034e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32403,Q#2351 - >seq8998,non-specific,197320,9,229,1.43006e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32404,Q#2351 - >seq8998,non-specific,197321,7,236,6.88367e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32405,Q#2351 - >seq8998,specific,335306,10,229,2.2037299999999997e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32406,Q#2351 - >seq8998,non-specific,273186,9,237,2.93314e-14,73.8524,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32407,Q#2351 - >seq8998,non-specific,272954,9,236,8.64206e-14,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32408,Q#2351 - >seq8998,non-specific,197319,13,236,1.39889e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32409,Q#2351 - >seq8998,non-specific,197322,8,236,1.46541e-10,63.4902,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32410,Q#2351 - >seq8998,non-specific,197336,9,194,2.4505000000000005e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32411,Q#2351 - >seq8998,non-specific,236970,9,237,1.77686e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32412,Q#2351 - >seq8998,non-specific,339261,108,232,9.36097e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32413,Q#2351 - >seq8998,non-specific,197311,30,236,2.87329e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32414,Q#2351 - >seq8998,non-specific,224117,266,389,0.00181214,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32415,Q#2351 - >seq8998,superfamily,224117,266,389,0.00181214,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32416,Q#2351 - >seq8998,non-specific,235175,263,396,0.00567969,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32417,Q#2351 - >seq8998,superfamily,235175,263,396,0.00567969,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs2_gorilla.pars.frame3,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32418,Q#2352 - >seq8999,specific,311990,1112,1130,0.000714608,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs2_gorilla.pars.frame1,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32419,Q#2352 - >seq8999,superfamily,311990,1112,1130,0.000714608,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs2_gorilla.pars.frame1,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32420,Q#2354 - >seq9001,specific,197310,9,236,1.8991199999999995e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32421,Q#2354 - >seq9001,superfamily,351117,9,236,1.8991199999999995e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32422,Q#2354 - >seq9001,specific,238827,506,767,2.75317e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32423,Q#2354 - >seq9001,superfamily,295487,506,767,2.75317e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32424,Q#2354 - >seq9001,non-specific,197306,9,236,4.22173e-36,137.22799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32425,Q#2354 - >seq9001,specific,333820,512,767,1.4657e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32426,Q#2354 - >seq9001,superfamily,333820,512,767,1.4657e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32427,Q#2354 - >seq9001,non-specific,197320,7,229,2.0294200000000002e-24,103.749,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32428,Q#2354 - >seq9001,non-specific,223780,7,229,5.398880000000001e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32429,Q#2354 - >seq9001,non-specific,197307,9,236,9.51981e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32430,Q#2354 - >seq9001,specific,335306,10,229,1.41536e-20,91.5377,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32431,Q#2354 - >seq9001,non-specific,197321,7,236,5.954820000000001e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32432,Q#2354 - >seq9001,non-specific,273186,7,237,3.03477e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32433,Q#2354 - >seq9001,non-specific,272954,7,236,3.74761e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32434,Q#2354 - >seq9001,non-specific,197319,7,236,6.83051e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32435,Q#2354 - >seq9001,non-specific,197336,7,229,1.72793e-11,65.7115,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32436,Q#2354 - >seq9001,non-specific,238828,512,732,3.88652e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32437,Q#2354 - >seq9001,non-specific,197311,7,236,1.48655e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32438,Q#2354 - >seq9001,non-specific,275209,582,732,5.6823e-07,52.8452,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32439,Q#2354 - >seq9001,superfamily,275209,582,732,5.6823e-07,52.8452,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32440,Q#2354 - >seq9001,non-specific,339261,108,232,6.3902499999999995e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32441,Q#2354 - >seq9001,non-specific,236970,9,207,8.45945e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32442,Q#2354 - >seq9001,non-specific,238185,651,767,0.00019804799999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32443,Q#2354 - >seq9001,non-specific,197318,9,236,0.00101593,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32444,Q#2354 - >seq9001,non-specific,197314,7,236,0.00147856,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1MA3,ORF2,hs2_gorilla,pars,CompleteHit
32445,Q#2355 - >seq9002,specific,311990,1113,1131,0.000722262,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs2_gorilla.marg.frame1,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32446,Q#2355 - >seq9002,superfamily,311990,1113,1131,0.000722262,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs2_gorilla.marg.frame1,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32447,Q#2357 - >seq9004,specific,311990,1113,1131,0.00570374,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs2_gorilla.pars.frame1,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32448,Q#2357 - >seq9004,superfamily,311990,1113,1131,0.00570374,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs2_gorilla.pars.frame1,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32449,Q#2359 - >seq9006,specific,238827,523,766,7.31844e-55,190.195,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32450,Q#2359 - >seq9006,superfamily,295487,523,766,7.31844e-55,190.195,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32451,Q#2359 - >seq9006,specific,197310,9,233,1.2976999999999999e-54,190.255,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32452,Q#2359 - >seq9006,superfamily,351117,9,233,1.2976999999999999e-54,190.255,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32453,Q#2359 - >seq9006,specific,333820,523,766,3.5841399999999995e-29,115.08200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32454,Q#2359 - >seq9006,superfamily,333820,523,766,3.5841399999999995e-29,115.08200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32455,Q#2359 - >seq9006,non-specific,197306,9,233,1.36326e-26,109.493,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32456,Q#2359 - >seq9006,non-specific,223780,7,226,1.7974e-18,86.4983,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32457,Q#2359 - >seq9006,non-specific,197320,7,226,2.91281e-17,82.5629,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32458,Q#2359 - >seq9006,non-specific,197307,9,233,3.0941e-17,82.7209,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32459,Q#2359 - >seq9006,specific,335306,10,226,5.10329e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32460,Q#2359 - >seq9006,non-specific,272954,7,233,2.05878e-12,68.5637,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32461,Q#2359 - >seq9006,non-specific,273186,7,234,1.5655e-11,65.7632,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32462,Q#2359 - >seq9006,non-specific,197319,7,233,5.81617e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32463,Q#2359 - >seq9006,non-specific,197321,7,233,5.32153e-10,61.413999999999994,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32464,Q#2359 - >seq9006,non-specific,238828,577,732,9.33098e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32465,Q#2359 - >seq9006,non-specific,275209,582,790,4.53989e-05,47.0672,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32466,Q#2359 - >seq9006,superfamily,275209,582,790,4.53989e-05,47.0672,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32467,Q#2359 - >seq9006,non-specific,235175,288,459,0.00044556800000000003,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32468,Q#2359 - >seq9006,superfamily,235175,288,459,0.00044556800000000003,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA8,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32469,Q#2359 - >seq9006,non-specific,197311,7,233,0.00174166,41.1233,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,pars,CompleteHit
32470,Q#2359 - >seq9006,non-specific,334125,209,407,0.0017714000000000002,42.1364,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32471,Q#2359 - >seq9006,superfamily,334125,209,407,0.0017714000000000002,42.1364,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA8.ORF2.hs2_gorilla.pars.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32472,Q#2360 - >seq9007,specific,197310,9,236,2.0752299999999997e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32473,Q#2360 - >seq9007,superfamily,351117,9,236,2.0752299999999997e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32474,Q#2360 - >seq9007,specific,238827,507,768,3.008449999999999e-63,214.077,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32475,Q#2360 - >seq9007,superfamily,295487,507,768,3.008449999999999e-63,214.077,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32476,Q#2360 - >seq9007,non-specific,197306,9,236,4.30761e-36,137.22799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32477,Q#2360 - >seq9007,specific,333820,513,768,1.5695499999999998e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32478,Q#2360 - >seq9007,superfamily,333820,513,768,1.5695499999999998e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32479,Q#2360 - >seq9007,non-specific,197320,7,229,2.0120299999999998e-24,103.749,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32480,Q#2360 - >seq9007,non-specific,223780,7,229,5.507430000000001e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32481,Q#2360 - >seq9007,non-specific,197307,9,236,9.52856e-21,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32482,Q#2360 - >seq9007,specific,335306,10,229,1.41663e-20,91.5377,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32483,Q#2360 - >seq9007,non-specific,197321,7,236,5.9603e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32484,Q#2360 - >seq9007,non-specific,273186,7,237,3.0375499999999997e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32485,Q#2360 - >seq9007,non-specific,272954,7,236,3.7866100000000005e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32486,Q#2360 - >seq9007,non-specific,197319,7,236,6.836769999999999e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32487,Q#2360 - >seq9007,non-specific,197336,7,229,1.7295e-11,65.7115,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32488,Q#2360 - >seq9007,non-specific,238828,513,733,4.19353e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32489,Q#2360 - >seq9007,non-specific,197311,7,236,1.57385e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32490,Q#2360 - >seq9007,non-specific,275209,583,733,5.63774e-07,52.8452,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32491,Q#2360 - >seq9007,superfamily,275209,583,733,5.63774e-07,52.8452,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32492,Q#2360 - >seq9007,non-specific,339261,108,232,6.52059e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32493,Q#2360 - >seq9007,non-specific,236970,9,207,8.77788e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32494,Q#2360 - >seq9007,non-specific,238185,652,768,0.00020015200000000002,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32495,Q#2360 - >seq9007,non-specific,197318,9,236,0.00101682,42.2835,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32496,Q#2360 - >seq9007,non-specific,197314,7,236,0.00147985,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1MA3,ORF2,hs2_gorilla,marg,CompleteHit
32497,Q#2360 - >seq9007,non-specific,334125,212,408,0.00508549,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32498,Q#2360 - >seq9007,superfamily,334125,212,408,0.00508549,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA3.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32499,Q#2362 - >seq9009,specific,311990,1118,1136,0.00584168,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs2_gorilla.marg.frame1,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32500,Q#2362 - >seq9009,superfamily,311990,1118,1136,0.00584168,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA8.ORF2.hs2_gorilla.marg.frame1,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32501,Q#2363 - >seq9010,non-specific,197310,5,66,1.26343e-07,53.5093,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs6_sqmonkey.marg.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
32502,Q#2363 - >seq9010,superfamily,351117,5,66,1.26343e-07,53.5093,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs6_sqmonkey.marg.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
32503,Q#2364 - >seq9011,specific,197310,39,227,3.42093e-30,119.764,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,CompleteHit
32504,Q#2364 - >seq9011,superfamily,351117,39,227,3.42093e-30,119.764,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,CompleteHit
32505,Q#2364 - >seq9011,non-specific,238827,504,676,1.01139e-16,80.413,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
32506,Q#2364 - >seq9011,superfamily,295487,504,676,1.01139e-16,80.413,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
32507,Q#2364 - >seq9011,non-specific,197306,60,227,4.9210199999999995e-14,72.8993,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32508,Q#2364 - >seq9011,non-specific,197320,59,220,6.081950000000001e-10,60.9918,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32509,Q#2364 - >seq9011,non-specific,223780,59,220,8.032539999999999e-10,60.6899,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32510,Q#2364 - >seq9011,non-specific,333820,508,679,1.1234e-08,55.7614,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs6_sqmonkey,marg,CompleteHit
32511,Q#2364 - >seq9011,superfamily,333820,508,679,1.1234e-08,55.7614,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs6_sqmonkey,marg,CompleteHit
32512,Q#2364 - >seq9011,specific,335306,59,220,1.3057700000000002e-07,53.403,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32513,Q#2364 - >seq9011,non-specific,197322,98,220,4.2766999999999996e-07,53.0898,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32514,Q#2364 - >seq9011,non-specific,197307,55,227,2.1513400000000003e-06,50.3641,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32515,Q#2364 - >seq9011,non-specific,197321,55,227,1.60456e-05,47.5468,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32516,Q#2364 - >seq9011,non-specific,197319,97,227,0.000109849,44.9601,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32517,Q#2364 - >seq9011,non-specific,273186,97,228,0.000278611,43.8068,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32518,Q#2364 - >seq9011,non-specific,339261,99,223,0.000551517,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1ME1,ORF2,hs6_sqmonkey,marg,CompleteHit
32519,Q#2364 - >seq9011,non-specific,272954,55,198,0.00484999,40.0589,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs6_sqmonkey.marg.frame2,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
32520,Q#2366 - >seq9013,specific,311990,1155,1173,0.000264581,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs2_gorilla.pars.frame1,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32521,Q#2366 - >seq9013,superfamily,311990,1155,1173,0.000264581,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs2_gorilla.pars.frame1,1909181907_L1PA14.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs2_gorilla,pars,CompleteHit
32522,Q#2369 - >seq9016,specific,197310,9,235,1.07511e-56,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32523,Q#2369 - >seq9016,superfamily,351117,9,235,1.07511e-56,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32524,Q#2369 - >seq9016,specific,238827,526,771,3.92777e-55,190.965,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32525,Q#2369 - >seq9016,superfamily,295487,526,771,3.92777e-55,190.965,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32526,Q#2369 - >seq9016,specific,333820,526,771,2.51072e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32527,Q#2369 - >seq9016,superfamily,333820,526,771,2.51072e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32528,Q#2369 - >seq9016,non-specific,197306,9,235,8.74224e-29,116.042,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32529,Q#2369 - >seq9016,non-specific,223780,7,228,5.591470000000001e-17,82.2611,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32530,Q#2369 - >seq9016,non-specific,197320,7,228,6.5318e-17,81.7925,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32531,Q#2369 - >seq9016,non-specific,197307,9,235,6.81228e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32532,Q#2369 - >seq9016,specific,335306,10,228,1.80611e-13,71.1221,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32533,Q#2369 - >seq9016,non-specific,272954,7,235,1.21584e-11,66.2525,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32534,Q#2369 - >seq9016,non-specific,197319,7,235,4.99322e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32535,Q#2369 - >seq9016,non-specific,273186,7,236,1.61992e-10,62.6816,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32536,Q#2369 - >seq9016,non-specific,197321,7,235,2.79763e-10,62.1844,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32537,Q#2369 - >seq9016,non-specific,238828,580,735,9.920389999999999e-09,56.8256,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32538,Q#2369 - >seq9016,non-specific,275209,585,795,3.16227e-05,47.4524,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32539,Q#2369 - >seq9016,superfamily,275209,585,795,3.16227e-05,47.4524,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32540,Q#2369 - >seq9016,non-specific,197311,37,235,0.00222232,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA8,ORF2,hs2_gorilla,marg,CompleteHit
32541,Q#2369 - >seq9016,non-specific,235175,306,462,0.00560472,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA8,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32542,Q#2369 - >seq9016,superfamily,235175,306,462,0.00560472,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA8.ORF2.hs2_gorilla.marg.frame3,1909181907_L1MA8.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA8,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32543,Q#2370 - >seq9017,specific,197310,5,232,5.19881e-44,159.439,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32544,Q#2370 - >seq9017,superfamily,351117,5,232,5.19881e-44,159.439,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32545,Q#2370 - >seq9017,non-specific,197306,5,232,3.7829599999999997e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32546,Q#2370 - >seq9017,non-specific,238827,505,696,5.1654e-15,75.4054,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
32547,Q#2370 - >seq9017,superfamily,295487,505,696,5.1654e-15,75.4054,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
32548,Q#2370 - >seq9017,non-specific,223780,5,225,1.59815e-12,68.7791,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32549,Q#2370 - >seq9017,non-specific,197320,5,225,3.03613e-11,64.8438,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32550,Q#2370 - >seq9017,non-specific,197307,5,232,7.1892e-11,63.8461,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32551,Q#2370 - >seq9017,specific,335306,6,225,1.30969e-10,62.2626,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32552,Q#2370 - >seq9017,non-specific,197321,3,232,1.40702e-09,59.8732,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32553,Q#2370 - >seq9017,non-specific,273186,5,233,3.7520600000000003e-07,52.6664,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32554,Q#2370 - >seq9017,non-specific,197322,103,225,4.23028e-07,53.0898,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
32555,Q#2370 - >seq9017,non-specific,272954,5,203,2.57002e-06,50.0741,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32556,Q#2370 - >seq9017,non-specific,197319,5,232,4.01973e-06,49.5825,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32557,Q#2370 - >seq9017,non-specific,333820,511,603,0.000123393,43.8202,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
32558,Q#2370 - >seq9017,superfamily,333820,511,603,0.000123393,43.8202,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1ME1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
32559,Q#2370 - >seq9017,non-specific,339261,104,228,0.0007806810000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1ME1.ORF2.hs6_sqmonkey.pars.frame3,1909181907_L1ME1.RM_HPGPNRMPCCS_1709081336.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1ME1,ORF2,hs6_sqmonkey,pars,CompleteHit
32560,Q#2373 - >seq9020,non-specific,238827,475,505,3.31872e-05,46.1302,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32561,Q#2373 - >seq9020,superfamily,295487,475,505,3.31872e-05,46.1302,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MC1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32562,Q#2374 - >seq9021,specific,197310,9,237,3.988e-49,174.46200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32563,Q#2374 - >seq9021,superfamily,351117,9,237,3.988e-49,174.46200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32564,Q#2374 - >seq9021,specific,238827,510,760,2.4969499999999996e-42,154.371,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32565,Q#2374 - >seq9021,superfamily,295487,510,760,2.4969499999999996e-42,154.371,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32566,Q#2374 - >seq9021,non-specific,333820,516,749,1.92942e-23,98.9037,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32567,Q#2374 - >seq9021,superfamily,333820,516,749,1.92942e-23,98.9037,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32568,Q#2374 - >seq9021,non-specific,197306,9,237,3.16481e-22,96.7816,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32569,Q#2374 - >seq9021,non-specific,223780,9,238,9.33817e-14,72.6311,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32570,Q#2374 - >seq9021,non-specific,197307,9,237,6.6589300000000006e-12,66.9277,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32571,Q#2374 - >seq9021,specific,335306,10,230,1.0162000000000001e-11,65.7294,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32572,Q#2374 - >seq9021,non-specific,238828,581,706,1.27147e-10,62.6036,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32573,Q#2374 - >seq9021,non-specific,273186,9,238,1.33329e-10,63.0668,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32574,Q#2374 - >seq9021,non-specific,197320,9,222,2.75118e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32575,Q#2374 - >seq9021,non-specific,272954,9,237,1.88353e-07,53.5409,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32576,Q#2374 - >seq9021,non-specific,275209,586,670,1.2244400000000001e-06,52.0748,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32577,Q#2374 - >seq9021,superfamily,275209,586,670,1.2244400000000001e-06,52.0748,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32578,Q#2374 - >seq9021,non-specific,197321,7,237,5.72071e-06,49.0876,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32579,Q#2374 - >seq9021,non-specific,197322,8,230,1.44326e-05,48.4674,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32580,Q#2374 - >seq9021,non-specific,339261,109,233,8.56458e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs2_gorilla,marg,CompleteHit
32581,Q#2374 - >seq9021,non-specific,274009,307,450,0.00166721,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32582,Q#2374 - >seq9021,superfamily,274009,307,450,0.00166721,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32583,Q#2377 - >seq9024,specific,197310,9,236,5.863499999999999e-50,176.773,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32584,Q#2377 - >seq9024,superfamily,351117,9,236,5.863499999999999e-50,176.773,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32585,Q#2377 - >seq9024,non-specific,197306,9,236,1.3129000000000001e-23,101.01899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32586,Q#2377 - >seq9024,non-specific,238827,510,609,8.362189999999999e-20,89.2726,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32587,Q#2377 - >seq9024,superfamily,295487,510,609,8.362189999999999e-20,89.2726,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32588,Q#2377 - >seq9024,non-specific,223780,9,237,1.4753e-15,77.6387,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32589,Q#2377 - >seq9024,non-specific,197307,9,236,2.46313e-13,71.1649,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32590,Q#2377 - >seq9024,specific,335306,10,229,3.82817e-13,69.9666,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32591,Q#2377 - >seq9024,non-specific,273186,9,237,3.0315599999999997e-12,67.6892,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32592,Q#2377 - >seq9024,non-specific,197320,9,221,5.16152e-12,67.155,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32593,Q#2377 - >seq9024,non-specific,272954,9,236,5.10845e-09,58.1633,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32594,Q#2377 - >seq9024,non-specific,333820,516,607,1.3644199999999999e-08,55.7614,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32595,Q#2377 - >seq9024,superfamily,333820,516,607,1.3644199999999999e-08,55.7614,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32596,Q#2377 - >seq9024,non-specific,197321,7,236,1.0232e-07,54.0952,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32597,Q#2377 - >seq9024,non-specific,197319,9,236,1.06874e-05,48.0417,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32598,Q#2377 - >seq9024,non-specific,339261,108,232,9.01143e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32599,Q#2377 - >seq9024,non-specific,197322,107,229,0.00014093799999999998,45.0006,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32600,Q#2377 - >seq9024,non-specific,274009,307,450,0.00125378,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32601,Q#2377 - >seq9024,superfamily,274009,307,450,0.00125378,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32602,Q#2377 - >seq9024,non-specific,197336,9,194,0.00131366,41.8291,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs2_gorilla,pars,CompleteHit
32603,Q#2377 - >seq9024,non-specific,235175,307,450,0.0053008000000000005,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32604,Q#2377 - >seq9024,superfamily,235175,307,450,0.0053008000000000005,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC1.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32605,Q#2378 - >seq9025,non-specific,238827,593,699,4.86757e-17,81.1834,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32606,Q#2378 - >seq9025,superfamily,295487,593,699,4.86757e-17,81.1834,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32607,Q#2378 - >seq9025,non-specific,333820,552,688,1.33142e-07,52.6798,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32608,Q#2378 - >seq9025,superfamily,333820,552,688,1.33142e-07,52.6798,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32609,Q#2378 - >seq9025,non-specific,238828,533,645,3.6041000000000004e-06,49.1216,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32610,Q#2378 - >seq9025,superfamily,295487,533,645,3.6041000000000004e-06,49.1216,cl02808,RT_like superfamily,NC, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MC1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MC1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32611,Q#2379 - >seq9026,specific,197310,3,230,5.076419999999999e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32612,Q#2379 - >seq9026,superfamily,351117,3,230,5.076419999999999e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32613,Q#2379 - >seq9026,specific,238827,501,762,2.3488099999999995e-57,197.514,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,CompleteHit
32614,Q#2379 - >seq9026,superfamily,295487,501,762,2.3488099999999995e-57,197.514,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,CompleteHit
32615,Q#2379 - >seq9026,non-specific,197306,3,230,7.892919999999998e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32616,Q#2379 - >seq9026,specific,333820,507,762,1.1322899999999999e-29,116.62299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,CompleteHit
32617,Q#2379 - >seq9026,superfamily,333820,507,762,1.1322899999999999e-29,116.62299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,CompleteHit
32618,Q#2379 - >seq9026,non-specific,197320,1,215,2.7624000000000003e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32619,Q#2379 - >seq9026,non-specific,223780,1,219,9.419229999999999e-21,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32620,Q#2379 - >seq9026,specific,335306,4,223,2.29893e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32621,Q#2379 - >seq9026,non-specific,197307,3,223,4.06068e-17,82.3357,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32622,Q#2379 - >seq9026,non-specific,197321,1,223,5.69711e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32623,Q#2379 - >seq9026,non-specific,273186,1,231,6.97674e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32624,Q#2379 - >seq9026,non-specific,272954,1,201,1.92845e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32625,Q#2379 - >seq9026,non-specific,197319,1,230,9.346789999999999e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32626,Q#2379 - >seq9026,non-specific,197336,1,198,2.40837e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32627,Q#2379 - >seq9026,non-specific,238828,577,728,7.44237e-09,57.2108,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,N-TerminusTruncated
32628,Q#2379 - >seq9026,non-specific,197311,1,198,3.21456e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32629,Q#2379 - >seq9026,non-specific,275209,578,786,1.86085e-05,48.2228,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,N-TerminusTruncated
32630,Q#2379 - >seq9026,superfamily,275209,578,786,1.86085e-05,48.2228,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs0_human,marg,N-TerminusTruncated
32631,Q#2379 - >seq9026,non-specific,236970,3,201,2.57269e-05,47.1962,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,marg,CompleteHit
32632,Q#2379 - >seq9026,non-specific,335313,39,132,0.00434429,40.888000000000005,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA9,ORF2,hs0_human,marg,N-TerminusTruncated
32633,Q#2379 - >seq9026,superfamily,354836,39,132,0.00434429,40.888000000000005,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA9,ORF2,hs0_human,marg,N-TerminusTruncated
32634,Q#2379 - >seq9026,non-specific,339261,102,225,0.00484857,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs0_human.marg.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs0_human,marg,CompleteHit
32635,Q#2380 - >seq9027,specific,197310,5,232,1.76312e-45,163.67600000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32636,Q#2380 - >seq9027,superfamily,351117,5,232,1.76312e-45,163.67600000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32637,Q#2380 - >seq9027,specific,238827,574,766,3.59727e-27,110.459,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32638,Q#2380 - >seq9027,superfamily,295487,574,766,3.59727e-27,110.459,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32639,Q#2380 - >seq9027,non-specific,197306,5,232,3.13665e-23,99.8632,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32640,Q#2380 - >seq9027,non-specific,333820,581,745,8.188350000000001e-17,79.6438,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32641,Q#2380 - >seq9027,superfamily,333820,581,745,8.188350000000001e-17,79.6438,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32642,Q#2380 - >seq9027,non-specific,223780,5,225,4.84112e-16,79.1795,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32643,Q#2380 - >seq9027,non-specific,197307,5,232,3.24123e-13,70.7797,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32644,Q#2380 - >seq9027,specific,335306,6,225,7.85613e-12,66.1146,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32645,Q#2380 - >seq9027,non-specific,238828,577,745,8.00527e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32646,Q#2380 - >seq9027,non-specific,273186,5,233,4.00708e-11,64.6076,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32647,Q#2380 - >seq9027,non-specific,197320,5,217,2.7894700000000003e-10,62.1474,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32648,Q#2380 - >seq9027,non-specific,197321,3,232,9.49923e-09,57.562,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32649,Q#2380 - >seq9027,non-specific,275209,582,732,8.9586e-08,55.5416,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32650,Q#2380 - >seq9027,superfamily,275209,582,732,8.9586e-08,55.5416,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32651,Q#2380 - >seq9027,non-specific,272954,5,203,2.04697e-06,50.4593,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32652,Q#2380 - >seq9027,non-specific,339261,104,228,2.73731e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32653,Q#2380 - >seq9027,non-specific,197322,103,232,3.4973400000000002e-06,50.0082,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32654,Q#2380 - >seq9027,non-specific,238185,653,745,0.00463408,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,pars,CompleteHit
32655,Q#2382 - >seq9029,specific,197310,3,230,3.0565199999999994e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32656,Q#2382 - >seq9029,superfamily,351117,3,230,3.0565199999999994e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32657,Q#2382 - >seq9029,non-specific,197306,3,230,1.19705e-33,129.909,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32658,Q#2382 - >seq9029,non-specific,197320,1,215,3.34809e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32659,Q#2382 - >seq9029,non-specific,223780,1,219,6.338640000000001e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32660,Q#2382 - >seq9029,specific,335306,4,223,2.15985e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32661,Q#2382 - >seq9029,non-specific,197307,3,223,1.84086e-17,83.1061,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32662,Q#2382 - >seq9029,non-specific,197321,1,223,5.39624e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32663,Q#2382 - >seq9029,non-specific,273186,1,231,6.79688e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32664,Q#2382 - >seq9029,non-specific,272954,1,201,1.02084e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32665,Q#2382 - >seq9029,non-specific,197319,1,230,3.84356e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32666,Q#2382 - >seq9029,non-specific,197336,1,198,2.2616e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32667,Q#2382 - >seq9029,non-specific,197311,1,198,1.5507e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32668,Q#2382 - >seq9029,non-specific,236970,3,201,1.7177100000000002e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs0_human,pars,CompleteHit
32669,Q#2382 - >seq9029,non-specific,335313,39,132,0.00364864,40.888000000000005,pfam03403,PAF-AH_p_II,N,cl21494,"Platelet-activating factor acetylhydrolase, isoform II; Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA9,ORF2,hs0_human,pars,N-TerminusTruncated
32670,Q#2382 - >seq9029,superfamily,354836,39,132,0.00364864,40.888000000000005,cl21494,Abhydrolase superfamily,N, - ,"alpha/beta hydrolases; A functionally diverse superfamily containing proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases. The catalytic apparatus typically involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine, and often the mechanism involves a nucleophilic attack on a carbonyl carbon atom.",L1MA9.ORF2.hs0_human.pars.frame3,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA9,ORF2,hs0_human,pars,N-TerminusTruncated
32671,Q#2383 - >seq9030,specific,311990,1152,1170,0.00717188,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs0_human.pars.frame2,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs0_human,pars,CompleteHit
32672,Q#2383 - >seq9030,superfamily,311990,1152,1170,0.00717188,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs0_human.pars.frame2,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs0_human,pars,CompleteHit
32673,Q#2384 - >seq9031,specific,238827,462,711,3.714119999999999e-57,196.743,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,CompleteHit
32674,Q#2384 - >seq9031,superfamily,295487,462,711,3.714119999999999e-57,196.743,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,CompleteHit
32675,Q#2384 - >seq9031,specific,333820,468,692,1.63714e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,CompleteHit
32676,Q#2384 - >seq9031,superfamily,333820,468,692,1.63714e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,CompleteHit
32677,Q#2384 - >seq9031,non-specific,238828,534,689,1.0686600000000001e-09,59.9072,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,N-TerminusTruncated
32678,Q#2384 - >seq9031,non-specific,275209,539,724,1.65833e-06,51.3044,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,N-TerminusTruncated
32679,Q#2384 - >seq9031,superfamily,275209,539,724,1.65833e-06,51.3044,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs0_human.pars.frame1,1909181908_L1MA9.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA9,ORF2,hs0_human,pars,N-TerminusTruncated
32680,Q#2385 - >seq9032,specific,197310,9,236,3.590959999999999e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32681,Q#2385 - >seq9032,superfamily,351117,9,236,3.590959999999999e-63,214.908,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32682,Q#2385 - >seq9032,specific,238827,509,770,7.89618e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32683,Q#2385 - >seq9032,superfamily,295487,509,770,7.89618e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32684,Q#2385 - >seq9032,non-specific,197306,9,236,8.428359999999999e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32685,Q#2385 - >seq9032,specific,333820,515,770,3.4813999999999996e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32686,Q#2385 - >seq9032,superfamily,333820,515,770,3.4813999999999996e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32687,Q#2385 - >seq9032,non-specific,197320,7,229,1.9228100000000002e-24,103.749,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32688,Q#2385 - >seq9032,non-specific,223780,7,229,1.33296e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32689,Q#2385 - >seq9032,specific,335306,10,229,7.26292e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32690,Q#2385 - >seq9032,non-specific,197307,9,229,1.9329200000000002e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32691,Q#2385 - >seq9032,non-specific,197321,7,229,5.3759e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32692,Q#2385 - >seq9032,non-specific,272954,7,207,1.2750400000000001e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32693,Q#2385 - >seq9032,non-specific,273186,7,237,2.54918e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32694,Q#2385 - >seq9032,non-specific,197319,7,236,2.83666e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32695,Q#2385 - >seq9032,non-specific,238828,515,770,8.4145e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32696,Q#2385 - >seq9032,non-specific,197336,7,229,2.23393e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32697,Q#2385 - >seq9032,non-specific,275209,466,794,4.97208e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32698,Q#2385 - >seq9032,superfamily,275209,466,794,4.97208e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32699,Q#2385 - >seq9032,non-specific,197311,7,204,2.14621e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32700,Q#2385 - >seq9032,non-specific,236970,9,229,2.95715e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32701,Q#2385 - >seq9032,non-specific,238185,655,770,6.64177e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32702,Q#2385 - >seq9032,non-specific,235175,307,468,0.000121795,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32703,Q#2385 - >seq9032,superfamily,235175,307,468,0.000121795,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32704,Q#2385 - >seq9032,non-specific,339261,108,231,0.0006625530000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32705,Q#2385 - >seq9032,non-specific,197318,9,230,0.00417202,40.3575,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32706,Q#2385 - >seq9032,specific,311990,1269,1287,0.00510542,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32707,Q#2385 - >seq9032,superfamily,311990,1269,1287,0.00510542,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA9,ORF2,hs4_gibbon,marg,CompleteHit
32708,Q#2385 - >seq9032,non-specific,274009,307,502,0.00854914,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32709,Q#2385 - >seq9032,superfamily,274009,307,502,0.00854914,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA9.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32710,Q#2386 - >seq9033,non-specific,240274,163,394,0.00271775,41.8993,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MA9.ORF2.hs4_gibbon.marg.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA9,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32711,Q#2386 - >seq9033,superfamily,240274,163,394,0.00271775,41.8993,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MA9.ORF2.hs4_gibbon.marg.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MA9,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32712,Q#2388 - >seq9035,specific,197310,9,236,2.1525799999999997e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32713,Q#2388 - >seq9035,superfamily,351117,9,236,2.1525799999999997e-63,214.908,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32714,Q#2388 - >seq9035,non-specific,197306,9,236,7.63836e-35,133.376,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32715,Q#2388 - >seq9035,non-specific,223780,7,229,6.035239999999999e-25,105.37299999999999,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32716,Q#2388 - >seq9035,non-specific,197320,7,229,7.98679e-25,104.905,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32717,Q#2388 - >seq9035,non-specific,197307,9,229,3.2907300000000002e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32718,Q#2388 - >seq9035,specific,335306,10,229,6.42825e-20,89.6117,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32719,Q#2388 - >seq9035,non-specific,197321,7,229,6.053769999999999e-18,84.52600000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32720,Q#2388 - >seq9035,non-specific,272954,7,207,3.0772500000000005e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32721,Q#2388 - >seq9035,non-specific,197319,7,236,2.9289299999999997e-16,79.6281,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32722,Q#2388 - >seq9035,non-specific,273186,7,237,3.9469599999999997e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32723,Q#2388 - >seq9035,non-specific,197336,7,229,1.97551e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32724,Q#2388 - >seq9035,non-specific,236970,9,229,3.3088000000000005e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32725,Q#2388 - >seq9035,non-specific,197311,7,204,1.53625e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32726,Q#2388 - >seq9035,non-specific,339261,108,231,0.00038701400000000003,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32727,Q#2388 - >seq9035,non-specific,197318,9,230,0.00117419,41.8983,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA9.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32728,Q#2390 - >seq9037,non-specific,238827,473,503,4.67339e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32729,Q#2390 - >seq9037,superfamily,295487,473,503,4.67339e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32730,Q#2391 - >seq9038,specific,238827,491,751,1.7842499999999998e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32731,Q#2391 - >seq9038,superfamily,295487,491,751,1.7842499999999998e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32732,Q#2391 - >seq9038,specific,333820,497,751,6.26114e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32733,Q#2391 - >seq9038,superfamily,333820,497,751,6.26114e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32734,Q#2391 - >seq9038,non-specific,238828,497,720,3.40287e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32735,Q#2391 - >seq9038,non-specific,275209,448,790,3.34101e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32736,Q#2391 - >seq9038,superfamily,275209,448,790,3.34101e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32737,Q#2391 - >seq9038,non-specific,235175,291,450,5.57887e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA9,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32738,Q#2391 - >seq9038,superfamily,235175,291,450,5.57887e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA9,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32739,Q#2391 - >seq9038,non-specific,238185,637,717,0.00115552,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32740,Q#2391 - >seq9038,specific,311990,1222,1240,0.00425007,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32741,Q#2391 - >seq9038,superfamily,311990,1222,1240,0.00425007,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs4_gibbon,pars,CompleteHit
32742,Q#2391 - >seq9038,non-specific,274009,291,484,0.00427592,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA9,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32743,Q#2391 - >seq9038,superfamily,274009,291,484,0.00427592,41.2067,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA9.ORF2.hs4_gibbon.pars.frame2,1909181908_L1MA9.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1MA9,ORF2,hs4_gibbon,pars,C-TerminusTruncated
32744,Q#2392 - >seq9039,specific,197310,5,232,2.89519e-45,163.291,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32745,Q#2392 - >seq9039,superfamily,351117,5,232,2.89519e-45,163.291,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32746,Q#2392 - >seq9039,specific,238827,572,764,7.279849999999999e-27,109.68799999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32747,Q#2392 - >seq9039,superfamily,295487,572,764,7.279849999999999e-27,109.68799999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32748,Q#2392 - >seq9039,non-specific,197306,5,232,5.427829999999999e-23,99.0928,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32749,Q#2392 - >seq9039,non-specific,333820,579,743,1.20606e-16,79.2586,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32750,Q#2392 - >seq9039,superfamily,333820,579,743,1.20606e-16,79.2586,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32751,Q#2392 - >seq9039,non-specific,223780,5,225,1.39312e-15,78.0239,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32752,Q#2392 - >seq9039,non-specific,197307,5,232,7.08159e-13,69.6241,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32753,Q#2392 - >seq9039,specific,335306,6,225,8.03973e-12,66.1146,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32754,Q#2392 - >seq9039,non-specific,238828,575,743,1.23939e-11,65.6852,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32755,Q#2392 - >seq9039,non-specific,273186,5,233,1.0286100000000002e-10,63.452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32756,Q#2392 - >seq9039,non-specific,197320,5,217,5.07073e-10,61.376999999999995,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32757,Q#2392 - >seq9039,non-specific,197321,3,232,1.70497e-08,56.7916,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32758,Q#2392 - >seq9039,non-specific,275209,580,730,1.2172700000000002e-07,55.1564,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32759,Q#2392 - >seq9039,superfamily,275209,580,730,1.2172700000000002e-07,55.1564,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32760,Q#2392 - >seq9039,non-specific,339261,104,228,3.49445e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32761,Q#2392 - >seq9039,non-specific,197322,103,232,3.5807800000000004e-06,50.0082,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32762,Q#2392 - >seq9039,non-specific,272954,5,203,3.8177e-06,49.6889,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32763,Q#2392 - >seq9039,non-specific,238185,651,743,0.00678749,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MC1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs4_gibbon,marg,CompleteHit
32764,Q#2393 - >seq9040,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32765,Q#2393 - >seq9040,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32766,Q#2393 - >seq9040,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32767,Q#2393 - >seq9040,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32768,Q#2393 - >seq9040,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32769,Q#2393 - >seq9040,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32770,Q#2393 - >seq9040,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32771,Q#2393 - >seq9040,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32772,Q#2393 - >seq9040,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32773,Q#2393 - >seq9040,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32774,Q#2393 - >seq9040,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32775,Q#2393 - >seq9040,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32776,Q#2393 - >seq9040,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32777,Q#2393 - >seq9040,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32778,Q#2393 - >seq9040,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32779,Q#2393 - >seq9040,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32780,Q#2393 - >seq9040,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32781,Q#2393 - >seq9040,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32782,Q#2393 - >seq9040,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32783,Q#2393 - >seq9040,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32784,Q#2393 - >seq9040,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32785,Q#2393 - >seq9040,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32786,Q#2393 - >seq9040,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32787,Q#2393 - >seq9040,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32788,Q#2393 - >seq9040,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32789,Q#2393 - >seq9040,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32790,Q#2393 - >seq9040,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32791,Q#2393 - >seq9040,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32792,Q#2393 - >seq9040,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32793,Q#2393 - >seq9040,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32794,Q#2393 - >seq9040,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32795,Q#2393 - >seq9040,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32796,Q#2393 - >seq9040,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32797,Q#2393 - >seq9040,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32798,Q#2393 - >seq9040,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32799,Q#2393 - >seq9040,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32800,Q#2393 - >seq9040,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32801,Q#2393 - >seq9040,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32802,Q#2393 - >seq9040,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32803,Q#2393 - >seq9040,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32804,Q#2393 - >seq9040,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32805,Q#2393 - >seq9040,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32806,Q#2393 - >seq9040,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32807,Q#2393 - >seq9040,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32808,Q#2393 - >seq9040,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32809,Q#2393 - >seq9040,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32810,Q#2393 - >seq9040,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32811,Q#2393 - >seq9040,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32812,Q#2393 - >seq9040,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32813,Q#2393 - >seq9040,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32814,Q#2393 - >seq9040,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
32815,Q#2393 - >seq9040,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32816,Q#2393 - >seq9040,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32817,Q#2393 - >seq9040,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32818,Q#2393 - >seq9040,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32819,Q#2393 - >seq9040,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
32820,Q#2393 - >seq9040,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32821,Q#2393 - >seq9040,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32822,Q#2393 - >seq9040,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32823,Q#2393 - >seq9040,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32824,Q#2393 - >seq9040,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,marg,CompleteHit
32825,Q#2393 - >seq9040,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32826,Q#2393 - >seq9040,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32827,Q#2393 - >seq9040,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.marg.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
32828,Q#2396 - >seq9043,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32829,Q#2396 - >seq9043,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32830,Q#2396 - >seq9043,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32831,Q#2396 - >seq9043,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32832,Q#2396 - >seq9043,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32833,Q#2396 - >seq9043,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32834,Q#2396 - >seq9043,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32835,Q#2396 - >seq9043,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32836,Q#2396 - >seq9043,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32837,Q#2396 - >seq9043,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32838,Q#2396 - >seq9043,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32839,Q#2396 - >seq9043,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32840,Q#2396 - >seq9043,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32841,Q#2396 - >seq9043,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32842,Q#2396 - >seq9043,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32843,Q#2396 - >seq9043,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32844,Q#2396 - >seq9043,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32845,Q#2396 - >seq9043,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32846,Q#2396 - >seq9043,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32847,Q#2396 - >seq9043,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32848,Q#2396 - >seq9043,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32849,Q#2396 - >seq9043,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32850,Q#2396 - >seq9043,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32851,Q#2396 - >seq9043,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32852,Q#2396 - >seq9043,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32853,Q#2396 - >seq9043,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32854,Q#2396 - >seq9043,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32855,Q#2396 - >seq9043,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32856,Q#2396 - >seq9043,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32857,Q#2396 - >seq9043,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32858,Q#2396 - >seq9043,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32859,Q#2396 - >seq9043,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32860,Q#2396 - >seq9043,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32861,Q#2396 - >seq9043,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32862,Q#2396 - >seq9043,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32863,Q#2396 - >seq9043,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32864,Q#2396 - >seq9043,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32865,Q#2396 - >seq9043,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32866,Q#2396 - >seq9043,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32867,Q#2396 - >seq9043,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32868,Q#2396 - >seq9043,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32869,Q#2396 - >seq9043,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32870,Q#2396 - >seq9043,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32871,Q#2396 - >seq9043,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32872,Q#2396 - >seq9043,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32873,Q#2396 - >seq9043,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32874,Q#2396 - >seq9043,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32875,Q#2396 - >seq9043,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32876,Q#2396 - >seq9043,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32877,Q#2396 - >seq9043,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32878,Q#2396 - >seq9043,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
32879,Q#2396 - >seq9043,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32880,Q#2396 - >seq9043,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32881,Q#2396 - >seq9043,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32882,Q#2396 - >seq9043,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32883,Q#2396 - >seq9043,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
32884,Q#2396 - >seq9043,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32885,Q#2396 - >seq9043,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32886,Q#2396 - >seq9043,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32887,Q#2396 - >seq9043,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32888,Q#2396 - >seq9043,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs2_gorilla,pars,CompleteHit
32889,Q#2396 - >seq9043,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32890,Q#2396 - >seq9043,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32891,Q#2396 - >seq9043,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs2_gorilla.pars.frame3,1909181908_L1PA3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
32892,Q#2399 - >seq9046,specific,197310,9,236,2.8951999999999992e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32893,Q#2399 - >seq9046,superfamily,351117,9,236,2.8951999999999992e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32894,Q#2399 - >seq9046,non-specific,197306,9,236,6.402519999999999e-47,168.044,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32895,Q#2399 - >seq9046,non-specific,197307,9,236,5.6644e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32896,Q#2399 - >seq9046,non-specific,223780,9,237,3.03223e-23,100.365,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32897,Q#2399 - >seq9046,non-specific,197320,9,229,2.94314e-22,97.2005,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32898,Q#2399 - >seq9046,non-specific,197321,7,236,8.607149999999999e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32899,Q#2399 - >seq9046,specific,335306,10,229,1.0779700000000002e-18,86.1449,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32900,Q#2399 - >seq9046,non-specific,272954,9,236,9.389e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32901,Q#2399 - >seq9046,non-specific,273186,9,237,1.80813e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32902,Q#2399 - >seq9046,non-specific,197319,13,236,2.2403899999999998e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32903,Q#2399 - >seq9046,non-specific,197336,9,229,4.72553e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32904,Q#2399 - >seq9046,non-specific,197322,8,236,1.2813e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32905,Q#2399 - >seq9046,non-specific,236970,9,237,2.69207e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32906,Q#2399 - >seq9046,non-specific,339261,108,232,2.11937e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32907,Q#2399 - >seq9046,non-specific,197311,37,236,7.215030000000001e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32908,Q#2399 - >seq9046,specific,311990,1190,1208,0.00023297599999999997,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32909,Q#2399 - >seq9046,superfamily,311990,1190,1208,0.00023297599999999997,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs4_gibbon.marg.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32910,Q#2400 - >seq9047,specific,238827,483,745,9.138999999999999e-69,229.87,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32911,Q#2400 - >seq9047,superfamily,295487,483,745,9.138999999999999e-69,229.87,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32912,Q#2400 - >seq9047,specific,333820,489,745,4.09274e-36,135.112,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32913,Q#2400 - >seq9047,superfamily,333820,489,745,4.09274e-36,135.112,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32914,Q#2400 - >seq9047,non-specific,238828,489,710,1.84618e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32915,Q#2400 - >seq9047,non-specific,275209,440,773,4.4309e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32916,Q#2400 - >seq9047,superfamily,275209,440,773,4.4309e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32917,Q#2400 - >seq9047,non-specific,238185,629,745,1.2053700000000002e-06,47.7308,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,CompleteHit
32918,Q#2400 - >seq9047,specific,225881,455,712,0.000286328,44.4445,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32919,Q#2400 - >seq9047,superfamily,225881,455,712,0.000286328,44.4445,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.marg.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,marg,N-TerminusTruncated
32920,Q#2402 - >seq9049,non-specific,239242,1091,1156,0.00161257,41.7102,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA13.ORF2.hs4_gibbon.marg.frame1,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32921,Q#2402 - >seq9049,superfamily,355772,1091,1156,0.00161257,41.7102,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA13.ORF2.hs4_gibbon.marg.frame1,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs4_gibbon,marg,BothTerminiTruncated
32922,Q#2403 - >seq9050,specific,238827,482,743,1.2795699999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32923,Q#2403 - >seq9050,superfamily,295487,482,743,1.2795699999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32924,Q#2403 - >seq9050,specific,333820,488,743,5.80853e-35,131.64600000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32925,Q#2403 - >seq9050,superfamily,333820,488,743,5.80853e-35,131.64600000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32926,Q#2403 - >seq9050,non-specific,238828,488,708,2.81126e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32927,Q#2403 - >seq9050,non-specific,275209,439,771,5.36896e-07,52.8452,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32928,Q#2403 - >seq9050,superfamily,275209,439,771,5.36896e-07,52.8452,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32929,Q#2403 - >seq9050,non-specific,238185,627,743,6.47414e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32930,Q#2403 - >seq9050,specific,311990,1209,1227,0.000243595,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32931,Q#2403 - >seq9050,superfamily,311990,1209,1227,0.000243595,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32932,Q#2403 - >seq9050,specific,225881,454,710,0.00603719,40.2073,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32933,Q#2403 - >seq9050,superfamily,225881,454,710,0.00603719,40.2073,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.pars.frame2,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs4_gibbon,pars,N-TerminusTruncated
32934,Q#2405 - >seq9052,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32935,Q#2405 - >seq9052,superfamily,335182,157,254,1.3475099999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32936,Q#2405 - >seq9052,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32937,Q#2405 - >seq9052,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32938,Q#2405 - >seq9052,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32939,Q#2405 - >seq9052,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,marg,CompleteHit
32940,Q#2405 - >seq9052,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,marg,CompleteHit
32941,Q#2405 - >seq9052,superfamily,340204,112,154,9.18373e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,marg,CompleteHit
32942,Q#2405 - >seq9052,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,marg,CompleteHit
32943,Q#2405 - >seq9052,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32944,Q#2405 - >seq9052,superfamily,274009,47,151,0.00016673599999999998,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32945,Q#2405 - >seq9052,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32946,Q#2405 - >seq9052,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32947,Q#2405 - >seq9052,superfamily,274008,47,212,0.00457316,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32948,Q#2405 - >seq9052,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,marg,BothTerminiTruncated
32949,Q#2405 - >seq9052,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,marg,N-TerminusTruncated
32950,Q#2405 - >seq9052,superfamily,313022,4,154,0.00492406,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,marg,N-TerminusTruncated
32951,Q#2405 - >seq9052,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.marg.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,marg,N-TerminusTruncated
32952,Q#2408 - >seq9055,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32953,Q#2408 - >seq9055,superfamily,335182,157,254,1.3475099999999998e-48,158.235,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32954,Q#2408 - >seq9055,non-specific,335182,157,254,1.3475099999999998e-48,158.235,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32955,Q#2408 - >seq9055,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32956,Q#2408 - >seq9055,superfamily,340205,257,321,2.1353099999999998e-33,117.822,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32957,Q#2408 - >seq9055,non-specific,340205,257,321,2.1353099999999998e-33,117.822,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1P2,ORF1,hs0_human,pars,CompleteHit
32958,Q#2408 - >seq9055,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,pars,CompleteHit
32959,Q#2408 - >seq9055,superfamily,340204,112,154,9.18373e-11,56.262,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,pars,CompleteHit
32960,Q#2408 - >seq9055,non-specific,340204,112,154,9.18373e-11,56.262,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1P2,ORF1,hs0_human,pars,CompleteHit
32961,Q#2408 - >seq9055,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32962,Q#2408 - >seq9055,superfamily,274009,47,151,0.00016673599999999998,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32963,Q#2408 - >seq9055,non-specific,274009,47,151,0.00016673599999999998,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32964,Q#2408 - >seq9055,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32965,Q#2408 - >seq9055,superfamily,274008,47,212,0.00457316,38.8843,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32966,Q#2408 - >seq9055,non-specific,274008,47,212,0.00457316,38.8843,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF1,hs0_human,pars,BothTerminiTruncated
32967,Q#2408 - >seq9055,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,pars,N-TerminusTruncated
32968,Q#2408 - >seq9055,superfamily,313022,4,154,0.00492406,38.6762,cl25928,Macoilin superfamily,N, - ,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,pars,N-TerminusTruncated
32969,Q#2408 - >seq9055,non-specific,313022,4,154,0.00492406,38.6762,pfam09726,Macoilin,N,cl25928,"Macoilin family; The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.",L1P2.ORF1.hs0_human.pars.frame3,1909181908_L1P2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Membrane,L1P2,ORF1,hs0_human,pars,N-TerminusTruncated
32970,Q#2411 - >seq9058,specific,197310,9,235,3.8328299999999996e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32971,Q#2411 - >seq9058,superfamily,351117,9,235,3.8328299999999996e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32972,Q#2411 - >seq9058,non-specific,197306,9,235,1.1137600000000002e-47,170.355,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32973,Q#2411 - >seq9058,non-specific,197307,9,235,2.0946700000000002e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32974,Q#2411 - >seq9058,non-specific,223780,9,236,9.642610000000002e-24,101.906,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32975,Q#2411 - >seq9058,non-specific,197320,9,228,5.44053e-23,99.5117,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32976,Q#2411 - >seq9058,non-specific,197321,7,235,1.19125e-20,92.6152,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32977,Q#2411 - >seq9058,specific,335306,10,228,1.35023e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32978,Q#2411 - >seq9058,non-specific,272954,9,235,1.6062299999999999e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32979,Q#2411 - >seq9058,non-specific,273186,9,236,8.63984e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32980,Q#2411 - >seq9058,non-specific,197319,13,235,7.834770000000001e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32981,Q#2411 - >seq9058,non-specific,197336,9,228,3.0059e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32982,Q#2411 - >seq9058,non-specific,236970,9,236,8.26228e-11,63.7598,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32983,Q#2411 - >seq9058,non-specific,197322,8,235,8.400889999999999e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32984,Q#2411 - >seq9058,non-specific,197311,37,235,1.74625e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32985,Q#2411 - >seq9058,non-specific,339261,108,231,3.3165399999999998e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs4_gibbon,pars,CompleteHit
32986,Q#2411 - >seq9058,non-specific,239242,1106,1171,0.00163605,41.7102,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32987,Q#2411 - >seq9058,superfamily,355772,1106,1171,0.00163605,41.7102,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA13.ORF2.hs4_gibbon.pars.frame3,1909181908_L1PA13.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs4_gibbon,pars,BothTerminiTruncated
32988,Q#2413 - >seq9060,specific,238827,510,772,3.39668e-60,205.60299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32989,Q#2413 - >seq9060,superfamily,295487,510,772,3.39668e-60,205.60299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32990,Q#2413 - >seq9060,specific,333820,516,772,1.95507e-28,113.156,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32991,Q#2413 - >seq9060,superfamily,333820,516,772,1.95507e-28,113.156,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32992,Q#2413 - >seq9060,specific,197310,9,237,1.6019699999999999e-27,112.06,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32993,Q#2413 - >seq9060,superfamily,351117,9,237,1.6019699999999999e-27,112.06,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32994,Q#2413 - >seq9060,non-specific,197306,9,237,1.20802e-13,71.7437,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32995,Q#2413 - >seq9060,specific,335306,10,193,4.81318e-11,63.8034,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32996,Q#2413 - >seq9060,non-specific,238828,516,737,5.3695800000000005e-06,48.7364,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
32997,Q#2413 - >seq9060,non-specific,223780,7,43,1.53344e-05,47.9783,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32998,Q#2413 - >seq9060,non-specific,197320,7,43,0.000132127,44.8134,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
32999,Q#2413 - >seq9060,non-specific,197321,7,43,0.00017529,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
33000,Q#2413 - >seq9060,non-specific,272954,7,53,0.00028268,43.9109,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
33001,Q#2413 - >seq9060,non-specific,275209,467,791,0.00033171199999999996,44.3708,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
33002,Q#2413 - >seq9060,superfamily,275209,467,791,0.00033171199999999996,44.3708,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
33003,Q#2413 - >seq9060,non-specific,197336,7,43,0.0007085430000000001,42.5995,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
33004,Q#2413 - >seq9060,non-specific,197307,9,43,0.000774548,42.6601,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
33005,Q#2413 - >seq9060,non-specific,273186,7,53,0.00135926,41.8808,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,C-TerminusTruncated
33006,Q#2413 - >seq9060,specific,311990,1240,1258,0.00357802,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
33007,Q#2413 - >seq9060,superfamily,311990,1240,1258,0.00357802,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA3,ORF2,hs4_gibbon,marg,CompleteHit
33008,Q#2413 - >seq9060,non-specific,334125,213,410,0.0073338000000000006,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33009,Q#2413 - >seq9060,superfamily,334125,213,410,0.0073338000000000006,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33010,Q#2415 - >seq9062,specific,197310,9,236,3.5188399999999998e-65,220.301,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33011,Q#2415 - >seq9062,superfamily,351117,9,236,3.5188399999999998e-65,220.301,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33012,Q#2415 - >seq9062,specific,238827,504,766,5.6017299999999986e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33013,Q#2415 - >seq9062,superfamily,295487,504,766,5.6017299999999986e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33014,Q#2415 - >seq9062,non-specific,197306,9,236,1.705e-34,132.605,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33015,Q#2415 - >seq9062,specific,333820,510,766,6.507809999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33016,Q#2415 - >seq9062,superfamily,333820,510,766,6.507809999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33017,Q#2415 - >seq9062,non-specific,197307,9,236,1.92769e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33018,Q#2415 - >seq9062,non-specific,197320,7,229,1.1056999999999998e-22,98.7413,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33019,Q#2415 - >seq9062,non-specific,223780,7,229,1.37458e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33020,Q#2415 - >seq9062,specific,335306,10,229,4.437699999999999e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33021,Q#2415 - >seq9062,non-specific,273186,7,237,1.3456999999999999e-16,80.786,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33022,Q#2415 - >seq9062,non-specific,197321,7,236,1.55429e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33023,Q#2415 - >seq9062,non-specific,272954,7,236,1.16655e-15,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33024,Q#2415 - >seq9062,non-specific,197319,7,236,3.8498e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33025,Q#2415 - >seq9062,non-specific,238828,510,731,9.9363e-12,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33026,Q#2415 - >seq9062,non-specific,275209,447,785,2.0049599999999997e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33027,Q#2415 - >seq9062,superfamily,275209,447,785,2.0049599999999997e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33028,Q#2415 - >seq9062,non-specific,197336,7,194,3.0437799999999997e-10,61.8595,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33029,Q#2415 - >seq9062,non-specific,236970,9,229,1.20716e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33030,Q#2415 - >seq9062,non-specific,197322,8,236,3.00043e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33031,Q#2415 - >seq9062,non-specific,197318,9,236,1.52208e-06,50.7579,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33032,Q#2415 - >seq9062,non-specific,197311,7,236,3.7588800000000004e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33033,Q#2415 - >seq9062,non-specific,238185,650,766,0.000170971,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33034,Q#2415 - >seq9062,non-specific,339261,108,232,0.00165698,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33035,Q#2415 - >seq9062,specific,311990,1233,1251,0.00412209,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33036,Q#2415 - >seq9062,superfamily,311990,1233,1251,0.00412209,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs2_gorilla,marg,CompleteHit
33037,Q#2415 - >seq9062,non-specific,223496,281,457,0.00554186,40.8991,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
33038,Q#2415 - >seq9062,superfamily,223496,281,457,0.00554186,40.8991,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.marg.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
33039,Q#2418 - >seq9065,specific,238827,601,718,6.50307e-30,118.54799999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33040,Q#2418 - >seq9065,superfamily,295487,601,718,6.50307e-30,118.54799999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33041,Q#2418 - >seq9065,non-specific,333820,583,718,4.1827300000000003e-14,71.5546,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33042,Q#2418 - >seq9065,superfamily,333820,583,718,4.1827300000000003e-14,71.5546,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33043,Q#2418 - >seq9065,non-specific,238828,562,683,3.65318e-07,52.2032,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33044,Q#2418 - >seq9065,non-specific,238185,602,718,7.30227e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33045,Q#2418 - >seq9065,non-specific,275209,554,737,0.00206866,41.6744,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33046,Q#2418 - >seq9065,superfamily,275209,554,737,0.00206866,41.6744,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs2_gorilla.pars.frame3,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33047,Q#2419 - >seq9066,specific,311990,1121,1139,0.00076177,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33048,Q#2419 - >seq9066,superfamily,311990,1121,1139,0.00076177,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs2_gorilla.pars.frame2,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33049,Q#2420 - >seq9067,specific,197310,8,235,4.2492699999999996e-64,217.21900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33050,Q#2420 - >seq9067,superfamily,351117,8,235,4.2492699999999996e-64,217.21900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33051,Q#2420 - >seq9067,non-specific,197306,8,235,5.07246e-34,131.064,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33052,Q#2420 - >seq9067,specific,238827,503,600,3.8065399999999996e-29,116.23700000000001,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33053,Q#2420 - >seq9067,superfamily,295487,503,600,3.8065399999999996e-29,116.23700000000001,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33054,Q#2420 - >seq9067,non-specific,197307,8,235,1.07257e-23,101.596,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33055,Q#2420 - >seq9067,non-specific,223780,6,228,4.413859999999999e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33056,Q#2420 - >seq9067,non-specific,197320,6,228,6.900879999999999e-23,99.1265,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33057,Q#2420 - >seq9067,specific,335306,9,228,4.29417e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33058,Q#2420 - >seq9067,non-specific,273186,6,236,1.0377299999999999e-16,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33059,Q#2420 - >seq9067,non-specific,197321,6,235,1.57549e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33060,Q#2420 - >seq9067,non-specific,272954,6,235,7.45613e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33061,Q#2420 - >seq9067,non-specific,197319,6,235,1.84173e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33062,Q#2420 - >seq9067,non-specific,333820,509,620,4.49138e-11,63.0802,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33063,Q#2420 - >seq9067,superfamily,333820,509,620,4.49138e-11,63.0802,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33064,Q#2420 - >seq9067,non-specific,197336,6,193,2.94438e-10,61.8595,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33065,Q#2420 - >seq9067,non-specific,236970,8,228,1.10573e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33066,Q#2420 - >seq9067,non-specific,197322,7,235,2.90135e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33067,Q#2420 - >seq9067,non-specific,197318,8,235,2.52558e-06,49.9875,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33068,Q#2420 - >seq9067,non-specific,197311,6,235,3.6405699999999995e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33069,Q#2420 - >seq9067,non-specific,223496,280,456,0.0017664999999999998,42.4399,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33070,Q#2420 - >seq9067,superfamily,223496,280,456,0.0017664999999999998,42.4399,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1MA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33071,Q#2420 - >seq9067,non-specific,223496,318,499,0.00492661,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1MA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33072,Q#2420 - >seq9067,non-specific,339261,107,231,0.00552535,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1MA4,ORF2,hs2_gorilla,pars,CompleteHit
33073,Q#2420 - >seq9067,non-specific,235175,292,462,0.00714843,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33074,Q#2420 - >seq9067,superfamily,235175,292,462,0.00714843,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4.ORF2.hs2_gorilla.pars.frame1,1909181908_L1MA4.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1MA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33075,Q#2421 - >seq9068,specific,238827,504,765,4.027549999999999e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33076,Q#2421 - >seq9068,superfamily,295487,504,765,4.027549999999999e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33077,Q#2421 - >seq9068,specific,197310,9,235,4.6932599999999993e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33078,Q#2421 - >seq9068,superfamily,351117,9,235,4.6932599999999993e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33079,Q#2421 - >seq9068,specific,333820,510,765,5.9377799999999995e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33080,Q#2421 - >seq9068,superfamily,333820,510,765,5.9377799999999995e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33081,Q#2421 - >seq9068,non-specific,197306,9,235,2.1337200000000002e-30,120.664,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33082,Q#2421 - >seq9068,non-specific,197320,7,228,5.0583e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33083,Q#2421 - >seq9068,non-specific,197307,9,235,9.820610000000001e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33084,Q#2421 - >seq9068,non-specific,223780,7,228,2.2164e-18,86.1131,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33085,Q#2421 - >seq9068,specific,335306,10,228,3.08036e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33086,Q#2421 - >seq9068,non-specific,197321,7,235,5.70164e-14,72.97,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33087,Q#2421 - >seq9068,non-specific,273186,7,236,5.16503e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33088,Q#2421 - >seq9068,non-specific,272954,7,235,2.53237e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33089,Q#2421 - >seq9068,non-specific,197319,7,235,1.5306299999999999e-10,62.6793,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33090,Q#2421 - >seq9068,non-specific,238828,510,730,4.44721e-10,61.0628,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33091,Q#2421 - >seq9068,non-specific,275209,447,784,2.0868400000000002e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33092,Q#2421 - >seq9068,superfamily,275209,447,784,2.0868400000000002e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33093,Q#2421 - >seq9068,non-specific,197311,7,235,7.01148e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33094,Q#2421 - >seq9068,non-specific,197336,7,228,9.68624e-06,48.3775,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33095,Q#2421 - >seq9068,non-specific,197318,9,235,0.000144754,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33096,Q#2421 - >seq9068,non-specific,339261,107,231,0.00208882,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33097,Q#2421 - >seq9068,specific,311990,1233,1251,0.00412209,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33098,Q#2421 - >seq9068,superfamily,311990,1233,1251,0.00412209,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33099,Q#2421 - >seq9068,non-specific,238185,649,765,0.00735292,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs1_chimp.marg.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,marg,CompleteHit
33100,Q#2423 - >seq9070,specific,238827,502,763,1.1626699999999999e-64,218.31400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33101,Q#2423 - >seq9070,superfamily,295487,502,763,1.1626699999999999e-64,218.31400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33102,Q#2423 - >seq9070,specific,197310,9,235,1.9583699999999996e-59,204.122,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33103,Q#2423 - >seq9070,superfamily,351117,9,235,1.9583699999999996e-59,204.122,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33104,Q#2423 - >seq9070,specific,333820,508,763,2.8199499999999998e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33105,Q#2423 - >seq9070,superfamily,333820,508,763,2.8199499999999998e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33106,Q#2423 - >seq9070,non-specific,197306,9,235,2.8640399999999998e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33107,Q#2423 - >seq9070,non-specific,197320,7,228,3.5160199999999995e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33108,Q#2423 - >seq9070,non-specific,197307,9,235,3.65486e-19,88.1137,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33109,Q#2423 - >seq9070,non-specific,223780,7,228,5.66803e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33110,Q#2423 - >seq9070,specific,335306,10,228,2.98638e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33111,Q#2423 - >seq9070,non-specific,197321,7,235,1.7922900000000003e-14,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33112,Q#2423 - >seq9070,non-specific,273186,7,236,2.3908000000000003e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33113,Q#2423 - >seq9070,non-specific,272954,7,235,1.0206200000000001e-12,69.3341,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33114,Q#2423 - >seq9070,non-specific,197319,7,235,3.85719e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33115,Q#2423 - >seq9070,non-specific,238828,508,728,2.48142e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33116,Q#2423 - >seq9070,non-specific,275209,445,782,1.2947899999999998e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33117,Q#2423 - >seq9070,superfamily,275209,445,782,1.2947899999999998e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33118,Q#2423 - >seq9070,non-specific,197311,7,235,6.80323e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33119,Q#2423 - >seq9070,non-specific,197336,7,228,9.39259e-06,48.3775,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33120,Q#2423 - >seq9070,non-specific,197318,9,235,0.00021664099999999997,44.2095,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33121,Q#2423 - >seq9070,non-specific,238185,647,763,0.00312269,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33122,Q#2423 - >seq9070,non-specific,339261,107,231,0.00414452,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs1_chimp,pars,CompleteHit
33123,Q#2423 - >seq9070,non-specific,274009,303,450,0.00567601,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
33124,Q#2423 - >seq9070,superfamily,274009,303,450,0.00567601,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MA4.ORF2.hs1_chimp.pars.frame3,1909181908_L1MA4.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
33125,Q#2426 - >seq9073,specific,238827,501,763,1.69517e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33126,Q#2426 - >seq9073,superfamily,295487,501,763,1.69517e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33127,Q#2426 - >seq9073,specific,197310,3,231,7.62981e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33128,Q#2426 - >seq9073,superfamily,351117,3,231,7.62981e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33129,Q#2426 - >seq9073,non-specific,197306,3,231,2.74447e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33130,Q#2426 - >seq9073,specific,333820,507,763,1.9689599999999998e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33131,Q#2426 - >seq9073,superfamily,333820,507,763,1.9689599999999998e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33132,Q#2426 - >seq9073,non-specific,197320,1,224,1.4843e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33133,Q#2426 - >seq9073,non-specific,223780,1,224,3.96064e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33134,Q#2426 - >seq9073,specific,335306,4,224,4.0799299999999997e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33135,Q#2426 - >seq9073,non-specific,197307,3,224,1.1623800000000001e-17,83.8765,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33136,Q#2426 - >seq9073,non-specific,197321,1,224,2.01658e-14,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33137,Q#2426 - >seq9073,non-specific,272954,1,202,5.80779e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33138,Q#2426 - >seq9073,non-specific,273186,1,232,2.25121e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33139,Q#2426 - >seq9073,non-specific,197319,1,231,5.802080000000001e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33140,Q#2426 - >seq9073,non-specific,238828,567,738,2.08468e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,N-TerminusTruncated
33141,Q#2426 - >seq9073,non-specific,197336,1,224,1.25295e-07,54.1555,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33142,Q#2426 - >seq9073,non-specific,197311,32,199,1.7445799999999999e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33143,Q#2426 - >seq9073,non-specific,275209,578,787,2.7175099999999997e-06,50.9192,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,N-TerminusTruncated
33144,Q#2426 - >seq9073,superfamily,275209,578,787,2.7175099999999997e-06,50.9192,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,N-TerminusTruncated
33145,Q#2426 - >seq9073,non-specific,238185,647,763,0.000880438,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs3_orang.marg.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33146,Q#2428 - >seq9075,non-specific,197310,84,216,4.572680000000001e-18,84.7105,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33147,Q#2428 - >seq9075,superfamily,351117,84,216,4.572680000000001e-18,84.7105,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33148,Q#2428 - >seq9075,non-specific,197306,84,208,2.3001000000000002e-08,55.9505,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33149,Q#2428 - >seq9075,non-specific,197320,96,195,2.5546100000000003e-05,47.1246,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33150,Q#2428 - >seq9075,non-specific,197307,96,195,0.00146515,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA3,ORF2,hs4_gibbon,marg,N-TerminusTruncated
33151,Q#2429 - >seq9076,specific,238827,510,772,3.39668e-60,205.60299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33152,Q#2429 - >seq9076,superfamily,295487,510,772,3.39668e-60,205.60299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33153,Q#2429 - >seq9076,specific,333820,516,772,1.95507e-28,113.156,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33154,Q#2429 - >seq9076,superfamily,333820,516,772,1.95507e-28,113.156,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33155,Q#2429 - >seq9076,specific,197310,9,237,1.6019699999999999e-27,112.06,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33156,Q#2429 - >seq9076,superfamily,351117,9,237,1.6019699999999999e-27,112.06,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33157,Q#2429 - >seq9076,non-specific,197306,9,237,1.20802e-13,71.7437,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33158,Q#2429 - >seq9076,specific,335306,10,193,4.81318e-11,63.8034,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33159,Q#2429 - >seq9076,non-specific,238828,516,737,5.3695800000000005e-06,48.7364,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33160,Q#2429 - >seq9076,non-specific,223780,7,43,1.53344e-05,47.9783,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33161,Q#2429 - >seq9076,non-specific,197320,7,43,0.000132127,44.8134,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33162,Q#2429 - >seq9076,non-specific,197321,7,43,0.00017529,44.4652,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33163,Q#2429 - >seq9076,non-specific,272954,7,53,0.00028268,43.9109,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33164,Q#2429 - >seq9076,non-specific,275209,467,791,0.00033171199999999996,44.3708,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33165,Q#2429 - >seq9076,superfamily,275209,467,791,0.00033171199999999996,44.3708,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33166,Q#2429 - >seq9076,non-specific,197336,7,43,0.0007085430000000001,42.5995,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33167,Q#2429 - >seq9076,non-specific,197307,9,43,0.000774548,42.6601,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33168,Q#2429 - >seq9076,non-specific,273186,7,53,0.00135926,41.8808,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,C-TerminusTruncated
33169,Q#2429 - >seq9076,specific,311990,1240,1258,0.00357802,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33170,Q#2429 - >seq9076,superfamily,311990,1240,1258,0.00357802,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1MA3,ORF2,hs4_gibbon,pars,CompleteHit
33171,Q#2429 - >seq9076,non-specific,334125,213,410,0.0073338000000000006,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33172,Q#2429 - >seq9076,superfamily,334125,213,410,0.0073338000000000006,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1MA3.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33173,Q#2431 - >seq9078,non-specific,197310,84,216,4.572680000000001e-18,84.7105,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA3.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33174,Q#2431 - >seq9078,superfamily,351117,84,216,4.572680000000001e-18,84.7105,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33175,Q#2431 - >seq9078,non-specific,197306,84,208,2.3001000000000002e-08,55.9505,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA3.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33176,Q#2431 - >seq9078,non-specific,197320,96,195,2.5546100000000003e-05,47.1246,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33177,Q#2431 - >seq9078,non-specific,197307,96,195,0.00146515,41.5045,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA3.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA3.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1MA3,ORF2,hs4_gibbon,pars,N-TerminusTruncated
33178,Q#2432 - >seq9079,specific,311990,1107,1125,0.0011028,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33179,Q#2432 - >seq9079,superfamily,311990,1107,1125,0.0011028,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs4_gibbon.pars.frame1,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33180,Q#2435 - >seq9082,specific,311990,1112,1130,0.00110757,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33181,Q#2435 - >seq9082,superfamily,311990,1112,1130,0.00110757,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs4_gibbon.marg.frame1,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33182,Q#2436 - >seq9083,specific,197310,9,236,4.34222e-65,220.301,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33183,Q#2436 - >seq9083,superfamily,351117,9,236,4.34222e-65,220.301,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33184,Q#2436 - >seq9083,specific,238827,508,770,6.047459999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33185,Q#2436 - >seq9083,superfamily,295487,508,770,6.047459999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33186,Q#2436 - >seq9083,non-specific,197306,9,236,1.87794e-33,129.524,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33187,Q#2436 - >seq9083,specific,333820,514,770,7.83899e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33188,Q#2436 - >seq9083,superfamily,333820,514,770,7.83899e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33189,Q#2436 - >seq9083,non-specific,197320,7,229,1.66134e-22,97.9709,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33190,Q#2436 - >seq9083,non-specific,223780,7,229,2.33512e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33191,Q#2436 - >seq9083,non-specific,197307,9,236,1.5464600000000002e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33192,Q#2436 - >seq9083,specific,335306,10,229,1.03867e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33193,Q#2436 - >seq9083,non-specific,197321,7,236,1.61107e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33194,Q#2436 - >seq9083,non-specific,272954,7,236,1.4321199999999999e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33195,Q#2436 - >seq9083,non-specific,273186,7,237,4.93784e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33196,Q#2436 - >seq9083,non-specific,197319,7,236,5.59211e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33197,Q#2436 - >seq9083,non-specific,238828,514,735,1.63276e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33198,Q#2436 - >seq9083,non-specific,275209,451,788,3.4378e-11,66.3272,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33199,Q#2436 - >seq9083,superfamily,275209,451,788,3.4378e-11,66.3272,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33200,Q#2436 - >seq9083,non-specific,197336,7,229,3.0388899999999996e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33201,Q#2436 - >seq9083,non-specific,236970,9,229,6.1283e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33202,Q#2436 - >seq9083,non-specific,197311,7,236,5.34442e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33203,Q#2436 - >seq9083,non-specific,197318,9,236,1.2951199999999999e-05,48.0615,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33204,Q#2436 - >seq9083,non-specific,238185,654,770,0.000708212,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33205,Q#2436 - >seq9083,specific,225881,481,678,0.0010720999999999999,42.5185,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
33206,Q#2436 - >seq9083,superfamily,225881,481,678,0.0010720999999999999,42.5185,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
33207,Q#2436 - >seq9083,non-specific,139971,7,236,0.00147814,41.6032,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33208,Q#2436 - >seq9083,non-specific,339261,108,232,0.00781578,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs4_gibbon.pars.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs4_gibbon,pars,CompleteHit
33209,Q#2437 - >seq9084,specific,311990,1120,1138,0.00175311,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs3_orang.marg.frame1,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33210,Q#2437 - >seq9084,superfamily,311990,1120,1138,0.00175311,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs3_orang.marg.frame1,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs3_orang,marg,CompleteHit
33211,Q#2438 - >seq9085,specific,238827,503,766,1.6448699999999996e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33212,Q#2438 - >seq9085,superfamily,295487,503,766,1.6448699999999996e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33213,Q#2438 - >seq9085,specific,197310,5,233,3.6964399999999995e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33214,Q#2438 - >seq9085,superfamily,351117,5,233,3.6964399999999995e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33215,Q#2438 - >seq9085,non-specific,197306,5,233,3.44821e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33216,Q#2438 - >seq9085,specific,333820,509,766,2.52812e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33217,Q#2438 - >seq9085,superfamily,333820,509,766,2.52812e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33218,Q#2438 - >seq9085,non-specific,197320,3,226,8.780700000000001e-22,96.0449,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33219,Q#2438 - >seq9085,non-specific,223780,3,226,2.2579499999999998e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33220,Q#2438 - >seq9085,specific,335306,6,226,3.99578e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33221,Q#2438 - >seq9085,non-specific,197307,5,226,8.408500000000001e-18,84.2617,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33222,Q#2438 - >seq9085,non-specific,197321,3,226,1.9014700000000002e-14,74.5108,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33223,Q#2438 - >seq9085,non-specific,272954,3,204,5.1289199999999994e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33224,Q#2438 - >seq9085,non-specific,273186,3,234,2.18344e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33225,Q#2438 - >seq9085,non-specific,197319,3,233,3.91191e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33226,Q#2438 - >seq9085,non-specific,238828,569,741,4.3501099999999996e-09,57.9812,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,N-TerminusTruncated
33227,Q#2438 - >seq9085,non-specific,197311,34,201,1.1111e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33228,Q#2438 - >seq9085,non-specific,197336,3,226,1.22708e-07,54.1555,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33229,Q#2438 - >seq9085,non-specific,275209,580,790,8.91982e-06,48.9932,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,N-TerminusTruncated
33230,Q#2438 - >seq9085,superfamily,275209,580,790,8.91982e-06,48.9932,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,N-TerminusTruncated
33231,Q#2438 - >seq9085,non-specific,238185,649,766,3.6731e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33232,Q#2438 - >seq9085,non-specific,235175,304,462,0.00271076,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA9,ORF2,hs3_orang,pars,BothTerminiTruncated
33233,Q#2438 - >seq9085,superfamily,235175,304,462,0.00271076,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA9,ORF2,hs3_orang,pars,BothTerminiTruncated
33234,Q#2438 - >seq9085,non-specific,223496,304,499,0.00725295,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA9,ORF2,hs3_orang,pars,BothTerminiTruncated
33235,Q#2438 - >seq9085,superfamily,223496,304,499,0.00725295,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs3_orang.pars.frame3,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA9,ORF2,hs3_orang,pars,BothTerminiTruncated
33236,Q#2439 - >seq9086,specific,311990,1151,1169,0.000321012,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs3_orang.pars.frame2,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33237,Q#2439 - >seq9086,superfamily,311990,1151,1169,0.000321012,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs3_orang.pars.frame2,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs3_orang,pars,CompleteHit
33238,Q#2439 - >seq9086,non-specific,273727,299,429,0.00750406,40.2618,TIGR01642,U2AF_lg,C,cl36941,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA9.ORF2.hs3_orang.pars.frame2,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA9,ORF2,hs3_orang,pars,C-TerminusTruncated
33239,Q#2439 - >seq9086,superfamily,273727,299,429,0.00750406,40.2618,cl36941,U2AF_lg superfamily,C, - ,"U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.",L1MA9.ORF2.hs3_orang.pars.frame2,1909181908_L1MA9.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1MA9,ORF2,hs3_orang,pars,C-TerminusTruncated
33240,Q#2442 - >seq9089,specific,311990,1113,1131,0.00100769,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs0_human.marg.frame2,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4,ORF2,hs0_human,marg,CompleteHit
33241,Q#2442 - >seq9089,superfamily,311990,1113,1131,0.00100769,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs0_human.marg.frame2,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1MA4,ORF2,hs0_human,marg,CompleteHit
33242,Q#2443 - >seq9090,specific,238827,512,756,8.735230000000001e-58,198.669,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,CompleteHit
33243,Q#2443 - >seq9090,superfamily,295487,512,756,8.735230000000001e-58,198.669,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,CompleteHit
33244,Q#2443 - >seq9090,specific,197310,22,224,1.51632e-39,146.72799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs0_human,pars,CompleteHit
33245,Q#2443 - >seq9090,superfamily,351117,22,224,1.51632e-39,146.72799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,pars,CompleteHit
33246,Q#2443 - >seq9090,specific,333820,512,756,4.42775e-29,115.08200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,CompleteHit
33247,Q#2443 - >seq9090,superfamily,333820,512,756,4.42775e-29,115.08200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,CompleteHit
33248,Q#2443 - >seq9090,non-specific,197306,60,224,5.78973e-17,81.7588,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33249,Q#2443 - >seq9090,non-specific,197320,96,217,4.86376e-11,64.4586,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33250,Q#2443 - >seq9090,non-specific,238828,566,721,4.689080000000001e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33251,Q#2443 - >seq9090,non-specific,223780,60,217,1.3042899999999998e-09,60.3047,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33252,Q#2443 - >seq9090,non-specific,197307,60,224,6.57551e-09,58.0681,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33253,Q#2443 - >seq9090,specific,335306,60,217,6.28619e-08,54.5586,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33254,Q#2443 - >seq9090,non-specific,275209,571,775,1.26425e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33255,Q#2443 - >seq9090,superfamily,275209,571,775,1.26425e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33256,Q#2443 - >seq9090,non-specific,273186,22,225,2.12347e-07,53.4368,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs0_human,pars,CompleteHit
33257,Q#2443 - >seq9090,non-specific,197319,96,224,1.0898700000000002e-06,51.1233,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33258,Q#2443 - >seq9090,non-specific,272954,22,224,6.109960000000001e-05,45.8369,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs0_human,pars,CompleteHit
33259,Q#2443 - >seq9090,non-specific,238185,640,756,0.000110067,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs0_human,pars,CompleteHit
33260,Q#2443 - >seq9090,non-specific,197321,96,224,0.000240075,44.08,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs0_human,pars,N-TerminusTruncated
33261,Q#2443 - >seq9090,non-specific,235175,279,453,0.00964903,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4,ORF2,hs0_human,pars,BothTerminiTruncated
33262,Q#2443 - >seq9090,superfamily,235175,279,453,0.00964903,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA4.ORF2.hs0_human.pars.frame3,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA4,ORF2,hs0_human,pars,BothTerminiTruncated
33263,Q#2445 - >seq9092,specific,238827,518,762,7.06833e-58,199.054,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,CompleteHit
33264,Q#2445 - >seq9092,superfamily,295487,518,762,7.06833e-58,199.054,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,CompleteHit
33265,Q#2445 - >seq9092,specific,197310,5,229,2.6403e-49,174.847,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33266,Q#2445 - >seq9092,superfamily,351117,5,229,2.6403e-49,174.847,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33267,Q#2445 - >seq9092,specific,333820,518,762,3.31203e-29,115.46700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,CompleteHit
33268,Q#2445 - >seq9092,superfamily,333820,518,762,3.31203e-29,115.46700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,CompleteHit
33269,Q#2445 - >seq9092,non-specific,197306,5,229,4.63526e-25,105.256,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33270,Q#2445 - >seq9092,non-specific,223780,3,222,1.95852e-16,80.3351,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33271,Q#2445 - >seq9092,non-specific,197320,3,222,5.46525e-15,76.0145,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33272,Q#2445 - >seq9092,non-specific,197307,5,229,4.68838e-14,73.0909,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33273,Q#2445 - >seq9092,non-specific,273186,3,230,2.96421e-13,70.7708,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33274,Q#2445 - >seq9092,specific,335306,6,222,2.24595e-11,64.959,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33275,Q#2445 - >seq9092,non-specific,272954,3,229,4.82327e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33276,Q#2445 - >seq9092,non-specific,238828,572,727,4.2286600000000003e-10,61.0628,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,N-TerminusTruncated
33277,Q#2445 - >seq9092,non-specific,197321,3,229,1.4830899999999999e-09,59.8732,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33278,Q#2445 - >seq9092,non-specific,197319,3,229,7.55875e-09,57.6717,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33279,Q#2445 - >seq9092,non-specific,275209,577,781,1.23194e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,N-TerminusTruncated
33280,Q#2445 - >seq9092,superfamily,275209,577,781,1.23194e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,N-TerminusTruncated
33281,Q#2445 - >seq9092,non-specific,238185,646,762,0.00010883899999999999,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1MA4,ORF2,hs0_human,marg,CompleteHit
33282,Q#2445 - >seq9092,non-specific,197322,101,229,0.00173561,41.919,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,N-TerminusTruncated
33283,Q#2445 - >seq9092,non-specific,197336,3,222,0.00259556,41.0587,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs0_human.marg.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1MA4,ORF2,hs0_human,marg,CompleteHit
33284,Q#2446 - >seq9093,specific,311990,1115,1133,0.000895167,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs0_human.pars.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs0_human,pars,CompleteHit
33285,Q#2446 - >seq9093,superfamily,311990,1115,1133,0.000895167,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs0_human.pars.frame1,1909181908_L1MA4.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs0_human,pars,CompleteHit
33286,Q#2447 - >seq9094,specific,238827,506,767,1.32001e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33287,Q#2447 - >seq9094,superfamily,295487,506,767,1.32001e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33288,Q#2447 - >seq9094,specific,197310,9,235,1.7376500000000001e-53,186.78799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33289,Q#2447 - >seq9094,superfamily,351117,9,235,1.7376500000000001e-53,186.78799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33290,Q#2447 - >seq9094,specific,333820,512,767,2.6141400000000004e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33291,Q#2447 - >seq9094,superfamily,333820,512,767,2.6141400000000004e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33292,Q#2447 - >seq9094,non-specific,197306,9,235,8.84338e-27,110.264,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33293,Q#2447 - >seq9094,non-specific,223780,7,228,4.51658e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33294,Q#2447 - >seq9094,non-specific,197307,9,235,8.06883e-18,84.2617,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33295,Q#2447 - >seq9094,non-specific,197320,7,228,1.51522e-17,83.7185,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33296,Q#2447 - >seq9094,non-specific,273186,7,236,4.11105e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33297,Q#2447 - >seq9094,non-specific,197321,7,235,8.73551e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33298,Q#2447 - >seq9094,non-specific,238828,512,732,6.66545e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33299,Q#2447 - >seq9094,non-specific,197319,7,235,7.21577e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33300,Q#2447 - >seq9094,non-specific,272954,7,235,2.20917e-11,65.4821,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33301,Q#2447 - >seq9094,non-specific,275209,449,786,2.57757e-11,66.7124,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33302,Q#2447 - >seq9094,superfamily,275209,449,786,2.57757e-11,66.7124,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33303,Q#2447 - >seq9094,specific,335306,10,228,5.33281e-11,63.8034,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33304,Q#2447 - >seq9094,non-specific,197336,7,228,1.7789599999999998e-06,50.6887,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33305,Q#2447 - >seq9094,non-specific,236970,9,228,1.40727e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33306,Q#2447 - >seq9094,non-specific,339261,107,231,6.23499e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33307,Q#2447 - >seq9094,non-specific,197311,46,235,6.9045e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33308,Q#2447 - >seq9094,non-specific,197322,8,235,0.000476927,43.4598,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33309,Q#2447 - >seq9094,non-specific,238185,651,767,0.00118327,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33310,Q#2447 - >seq9094,non-specific,223496,318,496,0.00428456,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
33311,Q#2447 - >seq9094,superfamily,223496,318,496,0.00428456,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1MA4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
33312,Q#2447 - >seq9094,specific,311990,1237,1255,0.004435499999999999,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33313,Q#2447 - >seq9094,superfamily,311990,1237,1255,0.004435499999999999,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs5_gmonkey.marg.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1MA4,ORF2,hs5_gmonkey,marg,CompleteHit
33314,Q#2450 - >seq9097,specific,238827,504,762,2.5621199999999997e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33315,Q#2450 - >seq9097,superfamily,295487,504,762,2.5621199999999997e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33316,Q#2450 - >seq9097,specific,197310,9,235,8.66002e-53,184.862,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33317,Q#2450 - >seq9097,superfamily,351117,9,235,8.66002e-53,184.862,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33318,Q#2450 - >seq9097,specific,333820,510,762,1.04539e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33319,Q#2450 - >seq9097,superfamily,333820,510,762,1.04539e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33320,Q#2450 - >seq9097,non-specific,197306,9,235,2.08132e-26,109.10799999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33321,Q#2450 - >seq9097,non-specific,223780,7,228,3.2576599999999997e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33322,Q#2450 - >seq9097,non-specific,197307,9,235,6.8346600000000006e-18,84.6469,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33323,Q#2450 - >seq9097,non-specific,197320,7,228,1.49305e-17,83.7185,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33324,Q#2450 - >seq9097,non-specific,273186,7,236,4.32528e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33325,Q#2450 - >seq9097,non-specific,197321,7,235,8.60867e-13,69.5032,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33326,Q#2450 - >seq9097,non-specific,197319,7,235,6.7244399999999996e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33327,Q#2450 - >seq9097,non-specific,272954,7,235,1.79091e-11,65.4821,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33328,Q#2450 - >seq9097,specific,335306,10,228,5.25718e-11,63.8034,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33329,Q#2450 - >seq9097,non-specific,238828,572,727,6.03967e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33330,Q#2450 - >seq9097,non-specific,275209,577,781,9.94468e-09,58.6232,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33331,Q#2450 - >seq9097,superfamily,275209,577,781,9.94468e-09,58.6232,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33332,Q#2450 - >seq9097,non-specific,197336,7,228,1.75362e-06,50.6887,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33333,Q#2450 - >seq9097,non-specific,236970,9,228,1.3747799999999999e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33334,Q#2450 - >seq9097,non-specific,197311,46,235,6.8088e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33335,Q#2450 - >seq9097,non-specific,339261,107,231,0.000145468,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33336,Q#2450 - >seq9097,non-specific,197322,8,235,0.00047014400000000003,43.4598,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33337,Q#2450 - >seq9097,non-specific,238185,646,762,0.000663596,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33338,Q#2450 - >seq9097,non-specific,223496,300,494,0.00319281,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
33339,Q#2450 - >seq9097,superfamily,223496,300,494,0.00319281,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA4.ORF2.hs5_gmonkey.pars.frame3,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
33340,Q#2452 - >seq9099,specific,311990,1099,1117,0.00133218,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs5_gmonkey.pars.frame1,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33341,Q#2452 - >seq9099,superfamily,311990,1099,1117,0.00133218,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA4.ORF2.hs5_gmonkey.pars.frame1,1909181908_L1MA4.RM_HPGPNRMPC_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1MA4,ORF2,hs5_gmonkey,pars,CompleteHit
33342,Q#2453 - >seq9100,specific,197310,9,236,4.456579999999999e-65,220.301,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33343,Q#2453 - >seq9100,superfamily,351117,9,236,4.456579999999999e-65,220.301,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33344,Q#2453 - >seq9100,specific,238827,510,772,5.5768599999999995e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33345,Q#2453 - >seq9100,superfamily,295487,510,772,5.5768599999999995e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33346,Q#2453 - >seq9100,non-specific,197306,9,236,1.86682e-33,129.524,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33347,Q#2453 - >seq9100,specific,333820,516,772,7.28163e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33348,Q#2453 - >seq9100,superfamily,333820,516,772,7.28163e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33349,Q#2453 - >seq9100,non-specific,197320,7,229,1.6674900000000002e-22,97.9709,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33350,Q#2453 - >seq9100,non-specific,223780,7,229,2.1931000000000003e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33351,Q#2453 - >seq9100,non-specific,197307,9,236,1.4801199999999999e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33352,Q#2453 - >seq9100,specific,335306,10,229,1.04241e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33353,Q#2453 - >seq9100,non-specific,197321,7,236,1.5137200000000002e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33354,Q#2453 - >seq9100,non-specific,272954,7,236,1.38431e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33355,Q#2453 - >seq9100,non-specific,273186,7,237,4.68433e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33356,Q#2453 - >seq9100,non-specific,197319,7,236,5.50831e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33357,Q#2453 - >seq9100,non-specific,275209,453,791,1.52661e-11,67.0976,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33358,Q#2453 - >seq9100,superfamily,275209,453,791,1.52661e-11,67.0976,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33359,Q#2453 - >seq9100,non-specific,238828,516,737,1.53424e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33360,Q#2453 - >seq9100,non-specific,197336,7,229,3.0499100000000003e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33361,Q#2453 - >seq9100,non-specific,236970,9,229,5.87776e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33362,Q#2453 - >seq9100,non-specific,197311,7,236,5.36313e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33363,Q#2453 - >seq9100,non-specific,197318,9,236,1.2763e-05,48.0615,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33364,Q#2453 - >seq9100,non-specific,238185,656,772,0.0006767489999999999,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33365,Q#2453 - >seq9100,specific,225881,483,680,0.00100325,42.5185,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
33366,Q#2453 - >seq9100,superfamily,225881,483,680,0.00100325,42.5185,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
33367,Q#2453 - >seq9100,non-specific,139971,7,236,0.00148334,41.6032,PRK13911,PRK13911, - ,cl00490,exodeoxyribonuclease III; Provisional,L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33368,Q#2453 - >seq9100,non-specific,339261,108,232,0.00784178,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA4.ORF2.hs4_gibbon.marg.frame3,1909181908_L1MA4.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA4,ORF2,hs4_gibbon,marg,CompleteHit
33369,Q#2456 - >seq9103,specific,311990,1183,1201,0.00035322699999999996,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs5_gmonkey.marg.frame2,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33370,Q#2456 - >seq9103,superfamily,311990,1183,1201,0.00035322699999999996,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs5_gmonkey.marg.frame2,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33371,Q#2458 - >seq9105,specific,238827,509,771,2.1535299999999992e-66,223.322,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33372,Q#2458 - >seq9105,superfamily,295487,509,771,2.1535299999999992e-66,223.322,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33373,Q#2458 - >seq9105,specific,197310,9,235,6.774669999999998e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33374,Q#2458 - >seq9105,superfamily,351117,9,235,6.774669999999998e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33375,Q#2458 - >seq9105,non-specific,197306,9,235,6.76716e-47,168.044,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33376,Q#2458 - >seq9105,specific,333820,515,771,1.99497e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33377,Q#2458 - >seq9105,superfamily,333820,515,771,1.99497e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33378,Q#2458 - >seq9105,non-specific,197307,9,235,7.176819999999999e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33379,Q#2458 - >seq9105,non-specific,197320,9,228,2.00876e-23,100.667,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33380,Q#2458 - >seq9105,non-specific,223780,9,236,3.3619999999999997e-23,100.365,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33381,Q#2458 - >seq9105,non-specific,197321,7,235,2.6794499999999997e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33382,Q#2458 - >seq9105,specific,335306,10,228,6.54572e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33383,Q#2458 - >seq9105,non-specific,273186,9,236,9.17211e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33384,Q#2458 - >seq9105,non-specific,272954,9,235,3.09529e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33385,Q#2458 - >seq9105,non-specific,197319,13,235,9.53716e-13,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33386,Q#2458 - >seq9105,non-specific,197336,9,228,2.82557e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33387,Q#2458 - >seq9105,non-specific,238828,515,736,4.94573e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33388,Q#2458 - >seq9105,non-specific,197322,8,235,1.8319700000000002e-10,63.4902,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33389,Q#2458 - >seq9105,non-specific,236970,9,236,6.660419999999999e-10,61.0634,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33390,Q#2458 - >seq9105,non-specific,275209,466,799,4.20495e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33391,Q#2458 - >seq9105,superfamily,275209,466,799,4.20495e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33392,Q#2458 - >seq9105,non-specific,339261,108,231,1.00132e-06,48.4875,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33393,Q#2458 - >seq9105,non-specific,197311,37,235,2.94362e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33394,Q#2458 - >seq9105,non-specific,238185,655,771,2.37944e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33395,Q#2458 - >seq9105,specific,311990,1239,1257,0.0035112999999999998,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33396,Q#2458 - >seq9105,superfamily,311990,1239,1257,0.0035112999999999998,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33397,Q#2458 - >seq9105,non-specific,197317,139,228,0.00509029,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33398,Q#2458 - >seq9105,specific,316774,304,362,0.00953451,36.9828,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33399,Q#2458 - >seq9105,superfamily,316774,304,362,0.00953451,36.9828,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs5_gmonkey,pars,CompleteHit
33400,Q#2458 - >seq9105,non-specific,224117,262,466,0.00999371,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33401,Q#2458 - >seq9105,superfamily,224117,262,466,0.00999371,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs5_gmonkey.pars.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA13,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
33402,Q#2460 - >seq9107,specific,238827,510,772,1.0270899999999999e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33403,Q#2460 - >seq9107,superfamily,295487,510,772,1.0270899999999999e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33404,Q#2460 - >seq9107,specific,197310,9,236,2.0860699999999997e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33405,Q#2460 - >seq9107,superfamily,351117,9,236,2.0860699999999997e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33406,Q#2460 - >seq9107,non-specific,197306,9,236,6.84752e-48,171.125,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33407,Q#2460 - >seq9107,specific,333820,516,772,9.93239e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33408,Q#2460 - >seq9107,superfamily,333820,516,772,9.93239e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33409,Q#2460 - >seq9107,non-specific,197307,9,236,1.07911e-26,110.07,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33410,Q#2460 - >seq9107,non-specific,223780,9,237,3.4722999999999996e-24,103.06200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33411,Q#2460 - >seq9107,non-specific,197320,9,229,3.59918e-23,99.8969,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33412,Q#2460 - >seq9107,non-specific,197321,7,236,2.11682e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33413,Q#2460 - >seq9107,specific,335306,10,229,5.125140000000001e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33414,Q#2460 - >seq9107,non-specific,273186,9,237,2.32524e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33415,Q#2460 - >seq9107,non-specific,272954,9,236,2.4453200000000004e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33416,Q#2460 - >seq9107,non-specific,197319,13,236,2.19308e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33417,Q#2460 - >seq9107,non-specific,197336,9,229,2.88549e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33418,Q#2460 - >seq9107,non-specific,238828,516,737,8.23812e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33419,Q#2460 - >seq9107,non-specific,197322,8,236,1.8170599999999998e-10,63.4902,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33420,Q#2460 - >seq9107,non-specific,236970,9,237,3.0370799999999996e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33421,Q#2460 - >seq9107,non-specific,275209,467,800,5.2018900000000005e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33422,Q#2460 - >seq9107,superfamily,275209,467,800,5.2018900000000005e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33423,Q#2460 - >seq9107,non-specific,339261,108,232,5.5016800000000005e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33424,Q#2460 - >seq9107,non-specific,197311,37,236,4.366880000000001e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33425,Q#2460 - >seq9107,non-specific,238185,656,772,5.657759999999999e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,CompleteHit
33426,Q#2460 - >seq9107,specific,225881,482,739,0.00203153,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
33427,Q#2460 - >seq9107,superfamily,225881,482,739,0.00203153,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
33428,Q#2460 - >seq9107,non-specific,197317,139,229,0.00407998,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
33429,Q#2460 - >seq9107,non-specific,224117,263,467,0.00455252,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
33430,Q#2460 - >seq9107,superfamily,224117,263,467,0.00455252,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
33431,Q#2460 - >seq9107,non-specific,274009,307,452,0.00722447,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
33432,Q#2460 - >seq9107,superfamily,274009,307,452,0.00722447,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
33433,Q#2460 - >seq9107,non-specific,235175,283,459,0.00919819,40.0472,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
33434,Q#2460 - >seq9107,superfamily,235175,283,459,0.00919819,40.0472,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA13.ORF2.hs5_gmonkey.marg.frame3,1909181910_L1PA13.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
33435,Q#2461 - >seq9108,specific,311990,1147,1165,0.00040470199999999995,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs2_gorilla.pars.frame2,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33436,Q#2461 - >seq9108,superfamily,311990,1147,1165,0.00040470199999999995,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs2_gorilla.pars.frame2,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33437,Q#2462 - >seq9109,specific,197310,3,231,1.4829699999999998e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33438,Q#2462 - >seq9109,superfamily,351117,3,231,1.4829699999999998e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33439,Q#2462 - >seq9109,specific,238827,499,761,1.95949e-60,206.373,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33440,Q#2462 - >seq9109,superfamily,295487,499,761,1.95949e-60,206.373,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33441,Q#2462 - >seq9109,non-specific,197306,3,231,4.33763e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33442,Q#2462 - >seq9109,specific,333820,505,761,1.0344499999999999e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33443,Q#2462 - >seq9109,superfamily,333820,505,761,1.0344499999999999e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33444,Q#2462 - >seq9109,non-specific,197320,3,224,1.0725899999999999e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33445,Q#2462 - >seq9109,non-specific,223780,3,224,6.1721e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33446,Q#2462 - >seq9109,non-specific,197307,3,224,1.40786e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33447,Q#2462 - >seq9109,specific,335306,4,224,4.9500099999999996e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33448,Q#2462 - >seq9109,non-specific,197321,1,224,2.7990400000000002e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33449,Q#2462 - >seq9109,non-specific,272954,3,202,1.3175e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33450,Q#2462 - >seq9109,non-specific,273186,3,232,1.81199e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33451,Q#2462 - >seq9109,non-specific,197319,3,231,2.17432e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33452,Q#2462 - >seq9109,non-specific,238828,505,729,2.0809699999999997e-09,59.1368,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33453,Q#2462 - >seq9109,non-specific,197336,3,224,1.78767e-07,53.7703,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33454,Q#2462 - >seq9109,non-specific,197311,32,199,4.11843e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33455,Q#2462 - >seq9109,non-specific,197322,2,224,5.03573e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33456,Q#2462 - >seq9109,non-specific,275209,456,728,1.0233e-06,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,C-TerminusTruncated
33457,Q#2462 - >seq9109,superfamily,275209,456,728,1.0233e-06,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,marg,C-TerminusTruncated
33458,Q#2462 - >seq9109,non-specific,236970,3,224,1.4124100000000001e-05,47.9666,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33459,Q#2462 - >seq9109,non-specific,339261,103,226,0.00250909,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33460,Q#2462 - >seq9109,non-specific,224259,298,457,0.00808738,39.6644,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA9,ORF2,hs2_gorilla,marg,N-TerminusTruncated
33461,Q#2462 - >seq9109,superfamily,224259,298,457,0.00808738,39.6644,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1MA9,ORF2,hs2_gorilla,marg,N-TerminusTruncated
33462,Q#2462 - >seq9109,non-specific,235175,288,490,0.00952632,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs2_gorilla,marg,BothTerminiTruncated
33463,Q#2462 - >seq9109,superfamily,235175,288,490,0.00952632,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA9.ORF2.hs2_gorilla.marg.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MA9,ORF2,hs2_gorilla,marg,BothTerminiTruncated
33464,Q#2464 - >seq9111,non-specific,227355,291,529,0.00047104,44.2984,COG5022,COG5022,NC,cl34868,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1MA9.ORF2.hs2_gorilla.marg.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MA9,ORF2,hs2_gorilla,marg,BothTerminiTruncated
33465,Q#2464 - >seq9111,superfamily,227355,291,529,0.00047104,44.2984,cl34868,COG5022 superfamily,NC, - ,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1MA9.ORF2.hs2_gorilla.marg.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1MA9,ORF2,hs2_gorilla,marg,BothTerminiTruncated
33466,Q#2464 - >seq9111,specific,311990,1115,1133,0.00194426,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs2_gorilla.marg.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33467,Q#2464 - >seq9111,superfamily,311990,1115,1133,0.00194426,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1MA9.ORF2.hs2_gorilla.marg.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1MA9,ORF2,hs2_gorilla,marg,CompleteHit
33468,Q#2465 - >seq9112,specific,238827,498,760,7.508109999999999e-62,210.225,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33469,Q#2465 - >seq9112,superfamily,295487,498,760,7.508109999999999e-62,210.225,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33470,Q#2465 - >seq9112,specific,197310,3,232,8.305119999999998e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33471,Q#2465 - >seq9112,superfamily,351117,3,232,8.305119999999998e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33472,Q#2465 - >seq9112,non-specific,197306,3,232,5.4297399999999994e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33473,Q#2465 - >seq9112,specific,333820,504,760,1.8821900000000002e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33474,Q#2465 - >seq9112,superfamily,333820,504,760,1.8821900000000002e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33475,Q#2465 - >seq9112,non-specific,197320,3,225,1.03598e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33476,Q#2465 - >seq9112,non-specific,223780,3,225,4.7480800000000005e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33477,Q#2465 - >seq9112,non-specific,197307,3,225,9.851810000000001e-20,90.0397,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33478,Q#2465 - >seq9112,specific,335306,4,225,4.39109e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33479,Q#2465 - >seq9112,non-specific,197321,1,225,3.6881e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33480,Q#2465 - >seq9112,non-specific,272954,3,203,1.2849200000000002e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33481,Q#2465 - >seq9112,non-specific,273186,3,233,3.9139e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33482,Q#2465 - >seq9112,non-specific,197319,3,232,1.93177e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33483,Q#2465 - >seq9112,non-specific,238828,504,728,6.86552e-10,60.2924,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33484,Q#2465 - >seq9112,non-specific,197336,3,225,2.33791e-07,53.3851,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33485,Q#2465 - >seq9112,non-specific,197311,33,200,2.84485e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33486,Q#2465 - >seq9112,non-specific,275209,456,727,1.5264300000000002e-05,48.608000000000004,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33487,Q#2465 - >seq9112,superfamily,275209,456,727,1.5264300000000002e-05,48.608000000000004,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MA9,ORF2,hs2_gorilla,pars,C-TerminusTruncated
33488,Q#2465 - >seq9112,non-specific,236970,3,225,1.85491e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33489,Q#2465 - >seq9112,non-specific,224259,298,457,0.00123156,41.9756,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA9,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33490,Q#2465 - >seq9112,superfamily,224259,298,457,0.00123156,41.9756,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1MA9,ORF2,hs2_gorilla,pars,N-TerminusTruncated
33491,Q#2465 - >seq9112,non-specific,235175,288,457,0.00148903,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33492,Q#2465 - >seq9112,superfamily,235175,288,457,0.00148903,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33493,Q#2465 - >seq9112,non-specific,339261,104,227,0.0019837,39.2427,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MA9,ORF2,hs2_gorilla,pars,CompleteHit
33494,Q#2465 - >seq9112,non-specific,223496,309,499,0.00254313,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33495,Q#2465 - >seq9112,superfamily,223496,309,499,0.00254313,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1MA9.ORF2.hs2_gorilla.pars.frame3,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33496,Q#2466 - >seq9113,non-specific,227355,291,528,0.0007865260000000001,43.528,COG5022,COG5022,NC,cl34868,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1MA9.ORF2.hs2_gorilla.pars.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33497,Q#2466 - >seq9113,superfamily,227355,291,528,0.0007865260000000001,43.528,cl34868,COG5022 superfamily,NC, - ,Myosin heavy chain  [General function prediction only]; Myosin heavy chain [Cytoskeleton].,L1MA9.ORF2.hs2_gorilla.pars.frame1,1909181910_L1MA9.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1MA9,ORF2,hs2_gorilla,pars,BothTerminiTruncated
33498,Q#2469 - >seq9116,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33499,Q#2469 - >seq9116,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33500,Q#2469 - >seq9116,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33501,Q#2469 - >seq9116,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33502,Q#2469 - >seq9116,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33503,Q#2469 - >seq9116,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33504,Q#2469 - >seq9116,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33505,Q#2469 - >seq9116,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33506,Q#2469 - >seq9116,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33507,Q#2469 - >seq9116,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33508,Q#2469 - >seq9116,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33509,Q#2469 - >seq9116,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33510,Q#2469 - >seq9116,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33511,Q#2469 - >seq9116,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33512,Q#2469 - >seq9116,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33513,Q#2469 - >seq9116,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33514,Q#2469 - >seq9116,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33515,Q#2469 - >seq9116,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33516,Q#2469 - >seq9116,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33517,Q#2469 - >seq9116,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33518,Q#2469 - >seq9116,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33519,Q#2469 - >seq9116,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33520,Q#2469 - >seq9116,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33521,Q#2469 - >seq9116,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33522,Q#2469 - >seq9116,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33523,Q#2469 - >seq9116,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33524,Q#2469 - >seq9116,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33525,Q#2469 - >seq9116,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33526,Q#2469 - >seq9116,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33527,Q#2469 - >seq9116,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33528,Q#2469 - >seq9116,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33529,Q#2469 - >seq9116,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33530,Q#2469 - >seq9116,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33531,Q#2469 - >seq9116,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33532,Q#2469 - >seq9116,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33533,Q#2469 - >seq9116,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33534,Q#2469 - >seq9116,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33535,Q#2469 - >seq9116,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33536,Q#2469 - >seq9116,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33537,Q#2469 - >seq9116,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33538,Q#2469 - >seq9116,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,N-TerminusTruncated
33539,Q#2469 - >seq9116,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,N-TerminusTruncated
33540,Q#2469 - >seq9116,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33541,Q#2469 - >seq9116,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,pars,CompleteHit
33542,Q#2469 - >seq9116,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33543,Q#2469 - >seq9116,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33544,Q#2469 - >seq9116,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33545,Q#2469 - >seq9116,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33546,Q#2469 - >seq9116,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33547,Q#2469 - >seq9116,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,N-TerminusTruncated
33548,Q#2469 - >seq9116,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,pars,N-TerminusTruncated
33549,Q#2469 - >seq9116,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33550,Q#2469 - >seq9116,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33551,Q#2469 - >seq9116,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,BothTerminiTruncated
33552,Q#2469 - >seq9116,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,BothTerminiTruncated
33553,Q#2469 - >seq9116,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,pars,BothTerminiTruncated
33554,Q#2469 - >seq9116,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33555,Q#2469 - >seq9116,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs0_human,pars,CompleteHit
33556,Q#2469 - >seq9116,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,pars,CompleteHit
33557,Q#2469 - >seq9116,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,pars,CompleteHit
33558,Q#2469 - >seq9116,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,pars,CompleteHit
33559,Q#2469 - >seq9116,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33560,Q#2469 - >seq9116,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33561,Q#2469 - >seq9116,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.pars.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,pars,C-TerminusTruncated
33562,Q#2472 - >seq9119,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33563,Q#2472 - >seq9119,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33564,Q#2472 - >seq9119,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33565,Q#2472 - >seq9119,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33566,Q#2472 - >seq9119,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33567,Q#2472 - >seq9119,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33568,Q#2472 - >seq9119,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33569,Q#2472 - >seq9119,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33570,Q#2472 - >seq9119,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33571,Q#2472 - >seq9119,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33572,Q#2472 - >seq9119,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33573,Q#2472 - >seq9119,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33574,Q#2472 - >seq9119,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33575,Q#2472 - >seq9119,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33576,Q#2472 - >seq9119,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33577,Q#2472 - >seq9119,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33578,Q#2472 - >seq9119,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33579,Q#2472 - >seq9119,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33580,Q#2472 - >seq9119,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33581,Q#2472 - >seq9119,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33582,Q#2472 - >seq9119,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33583,Q#2472 - >seq9119,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33584,Q#2472 - >seq9119,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33585,Q#2472 - >seq9119,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33586,Q#2472 - >seq9119,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33587,Q#2472 - >seq9119,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33588,Q#2472 - >seq9119,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33589,Q#2472 - >seq9119,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33590,Q#2472 - >seq9119,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33591,Q#2472 - >seq9119,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33592,Q#2472 - >seq9119,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33593,Q#2472 - >seq9119,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33594,Q#2472 - >seq9119,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33595,Q#2472 - >seq9119,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33596,Q#2472 - >seq9119,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33597,Q#2472 - >seq9119,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33598,Q#2472 - >seq9119,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33599,Q#2472 - >seq9119,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33600,Q#2472 - >seq9119,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33601,Q#2472 - >seq9119,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33602,Q#2472 - >seq9119,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,N-TerminusTruncated
33603,Q#2472 - >seq9119,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,N-TerminusTruncated
33604,Q#2472 - >seq9119,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33605,Q#2472 - >seq9119,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs0_human,marg,CompleteHit
33606,Q#2472 - >seq9119,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33607,Q#2472 - >seq9119,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33608,Q#2472 - >seq9119,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33609,Q#2472 - >seq9119,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33610,Q#2472 - >seq9119,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33611,Q#2472 - >seq9119,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,N-TerminusTruncated
33612,Q#2472 - >seq9119,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs0_human,marg,N-TerminusTruncated
33613,Q#2472 - >seq9119,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33614,Q#2472 - >seq9119,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33615,Q#2472 - >seq9119,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,BothTerminiTruncated
33616,Q#2472 - >seq9119,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,BothTerminiTruncated
33617,Q#2472 - >seq9119,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs0_human,marg,BothTerminiTruncated
33618,Q#2472 - >seq9119,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33619,Q#2472 - >seq9119,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs0_human,marg,CompleteHit
33620,Q#2472 - >seq9119,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,marg,CompleteHit
33621,Q#2472 - >seq9119,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,marg,CompleteHit
33622,Q#2472 - >seq9119,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs0_human,marg,CompleteHit
33623,Q#2472 - >seq9119,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33624,Q#2472 - >seq9119,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33625,Q#2472 - >seq9119,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs0_human.marg.frame3,1909181914_L1PA3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs0_human,marg,C-TerminusTruncated
33626,Q#2475 - >seq9122,non-specific,335182,155,251,6.303869999999999e-35,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33627,Q#2475 - >seq9122,superfamily,335182,155,251,6.303869999999999e-35,122.411,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33628,Q#2475 - >seq9122,non-specific,335182,155,251,6.303869999999999e-35,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33629,Q#2475 - >seq9122,non-specific,340205,254,317,2.99517e-23,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33630,Q#2475 - >seq9122,superfamily,340205,254,317,2.99517e-23,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33631,Q#2475 - >seq9122,non-specific,340205,254,317,2.99517e-23,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,marg,CompleteHit
33632,Q#2475 - >seq9122,non-specific,340204,111,153,3.4550300000000004e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,marg,CompleteHit
33633,Q#2475 - >seq9122,superfamily,340204,111,153,3.4550300000000004e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,marg,CompleteHit
33634,Q#2475 - >seq9122,non-specific,340204,111,153,3.4550300000000004e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,marg,CompleteHit
33635,Q#2475 - >seq9122,non-specific,237177,42,149,0.000104935,43.6134,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33636,Q#2475 - >seq9122,superfamily,237177,42,149,0.000104935,43.6134,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33637,Q#2475 - >seq9122,non-specific,237177,42,149,0.000104935,43.6134,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33638,Q#2475 - >seq9122,non-specific,274009,60,202,0.00010555200000000001,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33639,Q#2475 - >seq9122,superfamily,274009,60,202,0.00010555200000000001,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33640,Q#2475 - >seq9122,non-specific,274009,60,202,0.00010555200000000001,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33641,Q#2475 - >seq9122,non-specific,235175,49,155,0.000253548,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33642,Q#2475 - >seq9122,superfamily,235175,49,155,0.000253548,42.3584,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33643,Q#2475 - >seq9122,non-specific,235175,49,155,0.000253548,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33644,Q#2475 - >seq9122,non-specific,274008,45,150,0.000687633,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33645,Q#2475 - >seq9122,superfamily,274008,45,150,0.000687633,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33646,Q#2475 - >seq9122,non-specific,274008,45,150,0.000687633,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33647,Q#2475 - >seq9122,non-specific,129694,79,146,0.000964255,40.8005,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33648,Q#2475 - >seq9122,superfamily,129694,79,146,0.000964255,40.8005,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33649,Q#2475 - >seq9122,non-specific,129694,79,146,0.000964255,40.8005,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33650,Q#2475 - >seq9122,non-specific,275056,60,152,0.00135167,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33651,Q#2475 - >seq9122,superfamily,275056,60,152,0.00135167,39.2209,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33652,Q#2475 - >seq9122,non-specific,275056,60,152,0.00135167,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33653,Q#2475 - >seq9122,non-specific,274386,27,147,0.00140071,40.0346,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33654,Q#2475 - >seq9122,superfamily,274386,27,147,0.00140071,40.0346,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33655,Q#2475 - >seq9122,non-specific,274386,27,147,0.00140071,40.0346,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33656,Q#2475 - >seq9122,non-specific,235600,70,185,0.00171337,39.9108,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33657,Q#2475 - >seq9122,superfamily,235600,70,185,0.00171337,39.9108,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33658,Q#2475 - >seq9122,non-specific,235600,70,185,0.00171337,39.9108,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33659,Q#2475 - >seq9122,non-specific,224117,28,155,0.00181928,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33660,Q#2475 - >seq9122,superfamily,224117,28,155,0.00181928,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33661,Q#2475 - >seq9122,non-specific,224117,28,155,0.00181928,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33662,Q#2475 - >seq9122,non-specific,336159,60,145,0.00189785,39.6601,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33663,Q#2475 - >seq9122,superfamily,336159,60,145,0.00189785,39.6601,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33664,Q#2475 - >seq9122,non-specific,336159,60,145,0.00189785,39.6601,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,marg,N-TerminusTruncated
33665,Q#2475 - >seq9122,non-specific,274008,41,149,0.00199578,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33666,Q#2475 - >seq9122,non-specific,274008,41,149,0.00199578,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33667,Q#2475 - >seq9122,non-specific,235461,47,169,0.0026129,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33668,Q#2475 - >seq9122,superfamily,235461,47,169,0.0026129,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33669,Q#2475 - >seq9122,non-specific,235461,47,169,0.0026129,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33670,Q#2475 - >seq9122,non-specific,223671,70,161,0.00392625,38.4601,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33671,Q#2475 - >seq9122,superfamily,320984,70,161,0.00392625,38.4601,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33672,Q#2475 - >seq9122,non-specific,223671,70,161,0.00392625,38.4601,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33673,Q#2475 - >seq9122,non-specific,223250,47,150,0.00443786,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33674,Q#2475 - >seq9122,superfamily,223250,47,150,0.00443786,38.3481,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33675,Q#2475 - >seq9122,non-specific,223250,47,150,0.00443786,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33676,Q#2475 - >seq9122,non-specific,310273,60,193,0.0060823,38.1878,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33677,Q#2475 - >seq9122,superfamily,310273,60,193,0.0060823,38.1878,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33678,Q#2475 - >seq9122,non-specific,310273,60,193,0.0060823,38.1878,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33679,Q#2475 - >seq9122,non-specific,337663,82,147,0.00688108,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33680,Q#2475 - >seq9122,superfamily,337663,82,147,0.00688108,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33681,Q#2475 - >seq9122,non-specific,337663,82,147,0.00688108,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33682,Q#2475 - >seq9122,non-specific,274009,33,150,0.00731288,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33683,Q#2475 - >seq9122,non-specific,274009,33,150,0.00731288,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33684,Q#2475 - >seq9122,non-specific,112704,2,139,0.00780782,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33685,Q#2475 - >seq9122,superfamily,112704,2,139,0.00780782,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33686,Q#2475 - >seq9122,non-specific,112704,2,139,0.00780782,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB1,ORF1,hs0_human,marg,C-TerminusTruncated
33687,Q#2475 - >seq9122,non-specific,235175,60,144,0.00923573,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33688,Q#2475 - >seq9122,non-specific,235175,60,144,0.00923573,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33689,Q#2475 - >seq9122,non-specific,224117,49,201,0.00945289,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33690,Q#2475 - >seq9122,non-specific,224117,49,201,0.00945289,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33691,Q#2475 - >seq9122,non-specific,222878,57,150,0.00997457,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33692,Q#2475 - >seq9122,superfamily,222878,57,150,0.00997457,37.3013,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33693,Q#2475 - >seq9122,non-specific,222878,57,150,0.00997457,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.marg.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,marg,BothTerminiTruncated
33694,Q#2478 - >seq9125,non-specific,335182,155,251,6.303869999999999e-35,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33695,Q#2478 - >seq9125,superfamily,335182,155,251,6.303869999999999e-35,122.411,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33696,Q#2478 - >seq9125,non-specific,335182,155,251,6.303869999999999e-35,122.411,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33697,Q#2478 - >seq9125,non-specific,340205,254,317,2.99517e-23,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33698,Q#2478 - >seq9125,superfamily,340205,254,317,2.99517e-23,90.8584,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33699,Q#2478 - >seq9125,non-specific,340205,254,317,2.99517e-23,90.8584,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB1,ORF1,hs0_human,pars,CompleteHit
33700,Q#2478 - >seq9125,non-specific,340204,111,153,3.4550300000000004e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,pars,CompleteHit
33701,Q#2478 - >seq9125,superfamily,340204,111,153,3.4550300000000004e-06,43.1652,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,pars,CompleteHit
33702,Q#2478 - >seq9125,non-specific,340204,111,153,3.4550300000000004e-06,43.1652,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB1,ORF1,hs0_human,pars,CompleteHit
33703,Q#2478 - >seq9125,non-specific,237177,42,149,0.000104935,43.6134,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33704,Q#2478 - >seq9125,superfamily,237177,42,149,0.000104935,43.6134,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33705,Q#2478 - >seq9125,non-specific,237177,42,149,0.000104935,43.6134,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33706,Q#2478 - >seq9125,non-specific,274009,60,202,0.00010555200000000001,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33707,Q#2478 - >seq9125,superfamily,274009,60,202,0.00010555200000000001,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33708,Q#2478 - >seq9125,non-specific,274009,60,202,0.00010555200000000001,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33709,Q#2478 - >seq9125,non-specific,235175,49,155,0.000253548,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33710,Q#2478 - >seq9125,superfamily,235175,49,155,0.000253548,42.3584,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33711,Q#2478 - >seq9125,non-specific,235175,49,155,0.000253548,42.3584,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33712,Q#2478 - >seq9125,non-specific,274008,45,150,0.000687633,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33713,Q#2478 - >seq9125,superfamily,274008,45,150,0.000687633,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33714,Q#2478 - >seq9125,non-specific,274008,45,150,0.000687633,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33715,Q#2478 - >seq9125,non-specific,129694,79,146,0.000964255,40.8005,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33716,Q#2478 - >seq9125,superfamily,129694,79,146,0.000964255,40.8005,cl31018,rad50 superfamily,C, - ,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33717,Q#2478 - >seq9125,non-specific,129694,79,146,0.000964255,40.8005,TIGR00606,rad50,C,cl31018,"rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33718,Q#2478 - >seq9125,non-specific,275056,60,152,0.00135167,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33719,Q#2478 - >seq9125,superfamily,275056,60,152,0.00135167,39.2209,cl25512,SH3_and_anchor superfamily,N, - ,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33720,Q#2478 - >seq9125,non-specific,275056,60,152,0.00135167,39.2209,TIGR04211,SH3_and_anchor,N,cl25512,"SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33721,Q#2478 - >seq9125,non-specific,274386,27,147,0.00140071,40.0346,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33722,Q#2478 - >seq9125,superfamily,274386,27,147,0.00140071,40.0346,cl37208,pepcterm_ChnLen superfamily,NC, - ,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33723,Q#2478 - >seq9125,non-specific,274386,27,147,0.00140071,40.0346,TIGR03007,pepcterm_ChnLen,NC,cl37208,"polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33724,Q#2478 - >seq9125,non-specific,235600,70,185,0.00171337,39.9108,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33725,Q#2478 - >seq9125,superfamily,235600,70,185,0.00171337,39.9108,cl35381,PRK05771 superfamily,C, - ,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33726,Q#2478 - >seq9125,non-specific,235600,70,185,0.00171337,39.9108,PRK05771,PRK05771,C,cl35381,V-type ATP synthase subunit I; Validated,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33727,Q#2478 - >seq9125,non-specific,224117,28,155,0.00181928,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33728,Q#2478 - >seq9125,superfamily,224117,28,155,0.00181928,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33729,Q#2478 - >seq9125,non-specific,224117,28,155,0.00181928,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33730,Q#2478 - >seq9125,non-specific,336159,60,145,0.00189785,39.6601,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33731,Q#2478 - >seq9125,superfamily,336159,60,145,0.00189785,39.6601,cl38191,HOOK superfamily,N, - ,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33732,Q#2478 - >seq9125,non-specific,336159,60,145,0.00189785,39.6601,pfam05622,HOOK,N,cl38191,"HOOK protein; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_HOOK,L1PB1,ORF1,hs0_human,pars,N-TerminusTruncated
33733,Q#2478 - >seq9125,non-specific,274008,41,149,0.00199578,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33734,Q#2478 - >seq9125,non-specific,274008,41,149,0.00199578,39.6547,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33735,Q#2478 - >seq9125,non-specific,235461,47,169,0.0026129,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33736,Q#2478 - >seq9125,superfamily,235461,47,169,0.0026129,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33737,Q#2478 - >seq9125,non-specific,235461,47,169,0.0026129,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33738,Q#2478 - >seq9125,non-specific,223671,70,161,0.00392625,38.4601,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33739,Q#2478 - >seq9125,superfamily,320984,70,161,0.00392625,38.4601,cl00459,MIT_CorA-like superfamily,NC, - ,"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33740,Q#2478 - >seq9125,non-specific,223671,70,161,0.00392625,38.4601,COG0598,CorA,NC,cl00459,Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]; Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism].,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33741,Q#2478 - >seq9125,non-specific,223250,47,150,0.00443786,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33742,Q#2478 - >seq9125,superfamily,223250,47,150,0.00443786,38.3481,cl33789,SerS superfamily,C, - ,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33743,Q#2478 - >seq9125,non-specific,223250,47,150,0.00443786,38.3481,COG0172,SerS,C,cl33789,"Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33744,Q#2478 - >seq9125,non-specific,310273,60,193,0.0060823,38.1878,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33745,Q#2478 - >seq9125,superfamily,310273,60,193,0.0060823,38.1878,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33746,Q#2478 - >seq9125,non-specific,310273,60,193,0.0060823,38.1878,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33747,Q#2478 - >seq9125,non-specific,337663,82,147,0.00688108,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33748,Q#2478 - >seq9125,superfamily,337663,82,147,0.00688108,37.7895,cl25898,Atg14 superfamily,C, - ,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33749,Q#2478 - >seq9125,non-specific,337663,82,147,0.00688108,37.7895,pfam10186,Atg14,C,cl25898,"Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N-terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33750,Q#2478 - >seq9125,non-specific,274009,33,150,0.00731288,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33751,Q#2478 - >seq9125,non-specific,274009,33,150,0.00731288,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33752,Q#2478 - >seq9125,non-specific,112704,2,139,0.00780782,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33753,Q#2478 - >seq9125,superfamily,112704,2,139,0.00780782,36.9151,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33754,Q#2478 - >seq9125,non-specific,112704,2,139,0.00780782,36.9151,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB1,ORF1,hs0_human,pars,C-TerminusTruncated
33755,Q#2478 - >seq9125,non-specific,235175,60,144,0.00923573,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33756,Q#2478 - >seq9125,non-specific,235175,60,144,0.00923573,37.736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33757,Q#2478 - >seq9125,non-specific,224117,49,201,0.00945289,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33758,Q#2478 - >seq9125,non-specific,224117,49,201,0.00945289,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33759,Q#2478 - >seq9125,non-specific,222878,57,150,0.00997457,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33760,Q#2478 - >seq9125,superfamily,222878,57,150,0.00997457,37.3013,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33761,Q#2478 - >seq9125,non-specific,222878,57,150,0.00997457,37.3013,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PB1.ORF1.hs0_human.pars.frame3,1909181919_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF1.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF1,hs0_human,pars,BothTerminiTruncated
33762,Q#2480 - >seq9127,specific,238827,582,701,5.16191e-31,121.62899999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33763,Q#2480 - >seq9127,superfamily,295487,582,701,5.16191e-31,121.62899999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33764,Q#2480 - >seq9127,non-specific,333820,584,701,1.52892e-13,70.0138,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33765,Q#2480 - >seq9127,superfamily,333820,584,701,1.52892e-13,70.0138,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33766,Q#2480 - >seq9127,non-specific,238828,572,698,1.23258e-06,50.6624,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33767,Q#2480 - >seq9127,non-specific,238185,581,699,1.67945e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,CompleteHit
33768,Q#2480 - >seq9127,non-specific,275209,572,729,0.00025942,44.3708,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33769,Q#2480 - >seq9127,superfamily,275209,572,729,0.00025942,44.3708,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs0_human.marg.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33770,Q#2481 - >seq9128,specific,197310,9,236,2.7541700000000002e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33771,Q#2481 - >seq9128,superfamily,351117,9,236,2.7541700000000002e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33772,Q#2481 - >seq9128,specific,238827,510,629,9.776139999999999e-35,132.415,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs0_human,marg,C-TerminusTruncated
33773,Q#2481 - >seq9128,superfamily,295487,510,629,9.776139999999999e-35,132.415,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs0_human,marg,C-TerminusTruncated
33774,Q#2481 - >seq9128,non-specific,197306,9,236,2.6445599999999996e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33775,Q#2481 - >seq9128,non-specific,197307,9,236,2.66797e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33776,Q#2481 - >seq9128,non-specific,223780,9,237,8.255770000000001e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33777,Q#2481 - >seq9128,non-specific,197321,7,236,1.2322000000000001e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33778,Q#2481 - >seq9128,non-specific,197320,9,229,2.40317e-17,82.9481,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33779,Q#2481 - >seq9128,specific,335306,10,229,3.8829500000000003e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33780,Q#2481 - >seq9128,non-specific,273186,9,237,1.83165e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33781,Q#2481 - >seq9128,non-specific,333820,516,627,2.07185e-14,72.7102,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs0_human,marg,C-TerminusTruncated
33782,Q#2481 - >seq9128,superfamily,333820,516,627,2.07185e-14,72.7102,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs0_human,marg,C-TerminusTruncated
33783,Q#2481 - >seq9128,non-specific,197319,13,236,1.7611e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33784,Q#2481 - >seq9128,non-specific,272954,9,207,1.0338800000000002e-09,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33785,Q#2481 - >seq9128,non-specific,236970,9,237,5.83513e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33786,Q#2481 - >seq9128,non-specific,197322,8,236,7.613389999999999e-07,52.3194,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33787,Q#2481 - >seq9128,non-specific,197336,9,194,6.4040899999999995e-06,48.7627,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,marg,CompleteHit
33788,Q#2481 - >seq9128,non-specific,334125,211,412,6.419350000000001e-05,46.7588,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33789,Q#2481 - >seq9128,superfamily,334125,211,412,6.419350000000001e-05,46.7588,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33790,Q#2481 - >seq9128,non-specific,235175,294,469,0.000199879,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33791,Q#2481 - >seq9128,superfamily,235175,294,469,0.000199879,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33792,Q#2481 - >seq9128,non-specific,339261,108,232,0.0008814389999999999,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs0_human,marg,CompleteHit
33793,Q#2481 - >seq9128,non-specific,223266,211,465,0.00293079,41.8738,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33794,Q#2481 - >seq9128,superfamily,223266,211,465,0.00293079,41.8738,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33795,Q#2481 - >seq9128,non-specific,223496,316,500,0.00402583,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33796,Q#2481 - >seq9128,superfamily,223496,316,500,0.00402583,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33797,Q#2481 - >seq9128,non-specific,224117,301,467,0.00545709,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33798,Q#2481 - >seq9128,superfamily,224117,301,467,0.00545709,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33799,Q#2481 - >seq9128,non-specific,274009,301,458,0.00795769,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33800,Q#2481 - >seq9128,superfamily,274009,301,458,0.00795769,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,marg,BothTerminiTruncated
33801,Q#2481 - >seq9128,non-specific,313357,321,464,0.00857245,38.7868,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33802,Q#2481 - >seq9128,superfamily,321788,321,464,0.00857245,38.7868,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA17.ORF2.hs0_human.marg.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,marg,N-TerminusTruncated
33803,Q#2483 - >seq9130,specific,238827,582,699,4.0813599999999997e-29,116.23700000000001,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33804,Q#2483 - >seq9130,superfamily,295487,582,699,4.0813599999999997e-29,116.23700000000001,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33805,Q#2483 - >seq9130,non-specific,333820,584,699,3.4334000000000003e-13,68.8582,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33806,Q#2483 - >seq9130,superfamily,333820,584,699,3.4334000000000003e-13,68.8582,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33807,Q#2483 - >seq9130,non-specific,238828,572,666,1.60494e-06,50.2772,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33808,Q#2483 - >seq9130,non-specific,238185,581,670,0.000455616,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,CompleteHit
33809,Q#2483 - >seq9130,non-specific,275209,572,727,0.00498153,40.5188,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33810,Q#2483 - >seq9130,superfamily,275209,572,727,0.00498153,40.5188,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs0_human.pars.frame1,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33811,Q#2484 - >seq9131,specific,197310,9,236,2.8496299999999994e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33812,Q#2484 - >seq9131,superfamily,351117,9,236,2.8496299999999994e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33813,Q#2484 - >seq9131,specific,238827,510,629,1.02208e-34,132.415,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs0_human,pars,C-TerminusTruncated
33814,Q#2484 - >seq9131,superfamily,295487,510,629,1.02208e-34,132.415,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs0_human,pars,C-TerminusTruncated
33815,Q#2484 - >seq9131,non-specific,197306,9,236,2.5846099999999997e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33816,Q#2484 - >seq9131,non-specific,197307,9,236,2.535e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33817,Q#2484 - >seq9131,non-specific,223780,9,237,8.302810000000001e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33818,Q#2484 - >seq9131,non-specific,197321,7,236,1.2276e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33819,Q#2484 - >seq9131,non-specific,197320,9,229,2.3716999999999998e-17,82.9481,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33820,Q#2484 - >seq9131,specific,335306,10,229,3.8688199999999997e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33821,Q#2484 - >seq9131,non-specific,273186,9,237,1.7741999999999998e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33822,Q#2484 - >seq9131,non-specific,333820,516,627,2.1451e-14,72.7102,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs0_human,pars,C-TerminusTruncated
33823,Q#2484 - >seq9131,superfamily,333820,516,627,2.1451e-14,72.7102,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs0_human,pars,C-TerminusTruncated
33824,Q#2484 - >seq9131,non-specific,197319,13,236,1.5981399999999999e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33825,Q#2484 - >seq9131,non-specific,272954,9,207,1.0019100000000001e-09,60.4745,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33826,Q#2484 - >seq9131,non-specific,236970,9,237,5.81376e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33827,Q#2484 - >seq9131,non-specific,197322,8,236,7.65305e-07,52.3194,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33828,Q#2484 - >seq9131,non-specific,197336,9,194,6.38089e-06,48.7627,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs0_human,pars,CompleteHit
33829,Q#2484 - >seq9131,non-specific,334125,211,412,6.12512e-05,46.7588,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33830,Q#2484 - >seq9131,superfamily,334125,211,412,6.12512e-05,46.7588,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33831,Q#2484 - >seq9131,non-specific,235175,294,469,0.000195784,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33832,Q#2484 - >seq9131,superfamily,235175,294,469,0.000195784,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33833,Q#2484 - >seq9131,non-specific,339261,108,232,0.00092192,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs0_human,pars,CompleteHit
33834,Q#2484 - >seq9131,non-specific,223266,211,465,0.00292005,41.8738,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33835,Q#2484 - >seq9131,superfamily,223266,211,465,0.00292005,41.8738,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33836,Q#2484 - >seq9131,non-specific,223496,316,500,0.00401111,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33837,Q#2484 - >seq9131,superfamily,223496,316,500,0.00401111,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33838,Q#2484 - >seq9131,non-specific,224117,301,467,0.00534596,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33839,Q#2484 - >seq9131,superfamily,224117,301,467,0.00534596,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33840,Q#2484 - >seq9131,non-specific,274009,301,458,0.00786191,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33841,Q#2484 - >seq9131,superfamily,274009,301,458,0.00786191,40.4363,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs0_human,pars,BothTerminiTruncated
33842,Q#2484 - >seq9131,non-specific,313357,321,464,0.00854265,38.7868,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33843,Q#2484 - >seq9131,superfamily,321788,321,464,0.00854265,38.7868,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA17.ORF2.hs0_human.pars.frame3,1909181921_L1PA17.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs0_human,pars,N-TerminusTruncated
33844,Q#2485 - >seq9132,non-specific,338310,939,1001,0.00156635,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs6_sqmonkey.pars.frame1,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
33845,Q#2485 - >seq9132,superfamily,338310,939,1001,0.00156635,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs6_sqmonkey.pars.frame1,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
33846,Q#2487 - >seq9134,specific,238827,503,766,3.02288e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33847,Q#2487 - >seq9134,superfamily,295487,503,766,3.02288e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33848,Q#2487 - >seq9134,specific,197310,3,230,1.5749199999999999e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33849,Q#2487 - >seq9134,superfamily,351117,3,230,1.5749199999999999e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33850,Q#2487 - >seq9134,specific,333820,509,766,2.12525e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33851,Q#2487 - >seq9134,superfamily,333820,509,766,2.12525e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33852,Q#2487 - >seq9134,non-specific,197306,3,230,6.26443e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33853,Q#2487 - >seq9134,non-specific,197320,3,223,2.4346300000000002e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33854,Q#2487 - >seq9134,non-specific,223780,3,231,3.1575700000000005e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33855,Q#2487 - >seq9134,non-specific,197307,3,230,3.78312e-19,88.1137,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33856,Q#2487 - >seq9134,specific,335306,4,223,2.4346199999999998e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33857,Q#2487 - >seq9134,non-specific,273186,3,231,9.130339999999998e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33858,Q#2487 - >seq9134,non-specific,197321,1,230,4.2849499999999995e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33859,Q#2487 - >seq9134,non-specific,197319,7,230,7.97273e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33860,Q#2487 - >seq9134,non-specific,272954,3,230,9.24767e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33861,Q#2487 - >seq9134,non-specific,238828,509,763,6.912970000000001e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33862,Q#2487 - >seq9134,non-specific,197336,3,188,1.50861e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33863,Q#2487 - >seq9134,non-specific,197322,2,230,1.20485e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33864,Q#2487 - >seq9134,non-specific,275209,460,730,1.42222e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
33865,Q#2487 - >seq9134,superfamily,275209,460,730,1.42222e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
33866,Q#2487 - >seq9134,non-specific,236970,3,183,2.7422500000000003e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
33867,Q#2487 - >seq9134,non-specific,197311,24,230,1.84727e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33868,Q#2487 - >seq9134,non-specific,339261,102,226,0.000531628,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33869,Q#2487 - >seq9134,non-specific,239569,518,731,0.000955569,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33870,Q#2487 - >seq9134,non-specific,238185,649,764,0.00224554,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,pars,CompleteHit
33871,Q#2487 - >seq9134,non-specific,274009,301,450,0.00823363,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
33872,Q#2487 - >seq9134,superfamily,274009,301,450,0.00823363,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
33873,Q#2487 - >seq9134,non-specific,235175,300,437,0.00923351,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
33874,Q#2487 - >seq9134,superfamily,235175,300,437,0.00923351,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs6_sqmonkey.pars.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
33875,Q#2488 - >seq9135,non-specific,338310,939,1001,0.00156787,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs6_sqmonkey.marg.frame1,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
33876,Q#2488 - >seq9135,superfamily,338310,939,1001,0.00156787,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs6_sqmonkey.marg.frame1,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
33877,Q#2490 - >seq9137,specific,238827,503,766,2.9414299999999997e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33878,Q#2490 - >seq9137,superfamily,295487,503,766,2.9414299999999997e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33879,Q#2490 - >seq9137,specific,197310,3,230,1.5614500000000001e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33880,Q#2490 - >seq9137,superfamily,351117,3,230,1.5614500000000001e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33881,Q#2490 - >seq9137,specific,333820,509,766,2.0864099999999997e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33882,Q#2490 - >seq9137,superfamily,333820,509,766,2.0864099999999997e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33883,Q#2490 - >seq9137,non-specific,197306,3,230,6.27015e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33884,Q#2490 - >seq9137,non-specific,197320,3,223,2.3018899999999996e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33885,Q#2490 - >seq9137,non-specific,223780,3,231,3.04287e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33886,Q#2490 - >seq9137,non-specific,197307,3,230,3.78659e-19,88.1137,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33887,Q#2490 - >seq9137,specific,335306,4,223,2.4368000000000002e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33888,Q#2490 - >seq9137,non-specific,273186,3,231,8.9683e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33889,Q#2490 - >seq9137,non-specific,197321,1,230,4.2487400000000005e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33890,Q#2490 - >seq9137,non-specific,197319,7,230,7.90537e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33891,Q#2490 - >seq9137,non-specific,272954,3,230,9.169620000000001e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33892,Q#2490 - >seq9137,non-specific,238828,509,763,6.919160000000001e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33893,Q#2490 - >seq9137,non-specific,197336,3,188,1.4685399999999997e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33894,Q#2490 - >seq9137,non-specific,197322,2,230,1.2059600000000002e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33895,Q#2490 - >seq9137,non-specific,275209,460,730,1.3379799999999999e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
33896,Q#2490 - >seq9137,superfamily,275209,460,730,1.3379799999999999e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
33897,Q#2490 - >seq9137,non-specific,236970,3,183,2.74471e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
33898,Q#2490 - >seq9137,non-specific,197311,24,230,1.84888e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33899,Q#2490 - >seq9137,non-specific,339261,102,226,0.000553028,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33900,Q#2490 - >seq9137,non-specific,239569,518,731,0.000956398,41.7895,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33901,Q#2490 - >seq9137,non-specific,238185,649,764,0.00224737,38.486,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs6_sqmonkey,marg,CompleteHit
33902,Q#2490 - >seq9137,non-specific,274009,301,450,0.00817163,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
33903,Q#2490 - >seq9137,superfamily,274009,301,450,0.00817163,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
33904,Q#2490 - >seq9137,non-specific,235175,300,437,0.00908642,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
33905,Q#2490 - >seq9137,superfamily,235175,300,437,0.00908642,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs6_sqmonkey.marg.frame3,1909181930_L1PB1.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
33906,Q#2491 - >seq9138,non-specific,338310,951,1013,0.000947645,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs0_human.marg.frame2,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PB1,ORF2,hs0_human,marg,BothTerminiTruncated
33907,Q#2491 - >seq9138,superfamily,338310,951,1013,0.000947645,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs0_human.marg.frame2,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PB1,ORF2,hs0_human,marg,BothTerminiTruncated
33908,Q#2492 - >seq9139,specific,197310,3,230,6.62455e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33909,Q#2492 - >seq9139,superfamily,351117,3,230,6.62455e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33910,Q#2492 - >seq9139,non-specific,197306,3,230,1.1993800000000001e-33,129.909,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33911,Q#2492 - >seq9139,non-specific,223780,3,231,3.4525699999999994e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33912,Q#2492 - >seq9139,non-specific,197320,3,223,5.569069999999999e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33913,Q#2492 - >seq9139,non-specific,197307,3,230,8.01979e-21,93.1213,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33914,Q#2492 - >seq9139,specific,335306,4,223,3.52528e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33915,Q#2492 - >seq9139,non-specific,273186,3,231,2.0959e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33916,Q#2492 - >seq9139,non-specific,197319,7,230,2.49047e-16,80.0133,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33917,Q#2492 - >seq9139,non-specific,197321,1,230,7.49808e-16,78.3628,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33918,Q#2492 - >seq9139,non-specific,272954,3,230,1.62149e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33919,Q#2492 - >seq9139,non-specific,197336,3,188,1.5325799999999998e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33920,Q#2492 - >seq9139,non-specific,197322,2,230,3.9245e-09,59.253,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33921,Q#2492 - >seq9139,non-specific,236970,3,183,1.30143e-06,51.0482,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,marg,C-TerminusTruncated
33922,Q#2492 - >seq9139,non-specific,197311,24,230,1.3214100000000001e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,marg,CompleteHit
33923,Q#2492 - >seq9139,non-specific,339261,102,226,0.00147013,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs0_human.marg.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33924,Q#2493 - >seq9140,specific,238827,467,729,1.7594899999999998e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33925,Q#2493 - >seq9140,superfamily,295487,467,729,1.7594899999999998e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33926,Q#2493 - >seq9140,specific,333820,473,729,2.3046599999999995e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33927,Q#2493 - >seq9140,superfamily,333820,473,729,2.3046599999999995e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33928,Q#2493 - >seq9140,non-specific,238828,473,694,5.34963e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33929,Q#2493 - >seq9140,non-specific,275209,424,681,1.15807e-07,55.1564,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,C-TerminusTruncated
33930,Q#2493 - >seq9140,superfamily,275209,424,681,1.15807e-07,55.1564,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,C-TerminusTruncated
33931,Q#2493 - >seq9140,non-specific,238185,613,727,7.86014e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs0_human.marg.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB1,ORF2,hs0_human,marg,CompleteHit
33932,Q#2494 - >seq9141,specific,238827,466,723,1.6476999999999997e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33933,Q#2494 - >seq9141,superfamily,295487,466,723,1.6476999999999997e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33934,Q#2494 - >seq9141,specific,333820,472,696,3.28996e-34,129.72,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33935,Q#2494 - >seq9141,superfamily,333820,472,696,3.28996e-34,129.72,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33936,Q#2494 - >seq9141,non-specific,238828,472,693,5.88418e-14,72.2336,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33937,Q#2494 - >seq9141,non-specific,275209,423,680,1.70147e-08,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33938,Q#2494 - >seq9141,superfamily,275209,423,680,1.70147e-08,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33939,Q#2494 - >seq9141,non-specific,238185,612,689,0.0009042439999999999,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33940,Q#2494 - >seq9141,non-specific,317932,849,1008,0.00864199,39.3645,pfam15620,CENP-C_mid,C,cl21416,"Centromere assembly component CENP-C middle DNMT3B-binding region; CENP-C is a component of the centromere assembly complex in eukaryotes. CENP-C recruits the DNA methyltransferases DNMT3B, in order to establish the necessary epigenetic DNA-methylation essential for maintenance of chromatin structure and genomic stability. This middle region of CENP-C is the binding-domain for DNMT3B. Binding of CENP-C and DNMT3B to DNA occurs at both centromeric and peri-centromeric satellite repeats. CENP-C and DNMT3B regulate the histone code in these regions.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33941,Q#2494 - >seq9141,superfamily,317932,849,1008,0.00864199,39.3645,cl21416,CENP-C_mid superfamily,C, - ,"Centromere assembly component CENP-C middle DNMT3B-binding region; CENP-C is a component of the centromere assembly complex in eukaryotes. CENP-C recruits the DNA methyltransferases DNMT3B, in order to establish the necessary epigenetic DNA-methylation essential for maintenance of chromatin structure and genomic stability. This middle region of CENP-C is the binding-domain for DNMT3B. Binding of CENP-C and DNMT3B to DNA occurs at both centromeric and peri-centromeric satellite repeats. CENP-C and DNMT3B regulate the histone code in these regions.",L1PB1.ORF2.hs0_human.pars.frame1,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33942,Q#2495 - >seq9142,specific,311990,1168,1185,0.00458468,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs0_human.pars.frame2,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs0_human,pars,CompleteHit
33943,Q#2495 - >seq9142,superfamily,311990,1168,1185,0.00458468,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs0_human.pars.frame2,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs0_human,pars,CompleteHit
33944,Q#2496 - >seq9143,specific,197310,3,230,1.69567e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33945,Q#2496 - >seq9143,superfamily,351117,3,230,1.69567e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33946,Q#2496 - >seq9143,non-specific,197306,3,230,6.895919999999999e-34,130.679,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33947,Q#2496 - >seq9143,non-specific,223780,3,231,3.3652200000000003e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33948,Q#2496 - >seq9143,non-specific,197320,3,223,5.42898e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33949,Q#2496 - >seq9143,non-specific,197307,3,230,3.72702e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33950,Q#2496 - >seq9143,specific,335306,4,223,3.4391700000000005e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33951,Q#2496 - >seq9143,non-specific,197319,7,230,1.90037e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33952,Q#2496 - >seq9143,non-specific,273186,3,231,2.0434600000000001e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33953,Q#2496 - >seq9143,non-specific,197321,1,230,7.10712e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33954,Q#2496 - >seq9143,non-specific,272954,3,230,7.95552e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33955,Q#2496 - >seq9143,non-specific,197336,3,188,1.4946799999999998e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33956,Q#2496 - >seq9143,non-specific,197322,2,230,3.8251999999999996e-09,59.253,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33957,Q#2496 - >seq9143,non-specific,236970,3,183,6.55167e-07,51.8186,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs0_human,pars,C-TerminusTruncated
33958,Q#2496 - >seq9143,non-specific,197311,24,230,8.979500000000001e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs0_human,pars,CompleteHit
33959,Q#2496 - >seq9143,non-specific,338310,987,1049,0.00115697,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs0_human,pars,BothTerminiTruncated
33960,Q#2496 - >seq9143,superfamily,338310,987,1049,0.00115697,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs0_human,pars,BothTerminiTruncated
33961,Q#2496 - >seq9143,non-specific,339261,102,226,0.00123136,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs0_human.pars.frame3,1909181931_L1PB1.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs0_human,pars,CompleteHit
33962,Q#2497 - >seq9144,non-specific,238827,631,721,1.23427e-13,71.1682,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
33963,Q#2497 - >seq9144,superfamily,295487,631,721,1.23427e-13,71.1682,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
33964,Q#2497 - >seq9144,specific,311990,1190,1207,8.83959e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33965,Q#2497 - >seq9144,superfamily,311990,1190,1207,8.83959e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33966,Q#2497 - >seq9144,non-specific,333820,598,689,0.00118475,41.1238,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
33967,Q#2497 - >seq9144,superfamily,333820,598,689,0.00118475,41.1238,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.pars.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
33968,Q#2498 - >seq9145,specific,197310,3,230,9.612979999999998e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33969,Q#2498 - >seq9145,superfamily,351117,3,230,9.612979999999998e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33970,Q#2498 - >seq9145,specific,238827,502,681,6.5825800000000005e-46,164.386,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33971,Q#2498 - >seq9145,superfamily,295487,502,681,6.5825800000000005e-46,164.386,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33972,Q#2498 - >seq9145,non-specific,197306,3,230,3.9454999999999995e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33973,Q#2498 - >seq9145,non-specific,333820,508,677,2.2921099999999996e-24,101.215,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33974,Q#2498 - >seq9145,superfamily,333820,508,677,2.2921099999999996e-24,101.215,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33975,Q#2498 - >seq9145,non-specific,197307,3,230,9.62655e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33976,Q#2498 - >seq9145,non-specific,197320,3,223,2.54421e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33977,Q#2498 - >seq9145,non-specific,223780,3,231,2.34464e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33978,Q#2498 - >seq9145,non-specific,197321,1,230,3.6228e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33979,Q#2498 - >seq9145,non-specific,273186,3,231,2.0768000000000002e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33980,Q#2498 - >seq9145,specific,335306,4,223,7.5394e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33981,Q#2498 - >seq9145,non-specific,272954,3,230,9.97705e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33982,Q#2498 - >seq9145,non-specific,197319,7,230,6.38394e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33983,Q#2498 - >seq9145,non-specific,197336,3,188,4.49497e-11,64.5559,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33984,Q#2498 - >seq9145,non-specific,238828,508,663,2.7288e-09,58.7516,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33985,Q#2498 - >seq9145,non-specific,236970,3,231,4.3823999999999996e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33986,Q#2498 - >seq9145,non-specific,275209,458,663,4.9572699999999994e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33987,Q#2498 - >seq9145,superfamily,275209,458,663,4.9572699999999994e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33988,Q#2498 - >seq9145,non-specific,197322,2,230,1.1385500000000001e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33989,Q#2498 - >seq9145,non-specific,197311,1,140,2.17158e-06,49.5977,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33990,Q#2498 - >seq9145,non-specific,235175,285,443,2.67804e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
33991,Q#2498 - >seq9145,superfamily,235175,285,443,2.67804e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
33992,Q#2498 - >seq9145,non-specific,235175,300,455,5.3248800000000004e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
33993,Q#2498 - >seq9145,non-specific,274009,301,451,0.000138609,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33994,Q#2498 - >seq9145,superfamily,274009,301,451,0.000138609,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,pars,C-TerminusTruncated
33995,Q#2498 - >seq9145,non-specific,339261,102,226,0.00019892599999999999,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB2,ORF2,hs1_chimp,pars,CompleteHit
33996,Q#2498 - >seq9145,specific,225881,475,672,0.0025215,41.3629,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
33997,Q#2498 - >seq9145,superfamily,225881,475,672,0.0025215,41.3629,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,pars,BothTerminiTruncated
33998,Q#2498 - >seq9145,non-specific,334125,206,403,0.00323184,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
33999,Q#2498 - >seq9145,superfamily,334125,206,403,0.00323184,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs1_chimp.pars.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34000,Q#2500 - >seq9147,non-specific,238827,631,721,1.2237799999999999e-13,71.1682,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34001,Q#2500 - >seq9147,superfamily,295487,631,721,1.2237799999999999e-13,71.1682,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34002,Q#2500 - >seq9147,specific,311990,1191,1208,8.846719999999999e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34003,Q#2500 - >seq9147,superfamily,311990,1191,1208,8.846719999999999e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34004,Q#2500 - >seq9147,non-specific,333820,598,689,0.00117484,41.1238,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34005,Q#2500 - >seq9147,superfamily,333820,598,689,0.00117484,41.1238,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.marg.frame1,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34006,Q#2501 - >seq9148,specific,197310,3,230,9.444069999999997e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34007,Q#2501 - >seq9148,superfamily,351117,3,230,9.444069999999997e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34008,Q#2501 - >seq9148,specific,238827,502,681,6.33934e-46,164.386,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34009,Q#2501 - >seq9148,superfamily,295487,502,681,6.33934e-46,164.386,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34010,Q#2501 - >seq9148,non-specific,197306,3,230,3.76427e-32,125.67200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34011,Q#2501 - >seq9148,non-specific,333820,508,677,2.2722099999999997e-24,101.215,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34012,Q#2501 - >seq9148,superfamily,333820,508,677,2.2722099999999997e-24,101.215,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34013,Q#2501 - >seq9148,non-specific,197307,3,230,9.54467e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34014,Q#2501 - >seq9148,non-specific,197320,3,223,2.5466700000000002e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34015,Q#2501 - >seq9148,non-specific,223780,3,231,2.34692e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34016,Q#2501 - >seq9148,non-specific,197321,1,230,3.52487e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34017,Q#2501 - >seq9148,non-specific,273186,3,231,2.0788e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34018,Q#2501 - >seq9148,specific,335306,4,223,7.54648e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34019,Q#2501 - >seq9148,non-specific,272954,3,230,9.708149999999999e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34020,Q#2501 - >seq9148,non-specific,197319,7,230,5.70712e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34021,Q#2501 - >seq9148,non-specific,197336,3,188,4.49925e-11,64.5559,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34022,Q#2501 - >seq9148,non-specific,238828,508,663,2.68081e-09,58.7516,cd01651,RT_G2_intron,C,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34023,Q#2501 - >seq9148,non-specific,236970,3,231,4.38657e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34024,Q#2501 - >seq9148,non-specific,275209,458,663,4.918480000000001e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34025,Q#2501 - >seq9148,superfamily,275209,458,663,4.918480000000001e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34026,Q#2501 - >seq9148,non-specific,197322,2,230,1.13965e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34027,Q#2501 - >seq9148,non-specific,197311,1,140,2.17357e-06,49.5977,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34028,Q#2501 - >seq9148,non-specific,235175,285,443,2.658e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34029,Q#2501 - >seq9148,superfamily,235175,285,443,2.658e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34030,Q#2501 - >seq9148,non-specific,235175,300,455,5.2850200000000004e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34031,Q#2501 - >seq9148,non-specific,274009,301,451,0.000139922,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34032,Q#2501 - >seq9148,superfamily,274009,301,451,0.000139922,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34033,Q#2501 - >seq9148,non-specific,339261,102,226,0.000195288,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1PB2,ORF2,hs1_chimp,marg,CompleteHit
34034,Q#2501 - >seq9148,specific,225881,475,672,0.00241602,41.3629,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34035,Q#2501 - >seq9148,superfamily,225881,475,672,0.00241602,41.3629,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34036,Q#2501 - >seq9148,non-specific,334125,206,403,0.00320711,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34037,Q#2501 - >seq9148,superfamily,334125,206,403,0.00320711,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs1_chimp.marg.frame2,1909181932_L1PB2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1PB2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34038,Q#2505 - >seq9152,non-specific,338310,934,995,0.00453769,39.4788,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs2_gorilla.marg.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
34039,Q#2505 - >seq9152,superfamily,338310,934,995,0.00453769,39.4788,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs2_gorilla.marg.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
34040,Q#2506 - >seq9153,specific,238827,502,764,1.1238399999999999e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34041,Q#2506 - >seq9153,superfamily,295487,502,764,1.1238399999999999e-66,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34042,Q#2506 - >seq9153,specific,197310,3,230,1.84196e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34043,Q#2506 - >seq9153,superfamily,351117,3,230,1.84196e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34044,Q#2506 - >seq9153,specific,333820,508,764,4.744519999999999e-32,123.557,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34045,Q#2506 - >seq9153,superfamily,333820,508,764,4.744519999999999e-32,123.557,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34046,Q#2506 - >seq9153,non-specific,197306,3,230,3.3608899999999997e-31,122.975,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34047,Q#2506 - >seq9153,non-specific,197320,3,223,1.03071e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34048,Q#2506 - >seq9153,non-specific,197307,3,230,2.28428e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34049,Q#2506 - >seq9153,non-specific,223780,3,231,6.57299e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34050,Q#2506 - >seq9153,specific,335306,4,223,1.5710899999999999e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34051,Q#2506 - >seq9153,non-specific,197321,1,230,3.4400699999999994e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34052,Q#2506 - >seq9153,non-specific,273186,3,231,9.044819999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34053,Q#2506 - >seq9153,non-specific,272954,3,230,1.4523e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34054,Q#2506 - >seq9153,non-specific,197319,7,230,2.2692399999999997e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34055,Q#2506 - >seq9153,non-specific,238828,508,729,1.04428e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34056,Q#2506 - >seq9153,non-specific,197336,3,188,7.52064e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34057,Q#2506 - >seq9153,non-specific,236970,3,188,7.268430000000001e-08,54.9002,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
34058,Q#2506 - >seq9153,non-specific,275209,459,663,2.89029e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
34059,Q#2506 - >seq9153,superfamily,275209,459,663,2.89029e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
34060,Q#2506 - >seq9153,non-specific,197322,2,230,4.65989e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34061,Q#2506 - >seq9153,non-specific,197311,1,230,2.9308400000000002e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34062,Q#2506 - >seq9153,non-specific,339261,102,226,6.15966e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34063,Q#2506 - >seq9153,non-specific,238185,648,762,7.12906e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34064,Q#2506 - >seq9153,non-specific,235175,284,461,9.97685e-05,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
34065,Q#2506 - >seq9153,superfamily,235175,284,461,9.97685e-05,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
34066,Q#2506 - >seq9153,specific,311990,1234,1251,0.000623673,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34067,Q#2506 - >seq9153,superfamily,311990,1234,1251,0.000623673,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs2_gorilla,marg,CompleteHit
34068,Q#2506 - >seq9153,non-specific,274009,300,450,0.0017230000000000001,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
34069,Q#2506 - >seq9153,superfamily,274009,300,450,0.0017230000000000001,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
34070,Q#2506 - >seq9153,non-specific,274009,287,439,0.00548716,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.marg.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
34071,Q#2507 - >seq9154,specific,311990,1116,1133,0.000153482,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs2_gorilla.pars.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34072,Q#2507 - >seq9154,superfamily,311990,1116,1133,0.000153482,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs2_gorilla.pars.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34073,Q#2507 - >seq9154,non-specific,338310,934,995,0.00553766,39.0936,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs2_gorilla.pars.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
34074,Q#2507 - >seq9154,superfamily,338310,934,995,0.00553766,39.0936,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs2_gorilla.pars.frame1,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
34075,Q#2508 - >seq9155,specific,238827,502,764,8.734959999999999e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34076,Q#2508 - >seq9155,superfamily,295487,502,764,8.734959999999999e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34077,Q#2508 - >seq9155,specific,197310,3,230,7.870159999999999e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34078,Q#2508 - >seq9155,superfamily,351117,3,230,7.870159999999999e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34079,Q#2508 - >seq9155,specific,333820,508,764,2.12127e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34080,Q#2508 - >seq9155,superfamily,333820,508,764,2.12127e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34081,Q#2508 - >seq9155,non-specific,197306,3,230,5.30377e-31,122.205,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34082,Q#2508 - >seq9155,non-specific,197320,3,223,7.71923e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34083,Q#2508 - >seq9155,non-specific,197307,3,230,1.0541299999999999e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34084,Q#2508 - >seq9155,non-specific,223780,3,231,2.22771e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34085,Q#2508 - >seq9155,specific,335306,4,223,1.5500100000000002e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34086,Q#2508 - >seq9155,non-specific,197321,1,230,1.7376099999999998e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34087,Q#2508 - >seq9155,non-specific,273186,3,231,4.659269999999999e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34088,Q#2508 - >seq9155,non-specific,272954,3,230,7.2753800000000005e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34089,Q#2508 - >seq9155,non-specific,197319,7,230,9.81579e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34090,Q#2508 - >seq9155,non-specific,238828,508,729,6.810189999999999e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34091,Q#2508 - >seq9155,non-specific,197336,3,188,7.41842e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34092,Q#2508 - >seq9155,non-specific,236970,3,188,6.48593e-08,55.2854,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
34093,Q#2508 - >seq9155,non-specific,275209,459,663,1.69452e-07,54.7712,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
34094,Q#2508 - >seq9155,superfamily,275209,459,663,1.69452e-07,54.7712,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
34095,Q#2508 - >seq9155,non-specific,197322,2,230,4.59603e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34096,Q#2508 - >seq9155,non-specific,197311,1,230,3.8248e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34097,Q#2508 - >seq9155,non-specific,238185,648,762,4.45362e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34098,Q#2508 - >seq9155,non-specific,235175,284,461,4.949520000000001e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
34099,Q#2508 - >seq9155,superfamily,235175,284,461,4.949520000000001e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
34100,Q#2508 - >seq9155,non-specific,339261,102,226,0.00010658299999999999,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs2_gorilla,pars,CompleteHit
34101,Q#2508 - >seq9155,non-specific,274009,300,450,0.00128575,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
34102,Q#2508 - >seq9155,superfamily,274009,300,450,0.00128575,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
34103,Q#2508 - >seq9155,non-specific,274009,287,439,0.00382732,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs2_gorilla.pars.frame3,1909181937_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
34104,Q#2511 - >seq9158,specific,238827,510,772,1.7947999999999997e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34105,Q#2511 - >seq9158,superfamily,295487,510,772,1.7947999999999997e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34106,Q#2511 - >seq9158,specific,197310,9,236,5.644149999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34107,Q#2511 - >seq9158,superfamily,351117,9,236,5.644149999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34108,Q#2511 - >seq9158,non-specific,197306,9,236,1.38359e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34109,Q#2511 - >seq9158,specific,333820,516,772,3.20118e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34110,Q#2511 - >seq9158,superfamily,333820,516,772,3.20118e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34111,Q#2511 - >seq9158,non-specific,197307,9,236,2.3618599999999996e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34112,Q#2511 - >seq9158,non-specific,223780,9,238,1.4878199999999998e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34113,Q#2511 - >seq9158,non-specific,197320,8,236,2.27264e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34114,Q#2511 - >seq9158,non-specific,197321,7,236,6.97339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34115,Q#2511 - >seq9158,specific,335306,10,229,1.3230399999999998e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34116,Q#2511 - >seq9158,non-specific,273186,9,237,8.04911e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34117,Q#2511 - >seq9158,non-specific,272954,9,236,1.60657e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34118,Q#2511 - >seq9158,non-specific,197319,8,236,4.5166000000000005e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34119,Q#2511 - >seq9158,non-specific,197336,7,235,2.70283e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34120,Q#2511 - >seq9158,non-specific,238828,516,737,2.29704e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34121,Q#2511 - >seq9158,non-specific,197322,9,236,2.74255e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34122,Q#2511 - >seq9158,non-specific,275209,467,800,9.85612e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34123,Q#2511 - >seq9158,superfamily,275209,467,800,9.85612e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34124,Q#2511 - >seq9158,non-specific,236970,9,238,4.34079e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34125,Q#2511 - >seq9158,non-specific,339261,108,232,1.87998e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34126,Q#2511 - >seq9158,non-specific,197311,7,236,2.1839600000000002e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,pars,CompleteHit
34127,Q#2511 - >seq9158,non-specific,197317,139,229,1.41886e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,pars,N-TerminusTruncated
34128,Q#2511 - >seq9158,non-specific,238185,656,772,0.000175315,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1P2,ORF2,hs3_orang,pars,CompleteHit
34129,Q#2511 - >seq9158,non-specific,274009,305,453,0.000923842,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,C-TerminusTruncated
34130,Q#2511 - >seq9158,superfamily,274009,305,453,0.000923842,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,C-TerminusTruncated
34131,Q#2511 - >seq9158,non-specific,226098,138,239,0.00165528,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,pars,N-TerminusTruncated
34132,Q#2511 - >seq9158,non-specific,197314,7,192,0.0019687999999999997,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1P2,ORF2,hs3_orang,pars,C-TerminusTruncated
34133,Q#2511 - >seq9158,non-specific,235175,295,464,0.00370722,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,BothTerminiTruncated
34134,Q#2511 - >seq9158,superfamily,235175,295,464,0.00370722,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,BothTerminiTruncated
34135,Q#2511 - >seq9158,non-specific,274008,263,500,0.00560386,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,N-TerminusTruncated
34136,Q#2511 - >seq9158,superfamily,274008,263,500,0.00560386,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,pars,N-TerminusTruncated
34137,Q#2511 - >seq9158,non-specific,293702,337,451,0.00873155,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs3_orang,pars,C-TerminusTruncated
34138,Q#2511 - >seq9158,superfamily,293702,337,451,0.00873155,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs3_orang.pars.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1P2,ORF2,hs3_orang,pars,C-TerminusTruncated
34139,Q#2514 - >seq9161,specific,238827,510,772,1.4262599999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34140,Q#2514 - >seq9161,superfamily,295487,510,772,1.4262599999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34141,Q#2514 - >seq9161,specific,197310,9,236,5.060329999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34142,Q#2514 - >seq9161,superfamily,351117,9,236,5.060329999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34143,Q#2514 - >seq9161,non-specific,197306,9,236,1.64763e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34144,Q#2514 - >seq9161,specific,333820,516,772,2.96122e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34145,Q#2514 - >seq9161,superfamily,333820,516,772,2.96122e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34146,Q#2514 - >seq9161,non-specific,197307,9,236,2.40736e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34147,Q#2514 - >seq9161,non-specific,223780,9,238,1.5604e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34148,Q#2514 - >seq9161,non-specific,197320,8,236,2.1265300000000003e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34149,Q#2514 - >seq9161,non-specific,197321,7,236,7.175050000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34150,Q#2514 - >seq9161,specific,335306,10,229,1.33537e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34151,Q#2514 - >seq9161,non-specific,273186,9,237,8.682540000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34152,Q#2514 - >seq9161,non-specific,272954,9,236,1.66827e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34153,Q#2514 - >seq9161,non-specific,197319,8,236,4.4329400000000006e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34154,Q#2514 - >seq9161,non-specific,197336,7,235,2.80585e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34155,Q#2514 - >seq9161,non-specific,238828,516,737,2.2539e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34156,Q#2514 - >seq9161,non-specific,197322,9,236,2.76928e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34157,Q#2514 - >seq9161,non-specific,275209,467,800,9.60509e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34158,Q#2514 - >seq9161,superfamily,275209,467,800,9.60509e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34159,Q#2514 - >seq9161,non-specific,236970,9,238,4.3818299999999995e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34160,Q#2514 - >seq9161,non-specific,339261,108,232,1.82405e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34161,Q#2514 - >seq9161,non-specific,197311,7,236,2.04483e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1P2,ORF2,hs3_orang,marg,CompleteHit
34162,Q#2514 - >seq9161,non-specific,197317,139,229,1.45838e-06,50.6784,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,marg,N-TerminusTruncated
34163,Q#2514 - >seq9161,non-specific,238185,656,772,0.00017680299999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1P2,ORF2,hs3_orang,marg,CompleteHit
34164,Q#2514 - >seq9161,non-specific,274009,305,453,0.00090921,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,C-TerminusTruncated
34165,Q#2514 - >seq9161,superfamily,274009,305,453,0.00090921,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,C-TerminusTruncated
34166,Q#2514 - >seq9161,non-specific,226098,138,239,0.00167039,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1P2,ORF2,hs3_orang,marg,N-TerminusTruncated
34167,Q#2514 - >seq9161,non-specific,197314,7,192,0.00195139,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1P2,ORF2,hs3_orang,marg,C-TerminusTruncated
34168,Q#2514 - >seq9161,non-specific,235175,295,464,0.00335135,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,BothTerminiTruncated
34169,Q#2514 - >seq9161,superfamily,235175,295,464,0.00335135,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,BothTerminiTruncated
34170,Q#2514 - >seq9161,non-specific,274008,263,500,0.00494052,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,N-TerminusTruncated
34171,Q#2514 - >seq9161,superfamily,274008,263,500,0.00494052,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1P2,ORF2,hs3_orang,marg,N-TerminusTruncated
34172,Q#2514 - >seq9161,non-specific,293702,337,451,0.00808057,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs3_orang,marg,C-TerminusTruncated
34173,Q#2514 - >seq9161,superfamily,293702,337,451,0.00808057,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1P2.ORF2.hs3_orang.marg.frame3,1909181937_L1P2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1P2,ORF2,hs3_orang,marg,C-TerminusTruncated
34174,Q#2515 - >seq9162,specific,238827,510,772,2.706519999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34175,Q#2515 - >seq9162,superfamily,295487,510,772,2.706519999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34176,Q#2515 - >seq9162,specific,197310,9,236,6.410249999999998e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34177,Q#2515 - >seq9162,superfamily,351117,9,236,6.410249999999998e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34178,Q#2515 - >seq9162,non-specific,197306,9,236,1.2308099999999998e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34179,Q#2515 - >seq9162,specific,333820,516,772,1.96874e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34180,Q#2515 - >seq9162,superfamily,333820,516,772,1.96874e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34181,Q#2515 - >seq9162,non-specific,197307,9,236,8.57065e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34182,Q#2515 - >seq9162,non-specific,223780,9,238,2.48717e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34183,Q#2515 - >seq9162,non-specific,197320,8,236,2.41317e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34184,Q#2515 - >seq9162,non-specific,197321,7,236,2.76148e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34185,Q#2515 - >seq9162,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34186,Q#2515 - >seq9162,non-specific,273186,9,237,1.04383e-17,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34187,Q#2515 - >seq9162,non-specific,272954,9,236,3.0378700000000005e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34188,Q#2515 - >seq9162,non-specific,197319,8,236,6.8901e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34189,Q#2515 - >seq9162,non-specific,197336,7,235,1.60331e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34190,Q#2515 - >seq9162,non-specific,238828,516,737,4.03331e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34191,Q#2515 - >seq9162,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34192,Q#2515 - >seq9162,non-specific,236970,9,238,3.1690099999999997e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34193,Q#2515 - >seq9162,non-specific,275209,467,800,1.99905e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34194,Q#2515 - >seq9162,superfamily,275209,467,800,1.99905e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34195,Q#2515 - >seq9162,non-specific,339261,108,232,1.48153e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34196,Q#2515 - >seq9162,non-specific,197317,139,229,7.88565e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34197,Q#2515 - >seq9162,non-specific,197311,7,236,2.35025e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34198,Q#2515 - >seq9162,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34199,Q#2515 - >seq9162,non-specific,274009,305,453,0.000235913,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34200,Q#2515 - >seq9162,superfamily,274009,305,453,0.000235913,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34201,Q#2515 - >seq9162,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34202,Q#2515 - >seq9162,non-specific,197314,7,236,0.00267176,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34203,Q#2515 - >seq9162,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34204,Q#2515 - >seq9162,non-specific,235175,301,469,0.00527011,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34205,Q#2515 - >seq9162,superfamily,235175,301,469,0.00527011,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,marg,BothTerminiTruncated
34206,Q#2515 - >seq9162,specific,311990,1241,1259,0.00901839,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34207,Q#2515 - >seq9162,superfamily,311990,1241,1259,0.00901839,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs1_chimp,marg,CompleteHit
34208,Q#2515 - >seq9162,non-specific,293702,337,451,0.00979671,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34209,Q#2515 - >seq9162,superfamily,293702,337,451,0.00979671,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs1_chimp.marg.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs1_chimp,marg,C-TerminusTruncated
34210,Q#2516 - >seq9163,non-specific,130141,277,387,0.00624777,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.marg.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34211,Q#2516 - >seq9163,superfamily,130141,277,387,0.00624777,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.marg.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34212,Q#2516 - >seq9163,non-specific,130141,277,387,0.00624777,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.marg.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,marg,N-TerminusTruncated
34213,Q#2519 - >seq9166,non-specific,130141,277,387,0.00624777,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.pars.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34214,Q#2519 - >seq9166,superfamily,130141,277,387,0.00624777,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.pars.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34215,Q#2519 - >seq9166,non-specific,130141,277,387,0.00624777,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs1_chimp.pars.frame1,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34216,Q#2520 - >seq9167,specific,238827,510,772,2.706519999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34217,Q#2520 - >seq9167,superfamily,295487,510,772,2.706519999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34218,Q#2520 - >seq9167,specific,197310,9,236,6.410249999999998e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34219,Q#2520 - >seq9167,superfamily,351117,9,236,6.410249999999998e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34220,Q#2520 - >seq9167,non-specific,197306,9,236,1.2308099999999998e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34221,Q#2520 - >seq9167,specific,333820,516,772,1.96874e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34222,Q#2520 - >seq9167,superfamily,333820,516,772,1.96874e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34223,Q#2520 - >seq9167,non-specific,197307,9,236,8.57065e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34224,Q#2520 - >seq9167,non-specific,223780,9,238,2.48717e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34225,Q#2520 - >seq9167,non-specific,197320,8,236,2.41317e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34226,Q#2520 - >seq9167,non-specific,197321,7,236,2.76148e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34227,Q#2520 - >seq9167,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34228,Q#2520 - >seq9167,non-specific,273186,9,237,1.04383e-17,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34229,Q#2520 - >seq9167,non-specific,272954,9,236,3.0378700000000005e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34230,Q#2520 - >seq9167,non-specific,197319,8,236,6.8901e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34231,Q#2520 - >seq9167,non-specific,197336,7,235,1.60331e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34232,Q#2520 - >seq9167,non-specific,238828,516,737,4.03331e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34233,Q#2520 - >seq9167,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34234,Q#2520 - >seq9167,non-specific,236970,9,238,3.1690099999999997e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34235,Q#2520 - >seq9167,non-specific,275209,467,800,1.99905e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34236,Q#2520 - >seq9167,superfamily,275209,467,800,1.99905e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34237,Q#2520 - >seq9167,non-specific,339261,108,232,1.48153e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34238,Q#2520 - >seq9167,non-specific,197317,139,229,7.88565e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34239,Q#2520 - >seq9167,non-specific,197311,7,236,2.35025e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34240,Q#2520 - >seq9167,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34241,Q#2520 - >seq9167,non-specific,274009,305,453,0.000235913,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
34242,Q#2520 - >seq9167,superfamily,274009,305,453,0.000235913,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
34243,Q#2520 - >seq9167,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs1_chimp,pars,N-TerminusTruncated
34244,Q#2520 - >seq9167,non-specific,197314,7,236,0.00267176,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34245,Q#2520 - >seq9167,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34246,Q#2520 - >seq9167,non-specific,235175,301,469,0.00527011,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,pars,BothTerminiTruncated
34247,Q#2520 - >seq9167,superfamily,235175,301,469,0.00527011,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs1_chimp,pars,BothTerminiTruncated
34248,Q#2520 - >seq9167,specific,311990,1241,1259,0.00901839,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34249,Q#2520 - >seq9167,superfamily,311990,1241,1259,0.00901839,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs1_chimp,pars,CompleteHit
34250,Q#2520 - >seq9167,non-specific,293702,337,451,0.00979671,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
34251,Q#2520 - >seq9167,superfamily,293702,337,451,0.00979671,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs1_chimp.pars.frame3,1909181938_L1PA2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs1_chimp,pars,C-TerminusTruncated
34252,Q#2521 - >seq9168,non-specific,130141,277,387,0.00618274,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs0_human.pars.frame1,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs0_human,pars,N-TerminusTruncated
34253,Q#2521 - >seq9168,superfamily,130141,277,387,0.00618274,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs0_human.pars.frame1,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA2,ORF2,hs0_human,pars,N-TerminusTruncated
34254,Q#2523 - >seq9170,specific,238827,510,772,2.759629999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34255,Q#2523 - >seq9170,superfamily,295487,510,772,2.759629999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34256,Q#2523 - >seq9170,specific,197310,9,236,7.132039999999998e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34257,Q#2523 - >seq9170,superfamily,351117,9,236,7.132039999999998e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34258,Q#2523 - >seq9170,non-specific,197306,9,236,1.2308099999999998e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34259,Q#2523 - >seq9170,specific,333820,516,772,1.9498099999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34260,Q#2523 - >seq9170,superfamily,333820,516,772,1.9498099999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34261,Q#2523 - >seq9170,non-specific,197307,9,236,8.40858e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34262,Q#2523 - >seq9170,non-specific,223780,9,238,2.48717e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34263,Q#2523 - >seq9170,non-specific,197320,8,236,2.2793400000000004e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34264,Q#2523 - >seq9170,non-specific,197321,7,236,2.76148e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34265,Q#2523 - >seq9170,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34266,Q#2523 - >seq9170,non-specific,273186,9,237,1.0242999999999999e-17,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34267,Q#2523 - >seq9170,non-specific,272954,9,236,2.95323e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34268,Q#2523 - >seq9170,non-specific,197319,8,236,6.955e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34269,Q#2523 - >seq9170,non-specific,197336,7,235,1.58841e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34270,Q#2523 - >seq9170,non-specific,238828,516,737,3.9955999999999995e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34271,Q#2523 - >seq9170,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34272,Q#2523 - >seq9170,non-specific,236970,9,238,3.1690099999999997e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34273,Q#2523 - >seq9170,non-specific,275209,467,800,1.98136e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34274,Q#2523 - >seq9170,superfamily,275209,467,800,1.98136e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34275,Q#2523 - >seq9170,non-specific,339261,108,232,1.54012e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34276,Q#2523 - >seq9170,non-specific,197317,139,229,7.95834e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,pars,N-TerminusTruncated
34277,Q#2523 - >seq9170,non-specific,197311,7,236,2.3723500000000002e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,pars,CompleteHit
34278,Q#2523 - >seq9170,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34279,Q#2523 - >seq9170,non-specific,274009,305,453,0.000241975,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,pars,C-TerminusTruncated
34280,Q#2523 - >seq9170,superfamily,274009,305,453,0.000241975,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,pars,C-TerminusTruncated
34281,Q#2523 - >seq9170,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,pars,N-TerminusTruncated
34282,Q#2523 - >seq9170,non-specific,197314,7,236,0.00267176,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs0_human,pars,CompleteHit
34283,Q#2523 - >seq9170,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA2,ORF2,hs0_human,pars,CompleteHit
34284,Q#2523 - >seq9170,non-specific,235175,301,469,0.00518151,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,pars,BothTerminiTruncated
34285,Q#2523 - >seq9170,superfamily,235175,301,469,0.00518151,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,pars,BothTerminiTruncated
34286,Q#2523 - >seq9170,specific,311990,1241,1259,0.00910723,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs0_human,pars,CompleteHit
34287,Q#2523 - >seq9170,superfamily,311990,1241,1259,0.00910723,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA2,ORF2,hs0_human,pars,CompleteHit
34288,Q#2523 - >seq9170,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs0_human,pars,C-TerminusTruncated
34289,Q#2523 - >seq9170,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs0_human.pars.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs0_human,pars,C-TerminusTruncated
34290,Q#2524 - >seq9171,non-specific,130141,277,387,0.00618274,40.5733,TIGR01069,mutS2,N,cl31057,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs0_human.marg.frame1,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs0_human,marg,N-TerminusTruncated
34291,Q#2524 - >seq9171,superfamily,130141,277,387,0.00618274,40.5733,cl31057,mutS2 superfamily,N, - ,"MutS2 family protein; Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other]",L1PA2.ORF2.hs0_human.marg.frame1,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA2,ORF2,hs0_human,marg,N-TerminusTruncated
34292,Q#2526 - >seq9173,specific,238827,510,772,2.759629999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34293,Q#2526 - >seq9173,superfamily,295487,510,772,2.759629999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34294,Q#2526 - >seq9173,specific,197310,9,236,7.132039999999998e-65,219.53,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34295,Q#2526 - >seq9173,superfamily,351117,9,236,7.132039999999998e-65,219.53,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34296,Q#2526 - >seq9173,non-specific,197306,9,236,1.2308099999999998e-55,193.467,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34297,Q#2526 - >seq9173,specific,333820,516,772,1.9498099999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34298,Q#2526 - >seq9173,superfamily,333820,516,772,1.9498099999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34299,Q#2526 - >seq9173,non-specific,197307,9,236,8.40858e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34300,Q#2526 - >seq9173,non-specific,223780,9,238,2.48717e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34301,Q#2526 - >seq9173,non-specific,197320,8,236,2.2793400000000004e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34302,Q#2526 - >seq9173,non-specific,197321,7,236,2.76148e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34303,Q#2526 - >seq9173,specific,335306,10,229,1.74267e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34304,Q#2526 - >seq9173,non-specific,273186,9,237,1.0242999999999999e-17,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34305,Q#2526 - >seq9173,non-specific,272954,9,236,2.95323e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34306,Q#2526 - >seq9173,non-specific,197319,8,236,6.955e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34307,Q#2526 - >seq9173,non-specific,197336,7,235,1.58841e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34308,Q#2526 - >seq9173,non-specific,238828,516,737,3.9955999999999995e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34309,Q#2526 - >seq9173,non-specific,197322,9,236,2.813e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34310,Q#2526 - >seq9173,non-specific,236970,9,238,3.1690099999999997e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34311,Q#2526 - >seq9173,non-specific,275209,467,800,1.98136e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34312,Q#2526 - >seq9173,superfamily,275209,467,800,1.98136e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34313,Q#2526 - >seq9173,non-specific,339261,108,232,1.54012e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34314,Q#2526 - >seq9173,non-specific,197317,139,229,7.95834e-08,54.5304,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,marg,N-TerminusTruncated
34315,Q#2526 - >seq9173,non-specific,197311,7,236,2.3723500000000002e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA2,ORF2,hs0_human,marg,CompleteHit
34316,Q#2526 - >seq9173,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34317,Q#2526 - >seq9173,non-specific,274009,305,453,0.000241975,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,marg,C-TerminusTruncated
34318,Q#2526 - >seq9173,superfamily,274009,305,453,0.000241975,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,marg,C-TerminusTruncated
34319,Q#2526 - >seq9173,non-specific,226098,138,239,0.000571735,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA2,ORF2,hs0_human,marg,N-TerminusTruncated
34320,Q#2526 - >seq9173,non-specific,197314,7,236,0.00267176,40.7899,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA2,ORF2,hs0_human,marg,CompleteHit
34321,Q#2526 - >seq9173,non-specific,239569,525,748,0.00368242,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA2,ORF2,hs0_human,marg,CompleteHit
34322,Q#2526 - >seq9173,non-specific,235175,301,469,0.00518151,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,marg,BothTerminiTruncated
34323,Q#2526 - >seq9173,superfamily,235175,301,469,0.00518151,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA2,ORF2,hs0_human,marg,BothTerminiTruncated
34324,Q#2526 - >seq9173,specific,311990,1241,1259,0.00910723,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs0_human,marg,CompleteHit
34325,Q#2526 - >seq9173,superfamily,311990,1241,1259,0.00910723,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA2,ORF2,hs0_human,marg,CompleteHit
34326,Q#2526 - >seq9173,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs0_human,marg,C-TerminusTruncated
34327,Q#2526 - >seq9173,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA2.ORF2.hs0_human.marg.frame3,1909181940_L1PA2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA2,ORF2,hs0_human,marg,C-TerminusTruncated
34328,Q#2528 - >seq9175,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34329,Q#2528 - >seq9175,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34330,Q#2528 - >seq9175,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34331,Q#2528 - >seq9175,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34332,Q#2528 - >seq9175,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34333,Q#2528 - >seq9175,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34334,Q#2528 - >seq9175,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34335,Q#2528 - >seq9175,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34336,Q#2528 - >seq9175,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34337,Q#2528 - >seq9175,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34338,Q#2528 - >seq9175,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34339,Q#2528 - >seq9175,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34340,Q#2528 - >seq9175,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34341,Q#2528 - >seq9175,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34342,Q#2528 - >seq9175,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34343,Q#2528 - >seq9175,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34344,Q#2528 - >seq9175,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34345,Q#2528 - >seq9175,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34346,Q#2528 - >seq9175,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34347,Q#2528 - >seq9175,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34348,Q#2528 - >seq9175,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34349,Q#2528 - >seq9175,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34350,Q#2528 - >seq9175,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34351,Q#2528 - >seq9175,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34352,Q#2528 - >seq9175,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34353,Q#2528 - >seq9175,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34354,Q#2528 - >seq9175,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34355,Q#2528 - >seq9175,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34356,Q#2528 - >seq9175,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34357,Q#2528 - >seq9175,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34358,Q#2528 - >seq9175,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34359,Q#2528 - >seq9175,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34360,Q#2528 - >seq9175,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34361,Q#2528 - >seq9175,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34362,Q#2528 - >seq9175,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34363,Q#2528 - >seq9175,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34364,Q#2528 - >seq9175,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34365,Q#2528 - >seq9175,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34366,Q#2528 - >seq9175,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34367,Q#2528 - >seq9175,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34368,Q#2528 - >seq9175,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
34369,Q#2528 - >seq9175,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
34370,Q#2528 - >seq9175,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34371,Q#2528 - >seq9175,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34372,Q#2528 - >seq9175,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34373,Q#2528 - >seq9175,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34374,Q#2528 - >seq9175,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34375,Q#2528 - >seq9175,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34376,Q#2528 - >seq9175,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34377,Q#2528 - >seq9175,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
34378,Q#2528 - >seq9175,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,marg,N-TerminusTruncated
34379,Q#2528 - >seq9175,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34380,Q#2528 - >seq9175,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34381,Q#2528 - >seq9175,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,BothTerminiTruncated
34382,Q#2528 - >seq9175,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,BothTerminiTruncated
34383,Q#2528 - >seq9175,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,marg,BothTerminiTruncated
34384,Q#2528 - >seq9175,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34385,Q#2528 - >seq9175,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34386,Q#2528 - >seq9175,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34387,Q#2528 - >seq9175,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34388,Q#2528 - >seq9175,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,marg,CompleteHit
34389,Q#2528 - >seq9175,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34390,Q#2528 - >seq9175,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34391,Q#2528 - >seq9175,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.marg.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,marg,C-TerminusTruncated
34392,Q#2532 - >seq9179,specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34393,Q#2532 - >seq9179,superfamily,295487,510,772,5.086149999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34394,Q#2532 - >seq9179,non-specific,238827,510,772,5.086149999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34395,Q#2532 - >seq9179,specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34396,Q#2532 - >seq9179,superfamily,351117,9,236,9.633769999999999e-65,219.145,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34397,Q#2532 - >seq9179,non-specific,197310,9,236,9.633769999999999e-65,219.145,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34398,Q#2532 - >seq9179,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34399,Q#2532 - >seq9179,non-specific,197306,9,236,3.07914e-55,192.31099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34400,Q#2532 - >seq9179,specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34401,Q#2532 - >seq9179,superfamily,333820,516,772,2.95395e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34402,Q#2532 - >seq9179,non-specific,333820,516,772,2.95395e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34403,Q#2532 - >seq9179,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34404,Q#2532 - >seq9179,non-specific,197307,9,236,3.69953e-26,108.529,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34405,Q#2532 - >seq9179,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34406,Q#2532 - >seq9179,non-specific,223780,9,238,2.32707e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34407,Q#2532 - >seq9179,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34408,Q#2532 - >seq9179,non-specific,197320,8,236,3.83225e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34409,Q#2532 - >seq9179,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34410,Q#2532 - >seq9179,non-specific,197321,7,236,3.83456e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34411,Q#2532 - >seq9179,specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34412,Q#2532 - >seq9179,non-specific,335306,10,229,2.86223e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34413,Q#2532 - >seq9179,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34414,Q#2532 - >seq9179,non-specific,273186,9,237,2.07358e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34415,Q#2532 - >seq9179,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34416,Q#2532 - >seq9179,non-specific,272954,9,236,3.8443699999999994e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34417,Q#2532 - >seq9179,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34418,Q#2532 - >seq9179,non-specific,197319,8,236,3.7453e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34419,Q#2532 - >seq9179,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34420,Q#2532 - >seq9179,non-specific,197336,7,235,7.179689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34421,Q#2532 - >seq9179,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34422,Q#2532 - >seq9179,non-specific,238828,516,737,2.10914e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34423,Q#2532 - >seq9179,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34424,Q#2532 - >seq9179,non-specific,197322,9,236,3.34143e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34425,Q#2532 - >seq9179,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34426,Q#2532 - >seq9179,superfamily,275209,467,800,3.95555e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34427,Q#2532 - >seq9179,non-specific,275209,467,800,3.95555e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34428,Q#2532 - >seq9179,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34429,Q#2532 - >seq9179,non-specific,236970,9,238,2.9571999999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34430,Q#2532 - >seq9179,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34431,Q#2532 - >seq9179,non-specific,339261,108,232,3.12559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34432,Q#2532 - >seq9179,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
34433,Q#2532 - >seq9179,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
34434,Q#2532 - >seq9179,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34435,Q#2532 - >seq9179,non-specific,197311,7,236,3.86635e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34436,Q#2532 - >seq9179,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34437,Q#2532 - >seq9179,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34438,Q#2532 - >seq9179,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34439,Q#2532 - >seq9179,superfamily,274009,305,453,0.000218625,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34440,Q#2532 - >seq9179,non-specific,274009,305,453,0.000218625,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34441,Q#2532 - >seq9179,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
34442,Q#2532 - >seq9179,non-specific,226098,138,239,0.00236741,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA3,ORF2,hs1_chimp,pars,N-TerminusTruncated
34443,Q#2532 - >seq9179,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34444,Q#2532 - >seq9179,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34445,Q#2532 - >seq9179,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,BothTerminiTruncated
34446,Q#2532 - >seq9179,superfamily,235175,301,469,0.00460168,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,BothTerminiTruncated
34447,Q#2532 - >seq9179,non-specific,235175,301,469,0.00460168,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA3,ORF2,hs1_chimp,pars,BothTerminiTruncated
34448,Q#2532 - >seq9179,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34449,Q#2532 - >seq9179,non-specific,239569,525,748,0.00827834,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34450,Q#2532 - >seq9179,specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34451,Q#2532 - >seq9179,superfamily,311990,1241,1259,0.00893041,34.57,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34452,Q#2532 - >seq9179,non-specific,311990,1241,1259,0.00893041,34.57,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA3,ORF2,hs1_chimp,pars,CompleteHit
34453,Q#2532 - >seq9179,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34454,Q#2532 - >seq9179,superfamily,293702,337,451,0.00988193,39.4123,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34455,Q#2532 - >seq9179,non-specific,293702,337,451,0.00988193,39.4123,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA3.ORF2.hs1_chimp.pars.frame3,1909181942_L1PA3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA3,ORF2,hs1_chimp,pars,C-TerminusTruncated
34456,Q#2535 - >seq9182,specific,238827,510,772,4.6599999999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34457,Q#2535 - >seq9182,superfamily,295487,510,772,4.6599999999999994e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34458,Q#2535 - >seq9182,non-specific,238827,510,772,4.6599999999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34459,Q#2535 - >seq9182,specific,197310,9,236,3.345989999999999e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34460,Q#2535 - >seq9182,superfamily,351117,9,236,3.345989999999999e-63,214.908,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34461,Q#2535 - >seq9182,non-specific,197310,9,236,3.345989999999999e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34462,Q#2535 - >seq9182,non-specific,197306,9,236,1.14412e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34463,Q#2535 - >seq9182,non-specific,197306,9,236,1.14412e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34464,Q#2535 - >seq9182,specific,333820,516,772,2.58027e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34465,Q#2535 - >seq9182,superfamily,333820,516,772,2.58027e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34466,Q#2535 - >seq9182,non-specific,333820,516,772,2.58027e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34467,Q#2535 - >seq9182,non-specific,197307,9,236,1.8959900000000002e-26,109.685,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34468,Q#2535 - >seq9182,non-specific,197307,9,236,1.8959900000000002e-26,109.685,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34469,Q#2535 - >seq9182,non-specific,223780,9,238,1.1625e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34470,Q#2535 - >seq9182,non-specific,223780,9,238,1.1625e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34471,Q#2535 - >seq9182,non-specific,197320,8,236,1.52531e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34472,Q#2535 - >seq9182,non-specific,197320,8,236,1.52531e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34473,Q#2535 - >seq9182,non-specific,197321,7,236,6.84339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34474,Q#2535 - >seq9182,non-specific,197321,7,236,6.84339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34475,Q#2535 - >seq9182,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34476,Q#2535 - >seq9182,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34477,Q#2535 - >seq9182,non-specific,273186,9,237,7.05224e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34478,Q#2535 - >seq9182,non-specific,273186,9,237,7.05224e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34479,Q#2535 - >seq9182,non-specific,272954,9,236,1.40891e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34480,Q#2535 - >seq9182,non-specific,272954,9,236,1.40891e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34481,Q#2535 - >seq9182,non-specific,197319,8,236,4.1524099999999996e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34482,Q#2535 - >seq9182,non-specific,197319,8,236,4.1524099999999996e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34483,Q#2535 - >seq9182,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34484,Q#2535 - >seq9182,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34485,Q#2535 - >seq9182,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34486,Q#2535 - >seq9182,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34487,Q#2535 - >seq9182,non-specific,238828,516,737,1.06056e-10,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34488,Q#2535 - >seq9182,non-specific,238828,516,737,1.06056e-10,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34489,Q#2535 - >seq9182,non-specific,275209,467,800,3.85115e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34490,Q#2535 - >seq9182,superfamily,275209,467,800,3.85115e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34491,Q#2535 - >seq9182,non-specific,275209,467,800,3.85115e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34492,Q#2535 - >seq9182,non-specific,236970,9,238,3.9294400000000004e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34493,Q#2535 - >seq9182,non-specific,236970,9,238,3.9294400000000004e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34494,Q#2535 - >seq9182,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34495,Q#2535 - >seq9182,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34496,Q#2535 - >seq9182,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34497,Q#2535 - >seq9182,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34498,Q#2535 - >seq9182,non-specific,197317,139,229,1.3199e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34499,Q#2535 - >seq9182,non-specific,197317,139,229,1.3199e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34500,Q#2535 - >seq9182,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34501,Q#2535 - >seq9182,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34502,Q#2535 - >seq9182,non-specific,274009,305,453,0.000831658,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34503,Q#2535 - >seq9182,superfamily,274009,305,453,0.000831658,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34504,Q#2535 - >seq9182,non-specific,274009,305,453,0.000831658,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34505,Q#2535 - >seq9182,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34506,Q#2535 - >seq9182,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34507,Q#2535 - >seq9182,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34508,Q#2535 - >seq9182,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34509,Q#2535 - >seq9182,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34510,Q#2535 - >seq9182,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34511,Q#2535 - >seq9182,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34512,Q#2535 - >seq9182,non-specific,235175,295,464,0.00301189,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,BothTerminiTruncated
34513,Q#2535 - >seq9182,superfamily,235175,295,464,0.00301189,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,BothTerminiTruncated
34514,Q#2535 - >seq9182,non-specific,235175,295,464,0.00301189,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,BothTerminiTruncated
34515,Q#2535 - >seq9182,non-specific,274008,263,500,0.00512821,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34516,Q#2535 - >seq9182,superfamily,274008,263,500,0.00512821,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34517,Q#2535 - >seq9182,non-specific,274008,263,500,0.00512821,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,pars,N-TerminusTruncated
34518,Q#2535 - >seq9182,non-specific,239569,525,748,0.00762789,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34519,Q#2535 - >seq9182,non-specific,239569,525,748,0.00762789,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,pars,CompleteHit
34520,Q#2535 - >seq9182,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34521,Q#2535 - >seq9182,superfamily,293702,337,451,0.00816746,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34522,Q#2535 - >seq9182,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.pars.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,pars,C-TerminusTruncated
34523,Q#2538 - >seq9185,specific,238827,510,772,4.6599999999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34524,Q#2538 - >seq9185,superfamily,295487,510,772,4.6599999999999994e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34525,Q#2538 - >seq9185,non-specific,238827,510,772,4.6599999999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34526,Q#2538 - >seq9185,specific,197310,9,236,3.345989999999999e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34527,Q#2538 - >seq9185,superfamily,351117,9,236,3.345989999999999e-63,214.908,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34528,Q#2538 - >seq9185,non-specific,197310,9,236,3.345989999999999e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34529,Q#2538 - >seq9185,non-specific,197306,9,236,1.14412e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34530,Q#2538 - >seq9185,non-specific,197306,9,236,1.14412e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34531,Q#2538 - >seq9185,specific,333820,516,772,2.58027e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34532,Q#2538 - >seq9185,superfamily,333820,516,772,2.58027e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34533,Q#2538 - >seq9185,non-specific,333820,516,772,2.58027e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34534,Q#2538 - >seq9185,non-specific,197307,9,236,1.8959900000000002e-26,109.685,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34535,Q#2538 - >seq9185,non-specific,197307,9,236,1.8959900000000002e-26,109.685,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34536,Q#2538 - >seq9185,non-specific,223780,9,238,1.1625e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34537,Q#2538 - >seq9185,non-specific,223780,9,238,1.1625e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34538,Q#2538 - >seq9185,non-specific,197320,8,236,1.52531e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34539,Q#2538 - >seq9185,non-specific,197320,8,236,1.52531e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34540,Q#2538 - >seq9185,non-specific,197321,7,236,6.84339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34541,Q#2538 - >seq9185,non-specific,197321,7,236,6.84339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34542,Q#2538 - >seq9185,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34543,Q#2538 - >seq9185,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34544,Q#2538 - >seq9185,non-specific,273186,9,237,7.05224e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34545,Q#2538 - >seq9185,non-specific,273186,9,237,7.05224e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34546,Q#2538 - >seq9185,non-specific,272954,9,236,1.40891e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34547,Q#2538 - >seq9185,non-specific,272954,9,236,1.40891e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34548,Q#2538 - >seq9185,non-specific,197319,8,236,4.1524099999999996e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34549,Q#2538 - >seq9185,non-specific,197319,8,236,4.1524099999999996e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34550,Q#2538 - >seq9185,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34551,Q#2538 - >seq9185,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34552,Q#2538 - >seq9185,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34553,Q#2538 - >seq9185,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34554,Q#2538 - >seq9185,non-specific,238828,516,737,1.06056e-10,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34555,Q#2538 - >seq9185,non-specific,238828,516,737,1.06056e-10,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34556,Q#2538 - >seq9185,non-specific,275209,467,800,3.85115e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34557,Q#2538 - >seq9185,superfamily,275209,467,800,3.85115e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34558,Q#2538 - >seq9185,non-specific,275209,467,800,3.85115e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34559,Q#2538 - >seq9185,non-specific,236970,9,238,3.9294400000000004e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34560,Q#2538 - >seq9185,non-specific,236970,9,238,3.9294400000000004e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34561,Q#2538 - >seq9185,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34562,Q#2538 - >seq9185,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34563,Q#2538 - >seq9185,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34564,Q#2538 - >seq9185,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34565,Q#2538 - >seq9185,non-specific,197317,139,229,1.3199e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34566,Q#2538 - >seq9185,non-specific,197317,139,229,1.3199e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34567,Q#2538 - >seq9185,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34568,Q#2538 - >seq9185,non-specific,238185,656,772,0.000182904,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34569,Q#2538 - >seq9185,non-specific,274009,305,453,0.000831658,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34570,Q#2538 - >seq9185,superfamily,274009,305,453,0.000831658,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34571,Q#2538 - >seq9185,non-specific,274009,305,453,0.000831658,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34572,Q#2538 - >seq9185,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34573,Q#2538 - >seq9185,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34574,Q#2538 - >seq9185,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34575,Q#2538 - >seq9185,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34576,Q#2538 - >seq9185,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34577,Q#2538 - >seq9185,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34578,Q#2538 - >seq9185,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34579,Q#2538 - >seq9185,non-specific,235175,295,464,0.00301189,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,BothTerminiTruncated
34580,Q#2538 - >seq9185,superfamily,235175,295,464,0.00301189,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,BothTerminiTruncated
34581,Q#2538 - >seq9185,non-specific,235175,295,464,0.00301189,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,BothTerminiTruncated
34582,Q#2538 - >seq9185,non-specific,274008,263,500,0.00512821,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34583,Q#2538 - >seq9185,superfamily,274008,263,500,0.00512821,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34584,Q#2538 - >seq9185,non-specific,274008,263,500,0.00512821,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs1_chimp,marg,N-TerminusTruncated
34585,Q#2538 - >seq9185,non-specific,239569,525,748,0.00762789,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34586,Q#2538 - >seq9185,non-specific,239569,525,748,0.00762789,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs1_chimp,marg,CompleteHit
34587,Q#2538 - >seq9185,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34588,Q#2538 - >seq9185,superfamily,293702,337,451,0.00816746,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34589,Q#2538 - >seq9185,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs1_chimp.marg.frame3,1909181944_L1PA4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs1_chimp,marg,C-TerminusTruncated
34590,Q#2541 - >seq9188,specific,238827,510,772,1.0044299999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34591,Q#2541 - >seq9188,superfamily,295487,510,772,1.0044299999999998e-66,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34592,Q#2541 - >seq9188,non-specific,238827,510,772,1.0044299999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34593,Q#2541 - >seq9188,specific,197310,9,236,3.758469999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34594,Q#2541 - >seq9188,superfamily,351117,9,236,3.758469999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34595,Q#2541 - >seq9188,non-specific,197310,9,236,3.758469999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34596,Q#2541 - >seq9188,non-specific,197306,9,236,1.2123200000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34597,Q#2541 - >seq9188,non-specific,197306,9,236,1.2123200000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34598,Q#2541 - >seq9188,specific,333820,516,772,2.32014e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34599,Q#2541 - >seq9188,superfamily,333820,516,772,2.32014e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34600,Q#2541 - >seq9188,non-specific,333820,516,772,2.32014e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34601,Q#2541 - >seq9188,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34602,Q#2541 - >seq9188,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34603,Q#2541 - >seq9188,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34604,Q#2541 - >seq9188,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34605,Q#2541 - >seq9188,non-specific,197320,8,236,1.67731e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34606,Q#2541 - >seq9188,non-specific,197320,8,236,1.67731e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34607,Q#2541 - >seq9188,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34608,Q#2541 - >seq9188,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34609,Q#2541 - >seq9188,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34610,Q#2541 - >seq9188,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34611,Q#2541 - >seq9188,non-specific,273186,9,237,7.25534e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34612,Q#2541 - >seq9188,non-specific,273186,9,237,7.25534e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34613,Q#2541 - >seq9188,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34614,Q#2541 - >seq9188,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34615,Q#2541 - >seq9188,non-specific,197319,8,236,4.3928100000000003e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34616,Q#2541 - >seq9188,non-specific,197319,8,236,4.3928100000000003e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34617,Q#2541 - >seq9188,non-specific,197336,7,235,2.83324e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34618,Q#2541 - >seq9188,non-specific,197336,7,235,2.83324e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34619,Q#2541 - >seq9188,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34620,Q#2541 - >seq9188,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34621,Q#2541 - >seq9188,non-specific,238828,516,737,6.32987e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34622,Q#2541 - >seq9188,non-specific,238828,516,737,6.32987e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34623,Q#2541 - >seq9188,non-specific,275209,467,800,4.32437e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34624,Q#2541 - >seq9188,superfamily,275209,467,800,4.32437e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34625,Q#2541 - >seq9188,non-specific,275209,467,800,4.32437e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34626,Q#2541 - >seq9188,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34627,Q#2541 - >seq9188,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34628,Q#2541 - >seq9188,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34629,Q#2541 - >seq9188,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34630,Q#2541 - >seq9188,non-specific,197311,7,236,1.9858799999999998e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34631,Q#2541 - >seq9188,non-specific,197311,7,236,1.9858799999999998e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34632,Q#2541 - >seq9188,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34633,Q#2541 - >seq9188,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34634,Q#2541 - >seq9188,non-specific,238185,656,772,0.000318777,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34635,Q#2541 - >seq9188,non-specific,238185,656,772,0.000318777,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34636,Q#2541 - >seq9188,non-specific,274009,305,453,0.0008602680000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34637,Q#2541 - >seq9188,superfamily,274009,305,453,0.0008602680000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34638,Q#2541 - >seq9188,non-specific,274009,305,453,0.0008602680000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34639,Q#2541 - >seq9188,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34640,Q#2541 - >seq9188,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34641,Q#2541 - >seq9188,specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34642,Q#2541 - >seq9188,superfamily,311990,1241,1259,0.00199368,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34643,Q#2541 - >seq9188,non-specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,pars,CompleteHit
34644,Q#2541 - >seq9188,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34645,Q#2541 - >seq9188,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34646,Q#2541 - >seq9188,non-specific,235175,295,464,0.00298647,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,BothTerminiTruncated
34647,Q#2541 - >seq9188,superfamily,235175,295,464,0.00298647,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,BothTerminiTruncated
34648,Q#2541 - >seq9188,non-specific,235175,295,464,0.00298647,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,BothTerminiTruncated
34649,Q#2541 - >seq9188,non-specific,274008,263,500,0.00525992,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34650,Q#2541 - >seq9188,superfamily,274008,263,500,0.00525992,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34651,Q#2541 - >seq9188,non-specific,274008,263,500,0.00525992,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,pars,N-TerminusTruncated
34652,Q#2541 - >seq9188,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34653,Q#2541 - >seq9188,superfamily,293702,337,451,0.00816746,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34654,Q#2541 - >seq9188,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.pars.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,pars,C-TerminusTruncated
34655,Q#2544 - >seq9191,specific,238827,510,772,1.0044299999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34656,Q#2544 - >seq9191,superfamily,295487,510,772,1.0044299999999998e-66,224.092,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34657,Q#2544 - >seq9191,non-specific,238827,510,772,1.0044299999999998e-66,224.092,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34658,Q#2544 - >seq9191,specific,197310,9,236,3.758469999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34659,Q#2544 - >seq9191,superfamily,351117,9,236,3.758469999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34660,Q#2544 - >seq9191,non-specific,197310,9,236,3.758469999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34661,Q#2544 - >seq9191,non-specific,197306,9,236,1.2123200000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34662,Q#2544 - >seq9191,non-specific,197306,9,236,1.2123200000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34663,Q#2544 - >seq9191,specific,333820,516,772,2.32014e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34664,Q#2544 - >seq9191,superfamily,333820,516,772,2.32014e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34665,Q#2544 - >seq9191,non-specific,333820,516,772,2.32014e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34666,Q#2544 - >seq9191,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34667,Q#2544 - >seq9191,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34668,Q#2544 - >seq9191,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34669,Q#2544 - >seq9191,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34670,Q#2544 - >seq9191,non-specific,197320,8,236,1.67731e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34671,Q#2544 - >seq9191,non-specific,197320,8,236,1.67731e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34672,Q#2544 - >seq9191,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34673,Q#2544 - >seq9191,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34674,Q#2544 - >seq9191,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34675,Q#2544 - >seq9191,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34676,Q#2544 - >seq9191,non-specific,273186,9,237,7.25534e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34677,Q#2544 - >seq9191,non-specific,273186,9,237,7.25534e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34678,Q#2544 - >seq9191,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34679,Q#2544 - >seq9191,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34680,Q#2544 - >seq9191,non-specific,197319,8,236,4.3928100000000003e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34681,Q#2544 - >seq9191,non-specific,197319,8,236,4.3928100000000003e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34682,Q#2544 - >seq9191,non-specific,197336,7,235,2.83324e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34683,Q#2544 - >seq9191,non-specific,197336,7,235,2.83324e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34684,Q#2544 - >seq9191,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34685,Q#2544 - >seq9191,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34686,Q#2544 - >seq9191,non-specific,238828,516,737,6.32987e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34687,Q#2544 - >seq9191,non-specific,238828,516,737,6.32987e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34688,Q#2544 - >seq9191,non-specific,275209,467,800,4.32437e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34689,Q#2544 - >seq9191,superfamily,275209,467,800,4.32437e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34690,Q#2544 - >seq9191,non-specific,275209,467,800,4.32437e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34691,Q#2544 - >seq9191,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34692,Q#2544 - >seq9191,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34693,Q#2544 - >seq9191,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34694,Q#2544 - >seq9191,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34695,Q#2544 - >seq9191,non-specific,197311,7,236,1.9858799999999998e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34696,Q#2544 - >seq9191,non-specific,197311,7,236,1.9858799999999998e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34697,Q#2544 - >seq9191,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34698,Q#2544 - >seq9191,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34699,Q#2544 - >seq9191,non-specific,238185,656,772,0.000318777,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34700,Q#2544 - >seq9191,non-specific,238185,656,772,0.000318777,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34701,Q#2544 - >seq9191,non-specific,274009,305,453,0.0008602680000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34702,Q#2544 - >seq9191,superfamily,274009,305,453,0.0008602680000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34703,Q#2544 - >seq9191,non-specific,274009,305,453,0.0008602680000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34704,Q#2544 - >seq9191,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34705,Q#2544 - >seq9191,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34706,Q#2544 - >seq9191,specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34707,Q#2544 - >seq9191,superfamily,311990,1241,1259,0.00199368,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34708,Q#2544 - >seq9191,non-specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs3_orang,marg,CompleteHit
34709,Q#2544 - >seq9191,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34710,Q#2544 - >seq9191,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34711,Q#2544 - >seq9191,non-specific,235175,295,464,0.00298647,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,BothTerminiTruncated
34712,Q#2544 - >seq9191,superfamily,235175,295,464,0.00298647,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,BothTerminiTruncated
34713,Q#2544 - >seq9191,non-specific,235175,295,464,0.00298647,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,BothTerminiTruncated
34714,Q#2544 - >seq9191,non-specific,274008,263,500,0.00525992,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34715,Q#2544 - >seq9191,superfamily,274008,263,500,0.00525992,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34716,Q#2544 - >seq9191,non-specific,274008,263,500,0.00525992,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs3_orang,marg,N-TerminusTruncated
34717,Q#2544 - >seq9191,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34718,Q#2544 - >seq9191,superfamily,293702,337,451,0.00816746,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34719,Q#2544 - >seq9191,non-specific,293702,337,451,0.00816746,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs3_orang.marg.frame3,1909181946_L1PA4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs3_orang,marg,C-TerminusTruncated
34720,Q#2545 - >seq9192,specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34721,Q#2545 - >seq9192,superfamily,295487,510,772,4.797929999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34722,Q#2545 - >seq9192,non-specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34723,Q#2545 - >seq9192,specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34724,Q#2545 - >seq9192,superfamily,351117,9,236,3.722229999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34725,Q#2545 - >seq9192,non-specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34726,Q#2545 - >seq9192,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34727,Q#2545 - >seq9192,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34728,Q#2545 - >seq9192,specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34729,Q#2545 - >seq9192,superfamily,333820,516,772,2.6306099999999997e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34730,Q#2545 - >seq9192,non-specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34731,Q#2545 - >seq9192,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34732,Q#2545 - >seq9192,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34733,Q#2545 - >seq9192,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34734,Q#2545 - >seq9192,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34735,Q#2545 - >seq9192,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34736,Q#2545 - >seq9192,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34737,Q#2545 - >seq9192,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34738,Q#2545 - >seq9192,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34739,Q#2545 - >seq9192,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34740,Q#2545 - >seq9192,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34741,Q#2545 - >seq9192,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34742,Q#2545 - >seq9192,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34743,Q#2545 - >seq9192,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34744,Q#2545 - >seq9192,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34745,Q#2545 - >seq9192,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34746,Q#2545 - >seq9192,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34747,Q#2545 - >seq9192,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34748,Q#2545 - >seq9192,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34749,Q#2545 - >seq9192,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34750,Q#2545 - >seq9192,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34751,Q#2545 - >seq9192,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34752,Q#2545 - >seq9192,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34753,Q#2545 - >seq9192,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34754,Q#2545 - >seq9192,superfamily,275209,467,800,4.2102600000000006e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34755,Q#2545 - >seq9192,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34756,Q#2545 - >seq9192,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34757,Q#2545 - >seq9192,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34758,Q#2545 - >seq9192,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34759,Q#2545 - >seq9192,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34760,Q#2545 - >seq9192,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34761,Q#2545 - >seq9192,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34762,Q#2545 - >seq9192,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34763,Q#2545 - >seq9192,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34764,Q#2545 - >seq9192,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34765,Q#2545 - >seq9192,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34766,Q#2545 - >seq9192,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34767,Q#2545 - >seq9192,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34768,Q#2545 - >seq9192,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34769,Q#2545 - >seq9192,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34770,Q#2545 - >seq9192,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34771,Q#2545 - >seq9192,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34772,Q#2545 - >seq9192,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34773,Q#2545 - >seq9192,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34774,Q#2545 - >seq9192,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34775,Q#2545 - >seq9192,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34776,Q#2545 - >seq9192,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
34777,Q#2545 - >seq9192,superfamily,235175,295,464,0.00327835,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
34778,Q#2545 - >seq9192,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
34779,Q#2545 - >seq9192,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34780,Q#2545 - >seq9192,superfamily,274008,263,500,0.00539502,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34781,Q#2545 - >seq9192,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
34782,Q#2545 - >seq9192,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34783,Q#2545 - >seq9192,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,marg,CompleteHit
34784,Q#2545 - >seq9192,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34785,Q#2545 - >seq9192,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34786,Q#2545 - >seq9192,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.marg.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
34787,Q#2550 - >seq9197,specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34788,Q#2550 - >seq9197,superfamily,295487,510,772,4.797929999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34789,Q#2550 - >seq9197,non-specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34790,Q#2550 - >seq9197,specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34791,Q#2550 - >seq9197,superfamily,351117,9,236,3.722229999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34792,Q#2550 - >seq9197,non-specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34793,Q#2550 - >seq9197,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34794,Q#2550 - >seq9197,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34795,Q#2550 - >seq9197,specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34796,Q#2550 - >seq9197,superfamily,333820,516,772,2.6306099999999997e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34797,Q#2550 - >seq9197,non-specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34798,Q#2550 - >seq9197,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34799,Q#2550 - >seq9197,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34800,Q#2550 - >seq9197,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34801,Q#2550 - >seq9197,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34802,Q#2550 - >seq9197,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34803,Q#2550 - >seq9197,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34804,Q#2550 - >seq9197,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34805,Q#2550 - >seq9197,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34806,Q#2550 - >seq9197,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34807,Q#2550 - >seq9197,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34808,Q#2550 - >seq9197,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34809,Q#2550 - >seq9197,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34810,Q#2550 - >seq9197,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34811,Q#2550 - >seq9197,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34812,Q#2550 - >seq9197,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34813,Q#2550 - >seq9197,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34814,Q#2550 - >seq9197,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34815,Q#2550 - >seq9197,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34816,Q#2550 - >seq9197,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34817,Q#2550 - >seq9197,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34818,Q#2550 - >seq9197,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34819,Q#2550 - >seq9197,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34820,Q#2550 - >seq9197,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34821,Q#2550 - >seq9197,superfamily,275209,467,800,4.2102600000000006e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34822,Q#2550 - >seq9197,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34823,Q#2550 - >seq9197,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34824,Q#2550 - >seq9197,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34825,Q#2550 - >seq9197,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34826,Q#2550 - >seq9197,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34827,Q#2550 - >seq9197,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34828,Q#2550 - >seq9197,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34829,Q#2550 - >seq9197,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34830,Q#2550 - >seq9197,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34831,Q#2550 - >seq9197,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34832,Q#2550 - >seq9197,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34833,Q#2550 - >seq9197,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34834,Q#2550 - >seq9197,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34835,Q#2550 - >seq9197,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34836,Q#2550 - >seq9197,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34837,Q#2550 - >seq9197,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34838,Q#2550 - >seq9197,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34839,Q#2550 - >seq9197,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34840,Q#2550 - >seq9197,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34841,Q#2550 - >seq9197,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34842,Q#2550 - >seq9197,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34843,Q#2550 - >seq9197,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
34844,Q#2550 - >seq9197,superfamily,235175,295,464,0.00327835,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
34845,Q#2550 - >seq9197,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
34846,Q#2550 - >seq9197,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34847,Q#2550 - >seq9197,superfamily,274008,263,500,0.00539502,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34848,Q#2550 - >seq9197,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
34849,Q#2550 - >seq9197,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34850,Q#2550 - >seq9197,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs4_gibbon,pars,CompleteHit
34851,Q#2550 - >seq9197,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34852,Q#2550 - >seq9197,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34853,Q#2550 - >seq9197,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs4_gibbon.pars.frame3,1909181949_L1PA4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
34854,Q#2553 - >seq9200,specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34855,Q#2553 - >seq9200,superfamily,295487,510,772,1.6302099999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34856,Q#2553 - >seq9200,non-specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34857,Q#2553 - >seq9200,specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34858,Q#2553 - >seq9200,superfamily,351117,9,236,1.3895299999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34859,Q#2553 - >seq9200,non-specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34860,Q#2553 - >seq9200,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34861,Q#2553 - >seq9200,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34862,Q#2553 - >seq9200,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34863,Q#2553 - >seq9200,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34864,Q#2553 - >seq9200,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34865,Q#2553 - >seq9200,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34866,Q#2553 - >seq9200,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34867,Q#2553 - >seq9200,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34868,Q#2553 - >seq9200,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34869,Q#2553 - >seq9200,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34870,Q#2553 - >seq9200,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34871,Q#2553 - >seq9200,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34872,Q#2553 - >seq9200,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34873,Q#2553 - >seq9200,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34874,Q#2553 - >seq9200,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34875,Q#2553 - >seq9200,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34876,Q#2553 - >seq9200,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34877,Q#2553 - >seq9200,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34878,Q#2553 - >seq9200,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34879,Q#2553 - >seq9200,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34880,Q#2553 - >seq9200,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34881,Q#2553 - >seq9200,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34882,Q#2553 - >seq9200,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34883,Q#2553 - >seq9200,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34884,Q#2553 - >seq9200,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34885,Q#2553 - >seq9200,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34886,Q#2553 - >seq9200,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34887,Q#2553 - >seq9200,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34888,Q#2553 - >seq9200,superfamily,275209,467,800,1.02596e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34889,Q#2553 - >seq9200,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34890,Q#2553 - >seq9200,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34891,Q#2553 - >seq9200,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34892,Q#2553 - >seq9200,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34893,Q#2553 - >seq9200,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34894,Q#2553 - >seq9200,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34895,Q#2553 - >seq9200,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34896,Q#2553 - >seq9200,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34897,Q#2553 - >seq9200,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34898,Q#2553 - >seq9200,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34899,Q#2553 - >seq9200,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34900,Q#2553 - >seq9200,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34901,Q#2553 - >seq9200,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34902,Q#2553 - >seq9200,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34903,Q#2553 - >seq9200,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34904,Q#2553 - >seq9200,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34905,Q#2553 - >seq9200,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34906,Q#2553 - >seq9200,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34907,Q#2553 - >seq9200,specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34908,Q#2553 - >seq9200,superfamily,311990,1241,1259,0.00205315,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34909,Q#2553 - >seq9200,non-specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,pars,CompleteHit
34910,Q#2553 - >seq9200,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34911,Q#2553 - >seq9200,superfamily,274008,157,500,0.00350553,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34912,Q#2553 - >seq9200,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
34913,Q#2553 - >seq9200,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
34914,Q#2553 - >seq9200,superfamily,235175,295,464,0.00375458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
34915,Q#2553 - >seq9200,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
34916,Q#2553 - >seq9200,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34917,Q#2553 - >seq9200,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34918,Q#2553 - >seq9200,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.pars.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
34919,Q#2556 - >seq9203,specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34920,Q#2556 - >seq9203,superfamily,295487,510,772,1.6302099999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34921,Q#2556 - >seq9203,non-specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34922,Q#2556 - >seq9203,specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34923,Q#2556 - >seq9203,superfamily,351117,9,236,1.3895299999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34924,Q#2556 - >seq9203,non-specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34925,Q#2556 - >seq9203,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34926,Q#2556 - >seq9203,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34927,Q#2556 - >seq9203,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34928,Q#2556 - >seq9203,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34929,Q#2556 - >seq9203,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34930,Q#2556 - >seq9203,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34931,Q#2556 - >seq9203,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34932,Q#2556 - >seq9203,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34933,Q#2556 - >seq9203,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34934,Q#2556 - >seq9203,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34935,Q#2556 - >seq9203,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34936,Q#2556 - >seq9203,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34937,Q#2556 - >seq9203,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34938,Q#2556 - >seq9203,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34939,Q#2556 - >seq9203,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34940,Q#2556 - >seq9203,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34941,Q#2556 - >seq9203,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34942,Q#2556 - >seq9203,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34943,Q#2556 - >seq9203,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34944,Q#2556 - >seq9203,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34945,Q#2556 - >seq9203,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34946,Q#2556 - >seq9203,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34947,Q#2556 - >seq9203,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34948,Q#2556 - >seq9203,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34949,Q#2556 - >seq9203,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34950,Q#2556 - >seq9203,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34951,Q#2556 - >seq9203,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34952,Q#2556 - >seq9203,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34953,Q#2556 - >seq9203,superfamily,275209,467,800,1.02596e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34954,Q#2556 - >seq9203,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34955,Q#2556 - >seq9203,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34956,Q#2556 - >seq9203,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34957,Q#2556 - >seq9203,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34958,Q#2556 - >seq9203,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34959,Q#2556 - >seq9203,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34960,Q#2556 - >seq9203,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34961,Q#2556 - >seq9203,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34962,Q#2556 - >seq9203,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34963,Q#2556 - >seq9203,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34964,Q#2556 - >seq9203,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34965,Q#2556 - >seq9203,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34966,Q#2556 - >seq9203,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34967,Q#2556 - >seq9203,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34968,Q#2556 - >seq9203,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34969,Q#2556 - >seq9203,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34970,Q#2556 - >seq9203,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34971,Q#2556 - >seq9203,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34972,Q#2556 - >seq9203,specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34973,Q#2556 - >seq9203,superfamily,311990,1241,1259,0.00205315,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34974,Q#2556 - >seq9203,non-specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs5_gmonkey,marg,CompleteHit
34975,Q#2556 - >seq9203,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34976,Q#2556 - >seq9203,superfamily,274008,157,500,0.00350553,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34977,Q#2556 - >seq9203,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
34978,Q#2556 - >seq9203,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
34979,Q#2556 - >seq9203,superfamily,235175,295,464,0.00375458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
34980,Q#2556 - >seq9203,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
34981,Q#2556 - >seq9203,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34982,Q#2556 - >seq9203,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34983,Q#2556 - >seq9203,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs5_gmonkey.marg.frame3,1909181955_L1PA5.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
34984,Q#2557 - >seq9204,non-specific,197310,9,66,1.53005e-13,71.2285,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34985,Q#2557 - >seq9204,superfamily,351117,9,66,1.53005e-13,71.2285,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34986,Q#2557 - >seq9204,non-specific,197306,9,66,1.6385000000000003e-11,65.5805,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34987,Q#2557 - >seq9204,non-specific,223780,9,43,2.7680100000000003e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34988,Q#2557 - >seq9204,non-specific,197321,7,49,4.50871e-05,46.3912,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34989,Q#2557 - >seq9204,non-specific,197307,9,49,0.000205587,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34990,Q#2557 - >seq9204,non-specific,197336,7,43,0.000227352,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34991,Q#2557 - >seq9204,specific,335306,10,53,0.000509136,42.6174,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34992,Q#2557 - >seq9204,non-specific,197320,8,43,0.00078719,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34993,Q#2557 - >seq9204,non-specific,273186,9,43,0.00141544,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34994,Q#2557 - >seq9204,non-specific,272954,9,43,0.00874831,39.2885,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.marg.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
34995,Q#2558 - >seq9205,specific,238827,515,777,1.17043e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
34996,Q#2558 - >seq9205,superfamily,295487,515,777,1.17043e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
34997,Q#2558 - >seq9205,specific,197310,23,241,3.05701e-39,145.957,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,CompleteHit
34998,Q#2558 - >seq9205,superfamily,351117,23,241,3.05701e-39,145.957,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,CompleteHit
34999,Q#2558 - >seq9205,specific,333820,521,777,2.61661e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35000,Q#2558 - >seq9205,superfamily,333820,521,777,2.61661e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35001,Q#2558 - >seq9205,non-specific,197306,77,241,4.6176499999999994e-33,128.368,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35002,Q#2558 - >seq9205,non-specific,223780,77,243,4.70217e-13,70.3199,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35003,Q#2558 - >seq9205,non-specific,197307,77,241,6.39592e-13,70.0093,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35004,Q#2558 - >seq9205,non-specific,197320,77,226,4.9263199999999996e-12,67.155,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35005,Q#2558 - >seq9205,non-specific,238828,521,742,2.62967e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35006,Q#2558 - >seq9205,non-specific,275209,472,805,2.8318400000000003e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35007,Q#2558 - >seq9205,superfamily,275209,472,805,2.8318400000000003e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35008,Q#2558 - >seq9205,non-specific,273186,77,242,2.10439e-09,59.6,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35009,Q#2558 - >seq9205,non-specific,339261,113,237,8.3144e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35010,Q#2558 - >seq9205,non-specific,335306,77,234,8.14471e-08,54.1734,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35011,Q#2558 - >seq9205,non-specific,197321,77,241,4.19059e-07,52.5544,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35012,Q#2558 - >seq9205,non-specific,197322,96,241,6.677199999999999e-07,52.3194,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35013,Q#2558 - >seq9205,non-specific,272954,77,241,2.17555e-06,50.4593,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35014,Q#2558 - >seq9205,non-specific,197319,77,241,1.4033399999999998e-05,48.0417,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35015,Q#2558 - >seq9205,non-specific,236970,77,243,1.43265e-05,47.9666,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35016,Q#2558 - >seq9205,non-specific,197317,144,234,8.538629999999999e-05,45.2856,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35017,Q#2558 - >seq9205,non-specific,238185,661,777,0.000133139,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35018,Q#2558 - >seq9205,non-specific,197311,77,241,0.00018549400000000002,43.8197,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35019,Q#2558 - >seq9205,specific,311990,1246,1264,0.00103818,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35020,Q#2558 - >seq9205,superfamily,311990,1246,1264,0.00103818,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35021,Q#2558 - >seq9205,non-specific,274009,310,458,0.0015227,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
35022,Q#2558 - >seq9205,superfamily,274009,310,458,0.0015227,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
35023,Q#2558 - >seq9205,non-specific,235175,300,469,0.00172896,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA6,ORF2,hs3_orang,marg,BothTerminiTruncated
35024,Q#2558 - >seq9205,superfamily,235175,300,469,0.00172896,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA6,ORF2,hs3_orang,marg,BothTerminiTruncated
35025,Q#2558 - >seq9205,non-specific,226098,143,244,0.00211735,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,marg,N-TerminusTruncated
35026,Q#2558 - >seq9205,non-specific,239569,530,753,0.00680638,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA6,ORF2,hs3_orang,marg,CompleteHit
35027,Q#2558 - >seq9205,non-specific,293702,342,456,0.00910186,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
35028,Q#2558 - >seq9205,superfamily,293702,342,456,0.00910186,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs3_orang.marg.frame2,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1PA6,ORF2,hs3_orang,marg,C-TerminusTruncated
35029,Q#2562 - >seq9209,specific,238827,510,772,1.77935e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35030,Q#2562 - >seq9209,superfamily,295487,510,772,1.77935e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35031,Q#2562 - >seq9209,specific,197310,9,236,5.378569999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35032,Q#2562 - >seq9209,superfamily,351117,9,236,5.378569999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35033,Q#2562 - >seq9209,non-specific,197306,9,236,1.49002e-53,187.304,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35034,Q#2562 - >seq9209,specific,333820,516,772,3.0703299999999996e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35035,Q#2562 - >seq9209,superfamily,333820,516,772,3.0703299999999996e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35036,Q#2562 - >seq9209,non-specific,197307,9,236,7.19652e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35037,Q#2562 - >seq9209,non-specific,223780,9,238,3.92496e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35038,Q#2562 - >seq9209,non-specific,197320,8,221,8.50677e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35039,Q#2562 - >seq9209,specific,335306,10,229,1.1671599999999999e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35040,Q#2562 - >seq9209,non-specific,197321,7,236,5.84126e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35041,Q#2562 - >seq9209,non-specific,273186,9,237,1.92248e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35042,Q#2562 - >seq9209,non-specific,272954,9,236,2.96126e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35043,Q#2562 - >seq9209,non-specific,197336,7,235,1.9021300000000002e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35044,Q#2562 - >seq9209,non-specific,197319,8,236,2.30727e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35045,Q#2562 - >seq9209,non-specific,238828,516,737,2.79607e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35046,Q#2562 - >seq9209,non-specific,197322,9,236,3.549e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35047,Q#2562 - >seq9209,non-specific,275209,467,800,3.05418e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35048,Q#2562 - >seq9209,superfamily,275209,467,800,3.05418e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35049,Q#2562 - >seq9209,non-specific,339261,108,232,9.30204e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35050,Q#2562 - >seq9209,non-specific,236970,9,238,3.62756e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35051,Q#2562 - >seq9209,non-specific,197311,7,236,1.56585e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35052,Q#2562 - >seq9209,non-specific,197317,139,229,8.5013e-05,45.2856,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,pars,N-TerminusTruncated
35053,Q#2562 - >seq9209,non-specific,238185,656,772,0.00013004,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35054,Q#2562 - >seq9209,specific,311990,1241,1259,0.0010241,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35055,Q#2562 - >seq9209,superfamily,311990,1241,1259,0.0010241,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35056,Q#2562 - >seq9209,non-specific,274009,305,453,0.00135809,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs3_orang,pars,C-TerminusTruncated
35057,Q#2562 - >seq9209,superfamily,274009,305,453,0.00135809,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs3_orang,pars,C-TerminusTruncated
35058,Q#2562 - >seq9209,non-specific,235175,295,464,0.00139249,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs3_orang,pars,BothTerminiTruncated
35059,Q#2562 - >seq9209,superfamily,235175,295,464,0.00139249,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs3_orang,pars,BothTerminiTruncated
35060,Q#2562 - >seq9209,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA6,ORF2,hs3_orang,pars,C-TerminusTruncated
35061,Q#2562 - >seq9209,non-specific,226098,138,239,0.00210816,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs3_orang,pars,N-TerminusTruncated
35062,Q#2562 - >seq9209,non-specific,239569,525,748,0.00728882,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs3_orang,pars,CompleteHit
35063,Q#2562 - >seq9209,non-specific,293702,337,451,0.00852896,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs3_orang,pars,C-TerminusTruncated
35064,Q#2562 - >seq9209,superfamily,293702,337,451,0.00852896,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs3_orang.pars.frame3,1909181956_L1PA6.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs3_orang,pars,C-TerminusTruncated
35065,Q#2564 - >seq9211,specific,238827,503,765,9.13673e-68,227.174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35066,Q#2564 - >seq9211,superfamily,295487,503,765,9.13673e-68,227.174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35067,Q#2564 - >seq9211,specific,197310,3,230,1.9365299999999996e-59,204.122,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35068,Q#2564 - >seq9211,superfamily,351117,3,230,1.9365299999999996e-59,204.122,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35069,Q#2564 - >seq9211,specific,333820,509,765,2.42132e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35070,Q#2564 - >seq9211,superfamily,333820,509,765,2.42132e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35071,Q#2564 - >seq9211,non-specific,197306,3,230,2.41982e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35072,Q#2564 - >seq9211,non-specific,197320,3,223,1.19683e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35073,Q#2564 - >seq9211,non-specific,223780,3,231,2.82716e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35074,Q#2564 - >seq9211,non-specific,197307,3,230,3.36859e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35075,Q#2564 - >seq9211,specific,335306,4,223,1.69225e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35076,Q#2564 - >seq9211,non-specific,197321,1,230,3.01867e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35077,Q#2564 - >seq9211,non-specific,273186,3,231,3.4300800000000003e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35078,Q#2564 - >seq9211,non-specific,272954,3,230,6.83078e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35079,Q#2564 - >seq9211,non-specific,197319,7,230,7.151110000000001e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35080,Q#2564 - >seq9211,non-specific,238828,509,730,3.67327e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35081,Q#2564 - >seq9211,non-specific,197336,3,188,7.02976e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35082,Q#2564 - >seq9211,non-specific,236970,3,243,2.18283e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35083,Q#2564 - >seq9211,non-specific,275209,459,789,2.90101e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35084,Q#2564 - >seq9211,superfamily,275209,459,789,2.90101e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35085,Q#2564 - >seq9211,non-specific,197322,2,230,3.43491e-08,56.5566,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35086,Q#2564 - >seq9211,non-specific,238185,649,763,1.7871e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35087,Q#2564 - >seq9211,non-specific,197311,1,230,2.22024e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35088,Q#2564 - >seq9211,non-specific,339261,102,226,7.76934e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs4_gibbon,marg,CompleteHit
35089,Q#2564 - >seq9211,non-specific,235175,288,462,8.03486e-05,46.9808,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35090,Q#2564 - >seq9211,superfamily,235175,288,462,8.03486e-05,46.9808,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35091,Q#2564 - >seq9211,non-specific,274009,301,451,0.000534128,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35092,Q#2564 - >seq9211,superfamily,274009,301,451,0.000534128,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35093,Q#2564 - >seq9211,non-specific,274009,288,440,0.00297312,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35094,Q#2564 - >seq9211,non-specific,274009,305,456,0.0093895,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35095,Q#2566 - >seq9213,specific,238827,503,756,8.910339999999998e-65,218.31400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35096,Q#2566 - >seq9213,superfamily,295487,503,756,8.910339999999998e-65,218.31400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35097,Q#2566 - >seq9213,specific,197310,3,230,6.297929999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35098,Q#2566 - >seq9213,superfamily,351117,3,230,6.297929999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35099,Q#2566 - >seq9213,specific,333820,509,733,4.317369999999999e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35100,Q#2566 - >seq9213,superfamily,333820,509,733,4.317369999999999e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35101,Q#2566 - >seq9213,non-specific,197306,3,230,4.39208e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35102,Q#2566 - >seq9213,non-specific,197320,3,223,5.24803e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35103,Q#2566 - >seq9213,non-specific,197307,3,230,1.00876e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35104,Q#2566 - >seq9213,non-specific,223780,3,231,2.1376400000000003e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35105,Q#2566 - >seq9213,specific,335306,4,223,1.6180600000000002e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35106,Q#2566 - >seq9213,non-specific,197321,1,230,2.1247899999999999e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35107,Q#2566 - >seq9213,non-specific,272954,3,230,3.53494e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35108,Q#2566 - >seq9213,non-specific,273186,3,231,7.20684e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35109,Q#2566 - >seq9213,non-specific,197319,7,230,2.30196e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35110,Q#2566 - >seq9213,non-specific,238828,509,730,2.8429400000000006e-14,73.3892,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35111,Q#2566 - >seq9213,non-specific,197336,3,188,6.71749e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35112,Q#2566 - >seq9213,non-specific,236970,3,243,4.83724e-10,61.4486,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35113,Q#2566 - >seq9213,non-specific,275209,459,730,6.03156e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35114,Q#2566 - >seq9213,superfamily,275209,459,730,6.03156e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35115,Q#2566 - >seq9213,non-specific,197322,2,230,3.27987e-08,56.5566,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35116,Q#2566 - >seq9213,non-specific,197311,1,230,1.27578e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35117,Q#2566 - >seq9213,non-specific,235175,288,462,2.7477800000000003e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35118,Q#2566 - >seq9213,superfamily,235175,288,462,2.7477800000000003e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35119,Q#2566 - >seq9213,non-specific,339261,102,226,8.452399999999999e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs4_gibbon,pars,CompleteHit
35120,Q#2566 - >seq9213,non-specific,238185,649,726,0.000222668,41.1824,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35121,Q#2566 - >seq9213,non-specific,274009,301,451,0.0005647790000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35122,Q#2566 - >seq9213,superfamily,274009,301,451,0.0005647790000000001,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35123,Q#2566 - >seq9213,specific,225881,429,673,0.00248159,41.3629,COG3344,YkfC,C,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35124,Q#2566 - >seq9213,superfamily,225881,429,673,0.00248159,41.3629,cl34590,YkfC superfamily,C, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35125,Q#2566 - >seq9213,non-specific,338310,1015,1079,0.00261647,40.2492,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35126,Q#2566 - >seq9213,superfamily,338310,1015,1079,0.00261647,40.2492,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35127,Q#2566 - >seq9213,non-specific,274009,288,440,0.00319893,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35128,Q#2566 - >seq9213,non-specific,224259,307,462,0.00859838,39.2792,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35129,Q#2566 - >seq9213,superfamily,224259,307,462,0.00859838,39.2792,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35130,Q#2566 - >seq9213,non-specific,274009,305,456,0.00968745,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35131,Q#2568 - >seq9215,non-specific,338310,934,998,0.000656763,42.1752,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs4_gibbon.marg.frame1,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35132,Q#2568 - >seq9215,superfamily,338310,934,998,0.000656763,42.1752,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs4_gibbon.marg.frame1,1909182000_L1PBa.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35133,Q#2571 - >seq9218,specific,238827,510,772,1.8143099999999998e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35134,Q#2571 - >seq9218,superfamily,295487,510,772,1.8143099999999998e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35135,Q#2571 - >seq9218,specific,197310,9,236,1.3497399999999997e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35136,Q#2571 - >seq9218,superfamily,351117,9,236,1.3497399999999997e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35137,Q#2571 - >seq9218,non-specific,197306,9,236,2.3223999999999997e-53,186.918,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35138,Q#2571 - >seq9218,specific,333820,516,772,3.0703299999999996e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35139,Q#2571 - >seq9218,superfamily,333820,516,772,3.0703299999999996e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35140,Q#2571 - >seq9218,non-specific,197307,9,236,1.0742e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35141,Q#2571 - >seq9218,non-specific,223780,9,238,6.14706e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35142,Q#2571 - >seq9218,non-specific,197320,8,221,8.587889999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35143,Q#2571 - >seq9218,specific,335306,10,229,1.1234400000000001e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35144,Q#2571 - >seq9218,non-specific,197321,7,236,2.14037e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35145,Q#2571 - >seq9218,non-specific,273186,9,237,2.51278e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35146,Q#2571 - >seq9218,non-specific,272954,9,236,4.106319999999999e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35147,Q#2571 - >seq9218,non-specific,197319,8,236,2.21444e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35148,Q#2571 - >seq9218,non-specific,197336,7,235,4.5788999999999997e-14,73.4155,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35149,Q#2571 - >seq9218,non-specific,238828,516,737,2.82247e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35150,Q#2571 - >seq9218,non-specific,197322,9,236,3.48501e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35151,Q#2571 - >seq9218,non-specific,275209,467,800,3.25094e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35152,Q#2571 - >seq9218,superfamily,275209,467,800,3.25094e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35153,Q#2571 - >seq9218,non-specific,339261,108,232,1.1339200000000002e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35154,Q#2571 - >seq9218,non-specific,236970,9,238,9.90975e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35155,Q#2571 - >seq9218,non-specific,197311,7,236,1.23183e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35156,Q#2571 - >seq9218,non-specific,238185,656,772,0.00013004,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35157,Q#2571 - >seq9218,non-specific,197317,139,229,0.000147396,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35158,Q#2571 - >seq9218,non-specific,226098,138,239,0.000603284,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35159,Q#2571 - >seq9218,specific,311990,1241,1259,0.0010241,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35160,Q#2571 - >seq9218,superfamily,311990,1241,1259,0.0010241,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35161,Q#2571 - >seq9218,non-specific,274009,305,453,0.00140481,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35162,Q#2571 - >seq9218,superfamily,274009,305,453,0.00140481,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35163,Q#2571 - >seq9218,non-specific,235175,295,464,0.0015286,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35164,Q#2571 - >seq9218,superfamily,235175,295,464,0.0015286,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,pars,BothTerminiTruncated
35165,Q#2571 - >seq9218,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA6,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35166,Q#2571 - >seq9218,non-specific,239569,525,748,0.00742261,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,pars,CompleteHit
35167,Q#2571 - >seq9218,non-specific,293702,337,451,0.00860316,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35168,Q#2571 - >seq9218,superfamily,293702,337,451,0.00860316,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs4_gibbon.pars.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35169,Q#2574 - >seq9221,specific,238827,517,779,1.7843699999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35170,Q#2574 - >seq9221,superfamily,295487,517,779,1.7843699999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35171,Q#2574 - >seq9221,specific,197310,9,243,3.0354899999999994e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35172,Q#2574 - >seq9221,superfamily,351117,9,243,3.0354899999999994e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35173,Q#2574 - >seq9221,non-specific,197306,9,243,4.6169299999999996e-51,180.37,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35174,Q#2574 - >seq9221,specific,333820,523,779,2.77754e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35175,Q#2574 - >seq9221,superfamily,333820,523,779,2.77754e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35176,Q#2574 - >seq9221,non-specific,223780,9,245,7.93999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35177,Q#2574 - >seq9221,non-specific,197307,9,243,1.00747e-21,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35178,Q#2574 - >seq9221,non-specific,197320,8,228,1.7924599999999998e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35179,Q#2574 - >seq9221,specific,335306,10,236,4.66089e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35180,Q#2574 - >seq9221,non-specific,273186,9,244,8.86227e-18,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35181,Q#2574 - >seq9221,non-specific,197321,7,243,7.22232e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35182,Q#2574 - >seq9221,non-specific,272954,9,243,1.02405e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35183,Q#2574 - >seq9221,non-specific,197319,8,243,2.20998e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35184,Q#2574 - >seq9221,non-specific,197336,7,242,3.77187e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35185,Q#2574 - >seq9221,non-specific,238828,523,744,2.68429e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35186,Q#2574 - >seq9221,non-specific,275209,474,807,2.99313e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35187,Q#2574 - >seq9221,superfamily,275209,474,807,2.99313e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35188,Q#2574 - >seq9221,non-specific,339261,115,239,1.20882e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35189,Q#2574 - >seq9221,non-specific,197322,9,243,1.3422500000000002e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35190,Q#2574 - >seq9221,non-specific,236970,9,245,1.32362e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35191,Q#2574 - >seq9221,non-specific,197311,7,243,3.5439599999999996e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35192,Q#2574 - >seq9221,non-specific,238185,663,779,0.000132061,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35193,Q#2574 - >seq9221,non-specific,197317,146,236,0.00015374600000000002,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35194,Q#2574 - >seq9221,non-specific,226098,145,246,0.000606978,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35195,Q#2574 - >seq9221,specific,311990,1248,1266,0.000999827,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35196,Q#2574 - >seq9221,superfamily,311990,1248,1266,0.000999827,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35197,Q#2574 - >seq9221,non-specific,235175,302,471,0.00129831,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35198,Q#2574 - >seq9221,superfamily,235175,302,471,0.00129831,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35199,Q#2574 - >seq9221,non-specific,274009,312,460,0.00129905,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35200,Q#2574 - >seq9221,superfamily,274009,312,460,0.00129905,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35201,Q#2574 - >seq9221,non-specific,239569,532,755,0.00700662,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs4_gibbon,marg,CompleteHit
35202,Q#2574 - >seq9221,non-specific,293702,344,458,0.00836129,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35203,Q#2574 - >seq9221,superfamily,293702,344,458,0.00836129,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35204,Q#2574 - >seq9221,non-specific,274008,164,507,0.00893905,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35205,Q#2574 - >seq9221,superfamily,274008,164,507,0.00893905,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs4_gibbon.marg.frame3,1909182000_L1PA6.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35206,Q#2575 - >seq9222,specific,238827,503,756,4.497609999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35207,Q#2575 - >seq9222,superfamily,295487,503,756,4.497609999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35208,Q#2575 - >seq9222,specific,197310,3,230,3.9224499999999995e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35209,Q#2575 - >seq9222,superfamily,351117,3,230,3.9224499999999995e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35210,Q#2575 - >seq9222,specific,333820,509,733,3.2140599999999996e-34,129.72,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35211,Q#2575 - >seq9222,superfamily,333820,509,733,3.2140599999999996e-34,129.72,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35212,Q#2575 - >seq9222,non-specific,197306,3,230,4.12078e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35213,Q#2575 - >seq9222,non-specific,197320,3,243,9.664249999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35214,Q#2575 - >seq9222,non-specific,197307,3,230,3.5763499999999995e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35215,Q#2575 - >seq9222,non-specific,223780,3,231,6.24895e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35216,Q#2575 - >seq9222,non-specific,197321,1,230,1.14394e-16,81.0592,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35217,Q#2575 - >seq9222,specific,335306,4,223,1.57826e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35218,Q#2575 - >seq9222,non-specific,272954,3,243,2.0726299999999997e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35219,Q#2575 - >seq9222,non-specific,197319,7,230,5.57301e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35220,Q#2575 - >seq9222,non-specific,273186,3,231,8.483019999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35221,Q#2575 - >seq9222,non-specific,238828,509,730,3.6141199999999996e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35222,Q#2575 - >seq9222,non-specific,197336,3,188,2.4243099999999997e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35223,Q#2575 - >seq9222,non-specific,236970,3,243,3.88893e-10,61.8338,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35224,Q#2575 - >seq9222,non-specific,275209,459,730,7.743499999999999e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,C-TerminusTruncated
35225,Q#2575 - >seq9222,superfamily,275209,459,730,7.743499999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,C-TerminusTruncated
35226,Q#2575 - >seq9222,non-specific,197322,2,230,5.507139999999999e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35227,Q#2575 - >seq9222,non-specific,197311,1,230,1.3044100000000001e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,pars,CompleteHit
35228,Q#2575 - >seq9222,non-specific,339261,102,226,3.13746e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs0_human,pars,CompleteHit
35229,Q#2575 - >seq9222,non-specific,235175,288,462,3.54803e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35230,Q#2575 - >seq9222,superfamily,235175,288,462,3.54803e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35231,Q#2575 - >seq9222,non-specific,238185,649,726,0.000189707,41.5676,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,C-TerminusTruncated
35232,Q#2575 - >seq9222,non-specific,274009,301,451,0.00044619099999999997,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,pars,C-TerminusTruncated
35233,Q#2575 - >seq9222,superfamily,274009,301,451,0.00044619099999999997,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,pars,C-TerminusTruncated
35234,Q#2575 - >seq9222,specific,225881,476,673,0.00222014,41.3629,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35235,Q#2575 - >seq9222,superfamily,225881,476,673,0.00222014,41.3629,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35236,Q#2575 - >seq9222,non-specific,274009,288,440,0.00389142,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35237,Q#2575 - >seq9222,non-specific,338310,1015,1077,0.00503522,39.4788,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35238,Q#2575 - >seq9222,superfamily,338310,1015,1077,0.00503522,39.4788,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs0_human,pars,BothTerminiTruncated
35239,Q#2575 - >seq9222,non-specific,224259,307,462,0.00748873,39.6644,COG1340,COG1340,N,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs0_human,pars,N-TerminusTruncated
35240,Q#2575 - >seq9222,superfamily,224259,307,462,0.00748873,39.6644,cl34231,COG1340 superfamily,N, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PBa,ORF2,hs0_human,pars,N-TerminusTruncated
35241,Q#2575 - >seq9222,non-specific,334125,206,403,0.00829072,39.8252,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF2,hs0_human,pars,N-TerminusTruncated
35242,Q#2575 - >seq9222,superfamily,334125,206,403,0.00829072,39.8252,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs0_human.pars.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF2,hs0_human,pars,N-TerminusTruncated
35243,Q#2576 - >seq9223,non-specific,338310,934,996,0.00158401,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs0_human.marg.frame1,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs0_human,marg,BothTerminiTruncated
35244,Q#2576 - >seq9223,superfamily,338310,934,996,0.00158401,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs0_human.marg.frame1,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs0_human,marg,BothTerminiTruncated
35245,Q#2578 - >seq9225,specific,238827,503,765,4.745839999999999e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35246,Q#2578 - >seq9225,superfamily,295487,503,765,4.745839999999999e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35247,Q#2578 - >seq9225,specific,197310,3,230,2.1298e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35248,Q#2578 - >seq9225,superfamily,351117,3,230,2.1298e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35249,Q#2578 - >seq9225,specific,333820,509,765,1.8505799999999998e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35250,Q#2578 - >seq9225,superfamily,333820,509,765,1.8505799999999998e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35251,Q#2578 - >seq9225,non-specific,197306,3,230,1.8876099999999997e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35252,Q#2578 - >seq9225,non-specific,197320,3,243,1.4347e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35253,Q#2578 - >seq9225,non-specific,223780,3,231,5.28046e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35254,Q#2578 - >seq9225,non-specific,197307,3,230,1.2112000000000001e-18,86.5729,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35255,Q#2578 - >seq9225,specific,335306,4,223,1.6624599999999997e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35256,Q#2578 - >seq9225,non-specific,197321,1,230,2.21541e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35257,Q#2578 - >seq9225,non-specific,273186,3,231,3.43337e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35258,Q#2578 - >seq9225,non-specific,272954,3,243,4.65193e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35259,Q#2578 - >seq9225,non-specific,197319,7,230,2.11431e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35260,Q#2578 - >seq9225,non-specific,238828,509,730,3.9661e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35261,Q#2578 - >seq9225,non-specific,197336,3,188,2.55527e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35262,Q#2578 - >seq9225,non-specific,236970,3,243,1.34285e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35263,Q#2578 - >seq9225,non-specific,275209,459,789,3.40233e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35264,Q#2578 - >seq9225,superfamily,275209,459,789,3.40233e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35265,Q#2578 - >seq9225,non-specific,197322,2,230,5.807520000000001e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35266,Q#2578 - >seq9225,non-specific,238185,649,763,1.5175499999999999e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35267,Q#2578 - >seq9225,non-specific,197311,1,230,1.93422e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs0_human,marg,CompleteHit
35268,Q#2578 - >seq9225,non-specific,339261,102,226,3.4549000000000004e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs0_human,marg,CompleteHit
35269,Q#2578 - >seq9225,non-specific,235175,288,462,0.00012072799999999999,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,marg,BothTerminiTruncated
35270,Q#2578 - >seq9225,superfamily,235175,288,462,0.00012072799999999999,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,marg,BothTerminiTruncated
35271,Q#2578 - >seq9225,non-specific,274009,301,451,0.000355915,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,marg,C-TerminusTruncated
35272,Q#2578 - >seq9225,superfamily,274009,301,451,0.000355915,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,marg,C-TerminusTruncated
35273,Q#2578 - >seq9225,non-specific,274009,288,440,0.00323591,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs0_human.marg.frame3,1909182005_L1PBa.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs0_human,marg,BothTerminiTruncated
35274,Q#2580 - >seq9227,specific,238827,509,771,2.307949999999999e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35275,Q#2580 - >seq9227,superfamily,295487,509,771,2.307949999999999e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35276,Q#2580 - >seq9227,specific,197310,9,231,2.2016400000000002e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35277,Q#2580 - >seq9227,superfamily,351117,9,231,2.2016400000000002e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35278,Q#2580 - >seq9227,non-specific,197306,9,229,7.076829999999999e-41,150.71,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35279,Q#2580 - >seq9227,specific,333820,515,771,1.14702e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35280,Q#2580 - >seq9227,superfamily,333820,515,771,1.14702e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35281,Q#2580 - >seq9227,non-specific,197307,9,229,4.95385e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35282,Q#2580 - >seq9227,non-specific,197320,9,194,3.3501499999999995e-18,85.6445,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35283,Q#2580 - >seq9227,non-specific,223780,9,229,4.08848e-18,85.3427,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35284,Q#2580 - >seq9227,non-specific,197321,7,229,1.43361e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35285,Q#2580 - >seq9227,specific,335306,10,229,6.34934e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35286,Q#2580 - >seq9227,non-specific,272954,9,194,1.22136e-11,66.2525,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35287,Q#2580 - >seq9227,non-specific,238828,515,736,2.37903e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35288,Q#2580 - >seq9227,non-specific,273186,9,229,1.3393200000000001e-10,63.0668,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35289,Q#2580 - >seq9227,non-specific,197319,13,229,3.3318900000000006e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35290,Q#2580 - >seq9227,non-specific,197336,9,194,1.1743599999999999e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35291,Q#2580 - >seq9227,non-specific,275209,466,736,1.71286e-07,54.7712,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35292,Q#2580 - >seq9227,superfamily,275209,466,736,1.71286e-07,54.7712,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35293,Q#2580 - >seq9227,non-specific,197322,8,229,1.85048e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35294,Q#2580 - >seq9227,non-specific,339261,108,231,9.29275e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35295,Q#2580 - >seq9227,non-specific,197311,7,229,2.25637e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35296,Q#2580 - >seq9227,non-specific,238185,655,771,2.6251799999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35297,Q#2580 - >seq9227,non-specific,236970,9,194,2.9769699999999997e-05,47.1962,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35298,Q#2580 - >seq9227,specific,311990,1240,1258,0.000449132,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35299,Q#2580 - >seq9227,superfamily,311990,1240,1258,0.000449132,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs1_chimp,pars,CompleteHit
35300,Q#2580 - >seq9227,non-specific,223496,304,449,0.00049909,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PREC2,ORF2,hs1_chimp,pars,BothTerminiTruncated
35301,Q#2580 - >seq9227,superfamily,223496,304,449,0.00049909,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1PREC2,ORF2,hs1_chimp,pars,BothTerminiTruncated
35302,Q#2580 - >seq9227,non-specific,224117,266,387,0.00296066,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PREC2,ORF2,hs1_chimp,pars,BothTerminiTruncated
35303,Q#2580 - >seq9227,superfamily,224117,266,387,0.00296066,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PREC2,ORF2,hs1_chimp,pars,BothTerminiTruncated
35304,Q#2580 - >seq9227,non-specific,274009,307,457,0.00561082,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35305,Q#2580 - >seq9227,superfamily,274009,307,457,0.00561082,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PREC2,ORF2,hs1_chimp,pars,C-TerminusTruncated
35306,Q#2580 - >seq9227,specific,225881,481,738,0.00871936,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
35307,Q#2580 - >seq9227,superfamily,225881,481,738,0.00871936,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.pars.frame2,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PREC2,ORF2,hs1_chimp,pars,N-TerminusTruncated
35308,Q#2584 - >seq9231,specific,238827,510,772,2.3761599999999997e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35309,Q#2584 - >seq9231,superfamily,295487,510,772,2.3761599999999997e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35310,Q#2584 - >seq9231,specific,197310,9,231,2.1594999999999998e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35311,Q#2584 - >seq9231,superfamily,351117,9,231,2.1594999999999998e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35312,Q#2584 - >seq9231,non-specific,197306,9,229,7.076829999999999e-41,150.71,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35313,Q#2584 - >seq9231,specific,333820,516,772,1.21546e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35314,Q#2584 - >seq9231,superfamily,333820,516,772,1.21546e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35315,Q#2584 - >seq9231,non-specific,197307,9,229,5.1944999999999995e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35316,Q#2584 - >seq9231,non-specific,197320,9,194,3.51232e-18,85.6445,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35317,Q#2584 - >seq9231,non-specific,223780,9,229,4.20586e-18,85.3427,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35318,Q#2584 - >seq9231,non-specific,197321,7,229,1.4886e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35319,Q#2584 - >seq9231,specific,335306,10,229,6.34934e-15,75.3593,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35320,Q#2584 - >seq9231,non-specific,272954,9,194,1.2443000000000001e-11,66.2525,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35321,Q#2584 - >seq9231,non-specific,238828,516,737,2.35677e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35322,Q#2584 - >seq9231,non-specific,273186,9,229,1.3518e-10,63.0668,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35323,Q#2584 - >seq9231,non-specific,197319,13,229,3.4258300000000005e-10,61.9089,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35324,Q#2584 - >seq9231,non-specific,197336,9,194,1.19628e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35325,Q#2584 - >seq9231,non-specific,275209,467,737,1.79005e-07,54.386,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35326,Q#2584 - >seq9231,superfamily,275209,467,737,1.79005e-07,54.386,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35327,Q#2584 - >seq9231,non-specific,197322,8,229,1.85048e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35328,Q#2584 - >seq9231,non-specific,339261,108,231,9.38313e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35329,Q#2584 - >seq9231,non-specific,197311,7,229,2.17418e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35330,Q#2584 - >seq9231,non-specific,238185,656,772,2.6251799999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35331,Q#2584 - >seq9231,non-specific,236970,9,194,3.03095e-05,46.81100000000001,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35332,Q#2584 - >seq9231,specific,311990,1240,1258,0.00045355199999999997,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35333,Q#2584 - >seq9231,superfamily,311990,1240,1258,0.00045355199999999997,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs1_chimp,marg,CompleteHit
35334,Q#2584 - >seq9231,non-specific,224117,266,391,0.00197303,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs1_chimp,marg,BothTerminiTruncated
35335,Q#2584 - >seq9231,superfamily,224117,266,391,0.00197303,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs1_chimp,marg,BothTerminiTruncated
35336,Q#2584 - >seq9231,non-specific,274009,307,458,0.00590278,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35337,Q#2584 - >seq9231,superfamily,274009,307,458,0.00590278,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs1_chimp,marg,C-TerminusTruncated
35338,Q#2584 - >seq9231,specific,225881,482,739,0.00985085,39.4369,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
35339,Q#2584 - >seq9231,superfamily,225881,482,739,0.00985085,39.4369,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs1_chimp.marg.frame3,1909182005_L1PREC2.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs1_chimp,marg,N-TerminusTruncated
35340,Q#2585 - >seq9232,specific,238827,509,771,2.3727099999999996e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35341,Q#2585 - >seq9232,superfamily,295487,509,771,2.3727099999999996e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35342,Q#2585 - >seq9232,specific,197310,9,230,2.47785e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35343,Q#2585 - >seq9232,superfamily,351117,9,230,2.47785e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35344,Q#2585 - >seq9232,non-specific,197306,9,229,1.26486e-40,150.32399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35345,Q#2585 - >seq9232,specific,333820,515,771,4.424299999999999e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35346,Q#2585 - >seq9232,superfamily,333820,515,771,4.424299999999999e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35347,Q#2585 - >seq9232,non-specific,197307,9,229,2.63135e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35348,Q#2585 - >seq9232,non-specific,223780,9,229,6.692189999999999e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35349,Q#2585 - >seq9232,non-specific,197320,9,229,3.2664e-18,85.6445,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35350,Q#2585 - >seq9232,specific,335306,10,229,2.92636e-15,76.1297,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35351,Q#2585 - >seq9232,non-specific,197321,7,229,4.12306e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35352,Q#2585 - >seq9232,non-specific,272954,9,194,9.26513e-12,66.6377,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
35353,Q#2585 - >seq9232,non-specific,238828,515,736,2.11208e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35354,Q#2585 - >seq9232,non-specific,273186,9,229,4.75004e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35355,Q#2585 - >seq9232,non-specific,197319,13,229,5.26171e-10,61.1385,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35356,Q#2585 - >seq9232,non-specific,197336,9,194,8.36517e-10,60.7039,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35357,Q#2585 - >seq9232,non-specific,197322,8,229,6.296859999999999e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35358,Q#2585 - >seq9232,non-specific,275209,466,799,7.89869e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35359,Q#2585 - >seq9232,superfamily,275209,466,799,7.89869e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35360,Q#2585 - >seq9232,non-specific,238185,655,771,1.5571199999999998e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35361,Q#2585 - >seq9232,non-specific,339261,108,229,1.57325e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35362,Q#2585 - >seq9232,non-specific,236970,9,194,3.23665e-05,46.81100000000001,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,pars,C-TerminusTruncated
35363,Q#2585 - >seq9232,non-specific,197311,7,229,4.09692e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35364,Q#2585 - >seq9232,non-specific,224117,266,387,0.00246342,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
35365,Q#2585 - >seq9232,superfamily,224117,266,387,0.00246342,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
35366,Q#2585 - >seq9232,non-specific,235175,294,463,0.00258666,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
35367,Q#2585 - >seq9232,superfamily,235175,294,463,0.00258666,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs2_gorilla,pars,BothTerminiTruncated
35368,Q#2585 - >seq9232,specific,225881,481,738,0.00545912,40.2073,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
35369,Q#2585 - >seq9232,superfamily,225881,481,738,0.00545912,40.2073,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,pars,N-TerminusTruncated
35370,Q#2589 - >seq9236,specific,238827,510,772,2.7754999999999995e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35371,Q#2589 - >seq9236,superfamily,295487,510,772,2.7754999999999995e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35372,Q#2589 - >seq9236,specific,197310,9,230,3.3435499999999993e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35373,Q#2589 - >seq9236,superfamily,351117,9,230,3.3435499999999993e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35374,Q#2589 - >seq9236,non-specific,197306,9,229,7.49755e-41,150.71,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35375,Q#2589 - >seq9236,specific,333820,516,772,1.3648199999999999e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35376,Q#2589 - >seq9236,superfamily,333820,516,772,1.3648199999999999e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35377,Q#2589 - >seq9236,non-specific,197307,9,229,4.9070699999999994e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35378,Q#2589 - >seq9236,non-specific,223780,9,229,1.1984299999999997e-18,86.8835,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35379,Q#2589 - >seq9236,non-specific,197320,9,194,3.71732e-18,85.2593,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35380,Q#2589 - >seq9236,specific,335306,10,229,2.94468e-15,76.1297,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35381,Q#2589 - >seq9236,non-specific,197321,7,229,6.5763800000000006e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35382,Q#2589 - >seq9236,non-specific,272954,9,194,1.40431e-11,65.8673,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35383,Q#2589 - >seq9236,non-specific,238828,516,737,2.73915e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35384,Q#2589 - >seq9236,non-specific,273186,9,229,6.02954e-11,64.2224,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35385,Q#2589 - >seq9236,non-specific,197336,9,194,1.05103e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35386,Q#2589 - >seq9236,non-specific,197319,13,229,1.17362e-09,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35387,Q#2589 - >seq9236,non-specific,197322,8,229,6.3376499999999995e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35388,Q#2589 - >seq9236,non-specific,275209,467,800,1.38615e-07,54.7712,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35389,Q#2589 - >seq9236,superfamily,275209,467,800,1.38615e-07,54.7712,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35390,Q#2589 - >seq9236,non-specific,339261,108,229,5.5097e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35391,Q#2589 - >seq9236,non-specific,197311,7,229,1.48608e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35392,Q#2589 - >seq9236,non-specific,238185,656,772,2.67686e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35393,Q#2589 - >seq9236,non-specific,236970,9,194,3.2277199999999997e-05,46.81100000000001,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35394,Q#2589 - >seq9236,specific,311990,1240,1258,0.000467074,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35395,Q#2589 - >seq9236,superfamily,311990,1240,1258,0.000467074,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs2_gorilla,marg,CompleteHit
35396,Q#2589 - >seq9236,non-specific,224117,266,391,0.00256428,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
35397,Q#2589 - >seq9236,superfamily,224117,266,391,0.00256428,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs2_gorilla,marg,BothTerminiTruncated
35398,Q#2590 - >seq9237,specific,238827,510,772,5.918079999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35399,Q#2590 - >seq9237,superfamily,295487,510,772,5.918079999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35400,Q#2590 - >seq9237,specific,197310,9,230,1.2604199999999997e-60,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35401,Q#2590 - >seq9237,superfamily,351117,9,230,1.2604199999999997e-60,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35402,Q#2590 - >seq9237,non-specific,197306,9,229,1.3932900000000001e-42,155.717,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35403,Q#2590 - >seq9237,specific,333820,516,772,4.653229999999999e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35404,Q#2590 - >seq9237,superfamily,333820,516,772,4.653229999999999e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35405,Q#2590 - >seq9237,non-specific,197307,9,229,9.438519999999999e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35406,Q#2590 - >seq9237,non-specific,223780,9,229,2.57725e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35407,Q#2590 - >seq9237,non-specific,197320,9,229,9.267150000000001e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35408,Q#2590 - >seq9237,specific,335306,10,229,3.2877099999999996e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35409,Q#2590 - >seq9237,non-specific,197321,7,229,6.8983e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35410,Q#2590 - >seq9237,non-specific,273186,9,229,1.5824600000000001e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35411,Q#2590 - >seq9237,non-specific,272954,9,221,3.3149199999999998e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35412,Q#2590 - >seq9237,non-specific,197319,13,229,2.97976e-11,64.9905,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35413,Q#2590 - >seq9237,non-specific,238828,516,737,1.9113e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35414,Q#2590 - >seq9237,non-specific,197336,9,194,9.76082e-10,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35415,Q#2590 - >seq9237,non-specific,197322,8,229,2.8673300000000003e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35416,Q#2590 - >seq9237,non-specific,339261,108,229,1.42934e-07,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35417,Q#2590 - >seq9237,non-specific,197311,7,229,5.920779999999999e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35418,Q#2590 - >seq9237,non-specific,275209,467,737,1.21932e-06,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,C-TerminusTruncated
35419,Q#2590 - >seq9237,superfamily,275209,467,737,1.21932e-06,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,C-TerminusTruncated
35420,Q#2590 - >seq9237,non-specific,236970,9,221,2.6351799999999996e-06,50.2778,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35421,Q#2590 - >seq9237,non-specific,238185,656,772,2.3354099999999997e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35422,Q#2590 - >seq9237,specific,311990,1239,1257,0.000407235,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35423,Q#2590 - >seq9237,superfamily,311990,1239,1257,0.000407235,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs0_human,marg,CompleteHit
35424,Q#2590 - >seq9237,non-specific,224117,266,391,0.00182846,42.394,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,marg,BothTerminiTruncated
35425,Q#2590 - >seq9237,superfamily,224117,266,391,0.00182846,42.394,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs0_human,marg,BothTerminiTruncated
35426,Q#2590 - >seq9237,non-specific,274009,307,458,0.00352436,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,marg,C-TerminusTruncated
35427,Q#2590 - >seq9237,superfamily,274009,307,458,0.00352436,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,marg,C-TerminusTruncated
35428,Q#2590 - >seq9237,non-specific,223496,304,450,0.00487837,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PREC2,ORF2,hs0_human,marg,BothTerminiTruncated
35429,Q#2590 - >seq9237,superfamily,223496,304,450,0.00487837,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.marg.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PREC2,ORF2,hs0_human,marg,BothTerminiTruncated
35430,Q#2591 - >seq9238,specific,311990,1171,1189,1.4678499999999998e-05,42.6592,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs0_human.pars.frame2,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35431,Q#2591 - >seq9238,superfamily,311990,1171,1189,1.4678499999999998e-05,42.6592,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs0_human.pars.frame2,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35432,Q#2592 - >seq9239,specific,238827,510,772,3.0741299999999996e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35433,Q#2592 - >seq9239,superfamily,295487,510,772,3.0741299999999996e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35434,Q#2592 - >seq9239,specific,197310,9,230,8.632039999999998e-60,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35435,Q#2592 - >seq9239,superfamily,351117,9,230,8.632039999999998e-60,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35436,Q#2592 - >seq9239,non-specific,197306,9,229,1.89875e-42,155.332,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35437,Q#2592 - >seq9239,specific,333820,516,772,1.7073899999999998e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35438,Q#2592 - >seq9239,superfamily,333820,516,772,1.7073899999999998e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35439,Q#2592 - >seq9239,non-specific,197307,9,229,5.65518e-22,96.5881,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35440,Q#2592 - >seq9239,non-specific,223780,9,229,1.83487e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35441,Q#2592 - >seq9239,non-specific,197320,9,229,9.19094e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35442,Q#2592 - >seq9239,specific,335306,10,229,3.26137e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35443,Q#2592 - >seq9239,non-specific,197321,7,229,5.2038700000000003e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35444,Q#2592 - >seq9239,non-specific,273186,9,229,1.3772899999999999e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35445,Q#2592 - >seq9239,non-specific,272954,9,221,2.37231e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35446,Q#2592 - >seq9239,non-specific,197319,13,229,1.78811e-11,65.7609,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35447,Q#2592 - >seq9239,non-specific,238828,516,737,1.27888e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35448,Q#2592 - >seq9239,non-specific,197336,9,194,9.59276e-10,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35449,Q#2592 - >seq9239,non-specific,197322,8,229,2.84356e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35450,Q#2592 - >seq9239,non-specific,339261,108,229,3.42666e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35451,Q#2592 - >seq9239,non-specific,275209,467,737,9.96669e-07,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,C-TerminusTruncated
35452,Q#2592 - >seq9239,superfamily,275209,467,737,9.96669e-07,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,C-TerminusTruncated
35453,Q#2592 - >seq9239,non-specific,197311,7,229,1.4528899999999998e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35454,Q#2592 - >seq9239,non-specific,236970,9,221,2.2825099999999996e-06,50.2778,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35455,Q#2592 - >seq9239,non-specific,238185,656,772,1.19486e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs0_human,pars,CompleteHit
35456,Q#2592 - >seq9239,non-specific,224117,266,391,0.00139545,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,pars,BothTerminiTruncated
35457,Q#2592 - >seq9239,superfamily,224117,266,391,0.00139545,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs0_human,pars,BothTerminiTruncated
35458,Q#2592 - >seq9239,non-specific,274009,307,458,0.0023101,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,pars,C-TerminusTruncated
35459,Q#2592 - >seq9239,superfamily,274009,307,458,0.0023101,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs0_human,pars,C-TerminusTruncated
35460,Q#2592 - >seq9239,non-specific,223496,304,450,0.00316774,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PREC2,ORF2,hs0_human,pars,BothTerminiTruncated
35461,Q#2592 - >seq9239,superfamily,223496,304,450,0.00316774,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs0_human.pars.frame3,1909182005_L1PREC2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PREC2,ORF2,hs0_human,pars,BothTerminiTruncated
35462,Q#2596 - >seq9243,specific,311990,1132,1150,9.38441e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35463,Q#2596 - >seq9243,superfamily,311990,1132,1150,9.38441e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PREC2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PREC2,ORF2,hs2_gorilla,pars,CompleteHit
35464,Q#2599 - >seq9246,specific,238827,499,761,2.3067199999999997e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35465,Q#2599 - >seq9246,superfamily,295487,499,761,2.3067199999999997e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35466,Q#2599 - >seq9246,specific,333820,505,761,6.05288e-36,134.727,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35467,Q#2599 - >seq9246,superfamily,333820,505,761,6.05288e-36,134.727,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35468,Q#2599 - >seq9246,non-specific,238828,505,726,2.11943e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35469,Q#2599 - >seq9246,non-specific,275209,456,789,2.01205e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35470,Q#2599 - >seq9246,superfamily,275209,456,789,2.01205e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35471,Q#2599 - >seq9246,non-specific,238185,645,761,2.50423e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35472,Q#2599 - >seq9246,specific,311990,1229,1247,0.000388559,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35473,Q#2599 - >seq9246,superfamily,311990,1229,1247,0.000388559,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35474,Q#2599 - >seq9246,non-specific,235175,252,453,0.00247259,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35475,Q#2599 - >seq9246,superfamily,235175,252,453,0.00247259,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,marg,BothTerminiTruncated
35476,Q#2599 - >seq9246,non-specific,274009,296,447,0.00334819,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35477,Q#2599 - >seq9246,superfamily,274009,296,447,0.00334819,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35478,Q#2599 - >seq9246,specific,316774,294,346,0.00635154,37.368,pfam14282,FlxA,C,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35479,Q#2599 - >seq9246,superfamily,316774,294,346,0.00635154,37.368,cl16771,FlxA superfamily,C, - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA10.ORF2.hs4_gibbon.marg.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35480,Q#2600 - >seq9247,specific,238827,499,761,3.967059999999999e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35481,Q#2600 - >seq9247,superfamily,295487,499,761,3.967059999999999e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35482,Q#2600 - >seq9247,specific,333820,505,761,1.81067e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35483,Q#2600 - >seq9247,superfamily,333820,505,761,1.81067e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35484,Q#2600 - >seq9247,non-specific,238828,505,726,6.32505e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35485,Q#2600 - >seq9247,non-specific,275209,456,789,2.8734599999999997e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35486,Q#2600 - >seq9247,superfamily,275209,456,789,2.8734599999999997e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35487,Q#2600 - >seq9247,non-specific,238185,645,761,2.6314499999999997e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35488,Q#2600 - >seq9247,non-specific,235175,252,458,0.000326169,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,BothTerminiTruncated
35489,Q#2600 - >seq9247,superfamily,235175,252,458,0.000326169,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,BothTerminiTruncated
35490,Q#2600 - >seq9247,specific,311990,1230,1248,0.00042055,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35491,Q#2600 - >seq9247,superfamily,311990,1230,1248,0.00042055,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35492,Q#2600 - >seq9247,non-specific,274009,290,467,0.00120467,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,BothTerminiTruncated
35493,Q#2600 - >seq9247,superfamily,274009,290,467,0.00120467,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,BothTerminiTruncated
35494,Q#2600 - >seq9247,non-specific,274009,296,447,0.00229065,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
35495,Q#2600 - >seq9247,non-specific,274009,252,416,0.00326728,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,BothTerminiTruncated
35496,Q#2600 - >seq9247,non-specific,274009,295,445,0.00653558,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.pars.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
35497,Q#2601 - >seq9248,specific,197310,9,222,1.0448e-56,196.033,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35498,Q#2601 - >seq9248,superfamily,351117,9,222,1.0448e-56,196.033,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35499,Q#2601 - >seq9248,non-specific,197306,9,223,4.679819999999999e-46,165.732,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35500,Q#2601 - >seq9248,non-specific,197307,9,223,1.5541e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35501,Q#2601 - >seq9248,non-specific,223780,9,221,3.18588e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35502,Q#2601 - >seq9248,non-specific,197320,8,221,1.59673e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35503,Q#2601 - >seq9248,non-specific,197321,7,223,1.34018e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35504,Q#2601 - >seq9248,specific,335306,10,212,5.02206e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35505,Q#2601 - >seq9248,non-specific,272954,9,221,3.9700200000000006e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35506,Q#2601 - >seq9248,non-specific,273186,9,221,5.3965899999999996e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35507,Q#2601 - >seq9248,non-specific,197336,7,221,7.484089999999999e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35508,Q#2601 - >seq9248,non-specific,197319,8,223,2.88096e-11,64.9905,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35509,Q#2601 - >seq9248,non-specific,197322,9,222,2.18981e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35510,Q#2601 - >seq9248,non-specific,236970,9,221,3.31134e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35511,Q#2601 - >seq9248,non-specific,197311,7,204,8.65091e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35512,Q#2601 - >seq9248,non-specific,339261,108,217,0.000131032,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs1_chimp,pars,CompleteHit
35513,Q#2601 - >seq9248,non-specific,197314,7,192,0.00445848,40.0195,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.pars.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs1_chimp,pars,C-TerminusTruncated
35514,Q#2603 - >seq9250,non-specific,240420,219,425,0.00693348,40.3325,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs1_chimp.marg.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
35515,Q#2603 - >seq9250,superfamily,240420,219,425,0.00693348,40.3325,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs1_chimp.marg.frame2,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
35516,Q#2604 - >seq9251,specific,238827,510,772,2.97939e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35517,Q#2604 - >seq9251,superfamily,295487,510,772,2.97939e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35518,Q#2604 - >seq9251,specific,197310,9,236,8.089849999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35519,Q#2604 - >seq9251,superfamily,351117,9,236,8.089849999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35520,Q#2604 - >seq9251,non-specific,197306,9,236,1.06651e-47,170.355,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35521,Q#2604 - >seq9251,specific,333820,516,772,5.44693e-36,134.727,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35522,Q#2604 - >seq9251,superfamily,333820,516,772,5.44693e-36,134.727,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35523,Q#2604 - >seq9251,non-specific,197307,9,236,2.74624e-22,97.3585,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35524,Q#2604 - >seq9251,non-specific,223780,9,238,7.889279999999999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35525,Q#2604 - >seq9251,non-specific,197320,8,229,2.2837299999999996e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35526,Q#2604 - >seq9251,specific,335306,10,229,5.933980000000001e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35527,Q#2604 - >seq9251,non-specific,197321,7,236,2.49356e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35528,Q#2604 - >seq9251,non-specific,273186,9,237,1.3090000000000002e-16,80.786,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35529,Q#2604 - >seq9251,non-specific,272954,9,236,6.39841e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35530,Q#2604 - >seq9251,non-specific,197319,8,236,9.041540000000001e-13,69.6129,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35531,Q#2604 - >seq9251,non-specific,197336,7,229,3.19857e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35532,Q#2604 - >seq9251,non-specific,238828,516,737,1.05174e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35533,Q#2604 - >seq9251,non-specific,197322,9,236,4.3450500000000004e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35534,Q#2604 - >seq9251,non-specific,275209,467,800,1.99905e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35535,Q#2604 - >seq9251,superfamily,275209,467,800,1.99905e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35536,Q#2604 - >seq9251,non-specific,339261,108,232,1.37096e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35537,Q#2604 - >seq9251,non-specific,236970,9,238,3.0499800000000004e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35538,Q#2604 - >seq9251,non-specific,197311,7,236,6.51186e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35539,Q#2604 - >seq9251,non-specific,238185,656,772,4.7652200000000004e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35540,Q#2604 - >seq9251,non-specific,235175,263,469,0.000310467,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,BothTerminiTruncated
35541,Q#2604 - >seq9251,superfamily,235175,263,469,0.000310467,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,BothTerminiTruncated
35542,Q#2604 - >seq9251,specific,311990,1241,1259,0.000515927,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35543,Q#2604 - >seq9251,superfamily,311990,1241,1259,0.000515927,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs1_chimp,marg,CompleteHit
35544,Q#2604 - >seq9251,non-specific,274009,301,478,0.00142877,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,BothTerminiTruncated
35545,Q#2604 - >seq9251,superfamily,274009,301,478,0.00142877,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,BothTerminiTruncated
35546,Q#2604 - >seq9251,non-specific,197317,139,229,0.0017603999999999999,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
35547,Q#2604 - >seq9251,non-specific,274009,307,458,0.00267108,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,C-TerminusTruncated
35548,Q#2604 - >seq9251,non-specific,274009,263,427,0.00353068,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,BothTerminiTruncated
35549,Q#2604 - >seq9251,non-specific,197314,7,192,0.00518247,40.0195,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs1_chimp,marg,C-TerminusTruncated
35550,Q#2604 - >seq9251,non-specific,274009,306,456,0.00749266,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs1_chimp.marg.frame3,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs1_chimp,marg,N-TerminusTruncated
35551,Q#2605 - >seq9252,specific,238827,469,731,8.383189999999998e-70,232.952,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35552,Q#2605 - >seq9252,superfamily,295487,469,731,8.383189999999998e-70,232.952,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35553,Q#2605 - >seq9252,specific,333820,475,731,6.18014e-37,137.424,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35554,Q#2605 - >seq9252,superfamily,333820,475,731,6.18014e-37,137.424,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35555,Q#2605 - >seq9252,non-specific,238828,475,696,1.12307e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35556,Q#2605 - >seq9252,non-specific,275209,426,759,3.9845400000000004e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35557,Q#2605 - >seq9252,superfamily,275209,426,759,3.9845400000000004e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35558,Q#2605 - >seq9252,non-specific,238185,615,731,8.33497e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs2_gorilla.pars.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35559,Q#2607 - >seq9254,specific,197310,9,222,4.39337e-55,191.41099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35560,Q#2607 - >seq9254,superfamily,351117,9,222,4.39337e-55,191.41099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35561,Q#2607 - >seq9254,non-specific,197306,9,223,5.44381e-45,162.651,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35562,Q#2607 - >seq9254,non-specific,197307,9,223,9.10155e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35563,Q#2607 - >seq9254,non-specific,223780,9,221,1.1317899999999999e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35564,Q#2607 - >seq9254,non-specific,197320,8,221,4.3055100000000003e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35565,Q#2607 - >seq9254,non-specific,197321,7,223,4.9545e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35566,Q#2607 - >seq9254,specific,335306,10,212,1.87303e-15,76.5149,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35567,Q#2607 - >seq9254,non-specific,272954,9,221,2.8237300000000002e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35568,Q#2607 - >seq9254,non-specific,273186,9,221,5.69587e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35569,Q#2607 - >seq9254,non-specific,197336,7,221,3.92456e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35570,Q#2607 - >seq9254,non-specific,197319,8,223,8.44924e-11,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35571,Q#2607 - >seq9254,non-specific,197322,9,222,3.7848300000000005e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35572,Q#2607 - >seq9254,non-specific,236970,9,221,6.839579999999999e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35573,Q#2607 - >seq9254,non-specific,197311,7,204,2.10179e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35574,Q#2607 - >seq9254,specific,311990,1180,1198,2.9042199999999998e-05,41.5036,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35575,Q#2607 - >seq9254,superfamily,311990,1180,1198,2.9042199999999998e-05,41.5036,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35576,Q#2607 - >seq9254,non-specific,339261,108,217,2.93475e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs2_gorilla.pars.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs2_gorilla,pars,CompleteHit
35577,Q#2608 - >seq9255,specific,238827,469,731,5.142199999999999e-69,230.641,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35578,Q#2608 - >seq9255,superfamily,295487,469,731,5.142199999999999e-69,230.641,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35579,Q#2608 - >seq9255,specific,333820,475,731,3.3009800000000004e-36,135.498,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35580,Q#2608 - >seq9255,superfamily,333820,475,731,3.3009800000000004e-36,135.498,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35581,Q#2608 - >seq9255,non-specific,238828,475,696,2.81452e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35582,Q#2608 - >seq9255,non-specific,275209,426,759,1.1163099999999998e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35583,Q#2608 - >seq9255,superfamily,275209,426,759,1.1163099999999998e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35584,Q#2608 - >seq9255,non-specific,238185,615,731,2.15181e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35585,Q#2608 - >seq9255,specific,311990,1199,1217,0.000357805,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35586,Q#2608 - >seq9255,superfamily,311990,1199,1217,0.000357805,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs2_gorilla.marg.frame1,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35587,Q#2609 - >seq9256,non-specific,235175,256,379,0.00435713,41.2028,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35588,Q#2609 - >seq9256,superfamily,235175,256,379,0.00435713,41.2028,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35589,Q#2609 - >seq9256,non-specific,224117,200,479,0.00470279,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs2_gorilla,marg,N-TerminusTruncated
35590,Q#2609 - >seq9256,superfamily,224117,200,479,0.00470279,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1PA10,ORF2,hs2_gorilla,marg,N-TerminusTruncated
35591,Q#2609 - >seq9256,non-specific,235175,251,449,0.00552505,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs2_gorilla,marg,BothTerminiTruncated
35592,Q#2609 - >seq9256,non-specific,336322,236,361,0.00940074,39.8078,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1PA10,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35593,Q#2609 - >seq9256,superfamily,336322,236,361,0.00940074,39.8078,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA10.ORF2.hs2_gorilla.marg.frame2,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_CellDiv,L1PA10,ORF2,hs2_gorilla,marg,C-TerminusTruncated
35594,Q#2610 - >seq9257,non-specific,240420,204,410,0.00167067,42.2585,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs1_chimp.pars.frame1,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
35595,Q#2610 - >seq9257,superfamily,240420,204,410,0.00167067,42.2585,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs1_chimp.pars.frame1,1909182005_L1PA10.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF2,hs1_chimp,pars,N-TerminusTruncated
35596,Q#2612 - >seq9259,specific,197310,9,222,2.2094799999999996e-54,189.485,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35597,Q#2612 - >seq9259,superfamily,351117,9,222,2.2094799999999996e-54,189.485,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35598,Q#2612 - >seq9259,non-specific,197306,9,223,1.0612699999999999e-44,161.88,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35599,Q#2612 - >seq9259,non-specific,197307,9,223,7.403789999999999e-22,96.2029,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35600,Q#2612 - >seq9259,non-specific,223780,9,221,1.12409e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35601,Q#2612 - >seq9259,non-specific,197320,8,221,4.2764099999999996e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35602,Q#2612 - >seq9259,non-specific,197321,7,223,4.0761400000000005e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35603,Q#2612 - >seq9259,specific,335306,10,212,1.8607299999999998e-15,76.5149,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35604,Q#2612 - >seq9259,non-specific,272954,9,221,2.60156e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35605,Q#2612 - >seq9259,non-specific,273186,9,221,5.65758e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35606,Q#2612 - >seq9259,non-specific,197336,7,221,3.8983300000000004e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35607,Q#2612 - >seq9259,non-specific,197319,8,223,8.39299e-11,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35608,Q#2612 - >seq9259,non-specific,197322,9,222,3.75921e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35609,Q#2612 - >seq9259,non-specific,236970,9,221,7.045300000000001e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35610,Q#2612 - >seq9259,non-specific,197311,7,204,2.40013e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35611,Q#2612 - >seq9259,non-specific,339261,108,217,7.38209e-05,43.0947,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs2_gorilla.marg.frame3,1909182005_L1PA10.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs2_gorilla,marg,CompleteHit
35612,Q#2613 - >seq9260,non-specific,240420,204,411,0.00314592,41.4881,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs4_gibbon.marg.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35613,Q#2613 - >seq9260,superfamily,240420,204,411,0.00314592,41.4881,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs4_gibbon.marg.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF2,hs4_gibbon,marg,N-TerminusTruncated
35614,Q#2614 - >seq9261,specific,197310,9,222,2.6487199999999997e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35615,Q#2614 - >seq9261,superfamily,351117,9,222,2.6487199999999997e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35616,Q#2614 - >seq9261,non-specific,197306,9,223,4.8255e-46,165.732,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35617,Q#2614 - >seq9261,non-specific,197307,9,223,1.21621e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35618,Q#2614 - >seq9261,non-specific,223780,9,221,3.04542e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35619,Q#2614 - >seq9261,non-specific,197320,8,221,7.08297e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35620,Q#2614 - >seq9261,non-specific,197321,7,223,2.2358000000000004e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35621,Q#2614 - >seq9261,specific,335306,10,212,3.57142e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35622,Q#2614 - >seq9261,non-specific,272954,9,221,8.511480000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35623,Q#2614 - >seq9261,non-specific,273186,9,221,8.98094e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35624,Q#2614 - >seq9261,non-specific,197336,7,221,2.09043e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35625,Q#2614 - >seq9261,non-specific,197319,8,223,3.28889e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35626,Q#2614 - >seq9261,non-specific,197322,9,222,1.88068e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35627,Q#2614 - >seq9261,non-specific,236970,9,221,2.8223e-07,52.9742,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35628,Q#2614 - >seq9261,non-specific,197311,7,204,5.85969e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35629,Q#2614 - >seq9261,non-specific,339261,108,217,0.000371497,41.1687,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35630,Q#2614 - >seq9261,non-specific,197314,7,192,0.00594857,39.6343,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.pars.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35631,Q#2615 - >seq9262,non-specific,235175,257,379,0.00024771099999999996,45.0548,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35632,Q#2615 - >seq9262,superfamily,235175,257,379,0.00024771099999999996,45.0548,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35633,Q#2615 - >seq9262,non-specific,224117,201,479,0.00156582,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35634,Q#2615 - >seq9262,superfamily,224117,201,479,0.00156582,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35635,Q#2615 - >seq9262,non-specific,224259,290,436,0.00900694,39.2792,COG1340,COG1340,C,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35636,Q#2615 - >seq9262,superfamily,224259,290,436,0.00900694,39.2792,cl34231,COG1340 superfamily,C, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA10.ORF2.hs4_gibbon.pars.frame2,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA10,ORF2,hs4_gibbon,pars,C-TerminusTruncated
35637,Q#2616 - >seq9263,specific,238827,469,731,3.9617299999999996e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35638,Q#2616 - >seq9263,superfamily,295487,469,731,3.9617299999999996e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35639,Q#2616 - >seq9263,specific,333820,475,731,3.05544e-36,135.498,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35640,Q#2616 - >seq9263,superfamily,333820,475,731,3.05544e-36,135.498,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35641,Q#2616 - >seq9263,non-specific,238828,475,696,1.07618e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35642,Q#2616 - >seq9263,non-specific,275209,426,759,8.856939999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35643,Q#2616 - >seq9263,superfamily,275209,426,759,8.856939999999999e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35644,Q#2616 - >seq9263,non-specific,238185,615,731,1.87733e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35645,Q#2616 - >seq9263,specific,311990,1199,1217,0.00032443,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35646,Q#2616 - >seq9263,superfamily,311990,1199,1217,0.00032443,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA10,ORF2,hs4_gibbon,pars,CompleteHit
35647,Q#2616 - >seq9263,specific,225881,473,693,0.00558455,40.2073,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35648,Q#2616 - >seq9263,superfamily,225881,473,693,0.00558455,40.2073,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA10.ORF2.hs4_gibbon.pars.frame1,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs4_gibbon,pars,N-TerminusTruncated
35649,Q#2617 - >seq9264,specific,197310,9,222,1.3520699999999997e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35650,Q#2617 - >seq9264,superfamily,351117,9,222,1.3520699999999997e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35651,Q#2617 - >seq9264,non-specific,197306,9,223,1.00031e-46,167.658,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35652,Q#2617 - >seq9264,non-specific,197307,9,223,1.1784799999999999e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35653,Q#2617 - >seq9264,non-specific,223780,9,221,2.9502e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35654,Q#2617 - >seq9264,non-specific,197320,8,221,6.86298e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35655,Q#2617 - >seq9264,non-specific,197321,7,223,2.1665799999999998e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35656,Q#2617 - >seq9264,specific,335306,10,212,3.46363e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35657,Q#2617 - >seq9264,non-specific,272954,9,221,8.248330000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35658,Q#2617 - >seq9264,non-specific,273186,9,221,8.70369e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35659,Q#2617 - >seq9264,non-specific,197336,7,221,2.0262200000000002e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35660,Q#2617 - >seq9264,non-specific,197319,8,223,3.18822e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35661,Q#2617 - >seq9264,non-specific,197322,9,222,1.82172e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35662,Q#2617 - >seq9264,non-specific,236970,9,221,5.36496e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35663,Q#2617 - >seq9264,non-specific,197311,7,204,4.81056e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35664,Q#2617 - >seq9264,non-specific,339261,108,217,0.000110006,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs4_gibbon,marg,CompleteHit
35665,Q#2617 - >seq9264,non-specific,197314,7,192,0.00577365,39.6343,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs4_gibbon.marg.frame3,1909182005_L1PA10.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs4_gibbon,marg,C-TerminusTruncated
35666,Q#2618 - >seq9265,specific,238827,485,747,2.7306699999999994e-68,228.715,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35667,Q#2618 - >seq9265,superfamily,295487,485,747,2.7306699999999994e-68,228.715,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35668,Q#2618 - >seq9265,specific,333820,491,747,1.35909e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35669,Q#2618 - >seq9265,superfamily,333820,491,747,1.35909e-35,133.572,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35670,Q#2618 - >seq9265,non-specific,238828,491,712,1.4387600000000002e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35671,Q#2618 - >seq9265,non-specific,275209,442,775,5.31717e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35672,Q#2618 - >seq9265,superfamily,275209,442,775,5.31717e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35673,Q#2618 - >seq9265,non-specific,238185,622,747,4.9086e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35674,Q#2618 - >seq9265,specific,311990,1215,1233,0.000201389,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35675,Q#2618 - >seq9265,superfamily,311990,1215,1233,0.000201389,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs3_orang.marg.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35676,Q#2620 - >seq9267,specific,197310,9,236,3.779699999999999e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35677,Q#2620 - >seq9267,superfamily,351117,9,236,3.779699999999999e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35678,Q#2620 - >seq9267,non-specific,197306,9,236,5.24059e-50,176.903,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35679,Q#2620 - >seq9267,non-specific,197307,9,236,1.1443799999999998e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35680,Q#2620 - >seq9267,non-specific,223780,9,238,9.27789e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35681,Q#2620 - >seq9267,non-specific,197320,8,229,6.893569999999999e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35682,Q#2620 - >seq9267,non-specific,197321,7,236,2.41165e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35683,Q#2620 - >seq9267,specific,335306,10,229,1.1989900000000001e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35684,Q#2620 - >seq9267,non-specific,273186,9,237,1.44697e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35685,Q#2620 - >seq9267,non-specific,272954,9,236,5.34044e-17,82.0456,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35686,Q#2620 - >seq9267,non-specific,197319,8,236,1.3037200000000001e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35687,Q#2620 - >seq9267,non-specific,197336,7,229,4.4383999999999995e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35688,Q#2620 - >seq9267,non-specific,197322,9,236,1.01926e-10,64.2606,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35689,Q#2620 - >seq9267,non-specific,339261,108,232,3.0375400000000002e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35690,Q#2620 - >seq9267,non-specific,236970,9,238,1.46048e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35691,Q#2620 - >seq9267,non-specific,197311,7,236,9.64684e-08,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35692,Q#2620 - >seq9267,non-specific,197317,23,229,0.000206679,44.13,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35693,Q#2620 - >seq9267,non-specific,224117,266,423,0.000853515,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,pars,BothTerminiTruncated
35694,Q#2620 - >seq9267,superfamily,224117,266,423,0.000853515,43.5496,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA10,ORF2,hs3_orang,pars,BothTerminiTruncated
35695,Q#2620 - >seq9267,non-specific,235175,263,461,0.00447916,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,pars,BothTerminiTruncated
35696,Q#2620 - >seq9267,superfamily,235175,263,461,0.00447916,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,pars,BothTerminiTruncated
35697,Q#2620 - >seq9267,non-specific,224117,263,491,0.00782927,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.pars.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,pars,N-TerminusTruncated
35698,Q#2621 - >seq9268,specific,197310,9,236,3.7865699999999994e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35699,Q#2621 - >seq9268,superfamily,351117,9,236,3.7865699999999994e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35700,Q#2621 - >seq9268,non-specific,197306,9,236,5.14576e-50,176.903,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35701,Q#2621 - >seq9268,non-specific,197307,9,236,1.14551e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35702,Q#2621 - >seq9268,non-specific,223780,9,238,9.28713e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35703,Q#2621 - >seq9268,non-specific,197320,8,229,6.90038e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35704,Q#2621 - >seq9268,non-specific,197321,7,236,2.4836200000000003e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35705,Q#2621 - >seq9268,specific,335306,10,229,1.2001400000000001e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35706,Q#2621 - >seq9268,non-specific,273186,9,237,1.4483900000000003e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35707,Q#2621 - >seq9268,non-specific,272954,9,236,5.3457e-17,82.0456,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35708,Q#2621 - >seq9268,non-specific,197319,8,236,1.35495e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35709,Q#2621 - >seq9268,non-specific,197336,7,229,4.4427399999999997e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35710,Q#2621 - >seq9268,non-specific,197322,9,236,1.0202899999999999e-10,64.2606,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35711,Q#2621 - >seq9268,non-specific,339261,108,232,3.04023e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35712,Q#2621 - >seq9268,non-specific,236970,9,238,1.47533e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35713,Q#2621 - >seq9268,non-specific,197311,7,236,9.655889999999999e-08,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35714,Q#2621 - >seq9268,non-specific,197317,23,229,0.000206875,44.13,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs3_orang,marg,CompleteHit
35715,Q#2621 - >seq9268,non-specific,224117,266,423,0.000898833,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,marg,BothTerminiTruncated
35716,Q#2621 - >seq9268,superfamily,224117,266,423,0.000898833,43.5496,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA10,ORF2,hs3_orang,marg,BothTerminiTruncated
35717,Q#2621 - >seq9268,non-specific,235175,263,461,0.00448347,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,marg,BothTerminiTruncated
35718,Q#2621 - >seq9268,superfamily,235175,263,461,0.00448347,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,marg,BothTerminiTruncated
35719,Q#2621 - >seq9268,non-specific,224117,263,491,0.00790336,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs3_orang.marg.frame3,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs3_orang,marg,N-TerminusTruncated
35720,Q#2622 - >seq9269,specific,238827,485,747,2.6718399999999996e-68,228.715,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35721,Q#2622 - >seq9269,superfamily,295487,485,747,2.6718399999999996e-68,228.715,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35722,Q#2622 - >seq9269,specific,333820,491,747,1.28141e-35,133.572,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35723,Q#2622 - >seq9269,superfamily,333820,491,747,1.28141e-35,133.572,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35724,Q#2622 - >seq9269,non-specific,238828,491,712,1.38454e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35725,Q#2622 - >seq9269,non-specific,275209,442,775,5.03785e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35726,Q#2622 - >seq9269,superfamily,275209,442,775,5.03785e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35727,Q#2622 - >seq9269,non-specific,238185,622,747,4.90452e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35728,Q#2622 - >seq9269,specific,311990,1214,1232,0.00020123,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35729,Q#2622 - >seq9269,superfamily,311990,1214,1232,0.00020123,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs3_orang.pars.frame2,1909182005_L1PA10.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs3_orang,pars,CompleteHit
35730,Q#2623 - >seq9270,specific,238827,510,772,2.1825799999999995e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35731,Q#2623 - >seq9270,superfamily,295487,510,772,2.1825799999999995e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35732,Q#2623 - >seq9270,specific,197310,9,236,7.07063e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35733,Q#2623 - >seq9270,superfamily,351117,9,236,7.07063e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35734,Q#2623 - >seq9270,non-specific,197306,9,236,1.84539e-48,172.666,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35735,Q#2623 - >seq9270,specific,333820,516,772,4.36159e-36,135.112,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35736,Q#2623 - >seq9270,superfamily,333820,516,772,4.36159e-36,135.112,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35737,Q#2623 - >seq9270,non-specific,197307,9,236,1.3974700000000001e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35738,Q#2623 - >seq9270,non-specific,223780,9,238,5.8787199999999995e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35739,Q#2623 - >seq9270,non-specific,197320,8,229,8.28602e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35740,Q#2623 - >seq9270,non-specific,197321,7,236,3.83946e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35741,Q#2623 - >seq9270,specific,335306,10,229,4.09244e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35742,Q#2623 - >seq9270,non-specific,273186,9,237,1.8727599999999996e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35743,Q#2623 - >seq9270,non-specific,272954,9,236,1.24674e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35744,Q#2623 - >seq9270,non-specific,197336,7,229,8.18332e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35745,Q#2623 - >seq9270,non-specific,197319,8,236,9.126440000000001e-13,69.6129,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35746,Q#2623 - >seq9270,non-specific,238828,516,737,8.55105e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35747,Q#2623 - >seq9270,non-specific,197322,9,236,3.549e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35748,Q#2623 - >seq9270,non-specific,275209,467,800,1.6586199999999998e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35749,Q#2623 - >seq9270,superfamily,275209,467,800,1.6586199999999998e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35750,Q#2623 - >seq9270,non-specific,339261,108,232,1.1292799999999998e-08,54.2655,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35751,Q#2623 - >seq9270,non-specific,236970,9,238,3.97416e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35752,Q#2623 - >seq9270,non-specific,197311,7,236,3.141e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35753,Q#2623 - >seq9270,non-specific,238185,656,772,4.6278999999999995e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35754,Q#2623 - >seq9270,non-specific,235175,263,469,0.00011221700000000001,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
35755,Q#2623 - >seq9270,superfamily,235175,263,469,0.00011221700000000001,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
35756,Q#2623 - >seq9270,specific,311990,1241,1259,0.0004912730000000001,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35757,Q#2623 - >seq9270,superfamily,311990,1241,1259,0.0004912730000000001,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs5_gmonkey,marg,CompleteHit
35758,Q#2623 - >seq9270,non-specific,274009,307,458,0.00101877,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
35759,Q#2623 - >seq9270,superfamily,274009,307,458,0.00101877,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
35760,Q#2623 - >seq9270,non-specific,197317,139,229,0.00172915,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
35761,Q#2623 - >seq9270,non-specific,197314,7,192,0.00630932,39.6343,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
35762,Q#2623 - >seq9270,non-specific,274009,306,456,0.00957436,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.marg.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
35763,Q#2626 - >seq9273,specific,238827,498,760,3.4135999999999996e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35764,Q#2626 - >seq9273,superfamily,295487,498,760,3.4135999999999996e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35765,Q#2626 - >seq9273,specific,333820,504,760,1.5486e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35766,Q#2626 - >seq9273,superfamily,333820,504,760,1.5486e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35767,Q#2626 - >seq9273,non-specific,238828,504,725,5.27973e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35768,Q#2626 - >seq9273,non-specific,275209,455,788,2.35885e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35769,Q#2626 - >seq9273,superfamily,275209,455,788,2.35885e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35770,Q#2626 - >seq9273,non-specific,238185,644,760,2.50217e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35771,Q#2626 - >seq9273,non-specific,224117,200,489,8.05729e-05,47.0164,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
35772,Q#2626 - >seq9273,superfamily,224117,200,489,8.05729e-05,47.0164,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
35773,Q#2626 - >seq9273,non-specific,235175,251,457,0.000116675,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
35774,Q#2626 - >seq9273,superfamily,235175,251,457,0.000116675,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
35775,Q#2626 - >seq9273,specific,311990,1228,1246,0.00040773800000000005,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35776,Q#2626 - >seq9273,superfamily,311990,1228,1246,0.00040773800000000005,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35777,Q#2626 - >seq9273,non-specific,274009,295,446,0.0008573960000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
35778,Q#2626 - >seq9273,superfamily,274009,295,446,0.0008573960000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
35779,Q#2626 - >seq9273,non-specific,274009,294,444,0.00833651,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
35780,Q#2626 - >seq9273,non-specific,223496,279,415,0.00975991,40.1287,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
35781,Q#2626 - >seq9273,superfamily,223496,279,415,0.00975991,40.1287,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA10.ORF2.hs5_gmonkey.pars.frame2,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1PA10,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
35782,Q#2627 - >seq9274,non-specific,240274,252,514,0.00602167,40.7437,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1PA10.ORF2.hs5_gmonkey.pars.frame1,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
35783,Q#2627 - >seq9274,superfamily,240274,252,514,0.00602167,40.7437,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1PA10.ORF2.hs5_gmonkey.pars.frame1,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
35784,Q#2628 - >seq9275,specific,197310,9,222,1.0408699999999999e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35785,Q#2628 - >seq9275,superfamily,351117,9,222,1.0408699999999999e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35786,Q#2628 - >seq9275,non-specific,197306,9,223,1.11219e-46,167.273,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35787,Q#2628 - >seq9275,non-specific,197307,9,223,1.1784799999999999e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35788,Q#2628 - >seq9275,non-specific,223780,9,221,2.9502e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35789,Q#2628 - >seq9275,non-specific,197320,8,221,6.86298e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35790,Q#2628 - >seq9275,non-specific,197321,7,223,2.1665799999999998e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35791,Q#2628 - >seq9275,specific,335306,10,212,3.46363e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35792,Q#2628 - >seq9275,non-specific,272954,9,221,8.248330000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35793,Q#2628 - >seq9275,non-specific,273186,9,221,8.70369e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35794,Q#2628 - >seq9275,non-specific,197336,7,221,2.0262200000000002e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35795,Q#2628 - >seq9275,non-specific,197319,8,223,3.18822e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35796,Q#2628 - >seq9275,non-specific,197322,9,222,1.82172e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35797,Q#2628 - >seq9275,non-specific,236970,9,221,5.71854e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35798,Q#2628 - >seq9275,non-specific,197311,7,204,4.81056e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35799,Q#2628 - >seq9275,non-specific,339261,108,217,9.890760000000001e-05,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs5_gmonkey,pars,CompleteHit
35800,Q#2628 - >seq9275,non-specific,197314,7,192,0.00577365,39.6343,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs5_gmonkey.pars.frame3,1909182008_L1PA10.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA10,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
35801,Q#2629 - >seq9276,non-specific,240420,218,426,0.00837366,39.9473,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs6_sqmonkey.marg.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
35802,Q#2629 - >seq9276,superfamily,240420,218,426,0.00837366,39.9473,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs6_sqmonkey.marg.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1PA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
35803,Q#2631 - >seq9278,specific,238827,510,772,1.6591799999999995e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35804,Q#2631 - >seq9278,superfamily,295487,510,772,1.6591799999999995e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35805,Q#2631 - >seq9278,specific,197310,9,236,3.2568199999999996e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35806,Q#2631 - >seq9278,superfamily,351117,9,236,3.2568199999999996e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35807,Q#2631 - >seq9278,non-specific,197306,9,236,7.23766e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35808,Q#2631 - >seq9278,specific,333820,516,772,3.76989e-36,135.112,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35809,Q#2631 - >seq9278,superfamily,333820,516,772,3.76989e-36,135.112,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35810,Q#2631 - >seq9278,non-specific,197307,9,236,1.30396e-23,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35811,Q#2631 - >seq9278,non-specific,223780,9,238,8.26498e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35812,Q#2631 - >seq9278,non-specific,197320,8,236,7.458799999999999e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35813,Q#2631 - >seq9278,non-specific,197321,7,236,1.9231599999999998e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35814,Q#2631 - >seq9278,specific,335306,10,229,5.04227e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35815,Q#2631 - >seq9278,non-specific,273186,9,237,5.81229e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35816,Q#2631 - >seq9278,non-specific,272954,9,236,2.78841e-16,79.7345,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35817,Q#2631 - >seq9278,non-specific,197336,7,235,6.65612e-14,73.0303,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35818,Q#2631 - >seq9278,non-specific,197319,8,236,9.8261e-13,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35819,Q#2631 - >seq9278,non-specific,238828,516,737,1.36143e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35820,Q#2631 - >seq9278,non-specific,197322,9,236,8.18011e-12,67.7274,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35821,Q#2631 - >seq9278,non-specific,339261,108,232,2.54348e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35822,Q#2631 - >seq9278,non-specific,275209,467,800,1.7018599999999997e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35823,Q#2631 - >seq9278,superfamily,275209,467,800,1.7018599999999997e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35824,Q#2631 - >seq9278,non-specific,236970,9,238,5.61539e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35825,Q#2631 - >seq9278,non-specific,197311,7,236,7.28207e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35826,Q#2631 - >seq9278,non-specific,238185,656,772,4.2357799999999996e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35827,Q#2631 - >seq9278,specific,311990,1240,1258,0.000472036,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35828,Q#2631 - >seq9278,superfamily,311990,1240,1258,0.000472036,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA10,ORF2,hs6_sqmonkey,marg,CompleteHit
35829,Q#2631 - >seq9278,non-specific,274009,301,478,0.00123636,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
35830,Q#2631 - >seq9278,superfamily,274009,301,478,0.00123636,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
35831,Q#2631 - >seq9278,non-specific,197317,139,229,0.00183943,41.4336,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
35832,Q#2631 - >seq9278,non-specific,235175,263,464,0.00335979,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
35833,Q#2631 - >seq9278,superfamily,235175,263,464,0.00335979,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
35834,Q#2631 - >seq9278,non-specific,274009,306,456,0.00367983,41.5919,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs6_sqmonkey.marg.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
35835,Q#2632 - >seq9279,specific,238827,473,735,2.43644e-69,231.41099999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35836,Q#2632 - >seq9279,superfamily,295487,473,735,2.43644e-69,231.41099999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35837,Q#2632 - >seq9279,specific,333820,479,735,2.2177600000000003e-37,138.579,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35838,Q#2632 - >seq9279,superfamily,333820,479,735,2.2177600000000003e-37,138.579,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35839,Q#2632 - >seq9279,non-specific,238828,479,700,3.08288e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35840,Q#2632 - >seq9279,non-specific,275209,430,763,5.85112e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35841,Q#2632 - >seq9279,superfamily,275209,430,763,5.85112e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35842,Q#2632 - >seq9279,non-specific,238185,619,735,8.40609e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs6_sqmonkey.pars.frame1,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35843,Q#2633 - >seq9280,specific,197310,9,222,6.65924e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35844,Q#2633 - >seq9280,superfamily,351117,9,222,6.65924e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35845,Q#2633 - >seq9280,non-specific,197306,9,223,1.9021599999999994e-46,166.888,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35846,Q#2633 - >seq9280,non-specific,197307,9,221,4.12876e-22,96.9733,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35847,Q#2633 - >seq9280,non-specific,223780,9,221,3.76523e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35848,Q#2633 - >seq9280,non-specific,197320,8,221,5.993680000000001e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35849,Q#2633 - >seq9280,non-specific,197321,7,221,4.7303999999999994e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35850,Q#2633 - >seq9280,non-specific,272954,9,221,1.7559099999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35851,Q#2633 - >seq9280,specific,335306,10,212,4.37683e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35852,Q#2633 - >seq9280,non-specific,273186,9,221,3.03118e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35853,Q#2633 - >seq9280,non-specific,197336,7,221,3.48835e-13,70.7191,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35854,Q#2633 - >seq9280,non-specific,197319,8,221,3.90202e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35855,Q#2633 - >seq9280,non-specific,197322,9,221,6.856489999999999e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35856,Q#2633 - >seq9280,non-specific,236970,9,221,2.53926e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35857,Q#2633 - >seq9280,non-specific,197311,7,204,1.7691400000000002e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35858,Q#2633 - >seq9280,non-specific,339261,108,217,3.73799e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs6_sqmonkey.pars.frame3,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35859,Q#2634 - >seq9281,specific,311990,1160,1178,0.000116934,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35860,Q#2634 - >seq9281,superfamily,311990,1160,1178,0.000116934,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs6_sqmonkey,pars,CompleteHit
35861,Q#2634 - >seq9281,non-specific,274008,285,369,0.00144358,42.7363,TIGR02168,SMC_prok_B,C,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35862,Q#2634 - >seq9281,superfamily,274008,285,369,0.00144358,42.7363,cl37069,SMC_prok_B superfamily,C, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35863,Q#2634 - >seq9281,non-specific,287038,302,460,0.00727116,38.5795,pfam10018,Med4,C,cl10818,"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35864,Q#2634 - >seq9281,superfamily,287038,302,460,0.00727116,38.5795,cl10818,Med4 superfamily,C, - ,"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35865,Q#2634 - >seq9281,non-specific,336322,272,361,0.0091295,39.8078,pfam06160,EzrA,C,cl38199,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35866,Q#2634 - >seq9281,superfamily,336322,272,361,0.0091295,39.8078,cl38199,EzrA superfamily,C, - ,"Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.",L1PA10.ORF2.hs6_sqmonkey.pars.frame2,1909182014_L1PA10.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_CellDiv,L1PA10,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
35867,Q#2636 - >seq9283,specific,311990,1186,1204,5.24946e-05,41.1184,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs0_human.pars.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs0_human,pars,CompleteHit
35868,Q#2636 - >seq9283,superfamily,311990,1186,1204,5.24946e-05,41.1184,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs0_human.pars.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA10,ORF2,hs0_human,pars,CompleteHit
35869,Q#2636 - >seq9283,non-specific,224117,200,380,0.00108434,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs0_human.pars.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA10,ORF2,hs0_human,pars,BothTerminiTruncated
35870,Q#2636 - >seq9283,superfamily,224117,200,380,0.00108434,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs0_human.pars.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA10,ORF2,hs0_human,pars,BothTerminiTruncated
35871,Q#2637 - >seq9284,specific,238827,493,754,3.552909999999999e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35872,Q#2637 - >seq9284,superfamily,295487,493,754,3.552909999999999e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35873,Q#2637 - >seq9284,specific,197310,9,228,4.62774e-56,194.107,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35874,Q#2637 - >seq9284,superfamily,351117,9,228,4.62774e-56,194.107,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35875,Q#2637 - >seq9284,non-specific,197306,9,223,6.20961e-45,162.651,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35876,Q#2637 - >seq9284,specific,333820,499,754,1.0223099999999998e-33,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35877,Q#2637 - >seq9284,superfamily,333820,499,754,1.0223099999999998e-33,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35878,Q#2637 - >seq9284,non-specific,197307,9,226,4.88035e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35879,Q#2637 - >seq9284,non-specific,223780,9,221,1.3774299999999998e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35880,Q#2637 - >seq9284,non-specific,197320,8,221,1.90172e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35881,Q#2637 - >seq9284,non-specific,197321,7,224,3.11441e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35882,Q#2637 - >seq9284,specific,335306,10,212,1.32625e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35883,Q#2637 - >seq9284,non-specific,272954,9,221,1.60215e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35884,Q#2637 - >seq9284,non-specific,273186,9,221,9.52268e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35885,Q#2637 - >seq9284,non-specific,197336,7,221,1.08979e-12,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35886,Q#2637 - >seq9284,non-specific,238828,499,719,7.69037e-11,63.373999999999995,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35887,Q#2637 - >seq9284,non-specific,197319,8,223,9.04543e-10,60.3681,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35888,Q#2637 - >seq9284,non-specific,197322,9,222,3.2439499999999997e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35889,Q#2637 - >seq9284,non-specific,275209,450,782,9.06886e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35890,Q#2637 - >seq9284,superfamily,275209,450,782,9.06886e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35891,Q#2637 - >seq9284,non-specific,236970,9,221,1.0263200000000002e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35892,Q#2637 - >seq9284,non-specific,238185,629,754,4.64402e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35893,Q#2637 - >seq9284,non-specific,197311,7,204,1.26875e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,pars,CompleteHit
35894,Q#2637 - >seq9284,non-specific,339261,108,217,1.79857e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35895,Q#2637 - >seq9284,non-specific,239569,523,729,0.000659651,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,CompleteHit
35896,Q#2637 - >seq9284,specific,225881,497,716,0.0044448,40.5925,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,N-TerminusTruncated
35897,Q#2637 - >seq9284,superfamily,225881,497,716,0.0044448,40.5925,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA10.ORF2.hs0_human.pars.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA10,ORF2,hs0_human,pars,N-TerminusTruncated
35898,Q#2638 - >seq9285,non-specific,240420,202,412,0.000220809,44.9549,PTZ00441,PTZ00441,N,cl25523,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs0_human.marg.frame1,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF2,hs0_human,marg,N-TerminusTruncated
35899,Q#2638 - >seq9285,superfamily,240420,202,412,0.000220809,44.9549,cl25523,PTZ00441 superfamily,N, - ,sporozoite surface protein 2 (SSP2); Provisional,L1PA10.ORF2.hs0_human.marg.frame1,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PA10,ORF2,hs0_human,marg,N-TerminusTruncated
35900,Q#2639 - >seq9286,specific,238827,497,758,7.672019999999998e-65,218.7,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35901,Q#2639 - >seq9286,superfamily,295487,497,758,7.672019999999998e-65,218.7,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35902,Q#2639 - >seq9286,specific,333820,503,758,2.2063699999999998e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35903,Q#2639 - >seq9286,superfamily,333820,503,758,2.2063699999999998e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35904,Q#2639 - >seq9286,non-specific,238828,503,723,1.8699799999999998e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35905,Q#2639 - >seq9286,non-specific,275209,454,786,4.45852e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35906,Q#2639 - >seq9286,superfamily,275209,454,786,4.45852e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35907,Q#2639 - >seq9286,non-specific,238185,633,758,9.2357e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35908,Q#2639 - >seq9286,non-specific,224117,200,488,6.95878e-05,47.0164,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA10,ORF2,hs0_human,marg,N-TerminusTruncated
35909,Q#2639 - >seq9286,superfamily,224117,200,488,6.95878e-05,47.0164,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1PA10,ORF2,hs0_human,marg,N-TerminusTruncated
35910,Q#2639 - >seq9286,specific,311990,1225,1243,0.00043564300000000004,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs0_human,marg,CompleteHit
35911,Q#2639 - >seq9286,superfamily,311990,1225,1243,0.00043564300000000004,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA10,ORF2,hs0_human,marg,CompleteHit
35912,Q#2639 - >seq9286,non-specific,239569,527,733,0.0006888660000000001,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA10.ORF2.hs0_human.marg.frame2,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35913,Q#2640 - >seq9287,specific,197310,9,228,4.9432600000000005e-57,196.804,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35914,Q#2640 - >seq9287,superfamily,351117,9,228,4.9432600000000005e-57,196.804,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35915,Q#2640 - >seq9287,non-specific,197306,9,223,4.9962900000000005e-46,165.732,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35916,Q#2640 - >seq9287,non-specific,197307,9,226,5.00302e-22,96.5881,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35917,Q#2640 - >seq9287,non-specific,223780,9,221,1.0104299999999999e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35918,Q#2640 - >seq9287,non-specific,197320,8,221,1.78539e-19,89.1113,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35919,Q#2640 - >seq9287,non-specific,197321,7,224,4.2711800000000004e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35920,Q#2640 - >seq9287,non-specific,272954,9,221,5.24474e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35921,Q#2640 - >seq9287,specific,335306,10,212,1.24737e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35922,Q#2640 - >seq9287,non-specific,273186,9,221,8.85984e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35923,Q#2640 - >seq9287,non-specific,197336,7,221,1.02379e-12,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35924,Q#2640 - >seq9287,non-specific,197319,8,223,9.01989e-11,63.4497,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35925,Q#2640 - >seq9287,non-specific,197322,9,222,3.0439e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35926,Q#2640 - >seq9287,non-specific,236970,9,221,2.08129e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35927,Q#2640 - >seq9287,non-specific,197311,7,204,1.13049e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA10,ORF2,hs0_human,marg,CompleteHit
35928,Q#2640 - >seq9287,non-specific,339261,108,217,1.73263e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA10.ORF2.hs0_human.marg.frame3,1909182035_L1PA10.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA10,ORF2,hs0_human,marg,CompleteHit
35929,Q#2642 - >seq9289,specific,238827,509,771,4.1954099999999994e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35930,Q#2642 - >seq9289,superfamily,295487,509,771,4.1954099999999994e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35931,Q#2642 - >seq9289,specific,197310,9,236,3.0653699999999994e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35932,Q#2642 - >seq9289,superfamily,351117,9,236,3.0653699999999994e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35933,Q#2642 - >seq9289,non-specific,197306,9,236,3.18803e-48,171.896,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35934,Q#2642 - >seq9289,specific,333820,515,771,2.2838499999999995e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35935,Q#2642 - >seq9289,superfamily,333820,515,771,2.2838499999999995e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35936,Q#2642 - >seq9289,non-specific,197307,9,236,5.58852e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35937,Q#2642 - >seq9289,non-specific,223780,9,238,6.324930000000001e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35938,Q#2642 - >seq9289,non-specific,197320,8,229,5.04751e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35939,Q#2642 - >seq9289,non-specific,197321,7,236,1.3655100000000001e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35940,Q#2642 - >seq9289,specific,335306,10,229,4.04282e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35941,Q#2642 - >seq9289,non-specific,273186,9,237,7.04732e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35942,Q#2642 - >seq9289,non-specific,272954,9,236,7.48045e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35943,Q#2642 - >seq9289,non-specific,197319,8,236,2.15504e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35944,Q#2642 - >seq9289,non-specific,197336,7,229,5.93929e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35945,Q#2642 - >seq9289,non-specific,238828,515,723,3.66196e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35946,Q#2642 - >seq9289,non-specific,197322,9,236,1.3828799999999998e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35947,Q#2642 - >seq9289,non-specific,236970,9,238,3.03147e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35948,Q#2642 - >seq9289,non-specific,339261,108,232,4.50654e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35949,Q#2642 - >seq9289,non-specific,275209,466,799,1.49927e-07,54.7712,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35950,Q#2642 - >seq9289,superfamily,275209,466,799,1.49927e-07,54.7712,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35951,Q#2642 - >seq9289,non-specific,197311,7,236,1.42269e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35952,Q#2642 - >seq9289,non-specific,238185,655,771,0.000430165,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35953,Q#2642 - >seq9289,non-specific,197314,7,192,0.000488025,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs1_chimp,marg,C-TerminusTruncated
35954,Q#2642 - >seq9289,non-specific,274009,306,455,0.000525363,44.2883,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs1_chimp,marg,N-TerminusTruncated
35955,Q#2642 - >seq9289,superfamily,274009,306,455,0.000525363,44.2883,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs1_chimp,marg,N-TerminusTruncated
35956,Q#2642 - >seq9289,non-specific,224117,263,466,0.00203907,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs1_chimp,marg,N-TerminusTruncated
35957,Q#2642 - >seq9289,superfamily,224117,263,466,0.00203907,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs1_chimp,marg,N-TerminusTruncated
35958,Q#2642 - >seq9289,non-specific,197317,23,229,0.00255727,41.0484,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35959,Q#2642 - >seq9289,specific,316774,305,363,0.00450789,37.7532,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35960,Q#2642 - >seq9289,superfamily,316774,305,363,0.00450789,37.7532,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35961,Q#2642 - >seq9289,specific,311990,1238,1256,0.00457495,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35962,Q#2642 - >seq9289,superfamily,311990,1238,1256,0.00457495,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35963,Q#2642 - >seq9289,non-specific,197318,9,236,0.00514094,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,marg,CompleteHit
35964,Q#2642 - >seq9289,non-specific,274008,263,426,0.00964153,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs1_chimp,marg,BothTerminiTruncated
35965,Q#2642 - >seq9289,superfamily,274008,263,426,0.00964153,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs1_chimp.marg.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs1_chimp,marg,BothTerminiTruncated
35966,Q#2644 - >seq9291,specific,197310,9,222,3.23537e-55,191.796,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35967,Q#2644 - >seq9291,superfamily,351117,9,222,3.23537e-55,191.796,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35968,Q#2644 - >seq9291,non-specific,197306,9,223,6.5109e-46,165.347,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35969,Q#2644 - >seq9291,non-specific,197307,9,223,5.07482e-22,96.5881,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35970,Q#2644 - >seq9291,non-specific,223780,9,221,4.20642e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35971,Q#2644 - >seq9291,non-specific,197320,8,221,4.71505e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35972,Q#2644 - >seq9291,non-specific,197321,7,223,8.86508e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35973,Q#2644 - >seq9291,specific,335306,10,212,3.5076099999999997e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35974,Q#2644 - >seq9291,non-specific,272954,9,221,4.980780000000001e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35975,Q#2644 - >seq9291,non-specific,273186,9,221,4.0320099999999993e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35976,Q#2644 - >seq9291,non-specific,197336,7,221,1.59569e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35977,Q#2644 - >seq9291,non-specific,197319,8,223,9.99639e-12,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35978,Q#2644 - >seq9291,non-specific,197322,9,222,7.2076899999999995e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35979,Q#2644 - >seq9291,non-specific,236970,9,221,1.51425e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35980,Q#2644 - >seq9291,non-specific,197311,7,204,2.42936e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35981,Q#2644 - >seq9291,non-specific,197314,7,192,0.000457274,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs1_chimp,pars,C-TerminusTruncated
35982,Q#2644 - >seq9291,non-specific,339261,108,217,0.00125653,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35983,Q#2644 - >seq9291,non-specific,197318,9,148,0.0084694,39.2019,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs1_chimp.pars.frame3,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs1_chimp,pars,C-TerminusTruncated
35984,Q#2645 - >seq9292,specific,238827,468,730,1.1981799999999999e-65,221.011,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35985,Q#2645 - >seq9292,superfamily,295487,468,730,1.1981799999999999e-65,221.011,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35986,Q#2645 - >seq9292,specific,333820,474,730,2.51205e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35987,Q#2645 - >seq9292,superfamily,333820,474,730,2.51205e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35988,Q#2645 - >seq9292,non-specific,238828,474,682,1.18835e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35989,Q#2645 - >seq9292,non-specific,275209,425,758,8.137050000000001e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35990,Q#2645 - >seq9292,superfamily,275209,425,758,8.137050000000001e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35991,Q#2645 - >seq9292,non-specific,238185,614,730,0.000120949,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35992,Q#2645 - >seq9292,specific,225881,472,697,0.00217478,41.3629,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,N-TerminusTruncated
35993,Q#2645 - >seq9292,superfamily,225881,472,697,0.00217478,41.3629,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA11.ORF2.hs1_chimp.pars.frame1,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs1_chimp,pars,N-TerminusTruncated
35994,Q#2646 - >seq9293,specific,311990,1155,1173,0.0009274880000000001,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs1_chimp.pars.frame2,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35995,Q#2646 - >seq9293,superfamily,311990,1155,1173,0.0009274880000000001,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs1_chimp.pars.frame2,1909182036_L1PA11.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs1_chimp,pars,CompleteHit
35996,Q#2648 - >seq9295,specific,238827,498,760,1.4154799999999999e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
35997,Q#2648 - >seq9295,superfamily,295487,498,760,1.4154799999999999e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
35998,Q#2648 - >seq9295,specific,333820,504,760,1.66342e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
35999,Q#2648 - >seq9295,superfamily,333820,504,760,1.66342e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36000,Q#2648 - >seq9295,non-specific,238828,570,712,2.1145500000000003e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36001,Q#2648 - >seq9295,non-specific,275209,455,788,2.35063e-06,50.9192,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36002,Q#2648 - >seq9295,superfamily,275209,455,788,2.35063e-06,50.9192,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36003,Q#2648 - >seq9295,non-specific,238185,635,760,7.97422e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36004,Q#2648 - >seq9295,non-specific,224117,200,489,0.00023967200000000002,45.4756,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36005,Q#2648 - >seq9295,superfamily,224117,200,489,0.00023967200000000002,45.4756,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36006,Q#2648 - >seq9295,non-specific,235175,251,457,0.00031177,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36007,Q#2648 - >seq9295,superfamily,235175,251,457,0.00031177,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36008,Q#2648 - >seq9295,specific,311990,1227,1245,0.00046273099999999997,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36009,Q#2648 - >seq9295,superfamily,311990,1227,1245,0.00046273099999999997,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36010,Q#2648 - >seq9295,non-specific,274009,294,444,0.00545758,40.8215,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36011,Q#2648 - >seq9295,superfamily,274009,294,444,0.00545758,40.8215,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36012,Q#2648 - >seq9295,non-specific,274009,295,440,0.00929664,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs2_gorilla.pars.frame2,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36013,Q#2649 - >seq9296,specific,197310,9,222,2.37545e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36014,Q#2649 - >seq9296,superfamily,351117,9,222,2.37545e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36015,Q#2649 - >seq9296,non-specific,197306,9,223,7.07528e-46,164.96200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36016,Q#2649 - >seq9296,non-specific,197307,9,223,5.61345e-22,96.2029,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36017,Q#2649 - >seq9296,non-specific,223780,9,221,2.92236e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36018,Q#2649 - >seq9296,non-specific,197320,8,221,3.74109e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36019,Q#2649 - >seq9296,non-specific,197321,7,223,2.04723e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36020,Q#2649 - >seq9296,non-specific,272954,9,221,3.9580900000000005e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36021,Q#2649 - >seq9296,specific,335306,10,212,5.2115e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36022,Q#2649 - >seq9296,non-specific,273186,9,221,3.42474e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36023,Q#2649 - >seq9296,non-specific,197336,7,221,2.20378e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36024,Q#2649 - >seq9296,non-specific,197319,8,223,3.16295e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36025,Q#2649 - >seq9296,non-specific,236970,9,221,3.17952e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36026,Q#2649 - >seq9296,non-specific,197322,9,222,1.5830000000000003e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36027,Q#2649 - >seq9296,non-specific,197311,7,204,2.24905e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36028,Q#2649 - >seq9296,non-specific,197314,7,192,0.00044745,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36029,Q#2649 - >seq9296,non-specific,339261,108,217,0.000644726,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs2_gorilla,pars,CompleteHit
36030,Q#2649 - >seq9296,non-specific,197318,9,148,0.00693126,39.5871,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs2_gorilla.pars.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36031,Q#2650 - >seq9297,specific,311990,1149,1167,0.000176517,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs2_gorilla.marg.frame1,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36032,Q#2650 - >seq9297,superfamily,311990,1149,1167,0.000176517,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs2_gorilla.marg.frame1,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36033,Q#2652 - >seq9299,specific,238827,510,772,1.6094799999999996e-63,214.84799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36034,Q#2652 - >seq9299,superfamily,295487,510,772,1.6094799999999996e-63,214.84799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36035,Q#2652 - >seq9299,specific,197310,9,236,5.529619999999999e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36036,Q#2652 - >seq9299,superfamily,351117,9,236,5.529619999999999e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36037,Q#2652 - >seq9299,non-specific,197306,9,236,2.66938e-47,169.199,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36038,Q#2652 - >seq9299,specific,333820,516,772,6.12518e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36039,Q#2652 - >seq9299,superfamily,333820,516,772,6.12518e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36040,Q#2652 - >seq9299,non-specific,197307,9,236,1.58156e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36041,Q#2652 - >seq9299,non-specific,223780,9,238,1.076e-22,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36042,Q#2652 - >seq9299,non-specific,197320,8,229,2.02023e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36043,Q#2652 - >seq9299,non-specific,197321,7,236,7.20455e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36044,Q#2652 - >seq9299,specific,335306,10,229,6.0603199999999995e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36045,Q#2652 - >seq9299,non-specific,272954,9,236,2.49617e-16,80.1197,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36046,Q#2652 - >seq9299,non-specific,273186,9,237,2.75976e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36047,Q#2652 - >seq9299,non-specific,197319,8,236,1.04625e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36048,Q#2652 - >seq9299,non-specific,197336,7,229,8.27152e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36049,Q#2652 - >seq9299,non-specific,197322,9,236,3.08106e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36050,Q#2652 - >seq9299,non-specific,238828,582,724,2.00903e-09,59.1368,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36051,Q#2652 - >seq9299,non-specific,236970,9,238,3.0151e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36052,Q#2652 - >seq9299,non-specific,339261,108,232,1.7441600000000002e-07,50.7987,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36053,Q#2652 - >seq9299,non-specific,275209,467,800,7.46685e-07,52.46,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36054,Q#2652 - >seq9299,superfamily,275209,467,800,7.46685e-07,52.46,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36055,Q#2652 - >seq9299,non-specific,197311,7,236,1.96258e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36056,Q#2652 - >seq9299,non-specific,238185,647,772,4.21457e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36057,Q#2652 - >seq9299,non-specific,235175,263,469,0.00015746100000000002,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36058,Q#2652 - >seq9299,superfamily,235175,263,469,0.00015746100000000002,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36059,Q#2652 - >seq9299,non-specific,197314,7,192,0.00048119199999999997,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs2_gorilla,marg,C-TerminusTruncated
36060,Q#2652 - >seq9299,non-specific,224117,263,501,0.000834052,43.5496,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36061,Q#2652 - >seq9299,superfamily,224117,263,501,0.000834052,43.5496,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36062,Q#2652 - >seq9299,non-specific,197317,23,229,0.00584237,39.8928,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36063,Q#2652 - >seq9299,non-specific,197318,9,236,0.00622854,39.5871,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs2_gorilla,marg,CompleteHit
36064,Q#2652 - >seq9299,non-specific,274009,306,456,0.00724238,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36065,Q#2652 - >seq9299,superfamily,274009,306,456,0.00724238,40.4363,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs2_gorilla.marg.frame3,1909182101_L1PA11.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36066,Q#2653 - >seq9300,specific,238827,510,772,2.6777299999999994e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36067,Q#2653 - >seq9300,superfamily,295487,510,772,2.6777299999999994e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36068,Q#2653 - >seq9300,specific,197310,9,236,1.01802e-59,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36069,Q#2653 - >seq9300,superfamily,351117,9,236,1.01802e-59,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36070,Q#2653 - >seq9300,non-specific,197306,9,236,1.12795e-47,170.355,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36071,Q#2653 - >seq9300,specific,333820,516,772,3.10168e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36072,Q#2653 - >seq9300,superfamily,333820,516,772,3.10168e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36073,Q#2653 - >seq9300,non-specific,197307,9,236,7.58573e-23,98.8993,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36074,Q#2653 - >seq9300,non-specific,223780,9,238,5.86793e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36075,Q#2653 - >seq9300,non-specific,197320,8,229,4.7727499999999997e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36076,Q#2653 - >seq9300,non-specific,197321,7,236,3.38914e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36077,Q#2653 - >seq9300,specific,335306,10,229,6.153490000000001e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36078,Q#2653 - >seq9300,non-specific,273186,9,237,6.922189999999999e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36079,Q#2653 - >seq9300,non-specific,272954,9,236,7.21064e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36080,Q#2653 - >seq9300,non-specific,197319,8,236,9.02602e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36081,Q#2653 - >seq9300,non-specific,197336,7,229,8.72072e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36082,Q#2653 - >seq9300,non-specific,238828,582,724,9.63885e-11,62.9888,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,N-TerminusTruncated
36083,Q#2653 - >seq9300,non-specific,197322,9,236,3.1303199999999997e-10,62.7198,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36084,Q#2653 - >seq9300,non-specific,236970,9,238,3.5137199999999997e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36085,Q#2653 - >seq9300,non-specific,339261,108,232,6.7113e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36086,Q#2653 - >seq9300,non-specific,275209,467,800,1.09237e-07,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36087,Q#2653 - >seq9300,superfamily,275209,467,800,1.09237e-07,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36088,Q#2653 - >seq9300,non-specific,197311,7,236,1.71592e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36089,Q#2653 - >seq9300,non-specific,238185,656,772,0.00045644,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36090,Q#2653 - >seq9300,non-specific,197314,7,192,0.000497326,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs3_orang,marg,C-TerminusTruncated
36091,Q#2653 - >seq9300,specific,311990,1239,1257,0.0005304880000000001,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36092,Q#2653 - >seq9300,superfamily,311990,1239,1257,0.0005304880000000001,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36093,Q#2653 - >seq9300,specific,316774,305,363,0.000862665,39.6792,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36094,Q#2653 - >seq9300,superfamily,316774,305,363,0.000862665,39.6792,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36095,Q#2653 - >seq9300,non-specific,197318,9,236,0.00445848,39.9723,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36096,Q#2653 - >seq9300,non-specific,197317,23,229,0.00614558,39.8928,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,marg,CompleteHit
36097,Q#2653 - >seq9300,non-specific,274009,307,452,0.00916177,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs3_orang,marg,C-TerminusTruncated
36098,Q#2653 - >seq9300,superfamily,274009,307,452,0.00916177,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs3_orang,marg,C-TerminusTruncated
36099,Q#2653 - >seq9300,non-specific,224117,306,428,0.00919176,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs3_orang,marg,C-TerminusTruncated
36100,Q#2653 - >seq9300,superfamily,224117,306,428,0.00919176,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs3_orang,marg,C-TerminusTruncated
36101,Q#2653 - >seq9300,non-specific,274009,306,456,0.00923955,40.0511,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs3_orang,marg,N-TerminusTruncated
36102,Q#2653 - >seq9300,non-specific,274009,263,427,0.00931799,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.marg.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs3_orang,marg,BothTerminiTruncated
36103,Q#2656 - >seq9303,specific,238827,498,760,3.0210899999999994e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36104,Q#2656 - >seq9303,superfamily,295487,498,760,3.0210899999999994e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36105,Q#2656 - >seq9303,specific,333820,504,760,7.781299999999998e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36106,Q#2656 - >seq9303,superfamily,333820,504,760,7.781299999999998e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36107,Q#2656 - >seq9303,non-specific,238828,570,712,5.12823e-11,63.7592,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,N-TerminusTruncated
36108,Q#2656 - >seq9303,non-specific,275209,455,788,1.0510400000000001e-07,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36109,Q#2656 - >seq9303,superfamily,275209,455,788,1.0510400000000001e-07,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36110,Q#2656 - >seq9303,non-specific,238185,644,760,0.00023736,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36111,Q#2656 - >seq9303,specific,311990,1226,1244,0.000462369,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36112,Q#2656 - >seq9303,superfamily,311990,1226,1244,0.000462369,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36113,Q#2656 - >seq9303,specific,316774,293,351,0.00184132,38.9088,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36114,Q#2656 - >seq9303,superfamily,316774,293,351,0.00184132,38.9088,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36115,Q#2656 - >seq9303,non-specific,274009,294,444,0.0083215,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs3_orang,pars,N-TerminusTruncated
36116,Q#2656 - >seq9303,superfamily,274009,294,444,0.0083215,40.4363,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs3_orang,pars,N-TerminusTruncated
36117,Q#2656 - >seq9303,non-specific,274009,295,440,0.0084634,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs3_orang,pars,C-TerminusTruncated
36118,Q#2656 - >seq9303,non-specific,224117,294,416,0.00878319,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs3_orang,pars,C-TerminusTruncated
36119,Q#2656 - >seq9303,superfamily,224117,294,416,0.00878319,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA11,ORF2,hs3_orang,pars,C-TerminusTruncated
36120,Q#2656 - >seq9303,non-specific,274009,251,415,0.00905565,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs3_orang.pars.frame2,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs3_orang,pars,BothTerminiTruncated
36121,Q#2658 - >seq9305,specific,197310,9,222,2.35257e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36122,Q#2658 - >seq9305,superfamily,351117,9,222,2.35257e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36123,Q#2658 - >seq9305,non-specific,197306,9,223,7.07528e-46,164.96200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36124,Q#2658 - >seq9305,non-specific,197307,9,223,5.61345e-22,96.2029,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36125,Q#2658 - >seq9305,non-specific,223780,9,221,2.92236e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36126,Q#2658 - >seq9305,non-specific,197320,8,221,3.74109e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36127,Q#2658 - >seq9305,non-specific,197321,7,223,2.27133e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36128,Q#2658 - >seq9305,non-specific,272954,9,221,3.9580900000000005e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36129,Q#2658 - >seq9305,specific,335306,10,212,5.2115e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36130,Q#2658 - >seq9305,non-specific,273186,9,221,3.42474e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36131,Q#2658 - >seq9305,non-specific,197336,7,221,2.20378e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36132,Q#2658 - >seq9305,non-specific,197319,8,223,3.16295e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36133,Q#2658 - >seq9305,non-specific,236970,9,221,3.17952e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36134,Q#2658 - >seq9305,non-specific,197322,9,222,1.5830000000000003e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36135,Q#2658 - >seq9305,non-specific,197311,7,204,2.24905e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36136,Q#2658 - >seq9305,non-specific,197314,7,192,0.00044745,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs3_orang,pars,C-TerminusTruncated
36137,Q#2658 - >seq9305,non-specific,339261,108,217,0.0006084290000000001,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs3_orang,pars,CompleteHit
36138,Q#2658 - >seq9305,non-specific,197318,9,148,0.00693126,39.5871,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs3_orang.pars.frame3,1909182111_L1PA11.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs3_orang,pars,C-TerminusTruncated
36139,Q#2659 - >seq9306,specific,238827,468,730,2.2369999999999993e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36140,Q#2659 - >seq9306,superfamily,295487,468,730,2.2369999999999993e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36141,Q#2659 - >seq9306,specific,333820,474,730,1.96142e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36142,Q#2659 - >seq9306,superfamily,333820,474,730,1.96142e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36143,Q#2659 - >seq9306,non-specific,238828,474,695,8.36987e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36144,Q#2659 - >seq9306,non-specific,275209,425,758,2.7169e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36145,Q#2659 - >seq9306,superfamily,275209,425,758,2.7169e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36146,Q#2659 - >seq9306,non-specific,238185,614,730,5.58354e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36147,Q#2659 - >seq9306,specific,311990,1198,1216,0.00037515800000000006,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36148,Q#2659 - >seq9306,superfamily,311990,1198,1216,0.00037515800000000006,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs4_gibbon.pars.frame1,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36149,Q#2660 - >seq9307,non-specific,235175,256,380,0.00516261,40.8176,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF2.hs4_gibbon.pars.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36150,Q#2660 - >seq9307,superfamily,235175,256,380,0.00516261,40.8176,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PA11.ORF2.hs4_gibbon.pars.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36151,Q#2661 - >seq9308,specific,197310,9,222,9.45544e-56,193.33700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36152,Q#2661 - >seq9308,superfamily,351117,9,222,9.45544e-56,193.33700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36153,Q#2661 - >seq9308,non-specific,197306,9,223,9.26472e-46,164.96200000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36154,Q#2661 - >seq9308,non-specific,197307,9,223,1.41314e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36155,Q#2661 - >seq9308,non-specific,223780,9,221,5.773759999999999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36156,Q#2661 - >seq9308,non-specific,197320,8,221,5.24959e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36157,Q#2661 - >seq9308,non-specific,197321,7,223,2.3816500000000003e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36158,Q#2661 - >seq9308,specific,335306,10,212,2.41206e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36159,Q#2661 - >seq9308,non-specific,272954,9,221,3.56955e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36160,Q#2661 - >seq9308,non-specific,273186,9,221,5.97981e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36161,Q#2661 - >seq9308,non-specific,197336,7,221,1.84622e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36162,Q#2661 - >seq9308,non-specific,197319,8,223,3.7077e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36163,Q#2661 - >seq9308,non-specific,197322,9,222,3.3105999999999997e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36164,Q#2661 - >seq9308,non-specific,236970,9,221,1.28013e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36165,Q#2661 - >seq9308,non-specific,197311,7,204,2.6554499999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36166,Q#2661 - >seq9308,non-specific,197314,7,192,0.000459836,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36167,Q#2661 - >seq9308,non-specific,339261,108,217,0.00100192,40.0131,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs4_gibbon,pars,CompleteHit
36168,Q#2661 - >seq9308,non-specific,197318,9,148,0.009481,39.2019,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs4_gibbon.pars.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36169,Q#2663 - >seq9310,specific,238827,497,759,1.0284999999999998e-65,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36170,Q#2663 - >seq9310,superfamily,295487,497,759,1.0284999999999998e-65,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36171,Q#2663 - >seq9310,specific,333820,503,759,2.7152999999999995e-34,129.72,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36172,Q#2663 - >seq9310,superfamily,333820,503,759,2.7152999999999995e-34,129.72,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36173,Q#2663 - >seq9310,non-specific,238828,503,724,1.29844e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36174,Q#2663 - >seq9310,non-specific,275209,454,787,4.8750400000000005e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36175,Q#2663 - >seq9310,superfamily,275209,454,787,4.8750400000000005e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36176,Q#2663 - >seq9310,non-specific,238185,643,759,6.12408e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36177,Q#2663 - >seq9310,specific,311990,1227,1245,0.000383871,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36178,Q#2663 - >seq9310,superfamily,311990,1227,1245,0.000383871,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36179,Q#2663 - >seq9310,non-specific,274009,294,443,0.00372707,41.5919,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA11,ORF2,hs4_gibbon,marg,N-TerminusTruncated
36180,Q#2663 - >seq9310,superfamily,274009,294,443,0.00372707,41.5919,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PA11,ORF2,hs4_gibbon,marg,N-TerminusTruncated
36181,Q#2663 - >seq9310,specific,316774,293,351,0.00658728,37.368,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36182,Q#2663 - >seq9310,superfamily,316774,293,351,0.00658728,37.368,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PA11.ORF2.hs4_gibbon.marg.frame2,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36183,Q#2664 - >seq9311,specific,197310,9,222,3.7692199999999996e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36184,Q#2664 - >seq9311,superfamily,351117,9,222,3.7692199999999996e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36185,Q#2664 - >seq9311,non-specific,197306,9,223,2.33357e-46,166.503,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36186,Q#2664 - >seq9311,non-specific,197307,9,223,1.3719e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36187,Q#2664 - >seq9311,non-specific,223780,9,221,5.603919999999999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36188,Q#2664 - >seq9311,non-specific,197320,8,221,5.09615e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36189,Q#2664 - >seq9311,non-specific,197321,7,223,2.5174200000000003e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36190,Q#2664 - >seq9311,specific,335306,10,212,2.34361e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36191,Q#2664 - >seq9311,non-specific,272954,9,221,3.4657300000000003e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36192,Q#2664 - >seq9311,non-specific,273186,9,221,5.80619e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36193,Q#2664 - >seq9311,non-specific,197336,7,221,1.7929e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36194,Q#2664 - >seq9311,non-specific,197319,8,223,3.6007599999999997e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36195,Q#2664 - >seq9311,non-specific,236970,9,221,2.16071e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36196,Q#2664 - >seq9311,non-specific,197322,9,222,3.2131500000000002e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36197,Q#2664 - >seq9311,non-specific,197311,7,204,2.24692e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36198,Q#2664 - >seq9311,non-specific,339261,108,217,0.00032758900000000004,41.5539,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs4_gibbon,marg,CompleteHit
36199,Q#2664 - >seq9311,non-specific,197314,7,192,0.000447023,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36200,Q#2664 - >seq9311,non-specific,197318,9,148,0.00704974,39.2019,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs4_gibbon.marg.frame3,1909182113_L1PA11.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36201,Q#2665 - >seq9312,specific,238827,510,772,2.0928499999999995e-66,223.322,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36202,Q#2665 - >seq9312,superfamily,295487,510,772,2.0928499999999995e-66,223.322,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36203,Q#2665 - >seq9312,specific,197310,9,236,5.916869999999999e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36204,Q#2665 - >seq9312,superfamily,351117,9,236,5.916869999999999e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36205,Q#2665 - >seq9312,non-specific,197306,9,236,1.9235199999999996e-47,169.584,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36206,Q#2665 - >seq9312,specific,333820,516,772,1.7132e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36207,Q#2665 - >seq9312,superfamily,333820,516,772,1.7132e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36208,Q#2665 - >seq9312,non-specific,197307,9,236,1.5517200000000002e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36209,Q#2665 - >seq9312,non-specific,223780,9,238,1.5436600000000002e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36210,Q#2665 - >seq9312,non-specific,197320,8,229,7.61971e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36211,Q#2665 - >seq9312,non-specific,197321,7,236,3.7484900000000003e-19,88.37799999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36212,Q#2665 - >seq9312,specific,335306,10,229,1.16923e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36213,Q#2665 - >seq9312,non-specific,273186,9,237,5.04244e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36214,Q#2665 - >seq9312,non-specific,272954,9,236,5.35256e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36215,Q#2665 - >seq9312,non-specific,197319,8,236,3.71559e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36216,Q#2665 - >seq9312,non-specific,197336,7,229,1.76262e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36217,Q#2665 - >seq9312,non-specific,238828,516,724,1.90542e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36218,Q#2665 - >seq9312,non-specific,197322,9,236,8.724540000000001e-10,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36219,Q#2665 - >seq9312,non-specific,275209,467,800,6.28338e-09,59.0084,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36220,Q#2665 - >seq9312,superfamily,275209,467,800,6.28338e-09,59.0084,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36221,Q#2665 - >seq9312,non-specific,236970,9,238,7.26707e-09,57.9818,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36222,Q#2665 - >seq9312,non-specific,339261,108,232,1.04354e-07,51.5691,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36223,Q#2665 - >seq9312,non-specific,197311,7,236,9.202089999999999e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36224,Q#2665 - >seq9312,non-specific,238185,656,772,8.41967e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36225,Q#2665 - >seq9312,non-specific,197314,7,192,0.000424204,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
36226,Q#2665 - >seq9312,non-specific,224117,263,501,0.000710252,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
36227,Q#2665 - >seq9312,superfamily,224117,263,501,0.000710252,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA11,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
36228,Q#2665 - >seq9312,non-specific,197317,139,229,0.00261347,41.0484,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
36229,Q#2665 - >seq9312,non-specific,235175,263,498,0.00298593,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
36230,Q#2665 - >seq9312,superfamily,235175,263,498,0.00298593,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA11,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
36231,Q#2665 - >seq9312,specific,225881,514,739,0.00487312,40.5925,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
36232,Q#2665 - >seq9312,superfamily,225881,514,739,0.00487312,40.5925,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA11.ORF2.hs5_gmonkey.marg.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA11,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
36233,Q#2667 - >seq9314,specific,311990,1157,1175,0.000226968,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs5_gmonkey.marg.frame1,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36234,Q#2667 - >seq9314,superfamily,311990,1157,1175,0.000226968,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs5_gmonkey.marg.frame1,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA11,ORF2,hs5_gmonkey,marg,CompleteHit
36235,Q#2668 - >seq9315,specific,238827,491,753,4.20814e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36236,Q#2668 - >seq9315,superfamily,295487,491,753,4.20814e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36237,Q#2668 - >seq9315,specific,333820,497,753,9.464839999999999e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36238,Q#2668 - >seq9315,superfamily,333820,497,753,9.464839999999999e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36239,Q#2668 - >seq9315,non-specific,238828,497,705,3.50646e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36240,Q#2668 - >seq9315,non-specific,275209,448,781,3.89022e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36241,Q#2668 - >seq9315,superfamily,275209,448,781,3.89022e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36242,Q#2668 - >seq9315,non-specific,238185,637,753,0.000194519,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36243,Q#2668 - >seq9315,specific,311990,1221,1239,0.000382369,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36244,Q#2668 - >seq9315,superfamily,311990,1221,1239,0.000382369,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36245,Q#2668 - >seq9315,non-specific,224117,199,482,0.00043819199999999995,44.7052,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36246,Q#2668 - >seq9315,superfamily,224117,199,482,0.00043819199999999995,44.7052,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA11,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36247,Q#2668 - >seq9315,non-specific,274008,250,443,0.00356123,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
36248,Q#2668 - >seq9315,superfamily,274008,250,443,0.00356123,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA11,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
36249,Q#2668 - >seq9315,non-specific,214699,288,396,0.00927987,37.3253,smart00503,SynN, - ,cl29093,Syntaxin N-terminal domain; Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p,L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36250,Q#2668 - >seq9315,superfamily,355969,288,396,0.00927987,37.3253,cl29093,SynN superfamily, - , - ,"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain",L1PA11.ORF2.hs5_gmonkey.pars.frame2,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36251,Q#2670 - >seq9317,specific,197310,9,222,9.75663e-56,193.33700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36252,Q#2670 - >seq9317,superfamily,351117,9,222,9.75663e-56,193.33700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36253,Q#2670 - >seq9317,non-specific,197306,9,223,1.78431e-45,163.806,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36254,Q#2670 - >seq9317,non-specific,197307,9,223,1.28375e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36255,Q#2670 - >seq9317,non-specific,223780,9,221,1.13323e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36256,Q#2670 - >seq9317,non-specific,197320,8,221,1.41029e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36257,Q#2670 - >seq9317,non-specific,197321,7,223,2.8222600000000006e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36258,Q#2670 - >seq9317,specific,335306,10,212,1.0036300000000001e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36259,Q#2670 - >seq9317,non-specific,272954,9,221,1.49199e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36260,Q#2670 - >seq9317,non-specific,273186,9,221,1.1796199999999998e-13,71.9264,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36261,Q#2670 - >seq9317,non-specific,197336,7,221,4.69154e-12,67.2523,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36262,Q#2670 - >seq9317,non-specific,197319,8,223,2.77299e-11,64.9905,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36263,Q#2670 - >seq9317,non-specific,236970,9,221,9.11803e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36264,Q#2670 - >seq9317,non-specific,197322,9,222,4.44565e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36265,Q#2670 - >seq9317,non-specific,197311,7,204,0.000145882,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36266,Q#2670 - >seq9317,non-specific,197314,7,192,0.00039444800000000004,43.1011,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA11,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
36267,Q#2670 - >seq9317,non-specific,339261,108,217,0.000579746,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA11.ORF2.hs5_gmonkey.pars.frame3,1909182116_L1PA11.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA11,ORF2,hs5_gmonkey,pars,CompleteHit
36268,Q#2671 - >seq9318,specific,238827,472,734,1.44836e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36269,Q#2671 - >seq9318,superfamily,295487,472,734,1.44836e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36270,Q#2671 - >seq9318,specific,333820,478,734,1.5759100000000002e-34,130.49,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36271,Q#2671 - >seq9318,superfamily,333820,478,734,1.5759100000000002e-34,130.49,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36272,Q#2671 - >seq9318,non-specific,238828,478,699,8.557639999999999e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36273,Q#2671 - >seq9318,non-specific,275209,429,762,9.717689999999999e-08,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36274,Q#2671 - >seq9318,superfamily,275209,429,762,9.717689999999999e-08,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36275,Q#2671 - >seq9318,non-specific,238185,618,734,1.36388e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36276,Q#2671 - >seq9318,specific,225881,444,701,0.00285352,40.9777,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,N-TerminusTruncated
36277,Q#2671 - >seq9318,superfamily,225881,444,701,0.00285352,40.9777,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.pars.frame1,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA13,ORF2,hs1_chimp,pars,N-TerminusTruncated
36278,Q#2672 - >seq9319,specific,311990,1145,1163,6.11287e-05,40.7332,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs1_chimp.pars.frame2,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36279,Q#2672 - >seq9319,superfamily,311990,1145,1163,6.11287e-05,40.7332,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs1_chimp.pars.frame2,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36280,Q#2673 - >seq9320,specific,197310,9,236,1.5030599999999997e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36281,Q#2673 - >seq9320,superfamily,351117,9,236,1.5030599999999997e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36282,Q#2673 - >seq9320,non-specific,197306,9,236,3.49496e-48,171.896,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36283,Q#2673 - >seq9320,non-specific,197307,9,236,1.3338099999999999e-27,112.766,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36284,Q#2673 - >seq9320,non-specific,223780,9,237,1.6391e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36285,Q#2673 - >seq9320,non-specific,197320,9,229,2.2400599999999996e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36286,Q#2673 - >seq9320,non-specific,197321,7,236,3.42718e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36287,Q#2673 - >seq9320,specific,335306,10,229,1.3208500000000002e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36288,Q#2673 - >seq9320,non-specific,272954,9,236,3.01991e-17,82.816,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36289,Q#2673 - >seq9320,non-specific,273186,9,237,4.0224e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36290,Q#2673 - >seq9320,non-specific,197319,13,236,4.0116100000000005e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36291,Q#2673 - >seq9320,non-specific,197336,9,236,5.03954e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36292,Q#2673 - >seq9320,non-specific,197322,8,236,2.56493e-10,63.105,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36293,Q#2673 - >seq9320,non-specific,339261,108,232,1.48565e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36294,Q#2673 - >seq9320,non-specific,236970,9,237,1.1267200000000002e-08,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36295,Q#2673 - >seq9320,non-specific,197311,37,236,4.84593e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,pars,CompleteHit
36296,Q#2673 - >seq9320,non-specific,275316,252,389,0.00044280400000000004,44.2408,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA13,ORF2,hs1_chimp,pars,BothTerminiTruncated
36297,Q#2673 - >seq9320,superfamily,275316,252,389,0.00044280400000000004,44.2408,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA13.ORF2.hs1_chimp.pars.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Mycoplasma,L1PA13,ORF2,hs1_chimp,pars,BothTerminiTruncated
36298,Q#2676 - >seq9323,specific,238827,510,772,2.2235099999999996e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36299,Q#2676 - >seq9323,superfamily,295487,510,772,2.2235099999999996e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36300,Q#2676 - >seq9323,specific,197310,9,236,5.283189999999999e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36301,Q#2676 - >seq9323,superfamily,351117,9,236,5.283189999999999e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36302,Q#2676 - >seq9323,non-specific,197306,9,236,3.8393799999999995e-47,168.81400000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36303,Q#2676 - >seq9323,specific,333820,516,772,9.8364e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36304,Q#2676 - >seq9323,superfamily,333820,516,772,9.8364e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36305,Q#2676 - >seq9323,non-specific,197307,9,236,1.7686500000000002e-25,106.603,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36306,Q#2676 - >seq9323,non-specific,223780,9,237,2.59634e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36307,Q#2676 - >seq9323,non-specific,197320,9,229,5.672519999999999e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36308,Q#2676 - >seq9323,non-specific,197321,7,236,1.53484e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36309,Q#2676 - >seq9323,specific,335306,10,229,1.39276e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36310,Q#2676 - >seq9323,non-specific,272954,9,236,6.7570199999999995e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36311,Q#2676 - >seq9323,non-specific,273186,9,237,2.00605e-15,77.3192,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36312,Q#2676 - >seq9323,non-specific,197336,9,236,5.894689999999999e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36313,Q#2676 - >seq9323,non-specific,197319,13,236,6.273399999999999e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36314,Q#2676 - >seq9323,non-specific,238828,516,737,2.27183e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36315,Q#2676 - >seq9323,non-specific,197322,8,236,2.71036e-10,63.105,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36316,Q#2676 - >seq9323,non-specific,339261,108,232,2.99954e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36317,Q#2676 - >seq9323,non-specific,236970,9,237,2.63306e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36318,Q#2676 - >seq9323,non-specific,275209,467,800,1.38743e-07,54.7712,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36319,Q#2676 - >seq9323,superfamily,275209,467,800,1.38743e-07,54.7712,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36320,Q#2676 - >seq9323,non-specific,197311,37,236,7.69735e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36321,Q#2676 - >seq9323,non-specific,238185,656,772,5.09754e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36322,Q#2676 - >seq9323,specific,311990,1240,1258,0.000407551,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36323,Q#2676 - >seq9323,superfamily,311990,1240,1258,0.000407551,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs1_chimp,marg,CompleteHit
36324,Q#2676 - >seq9323,non-specific,223496,263,459,0.00540535,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA13,ORF2,hs1_chimp,marg,BothTerminiTruncated
36325,Q#2676 - >seq9323,superfamily,223496,263,459,0.00540535,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA13,ORF2,hs1_chimp,marg,BothTerminiTruncated
36326,Q#2676 - >seq9323,non-specific,224117,204,467,0.0062358000000000005,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs1_chimp,marg,N-TerminusTruncated
36327,Q#2676 - >seq9323,superfamily,224117,204,467,0.0062358000000000005,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF2,hs1_chimp,marg,N-TerminusTruncated
36328,Q#2676 - >seq9323,non-specific,274009,307,452,0.00835563,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs1_chimp,marg,C-TerminusTruncated
36329,Q#2676 - >seq9323,superfamily,274009,307,452,0.00835563,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs1_chimp.marg.frame3,1909182140_L1PA13.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs1_chimp,marg,C-TerminusTruncated
36330,Q#2677 - >seq9324,specific,238827,510,772,2.57209e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36331,Q#2677 - >seq9324,superfamily,295487,510,772,2.57209e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36332,Q#2677 - >seq9324,specific,197310,9,236,8.465999999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36333,Q#2677 - >seq9324,superfamily,351117,9,236,8.465999999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36334,Q#2677 - >seq9324,non-specific,197306,9,236,3.95453e-45,163.036,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36335,Q#2677 - >seq9324,specific,333820,516,772,9.282569999999999e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36336,Q#2677 - >seq9324,superfamily,333820,516,772,9.282569999999999e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36337,Q#2677 - >seq9324,non-specific,197307,9,236,3.478e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36338,Q#2677 - >seq9324,non-specific,223780,9,237,5.77448e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36339,Q#2677 - >seq9324,non-specific,197320,9,229,1.9220400000000002e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36340,Q#2677 - >seq9324,non-specific,197321,7,236,2.8884300000000004e-18,85.6816,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36341,Q#2677 - >seq9324,specific,335306,10,229,1.1120399999999998e-16,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36342,Q#2677 - >seq9324,non-specific,272954,9,236,2.63714e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36343,Q#2677 - >seq9324,non-specific,273186,9,237,7.16902e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36344,Q#2677 - >seq9324,non-specific,197319,13,236,1.00348e-11,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36345,Q#2677 - >seq9324,non-specific,238828,516,737,2.04868e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36346,Q#2677 - >seq9324,non-specific,197336,9,229,7.71022e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36347,Q#2677 - >seq9324,non-specific,275209,467,800,4.0287600000000005e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36348,Q#2677 - >seq9324,superfamily,275209,467,800,4.0287600000000005e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36349,Q#2677 - >seq9324,non-specific,197322,8,236,1.78489e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36350,Q#2677 - >seq9324,non-specific,236970,9,237,8.46234e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36351,Q#2677 - >seq9324,non-specific,339261,108,232,9.48222e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36352,Q#2677 - >seq9324,non-specific,238185,656,772,3.73167e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36353,Q#2677 - >seq9324,non-specific,197311,37,236,0.00032997,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36354,Q#2677 - >seq9324,specific,311990,1240,1258,0.000407551,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36355,Q#2677 - >seq9324,superfamily,311990,1240,1258,0.000407551,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs2_gorilla,marg,CompleteHit
36356,Q#2677 - >seq9324,non-specific,223496,224,459,0.003479,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA13,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36357,Q#2677 - >seq9324,superfamily,223496,224,459,0.003479,41.6695,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA13,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36358,Q#2677 - >seq9324,non-specific,224117,263,467,0.00602845,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36359,Q#2677 - >seq9324,superfamily,224117,263,467,0.00602845,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA13,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36360,Q#2677 - >seq9324,specific,225881,482,739,0.00911572,39.4369,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36361,Q#2677 - >seq9324,superfamily,225881,482,739,0.00911572,39.4369,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.marg.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs2_gorilla,marg,N-TerminusTruncated
36362,Q#2680 - >seq9327,specific,238827,480,742,1.2444999999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36363,Q#2680 - >seq9327,superfamily,295487,480,742,1.2444999999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36364,Q#2680 - >seq9327,specific,333820,486,742,2.2952099999999998e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36365,Q#2680 - >seq9327,superfamily,333820,486,742,2.2952099999999998e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36366,Q#2680 - >seq9327,non-specific,238828,486,739,2.62762e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36367,Q#2680 - >seq9327,non-specific,275209,437,770,1.30636e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36368,Q#2680 - >seq9327,superfamily,275209,437,770,1.30636e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36369,Q#2680 - >seq9327,non-specific,238185,626,742,3.7132199999999996e-06,46.5752,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36370,Q#2680 - >seq9327,specific,225881,452,709,0.000643728,43.2889,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36371,Q#2680 - >seq9327,superfamily,225881,452,709,0.000643728,43.2889,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.pars.frame2,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36372,Q#2681 - >seq9328,specific,311990,1159,1177,4.39081e-05,41.1184,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs2_gorilla.pars.frame1,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36373,Q#2681 - >seq9328,superfamily,311990,1159,1177,4.39081e-05,41.1184,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs2_gorilla.pars.frame1,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36374,Q#2682 - >seq9329,specific,197310,9,236,3.8278599999999994e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36375,Q#2682 - >seq9329,superfamily,351117,9,236,3.8278599999999994e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36376,Q#2682 - >seq9329,non-specific,197306,9,236,6.94471e-46,165.347,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36377,Q#2682 - >seq9329,non-specific,197307,9,236,4.0702699999999993e-25,105.448,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36378,Q#2682 - >seq9329,non-specific,223780,9,237,4.42918e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36379,Q#2682 - >seq9329,non-specific,197320,9,229,8.206799999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36380,Q#2682 - >seq9329,non-specific,197321,7,236,1.44063e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36381,Q#2682 - >seq9329,specific,335306,10,229,1.0359100000000002e-16,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36382,Q#2682 - >seq9329,non-specific,272954,9,236,1.45182e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36383,Q#2682 - >seq9329,non-specific,273186,9,237,1.47368e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36384,Q#2682 - >seq9329,non-specific,197319,13,236,8.644169999999999e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36385,Q#2682 - >seq9329,non-specific,197336,9,229,7.17566e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36386,Q#2682 - >seq9329,non-specific,236970,9,237,1.35296e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36387,Q#2682 - >seq9329,non-specific,197322,8,236,1.6589700000000002e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36388,Q#2682 - >seq9329,non-specific,339261,108,232,2.50087e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36389,Q#2682 - >seq9329,non-specific,197311,37,236,0.000170708,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs2_gorilla.pars.frame3,1909182149_L1PA13.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs2_gorilla,pars,CompleteHit
36390,Q#2683 - >seq9330,specific,238827,486,748,5.940849999999998e-68,227.55900000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36391,Q#2683 - >seq9330,superfamily,295487,486,748,5.940849999999998e-68,227.55900000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36392,Q#2683 - >seq9330,specific,333820,492,748,2.4818700000000003e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36393,Q#2683 - >seq9330,superfamily,333820,492,748,2.4818700000000003e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36394,Q#2683 - >seq9330,non-specific,238828,492,713,2.58096e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36395,Q#2683 - >seq9330,non-specific,275209,443,776,1.0168200000000001e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36396,Q#2683 - >seq9330,superfamily,275209,443,776,1.0168200000000001e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36397,Q#2683 - >seq9330,non-specific,238185,632,748,2.26065e-06,46.9604,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36398,Q#2683 - >seq9330,specific,311990,1197,1215,0.000100053,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36399,Q#2683 - >seq9330,superfamily,311990,1197,1215,0.000100053,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36400,Q#2683 - >seq9330,specific,225881,458,715,0.000499897,43.6741,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
36401,Q#2683 - >seq9330,superfamily,225881,458,715,0.000499897,43.6741,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.pars.frame2,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA13,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
36402,Q#2685 - >seq9332,specific,238827,509,771,3.3268300000000003e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36403,Q#2685 - >seq9332,superfamily,295487,509,771,3.3268300000000003e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36404,Q#2685 - >seq9332,specific,197310,9,236,4.390959999999999e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36405,Q#2685 - >seq9332,superfamily,351117,9,236,4.390959999999999e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36406,Q#2685 - >seq9332,non-specific,197306,9,236,2.8389e-46,166.503,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36407,Q#2685 - >seq9332,specific,333820,515,771,2.09186e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36408,Q#2685 - >seq9332,superfamily,333820,515,771,2.09186e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36409,Q#2685 - >seq9332,non-specific,197307,9,236,1.0387600000000003e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36410,Q#2685 - >seq9332,non-specific,223780,9,237,1.44862e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36411,Q#2685 - >seq9332,non-specific,197320,9,229,1.17428e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36412,Q#2685 - >seq9332,non-specific,197321,7,236,5.54322e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36413,Q#2685 - >seq9332,specific,335306,10,229,4.89045e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36414,Q#2685 - >seq9332,non-specific,273186,9,237,2.72442e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36415,Q#2685 - >seq9332,non-specific,272954,9,236,4.49697e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36416,Q#2685 - >seq9332,non-specific,197319,13,236,1.3319600000000001e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36417,Q#2685 - >seq9332,non-specific,238828,515,736,7.118930000000001e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36418,Q#2685 - >seq9332,non-specific,197336,9,229,6.14379e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36419,Q#2685 - >seq9332,non-specific,197322,8,236,3.54489e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36420,Q#2685 - >seq9332,non-specific,275209,466,799,8.51303e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36421,Q#2685 - >seq9332,superfamily,275209,466,799,8.51303e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36422,Q#2685 - >seq9332,non-specific,236970,9,237,2.30662e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36423,Q#2685 - >seq9332,non-specific,339261,108,232,5.24589e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36424,Q#2685 - >seq9332,non-specific,238185,655,771,1.28835e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36425,Q#2685 - >seq9332,non-specific,197311,37,236,0.000157211,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36426,Q#2685 - >seq9332,non-specific,235175,294,468,0.000167424,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
36427,Q#2685 - >seq9332,superfamily,235175,294,468,0.000167424,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
36428,Q#2685 - >seq9332,specific,311990,1215,1233,0.000259769,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36429,Q#2685 - >seq9332,superfamily,311990,1215,1233,0.000259769,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs6_sqmonkey,marg,CompleteHit
36430,Q#2685 - >seq9332,specific,225881,481,738,0.00109735,42.5185,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
36431,Q#2685 - >seq9332,superfamily,225881,481,738,0.00109735,42.5185,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
36432,Q#2685 - >seq9332,non-specific,274009,307,451,0.00975689,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
36433,Q#2685 - >seq9332,superfamily,274009,307,451,0.00975689,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs6_sqmonkey.marg.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
36434,Q#2686 - >seq9333,specific,197310,9,236,6.350299999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36435,Q#2686 - >seq9333,superfamily,351117,9,236,6.350299999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36436,Q#2686 - >seq9333,non-specific,197306,9,236,3.9226499999999996e-46,166.118,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36437,Q#2686 - >seq9333,non-specific,197307,9,236,8.06869e-25,104.677,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36438,Q#2686 - >seq9333,non-specific,223780,9,237,8.630360000000001e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36439,Q#2686 - >seq9333,non-specific,197320,9,229,1.13583e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36440,Q#2686 - >seq9333,non-specific,197321,7,236,1.1435e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36441,Q#2686 - >seq9333,specific,335306,10,229,4.73478e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36442,Q#2686 - >seq9333,non-specific,273186,9,237,2.63578e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36443,Q#2686 - >seq9333,non-specific,272954,9,236,3.60532e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36444,Q#2686 - >seq9333,non-specific,197319,13,236,1.0893600000000001e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36445,Q#2686 - >seq9333,non-specific,197336,9,229,5.94568e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36446,Q#2686 - >seq9333,non-specific,197322,8,236,3.42808e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36447,Q#2686 - >seq9333,non-specific,236970,9,237,1.52074e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36448,Q#2686 - >seq9333,non-specific,339261,108,232,9.10043e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36449,Q#2686 - >seq9333,non-specific,197311,37,236,0.000161042,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs6_sqmonkey,pars,CompleteHit
36450,Q#2686 - >seq9333,non-specific,239242,1135,1195,0.00641475,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
36451,Q#2686 - >seq9333,superfamily,355772,1135,1195,0.00641475,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA13.ORF2.hs6_sqmonkey.pars.frame3,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA13,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
36452,Q#2688 - >seq9335,non-specific,239242,1086,1146,0.00612301,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA13.ORF2.hs6_sqmonkey.marg.frame1,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
36453,Q#2688 - >seq9335,superfamily,355772,1086,1146,0.00612301,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA13.ORF2.hs6_sqmonkey.marg.frame1,1909182155_L1PA13.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
36454,Q#2690 - >seq9337,non-specific,239242,1078,1139,0.00803657,39.7842,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA13.ORF2.hs3_orang.marg.frame1,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs3_orang,marg,BothTerminiTruncated
36455,Q#2690 - >seq9337,superfamily,355772,1078,1139,0.00803657,39.7842,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA13.ORF2.hs3_orang.marg.frame1,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA13,ORF2,hs3_orang,marg,BothTerminiTruncated
36456,Q#2691 - >seq9338,specific,238827,509,771,2.4241399999999996e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36457,Q#2691 - >seq9338,superfamily,295487,509,771,2.4241399999999996e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36458,Q#2691 - >seq9338,specific,197310,9,236,2.786209999999999e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36459,Q#2691 - >seq9338,superfamily,351117,9,236,2.786209999999999e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36460,Q#2691 - >seq9338,non-specific,197306,9,236,3.5097599999999996e-45,163.421,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36461,Q#2691 - >seq9338,specific,333820,515,771,4.01005e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36462,Q#2691 - >seq9338,superfamily,333820,515,771,4.01005e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36463,Q#2691 - >seq9338,non-specific,197307,9,236,1.2621099999999999e-23,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36464,Q#2691 - >seq9338,non-specific,223780,9,237,4.53677e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36465,Q#2691 - >seq9338,non-specific,197320,9,229,4.0109800000000004e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36466,Q#2691 - >seq9338,non-specific,197321,7,236,1.46196e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36467,Q#2691 - >seq9338,specific,335306,10,229,1.9053999999999999e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36468,Q#2691 - >seq9338,non-specific,272954,9,236,3.28891e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36469,Q#2691 - >seq9338,non-specific,273186,9,237,4.77145e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36470,Q#2691 - >seq9338,non-specific,238828,515,736,2.55338e-13,70.6928,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36471,Q#2691 - >seq9338,non-specific,197319,13,236,8.58516e-13,69.6129,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36472,Q#2691 - >seq9338,non-specific,197336,9,194,1.0625900000000001e-10,63.4003,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36473,Q#2691 - >seq9338,non-specific,275209,466,799,1.8165100000000002e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36474,Q#2691 - >seq9338,superfamily,275209,466,799,1.8165100000000002e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36475,Q#2691 - >seq9338,non-specific,197322,8,236,1.55471e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36476,Q#2691 - >seq9338,non-specific,236970,9,237,1.0720299999999998e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36477,Q#2691 - >seq9338,non-specific,238185,655,771,3.4224300000000005e-06,46.5752,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36478,Q#2691 - >seq9338,non-specific,339261,108,232,2.96595e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36479,Q#2691 - >seq9338,specific,225881,405,738,0.00011659200000000001,45.6001,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36480,Q#2691 - >seq9338,superfamily,225881,405,738,0.00011659200000000001,45.6001,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36481,Q#2691 - >seq9338,non-specific,197311,37,146,0.000662206,42.2789,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,pars,C-TerminusTruncated
36482,Q#2691 - >seq9338,non-specific,274009,307,457,0.00967475,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF2,hs3_orang,pars,C-TerminusTruncated
36483,Q#2691 - >seq9338,superfamily,274009,307,457,0.00967475,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs3_orang.pars.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA13,ORF2,hs3_orang,pars,C-TerminusTruncated
36484,Q#2693 - >seq9340,specific,311990,1150,1168,0.00132822,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs3_orang.pars.frame1,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36485,Q#2693 - >seq9340,superfamily,311990,1150,1168,0.00132822,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs3_orang.pars.frame1,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA13,ORF2,hs3_orang,pars,CompleteHit
36486,Q#2694 - >seq9341,specific,238827,509,771,1.7930199999999995e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36487,Q#2694 - >seq9341,superfamily,295487,509,771,1.7930199999999995e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36488,Q#2694 - >seq9341,specific,197310,9,236,2.868e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36489,Q#2694 - >seq9341,superfamily,351117,9,236,2.868e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36490,Q#2694 - >seq9341,non-specific,197306,9,236,9.134539999999999e-45,161.88,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36491,Q#2694 - >seq9341,specific,333820,515,771,1.3130899999999998e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36492,Q#2694 - >seq9341,superfamily,333820,515,771,1.3130899999999998e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36493,Q#2694 - >seq9341,non-specific,197307,9,236,1.80357e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36494,Q#2694 - >seq9341,non-specific,223780,9,237,5.4444e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36495,Q#2694 - >seq9341,non-specific,197320,9,229,9.093149999999999e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36496,Q#2694 - >seq9341,non-specific,197321,7,236,1.77147e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36497,Q#2694 - >seq9341,specific,335306,10,229,1.94697e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36498,Q#2694 - >seq9341,non-specific,272954,9,236,1.60696e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36499,Q#2694 - >seq9341,non-specific,273186,9,237,2.2444899999999997e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36500,Q#2694 - >seq9341,non-specific,238828,515,736,1.75447e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36501,Q#2694 - >seq9341,non-specific,197319,13,236,1.92413e-11,65.3757,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36502,Q#2694 - >seq9341,non-specific,197336,9,194,1.0860700000000001e-10,63.4003,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36503,Q#2694 - >seq9341,non-specific,275209,466,799,1.38044e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36504,Q#2694 - >seq9341,superfamily,275209,466,799,1.38044e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36505,Q#2694 - >seq9341,non-specific,197322,8,236,1.58948e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36506,Q#2694 - >seq9341,non-specific,236970,9,237,1.63167e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36507,Q#2694 - >seq9341,non-specific,238185,655,771,2.70308e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36508,Q#2694 - >seq9341,non-specific,339261,108,232,2.72044e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36509,Q#2694 - >seq9341,non-specific,197311,37,146,0.0010322,41.5085,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA13,ORF2,hs3_orang,marg,C-TerminusTruncated
36510,Q#2694 - >seq9341,specific,225881,481,738,0.00358223,40.9777,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,N-TerminusTruncated
36511,Q#2694 - >seq9341,superfamily,225881,481,738,0.00358223,40.9777,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA13,ORF2,hs3_orang,marg,N-TerminusTruncated
36512,Q#2694 - >seq9341,specific,311990,1239,1257,0.00423323,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36513,Q#2694 - >seq9341,superfamily,311990,1239,1257,0.00423323,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA13,ORF2,hs3_orang,marg,CompleteHit
36514,Q#2694 - >seq9341,non-specific,274009,307,457,0.00955734,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs3_orang,marg,C-TerminusTruncated
36515,Q#2694 - >seq9341,superfamily,274009,307,457,0.00955734,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA13.ORF2.hs3_orang.marg.frame3,1909182155_L1PA13.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA13,ORF2,hs3_orang,marg,C-TerminusTruncated
36516,Q#2695 - >seq9342,specific,238827,510,772,1.3258499999999998e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36517,Q#2695 - >seq9342,superfamily,295487,510,772,1.3258499999999998e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36518,Q#2695 - >seq9342,specific,197310,9,236,4.9913399999999995e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36519,Q#2695 - >seq9342,superfamily,351117,9,236,4.9913399999999995e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36520,Q#2695 - >seq9342,non-specific,197306,9,236,8.653249999999999e-44,159.184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36521,Q#2695 - >seq9342,specific,333820,516,772,5.603699999999999e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36522,Q#2695 - >seq9342,superfamily,333820,516,772,5.603699999999999e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36523,Q#2695 - >seq9342,non-specific,197307,9,236,4.562819999999999e-25,105.448,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36524,Q#2695 - >seq9342,non-specific,223780,9,237,5.06123e-22,96.8987,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36525,Q#2695 - >seq9342,non-specific,197320,9,229,1.42314e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36526,Q#2695 - >seq9342,specific,335306,10,229,2.62129e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36527,Q#2695 - >seq9342,non-specific,197321,7,236,1.8997999999999998e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36528,Q#2695 - >seq9342,non-specific,273186,9,237,1.35551e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36529,Q#2695 - >seq9342,non-specific,272954,9,236,1.67041e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36530,Q#2695 - >seq9342,non-specific,197319,13,236,1.06264e-13,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36531,Q#2695 - >seq9342,non-specific,197322,8,236,6.51925e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36532,Q#2695 - >seq9342,non-specific,238828,516,737,7.44242e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36533,Q#2695 - >seq9342,non-specific,197336,9,194,6.66528e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36534,Q#2695 - >seq9342,non-specific,275209,467,800,1.7746099999999998e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36535,Q#2695 - >seq9342,superfamily,275209,467,800,1.7746099999999998e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36536,Q#2695 - >seq9342,non-specific,236970,9,237,8.9628e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36537,Q#2695 - >seq9342,non-specific,339261,108,232,1.31615e-07,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36538,Q#2695 - >seq9342,non-specific,197311,30,236,6.65044e-07,51.1385,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36539,Q#2695 - >seq9342,non-specific,238185,656,772,1.75176e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36540,Q#2695 - >seq9342,non-specific,235175,294,469,0.000214036,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs1_chimp,marg,BothTerminiTruncated
36541,Q#2695 - >seq9342,superfamily,235175,294,469,0.000214036,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs1_chimp,marg,BothTerminiTruncated
36542,Q#2695 - >seq9342,non-specific,224117,266,391,0.00113263,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs1_chimp,marg,BothTerminiTruncated
36543,Q#2695 - >seq9342,superfamily,224117,266,391,0.00113263,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs1_chimp.marg.frame3,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs1_chimp,marg,BothTerminiTruncated
36544,Q#2697 - >seq9344,specific,311990,1174,1192,0.000169913,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs1_chimp.marg.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36545,Q#2697 - >seq9344,superfamily,311990,1174,1192,0.000169913,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs1_chimp.marg.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs1_chimp,marg,CompleteHit
36546,Q#2698 - >seq9345,specific,197310,9,236,3.2521199999999995e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36547,Q#2698 - >seq9345,superfamily,351117,9,236,3.2521199999999995e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36548,Q#2698 - >seq9345,non-specific,197306,9,236,2.40212e-45,163.806,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36549,Q#2698 - >seq9345,non-specific,197307,9,236,4.11399e-27,111.226,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36550,Q#2698 - >seq9345,non-specific,223780,9,237,3.6019699999999997e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36551,Q#2698 - >seq9345,non-specific,197320,9,229,4.09606e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36552,Q#2698 - >seq9345,specific,335306,10,229,2.45226e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36553,Q#2698 - >seq9345,non-specific,197321,7,236,8.821799999999999e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36554,Q#2698 - >seq9345,non-specific,273186,9,237,2.62871e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36555,Q#2698 - >seq9345,non-specific,272954,9,236,9.2248e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36556,Q#2698 - >seq9345,non-specific,197319,13,236,1.0046e-15,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36557,Q#2698 - >seq9345,non-specific,197322,8,236,6.077489999999999e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36558,Q#2698 - >seq9345,non-specific,197336,9,194,5.5215999999999996e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36559,Q#2698 - >seq9345,non-specific,236970,9,237,7.51842e-09,57.9818,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36560,Q#2698 - >seq9345,non-specific,339261,108,232,7.62188e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36561,Q#2698 - >seq9345,non-specific,197311,30,236,1.57598e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36562,Q#2698 - >seq9345,non-specific,224117,266,389,0.00079403,43.5496,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA14,ORF2,hs1_chimp,pars,BothTerminiTruncated
36563,Q#2698 - >seq9345,superfamily,224117,266,389,0.00079403,43.5496,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA14,ORF2,hs1_chimp,pars,BothTerminiTruncated
36564,Q#2698 - >seq9345,non-specific,197318,9,236,0.00223876,41.1279,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA14.ORF2.hs1_chimp.pars.frame2,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36565,Q#2699 - >seq9346,specific,238827,482,744,3.59873e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36566,Q#2699 - >seq9346,superfamily,295487,482,744,3.59873e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36567,Q#2699 - >seq9346,specific,333820,488,744,8.69132e-36,134.342,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36568,Q#2699 - >seq9346,superfamily,333820,488,744,8.69132e-36,134.342,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36569,Q#2699 - >seq9346,non-specific,238828,488,741,2.6664799999999998e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36570,Q#2699 - >seq9346,non-specific,275209,439,772,8.640489999999999e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36571,Q#2699 - >seq9346,superfamily,275209,439,772,8.640489999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36572,Q#2699 - >seq9346,non-specific,238185,628,744,8.12817e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36573,Q#2699 - >seq9346,specific,311990,1212,1230,0.00189247,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36574,Q#2699 - >seq9346,superfamily,311990,1212,1230,0.00189247,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs1_chimp,pars,CompleteHit
36575,Q#2699 - >seq9346,specific,225881,454,726,0.008439,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,N-TerminusTruncated
36576,Q#2699 - >seq9346,superfamily,225881,454,726,0.008439,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs1_chimp.pars.frame1,1909182200_L1PA14.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs1_chimp,pars,N-TerminusTruncated
36577,Q#2702 - >seq9349,specific,238827,482,744,4.869219999999999e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36578,Q#2702 - >seq9349,superfamily,295487,482,744,4.869219999999999e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36579,Q#2702 - >seq9349,specific,333820,488,744,1.02427e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36580,Q#2702 - >seq9349,superfamily,333820,488,744,1.02427e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36581,Q#2702 - >seq9349,non-specific,238828,488,741,1.63989e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36582,Q#2702 - >seq9349,non-specific,275209,439,772,1.0045600000000001e-08,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36583,Q#2702 - >seq9349,superfamily,275209,439,772,1.0045600000000001e-08,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36584,Q#2702 - >seq9349,non-specific,238185,628,744,8.6177e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36585,Q#2702 - >seq9349,specific,311990,1212,1230,0.00185575,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36586,Q#2702 - >seq9349,superfamily,311990,1212,1230,0.00185575,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36587,Q#2702 - >seq9349,specific,225881,454,726,0.00873843,39.4369,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,N-TerminusTruncated
36588,Q#2702 - >seq9349,superfamily,225881,454,726,0.00873843,39.4369,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.pars.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs3_orang,pars,N-TerminusTruncated
36589,Q#2703 - >seq9350,specific,197310,9,236,1.7787299999999995e-63,215.293,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36590,Q#2703 - >seq9350,superfamily,351117,9,236,1.7787299999999995e-63,215.293,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36591,Q#2703 - >seq9350,non-specific,197306,9,236,3.74085e-46,166.118,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36592,Q#2703 - >seq9350,non-specific,197307,9,236,6.445999999999999e-27,110.84,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36593,Q#2703 - >seq9350,non-specific,223780,9,237,2.04886e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36594,Q#2703 - >seq9350,non-specific,197320,9,229,4.09606e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36595,Q#2703 - >seq9350,specific,335306,10,229,1.79048e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36596,Q#2703 - >seq9350,non-specific,197321,7,236,3.3954999999999998e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36597,Q#2703 - >seq9350,non-specific,273186,9,237,1.12047e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36598,Q#2703 - >seq9350,non-specific,197319,13,236,2.59887e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36599,Q#2703 - >seq9350,non-specific,272954,9,236,9.31324e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36600,Q#2703 - >seq9350,non-specific,197322,8,236,2.6276599999999997e-12,68.883,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36601,Q#2703 - >seq9350,non-specific,197336,9,194,2.46003e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36602,Q#2703 - >seq9350,non-specific,236970,9,237,7.798850000000001e-09,57.9818,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36603,Q#2703 - >seq9350,non-specific,339261,108,232,7.33202e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36604,Q#2703 - >seq9350,non-specific,197311,30,236,4.4518399999999997e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,pars,CompleteHit
36605,Q#2703 - >seq9350,non-specific,224117,266,389,0.0011424000000000002,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs3_orang,pars,BothTerminiTruncated
36606,Q#2703 - >seq9350,superfamily,224117,266,389,0.0011424000000000002,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs3_orang.pars.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs3_orang,pars,BothTerminiTruncated
36607,Q#2705 - >seq9352,specific,238827,482,744,4.693499999999999e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36608,Q#2705 - >seq9352,superfamily,295487,482,744,4.693499999999999e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36609,Q#2705 - >seq9352,specific,333820,488,744,9.95893e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36610,Q#2705 - >seq9352,superfamily,333820,488,744,9.95893e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36611,Q#2705 - >seq9352,non-specific,238828,488,741,1.5808e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36612,Q#2705 - >seq9352,non-specific,275209,439,772,9.70501e-09,58.6232,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36613,Q#2705 - >seq9352,superfamily,275209,439,772,9.70501e-09,58.6232,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36614,Q#2705 - >seq9352,non-specific,238185,628,744,8.624880000000001e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36615,Q#2705 - >seq9352,specific,311990,1213,1231,0.00185722,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36616,Q#2705 - >seq9352,superfamily,311990,1213,1231,0.00185722,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36617,Q#2705 - >seq9352,specific,225881,454,726,0.00867037,39.4369,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,N-TerminusTruncated
36618,Q#2705 - >seq9352,superfamily,225881,454,726,0.00867037,39.4369,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.marg.frame2,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs3_orang,marg,N-TerminusTruncated
36619,Q#2706 - >seq9353,specific,197310,9,236,1.64901e-63,215.678,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36620,Q#2706 - >seq9353,superfamily,351117,9,236,1.64901e-63,215.678,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36621,Q#2706 - >seq9353,non-specific,197306,9,236,3.7086300000000006e-46,166.118,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36622,Q#2706 - >seq9353,non-specific,197307,9,236,6.4523499999999995e-27,110.84,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36623,Q#2706 - >seq9353,non-specific,223780,9,237,2.0508900000000003e-22,98.0543,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36624,Q#2706 - >seq9353,non-specific,197320,9,229,4.1001e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36625,Q#2706 - >seq9353,specific,335306,10,229,1.7921900000000002e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36626,Q#2706 - >seq9353,non-specific,197321,7,236,3.27267e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36627,Q#2706 - >seq9353,non-specific,273186,9,237,1.12157e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36628,Q#2706 - >seq9353,non-specific,197319,13,236,2.60141e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36629,Q#2706 - >seq9353,non-specific,272954,9,236,9.32235e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36630,Q#2706 - >seq9353,non-specific,197322,8,236,2.63031e-12,68.883,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36631,Q#2706 - >seq9353,non-specific,197336,9,194,2.46241e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36632,Q#2706 - >seq9353,non-specific,236970,9,237,7.80642e-09,57.9818,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36633,Q#2706 - >seq9353,non-specific,339261,108,232,7.197610000000001e-08,51.9543,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36634,Q#2706 - >seq9353,non-specific,197311,30,236,4.45599e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs3_orang,marg,CompleteHit
36635,Q#2706 - >seq9353,non-specific,224117,266,389,0.0011729000000000002,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs3_orang,marg,BothTerminiTruncated
36636,Q#2706 - >seq9353,superfamily,224117,266,389,0.0011729000000000002,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs3_orang.marg.frame3,1909182204_L1PA14.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs3_orang,marg,BothTerminiTruncated
36637,Q#2708 - >seq9355,specific,238827,510,772,7.489759999999999e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36638,Q#2708 - >seq9355,superfamily,295487,510,772,7.489759999999999e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36639,Q#2708 - >seq9355,specific,197310,9,236,2.0597e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36640,Q#2708 - >seq9355,superfamily,351117,9,236,2.0597e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36641,Q#2708 - >seq9355,non-specific,197306,9,236,1.2744700000000002e-44,161.495,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36642,Q#2708 - >seq9355,specific,333820,516,772,7.500749999999999e-35,131.64600000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36643,Q#2708 - >seq9355,superfamily,333820,516,772,7.500749999999999e-35,131.64600000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36644,Q#2708 - >seq9355,non-specific,197307,9,236,6.50204e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36645,Q#2708 - >seq9355,non-specific,223780,9,237,4.7169699999999997e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36646,Q#2708 - >seq9355,non-specific,197320,9,229,7.263439999999999e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36647,Q#2708 - >seq9355,specific,335306,10,229,3.2683499999999996e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36648,Q#2708 - >seq9355,non-specific,197321,7,236,2.4550100000000003e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36649,Q#2708 - >seq9355,non-specific,273186,9,237,2.50072e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36650,Q#2708 - >seq9355,non-specific,272954,9,236,1.90703e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36651,Q#2708 - >seq9355,non-specific,197319,13,236,4.6622699999999995e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36652,Q#2708 - >seq9355,non-specific,238828,516,737,4.937939999999999e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36653,Q#2708 - >seq9355,non-specific,197322,8,236,1.0307999999999998e-11,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36654,Q#2708 - >seq9355,non-specific,197336,9,194,2.70861e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36655,Q#2708 - >seq9355,non-specific,275209,467,800,2.5911799999999997e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36656,Q#2708 - >seq9355,superfamily,275209,467,800,2.5911799999999997e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36657,Q#2708 - >seq9355,non-specific,236970,9,237,5.2399699999999996e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36658,Q#2708 - >seq9355,non-specific,339261,108,232,5.37605e-07,49.2579,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36659,Q#2708 - >seq9355,non-specific,197311,30,236,9.234659999999999e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36660,Q#2708 - >seq9355,non-specific,238185,656,772,1.0373099999999999e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,CompleteHit
36661,Q#2708 - >seq9355,specific,225881,482,739,0.000549509,43.2889,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,N-TerminusTruncated
36662,Q#2708 - >seq9355,superfamily,225881,482,739,0.000549509,43.2889,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs0_human,marg,N-TerminusTruncated
36663,Q#2708 - >seq9355,non-specific,235175,294,469,0.00115734,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs0_human,marg,BothTerminiTruncated
36664,Q#2708 - >seq9355,superfamily,235175,294,469,0.00115734,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs0_human,marg,BothTerminiTruncated
36665,Q#2708 - >seq9355,specific,311990,1224,1242,0.00200637,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA14,ORF2,hs0_human,marg,CompleteHit
36666,Q#2708 - >seq9355,superfamily,311990,1224,1242,0.00200637,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA14,ORF2,hs0_human,marg,CompleteHit
36667,Q#2708 - >seq9355,non-specific,224117,266,391,0.00342986,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs0_human,marg,BothTerminiTruncated
36668,Q#2708 - >seq9355,superfamily,224117,266,391,0.00342986,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs0_human,marg,BothTerminiTruncated
36669,Q#2708 - >seq9355,non-specific,197318,9,236,0.0042455,40.3575,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA14.ORF2.hs0_human.marg.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,marg,CompleteHit
36670,Q#2710 - >seq9357,specific,238827,473,735,3.0992499999999998e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36671,Q#2710 - >seq9357,superfamily,295487,473,735,3.0992499999999998e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36672,Q#2710 - >seq9357,specific,333820,479,735,2.0470699999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36673,Q#2710 - >seq9357,superfamily,333820,479,735,2.0470699999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36674,Q#2710 - >seq9357,non-specific,238828,479,700,1.5963e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36675,Q#2710 - >seq9357,non-specific,275209,430,763,1.5332699999999998e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36676,Q#2710 - >seq9357,superfamily,275209,430,763,1.5332699999999998e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36677,Q#2710 - >seq9357,non-specific,238185,619,735,4.888719999999999e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36678,Q#2710 - >seq9357,specific,225881,445,702,0.00016136299999999998,45.2149,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,N-TerminusTruncated
36679,Q#2710 - >seq9357,superfamily,225881,445,702,0.00016136299999999998,45.2149,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA14,ORF2,hs0_human,pars,N-TerminusTruncated
36680,Q#2710 - >seq9357,specific,311990,1187,1205,0.00180128,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs0_human,pars,CompleteHit
36681,Q#2710 - >seq9357,superfamily,311990,1187,1205,0.00180128,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs0_human.pars.frame1,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs0_human,pars,CompleteHit
36682,Q#2712 - >seq9359,specific,197310,9,236,5.617249999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36683,Q#2712 - >seq9359,superfamily,351117,9,236,5.617249999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36684,Q#2712 - >seq9359,non-specific,197306,9,236,3.8372899999999995e-45,163.036,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36685,Q#2712 - >seq9359,non-specific,197307,9,236,6.41746e-26,107.759,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36686,Q#2712 - >seq9359,non-specific,223780,9,237,3.87385e-23,99.9803,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36687,Q#2712 - >seq9359,non-specific,197320,9,229,6.94689e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36688,Q#2712 - >seq9359,specific,335306,10,229,3.1296600000000003e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36689,Q#2712 - >seq9359,non-specific,197321,7,236,7.27826e-18,84.52600000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36690,Q#2712 - >seq9359,non-specific,273186,9,237,2.39236e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36691,Q#2712 - >seq9359,non-specific,272954,9,236,3.24187e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36692,Q#2712 - >seq9359,non-specific,197319,13,236,4.51146e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36693,Q#2712 - >seq9359,non-specific,197322,8,236,9.85026e-12,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36694,Q#2712 - >seq9359,non-specific,197336,9,194,2.59248e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36695,Q#2712 - >seq9359,non-specific,236970,9,237,2.5998000000000002e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36696,Q#2712 - >seq9359,non-specific,197311,30,236,1.1284e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36697,Q#2712 - >seq9359,non-specific,339261,108,232,4.025069999999999e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs0_human,pars,CompleteHit
36698,Q#2712 - >seq9359,non-specific,197318,9,236,0.000669144,42.6687,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs0_human,pars,CompleteHit
36699,Q#2712 - >seq9359,non-specific,315083,301,362,0.00757404,37.4882,pfam12325,TMF_TATA_bd,C,cl26375,"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA14,ORF2,hs0_human,pars,C-TerminusTruncated
36700,Q#2712 - >seq9359,superfamily,315083,301,362,0.00757404,37.4882,cl26375,TMF_TATA_bd superfamily,C, - ,"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family.",L1PA14.ORF2.hs0_human.pars.frame3,1909182225_L1PA14.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA14,ORF2,hs0_human,pars,C-TerminusTruncated
36701,Q#2715 - >seq9362,specific,238827,509,771,1.5239099999999998e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36702,Q#2715 - >seq9362,superfamily,295487,509,771,1.5239099999999998e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36703,Q#2715 - >seq9362,specific,197310,9,236,6.0890899999999985e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36704,Q#2715 - >seq9362,superfamily,351117,9,236,6.0890899999999985e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36705,Q#2715 - >seq9362,non-specific,197306,9,236,5.95714e-42,153.791,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36706,Q#2715 - >seq9362,specific,333820,515,771,6.00794e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36707,Q#2715 - >seq9362,superfamily,333820,515,771,6.00794e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36708,Q#2715 - >seq9362,non-specific,197307,9,236,3.84948e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36709,Q#2715 - >seq9362,non-specific,223780,9,237,1.01774e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36710,Q#2715 - >seq9362,non-specific,197321,7,236,1.40679e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36711,Q#2715 - >seq9362,non-specific,197320,9,229,4.99802e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36712,Q#2715 - >seq9362,specific,335306,10,229,6.2068499999999994e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36713,Q#2715 - >seq9362,non-specific,197319,13,236,1.5382999999999999e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36714,Q#2715 - >seq9362,non-specific,273186,9,237,4.783e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36715,Q#2715 - >seq9362,non-specific,272954,9,236,1.22025e-11,66.2525,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36716,Q#2715 - >seq9362,non-specific,238828,515,736,1.51119e-09,59.522,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36717,Q#2715 - >seq9362,non-specific,197311,7,236,1.55446e-09,58.8425,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36718,Q#2715 - >seq9362,non-specific,197336,9,194,3.1235599999999995e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36719,Q#2715 - >seq9362,non-specific,197322,8,236,2.2302699999999998e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36720,Q#2715 - >seq9362,non-specific,339261,108,232,2.9416599999999996e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36721,Q#2715 - >seq9362,non-specific,223496,304,499,6.19577e-05,47.4475,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs1_chimp,pars,BothTerminiTruncated
36722,Q#2715 - >seq9362,superfamily,223496,304,499,6.19577e-05,47.4475,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs1_chimp,pars,BothTerminiTruncated
36723,Q#2715 - >seq9362,non-specific,275209,468,670,9.21288e-05,45.9116,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36724,Q#2715 - >seq9362,superfamily,275209,468,670,9.21288e-05,45.9116,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36725,Q#2715 - >seq9362,non-specific,238185,654,771,0.000394042,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36726,Q#2715 - >seq9362,non-specific,274009,307,457,0.000418122,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36727,Q#2715 - >seq9362,superfamily,274009,307,457,0.000418122,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36728,Q#2715 - >seq9362,non-specific,235175,263,463,0.000510633,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,pars,BothTerminiTruncated
36729,Q#2715 - >seq9362,superfamily,235175,263,463,0.000510633,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,pars,BothTerminiTruncated
36730,Q#2715 - >seq9362,specific,311990,1239,1257,0.0007842880000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36731,Q#2715 - >seq9362,superfamily,311990,1239,1257,0.0007842880000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs1_chimp,pars,CompleteHit
36732,Q#2715 - >seq9362,non-specific,234767,171,399,0.00173732,42.5176,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36733,Q#2715 - >seq9362,superfamily,234767,171,399,0.00173732,42.5176,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36734,Q#2715 - >seq9362,non-specific,224117,263,447,0.00466958,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36735,Q#2715 - >seq9362,superfamily,224117,263,447,0.00466958,41.2384,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs1_chimp.pars.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs1_chimp,pars,C-TerminusTruncated
36736,Q#2718 - >seq9365,specific,238827,510,772,1.5408699999999997e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36737,Q#2718 - >seq9365,superfamily,295487,510,772,1.5408699999999997e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36738,Q#2718 - >seq9365,specific,197310,9,236,6.399139999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36739,Q#2718 - >seq9365,superfamily,351117,9,236,6.399139999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36740,Q#2718 - >seq9365,non-specific,197306,9,236,5.90543e-42,153.791,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36741,Q#2718 - >seq9365,specific,333820,516,772,6.013159999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36742,Q#2718 - >seq9365,superfamily,333820,516,772,6.013159999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36743,Q#2718 - >seq9365,non-specific,197307,9,236,3.88978e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36744,Q#2718 - >seq9365,non-specific,223780,9,237,1.07826e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36745,Q#2718 - >seq9365,non-specific,197321,7,236,1.42148e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36746,Q#2718 - >seq9365,non-specific,197320,9,229,5.05018e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36747,Q#2718 - >seq9365,specific,335306,10,229,6.2123900000000004e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36748,Q#2718 - >seq9365,non-specific,197319,13,236,1.56881e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36749,Q#2718 - >seq9365,non-specific,273186,9,237,4.87768e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36750,Q#2718 - >seq9365,non-specific,272954,9,236,1.25594e-11,66.2525,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36751,Q#2718 - >seq9365,non-specific,238828,516,737,1.51253e-09,59.522,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36752,Q#2718 - >seq9365,non-specific,197311,7,236,1.57055e-09,58.8425,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36753,Q#2718 - >seq9365,non-specific,197336,9,194,3.1553500000000003e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36754,Q#2718 - >seq9365,non-specific,197322,8,236,2.23231e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36755,Q#2718 - >seq9365,non-specific,339261,108,232,2.97278e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36756,Q#2718 - >seq9365,non-specific,275209,469,671,9.38356e-05,45.9116,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,C-TerminusTruncated
36757,Q#2718 - >seq9365,superfamily,275209,469,671,9.38356e-05,45.9116,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,C-TerminusTruncated
36758,Q#2718 - >seq9365,non-specific,238185,655,772,0.000390538,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36759,Q#2718 - >seq9365,specific,311990,1240,1258,0.0007772460000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36760,Q#2718 - >seq9365,superfamily,311990,1240,1258,0.0007772460000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs1_chimp,marg,CompleteHit
36761,Q#2718 - >seq9365,non-specific,274009,307,458,0.00126698,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,marg,C-TerminusTruncated
36762,Q#2718 - >seq9365,superfamily,274009,307,458,0.00126698,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,marg,C-TerminusTruncated
36763,Q#2718 - >seq9365,non-specific,223496,304,500,0.00163495,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs1_chimp,marg,BothTerminiTruncated
36764,Q#2718 - >seq9365,superfamily,223496,304,500,0.00163495,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs1_chimp,marg,BothTerminiTruncated
36765,Q#2718 - >seq9365,non-specific,235175,263,464,0.00180781,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,marg,BothTerminiTruncated
36766,Q#2718 - >seq9365,superfamily,235175,263,464,0.00180781,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,marg,BothTerminiTruncated
36767,Q#2718 - >seq9365,non-specific,274009,305,458,0.0057065,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs1_chimp.marg.frame3,1909182229_L1PA15.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs1_chimp,marg,BothTerminiTruncated
36768,Q#2719 - >seq9366,specific,311990,1153,1171,0.000391431,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs2_gorilla.pars.frame1,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36769,Q#2719 - >seq9366,superfamily,311990,1153,1171,0.000391431,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs2_gorilla.pars.frame1,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36770,Q#2721 - >seq9368,specific,238827,509,771,2.6849599999999993e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36771,Q#2721 - >seq9368,superfamily,295487,509,771,2.6849599999999993e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36772,Q#2721 - >seq9368,specific,197310,9,236,1.0363399999999998e-59,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36773,Q#2721 - >seq9368,superfamily,351117,9,236,1.0363399999999998e-59,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36774,Q#2721 - >seq9368,non-specific,197306,9,236,1.58095e-40,149.939,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36775,Q#2721 - >seq9368,specific,333820,515,771,5.7345e-33,126.25299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36776,Q#2721 - >seq9368,superfamily,333820,515,771,5.7345e-33,126.25299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36777,Q#2721 - >seq9368,non-specific,197307,9,236,8.703520000000001e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36778,Q#2721 - >seq9368,non-specific,223780,9,237,8.22681e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36779,Q#2721 - >seq9368,non-specific,197321,7,236,1.44135e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36780,Q#2721 - >seq9368,non-specific,197320,9,194,1.15558e-18,86.8001,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36781,Q#2721 - >seq9368,specific,335306,10,229,7.91024e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36782,Q#2721 - >seq9368,non-specific,197319,13,236,3.09161e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36783,Q#2721 - >seq9368,non-specific,273186,9,237,4.85265e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36784,Q#2721 - >seq9368,non-specific,272954,9,194,5.4278e-11,64.3265,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36785,Q#2721 - >seq9368,non-specific,238828,515,736,2.1897999999999998e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36786,Q#2721 - >seq9368,non-specific,197336,9,194,1.62956e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36787,Q#2721 - >seq9368,non-specific,197322,8,236,3.4138199999999995e-08,56.5566,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36788,Q#2721 - >seq9368,non-specific,197311,7,236,1.7317e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36789,Q#2721 - >seq9368,non-specific,275209,468,799,2.16287e-06,51.3044,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36790,Q#2721 - >seq9368,superfamily,275209,468,799,2.16287e-06,51.3044,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36791,Q#2721 - >seq9368,non-specific,235175,263,468,2.87125e-06,51.6032,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36792,Q#2721 - >seq9368,superfamily,235175,263,468,2.87125e-06,51.6032,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36793,Q#2721 - >seq9368,non-specific,339261,108,232,2.46377e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36794,Q#2721 - >seq9368,non-specific,238185,654,771,4.88921e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,CompleteHit
36795,Q#2721 - >seq9368,non-specific,274009,307,457,0.000145609,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36796,Q#2721 - >seq9368,superfamily,274009,307,457,0.000145609,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36797,Q#2721 - >seq9368,non-specific,224117,263,447,0.00306793,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36798,Q#2721 - >seq9368,superfamily,224117,263,447,0.00306793,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,C-TerminusTruncated
36799,Q#2721 - >seq9368,non-specific,224117,266,427,0.00312026,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36800,Q#2721 - >seq9368,non-specific,313357,336,463,0.00330185,39.9424,pfam10112,Halogen_Hydrol,N,cl02059,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36801,Q#2721 - >seq9368,superfamily,321788,336,463,0.00330185,39.9424,cl02059,Halogen_Hydrol superfamily,N, - ,5-bromo-4-chloroindolyl phosphate hydrolysis protein; Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.,L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs2_gorilla,pars,N-TerminusTruncated
36802,Q#2721 - >seq9368,specific,225881,481,679,0.00491904,40.5925,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36803,Q#2721 - >seq9368,superfamily,225881,481,679,0.00491904,40.5925,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36804,Q#2721 - >seq9368,non-specific,274008,263,435,0.00707159,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36805,Q#2721 - >seq9368,superfamily,274008,263,435,0.00707159,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.pars.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,pars,BothTerminiTruncated
36806,Q#2724 - >seq9371,specific,238827,510,772,2.1454499999999995e-63,214.84799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36807,Q#2724 - >seq9371,superfamily,295487,510,772,2.1454499999999995e-63,214.84799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36808,Q#2724 - >seq9371,specific,197310,9,236,3.0428299999999995e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36809,Q#2724 - >seq9371,superfamily,351117,9,236,3.0428299999999995e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36810,Q#2724 - >seq9371,non-specific,197306,9,236,2.20519e-40,149.554,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36811,Q#2724 - >seq9371,specific,333820,516,772,6.43922e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36812,Q#2724 - >seq9371,superfamily,333820,516,772,6.43922e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36813,Q#2724 - >seq9371,non-specific,197307,9,236,8.09038e-21,93.1213,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36814,Q#2724 - >seq9371,non-specific,223780,9,237,8.829619999999999e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36815,Q#2724 - >seq9371,non-specific,197321,7,236,1.5470699999999998e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36816,Q#2724 - >seq9371,non-specific,197320,9,194,2.3632900000000002e-18,86.0297,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,C-TerminusTruncated
36817,Q#2724 - >seq9371,specific,335306,10,229,8.10464e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36818,Q#2724 - >seq9371,non-specific,273186,9,237,2.01882e-12,68.4596,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36819,Q#2724 - >seq9371,non-specific,197319,13,236,4.76026e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36820,Q#2724 - >seq9371,non-specific,272954,9,194,2.23656e-10,62.4005,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,C-TerminusTruncated
36821,Q#2724 - >seq9371,non-specific,238828,516,737,6.16829e-10,60.6776,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36822,Q#2724 - >seq9371,non-specific,197336,9,194,1.6700100000000001e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36823,Q#2724 - >seq9371,non-specific,197322,8,236,3.50025e-08,56.5566,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36824,Q#2724 - >seq9371,non-specific,197311,7,236,1.94735e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36825,Q#2724 - >seq9371,non-specific,275209,469,800,1.08396e-05,48.9932,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36826,Q#2724 - >seq9371,superfamily,275209,469,800,1.08396e-05,48.9932,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36827,Q#2724 - >seq9371,non-specific,339261,108,232,1.45161e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36828,Q#2724 - >seq9371,non-specific,238185,655,772,0.00022646,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36829,Q#2724 - >seq9371,non-specific,274009,307,458,0.000408389,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,C-TerminusTruncated
36830,Q#2724 - >seq9371,superfamily,274009,307,458,0.000408389,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,C-TerminusTruncated
36831,Q#2724 - >seq9371,specific,311990,1241,1259,0.0007778489999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36832,Q#2724 - >seq9371,superfamily,311990,1241,1259,0.0007778489999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs2_gorilla,marg,CompleteHit
36833,Q#2724 - >seq9371,non-specific,235175,263,464,0.000941945,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36834,Q#2724 - >seq9371,superfamily,235175,263,464,0.000941945,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36835,Q#2724 - >seq9371,non-specific,274008,263,436,0.0050805,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36836,Q#2724 - >seq9371,superfamily,274008,263,436,0.0050805,41.1955,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36837,Q#2724 - >seq9371,non-specific,274009,301,458,0.00736048,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36838,Q#2724 - >seq9371,non-specific,274008,267,427,0.00822561,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs2_gorilla.marg.frame3,1909182230_L1PA15.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs2_gorilla,marg,BothTerminiTruncated
36839,Q#2725 - >seq9372,specific,238827,510,772,1.9820599999999996e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36840,Q#2725 - >seq9372,superfamily,295487,510,772,1.9820599999999996e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36841,Q#2725 - >seq9372,specific,197310,9,236,2.9032699999999994e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36842,Q#2725 - >seq9372,superfamily,351117,9,236,2.9032699999999994e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36843,Q#2725 - >seq9372,non-specific,197306,9,236,3.54531e-41,151.865,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36844,Q#2725 - >seq9372,specific,333820,516,772,2.4881799999999996e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36845,Q#2725 - >seq9372,superfamily,333820,516,772,2.4881799999999996e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36846,Q#2725 - >seq9372,non-specific,197307,9,236,1.9107299999999998e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36847,Q#2725 - >seq9372,non-specific,223780,9,237,6.590960000000001e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36848,Q#2725 - >seq9372,non-specific,197320,9,194,8.76031e-19,87.1853,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36849,Q#2725 - >seq9372,non-specific,197321,7,236,1.7678e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36850,Q#2725 - >seq9372,specific,335306,10,229,3.3528699999999997e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36851,Q#2725 - >seq9372,non-specific,273186,9,237,8.7216e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36852,Q#2725 - >seq9372,non-specific,197319,13,236,5.0859800000000005e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36853,Q#2725 - >seq9372,non-specific,272954,9,194,1.7921700000000003e-10,62.7857,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36854,Q#2725 - >seq9372,non-specific,197336,9,194,4.41187e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36855,Q#2725 - >seq9372,non-specific,238828,516,737,4.23274e-09,57.9812,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36856,Q#2725 - >seq9372,non-specific,197322,8,236,1.33995e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36857,Q#2725 - >seq9372,non-specific,197311,7,236,2.0810300000000002e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36858,Q#2725 - >seq9372,non-specific,339261,108,232,1.4528099999999999e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36859,Q#2725 - >seq9372,non-specific,238185,655,772,1.94376e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36860,Q#2725 - >seq9372,non-specific,275209,469,800,4.63399e-05,47.0672,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36861,Q#2725 - >seq9372,superfamily,275209,469,800,4.63399e-05,47.0672,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36862,Q#2725 - >seq9372,specific,311990,1241,1259,0.000726868,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36863,Q#2725 - >seq9372,superfamily,311990,1241,1259,0.000726868,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs3_orang,marg,CompleteHit
36864,Q#2725 - >seq9372,non-specific,274009,307,458,0.00133532,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36865,Q#2725 - >seq9372,superfamily,274009,307,458,0.00133532,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36866,Q#2725 - >seq9372,non-specific,235175,263,464,0.00311577,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,marg,BothTerminiTruncated
36867,Q#2725 - >seq9372,superfamily,235175,263,464,0.00311577,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,marg,BothTerminiTruncated
36868,Q#2725 - >seq9372,non-specific,224241,309,388,0.00686961,40.0676,COG1322,RmuC,C,cl34228,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36869,Q#2725 - >seq9372,superfamily,224241,309,388,0.00686961,40.0676,cl34228,RmuC superfamily,C, - ,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1PA15.ORF2.hs3_orang.marg.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs3_orang,marg,C-TerminusTruncated
36870,Q#2729 - >seq9376,specific,238827,509,771,2.0508799999999997e-65,220.62599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36871,Q#2729 - >seq9376,superfamily,295487,509,771,2.0508799999999997e-65,220.62599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36872,Q#2729 - >seq9376,specific,197310,9,236,2.8927699999999996e-61,209.13,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36873,Q#2729 - >seq9376,superfamily,351117,9,236,2.8927699999999996e-61,209.13,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36874,Q#2729 - >seq9376,non-specific,197306,9,236,3.60439e-41,151.865,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36875,Q#2729 - >seq9376,specific,333820,515,771,2.4342299999999998e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36876,Q#2729 - >seq9376,superfamily,333820,515,771,2.4342299999999998e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36877,Q#2729 - >seq9376,non-specific,197307,9,236,1.94207e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36878,Q#2729 - >seq9376,non-specific,223780,9,237,6.7621e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36879,Q#2729 - >seq9376,non-specific,197320,9,194,8.98794e-19,87.1853,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36880,Q#2729 - >seq9376,non-specific,197321,7,236,1.8659400000000003e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36881,Q#2729 - >seq9376,specific,335306,10,229,3.34394e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36882,Q#2729 - >seq9376,non-specific,273186,9,237,9.029069999999999e-13,69.6152,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36883,Q#2729 - >seq9376,non-specific,197319,13,236,5.265e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36884,Q#2729 - >seq9376,non-specific,272954,9,194,1.7873400000000002e-10,62.7857,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36885,Q#2729 - >seq9376,non-specific,197336,9,194,4.48223e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36886,Q#2729 - >seq9376,non-specific,238828,515,736,4.34138e-09,57.9812,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36887,Q#2729 - >seq9376,non-specific,197322,8,236,1.33626e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36888,Q#2729 - >seq9376,non-specific,197311,7,236,2.15478e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36889,Q#2729 - >seq9376,non-specific,339261,108,232,1.43526e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36890,Q#2729 - >seq9376,non-specific,238185,654,771,1.958e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36891,Q#2729 - >seq9376,non-specific,275209,468,799,4.62146e-05,47.0672,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36892,Q#2729 - >seq9376,superfamily,275209,468,799,4.62146e-05,47.0672,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36893,Q#2729 - >seq9376,specific,311990,1239,1257,0.000718113,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36894,Q#2729 - >seq9376,superfamily,311990,1239,1257,0.000718113,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs3_orang,pars,CompleteHit
36895,Q#2729 - >seq9376,non-specific,235175,263,463,0.000760649,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36896,Q#2729 - >seq9376,superfamily,235175,263,463,0.000760649,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36897,Q#2729 - >seq9376,non-specific,274009,307,457,0.000982229,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36898,Q#2729 - >seq9376,superfamily,274009,307,457,0.000982229,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36899,Q#2729 - >seq9376,non-specific,224117,263,447,0.00249781,42.0088,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36900,Q#2729 - >seq9376,superfamily,224117,263,447,0.00249781,42.0088,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs3_orang,pars,C-TerminusTruncated
36901,Q#2729 - >seq9376,non-specific,274009,300,467,0.00406548,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36902,Q#2729 - >seq9376,non-specific,274475,255,427,0.00415837,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36903,Q#2729 - >seq9376,superfamily,274475,255,427,0.00415837,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36904,Q#2729 - >seq9376,non-specific,274008,263,435,0.00659084,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36905,Q#2729 - >seq9376,superfamily,274008,263,435,0.00659084,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs3_orang.pars.frame3,1909182239_L1PA15.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs3_orang,pars,BothTerminiTruncated
36906,Q#2732 - >seq9379,non-specific,239242,1076,1141,0.00156005,41.7102,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs4_gibbon.marg.frame1,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36907,Q#2732 - >seq9379,superfamily,355772,1076,1141,0.00156005,41.7102,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs4_gibbon.marg.frame1,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36908,Q#2733 - >seq9380,specific,238827,508,770,4.3351399999999993e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36909,Q#2733 - >seq9380,superfamily,295487,508,770,4.3351399999999993e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36910,Q#2733 - >seq9380,specific,197310,9,234,4.7340799999999995e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36911,Q#2733 - >seq9380,superfamily,351117,9,234,4.7340799999999995e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36912,Q#2733 - >seq9380,non-specific,197306,9,234,4.5935299999999994e-42,154.17600000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36913,Q#2733 - >seq9380,specific,333820,514,770,5.77264e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36914,Q#2733 - >seq9380,superfamily,333820,514,770,5.77264e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36915,Q#2733 - >seq9380,non-specific,197307,9,234,5.17867e-23,99.6696,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36916,Q#2733 - >seq9380,non-specific,223780,9,235,7.292430000000001e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36917,Q#2733 - >seq9380,non-specific,197321,7,234,2.8066700000000004e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36918,Q#2733 - >seq9380,non-specific,197320,9,227,4.1751799999999997e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36919,Q#2733 - >seq9380,specific,335306,10,227,2.49252e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36920,Q#2733 - >seq9380,non-specific,197319,13,234,1.77955e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36921,Q#2733 - >seq9380,non-specific,273186,9,235,2.9139200000000003e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36922,Q#2733 - >seq9380,non-specific,272954,9,234,3.25073e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36923,Q#2733 - >seq9380,non-specific,238828,514,735,1.33954e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36924,Q#2733 - >seq9380,non-specific,197336,9,192,1.6782299999999997e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36925,Q#2733 - >seq9380,non-specific,197311,7,234,7.17403e-10,59.9981,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36926,Q#2733 - >seq9380,non-specific,339261,108,230,7.381569999999999e-10,57.7323,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36927,Q#2733 - >seq9380,non-specific,197322,8,234,3.8562699999999996e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36928,Q#2733 - >seq9380,non-specific,275209,467,798,2.82795e-07,54.0008,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36929,Q#2733 - >seq9380,superfamily,275209,467,798,2.82795e-07,54.0008,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36930,Q#2733 - >seq9380,non-specific,238185,654,770,2.9485100000000003e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36931,Q#2733 - >seq9380,specific,311990,1239,1257,0.00067053,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36932,Q#2733 - >seq9380,superfamily,311990,1239,1257,0.00067053,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs4_gibbon,marg,CompleteHit
36933,Q#2733 - >seq9380,non-specific,274009,305,456,0.00109636,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36934,Q#2733 - >seq9380,superfamily,274009,305,456,0.00109636,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36935,Q#2733 - >seq9380,non-specific,235175,261,462,0.00176083,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36936,Q#2733 - >seq9380,superfamily,235175,261,462,0.00176083,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36937,Q#2733 - >seq9380,non-specific,224241,307,386,0.00576967,40.4528,COG1322,RmuC,C,cl34228,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36938,Q#2733 - >seq9380,superfamily,224241,307,386,0.00576967,40.4528,cl34228,RmuC superfamily,C, - ,"DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]; Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only].",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36939,Q#2733 - >seq9380,non-specific,274008,261,434,0.00605658,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36940,Q#2733 - >seq9380,superfamily,274008,261,434,0.00605658,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36941,Q#2733 - >seq9380,non-specific,274008,265,462,0.00705198,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36942,Q#2733 - >seq9380,non-specific,224117,261,446,0.00843909,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36943,Q#2733 - >seq9380,superfamily,224117,261,446,0.00843909,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,C-TerminusTruncated
36944,Q#2733 - >seq9380,non-specific,274009,298,466,0.00971165,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.marg.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,marg,BothTerminiTruncated
36945,Q#2734 - >seq9381,non-specific,239242,1107,1172,0.00160774,41.7102,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs4_gibbon.pars.frame2,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36946,Q#2734 - >seq9381,superfamily,355772,1107,1172,0.00160774,41.7102,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs4_gibbon.pars.frame2,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36947,Q#2735 - >seq9382,specific,311990,1155,1173,0.000391756,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs4_gibbon.pars.frame1,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36948,Q#2735 - >seq9382,superfamily,311990,1155,1173,0.000391756,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs4_gibbon.pars.frame1,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36949,Q#2736 - >seq9383,specific,238827,508,770,6.52018e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36950,Q#2736 - >seq9383,superfamily,295487,508,770,6.52018e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36951,Q#2736 - >seq9383,specific,197310,9,234,7.009649999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36952,Q#2736 - >seq9383,superfamily,351117,9,234,7.009649999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36953,Q#2736 - >seq9383,non-specific,197306,9,234,2.8827999999999995e-42,154.947,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36954,Q#2736 - >seq9383,specific,333820,514,770,7.28604e-35,131.64600000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36955,Q#2736 - >seq9383,superfamily,333820,514,770,7.28604e-35,131.64600000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36956,Q#2736 - >seq9383,non-specific,197307,9,234,7.38857e-24,101.98100000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36957,Q#2736 - >seq9383,non-specific,223780,9,235,9.52004e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36958,Q#2736 - >seq9383,non-specific,197321,7,234,3.70128e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36959,Q#2736 - >seq9383,non-specific,197320,9,227,2.44652e-19,88.7261,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36960,Q#2736 - >seq9383,specific,335306,10,227,2.437e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36961,Q#2736 - >seq9383,non-specific,197319,13,234,1.40017e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36962,Q#2736 - >seq9383,non-specific,273186,9,235,6.928330000000001e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36963,Q#2736 - >seq9383,non-specific,272954,9,234,7.983569999999999e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36964,Q#2736 - >seq9383,non-specific,238828,514,735,4.56544e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36965,Q#2736 - >seq9383,non-specific,197336,9,192,1.64042e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36966,Q#2736 - >seq9383,non-specific,197311,7,234,5.755800000000001e-10,60.3833,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36967,Q#2736 - >seq9383,non-specific,339261,108,230,1.12942e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36968,Q#2736 - >seq9383,non-specific,197322,8,234,3.7679699999999994e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36969,Q#2736 - >seq9383,non-specific,275209,467,798,7.827610000000001e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36970,Q#2736 - >seq9383,superfamily,275209,467,798,7.827610000000001e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36971,Q#2736 - >seq9383,non-specific,238185,654,770,6.5012e-06,45.8048,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,CompleteHit
36972,Q#2736 - >seq9383,non-specific,235175,261,462,0.000718662,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36973,Q#2736 - >seq9383,superfamily,235175,261,462,0.000718662,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36974,Q#2736 - >seq9383,non-specific,274009,305,456,0.00116616,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36975,Q#2736 - >seq9383,superfamily,274009,305,456,0.00116616,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36976,Q#2736 - >seq9383,specific,225881,480,715,0.0016374000000000002,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,N-TerminusTruncated
36977,Q#2736 - >seq9383,superfamily,225881,480,715,0.0016374000000000002,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs4_gibbon,pars,N-TerminusTruncated
36978,Q#2736 - >seq9383,non-specific,224117,261,446,0.00897885,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36979,Q#2736 - >seq9383,superfamily,224117,261,446,0.00897885,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,C-TerminusTruncated
36980,Q#2736 - >seq9383,non-specific,274008,261,434,0.00934726,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36981,Q#2736 - >seq9383,superfamily,274008,261,434,0.00934726,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs4_gibbon.pars.frame3,1909182245_L1PA15.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs4_gibbon,pars,BothTerminiTruncated
36982,Q#2737 - >seq9384,non-specific,239242,1088,1153,0.00544091,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs5_gmonkey.pars.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
36983,Q#2737 - >seq9384,superfamily,355772,1088,1153,0.00544091,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs5_gmonkey.pars.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
36984,Q#2738 - >seq9385,specific,238827,516,730,1.0800000000000002e-45,164.00099999999998,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36985,Q#2738 - >seq9385,superfamily,295487,516,730,1.0800000000000002e-45,164.00099999999998,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36986,Q#2738 - >seq9385,non-specific,333820,514,730,5.116480000000001e-24,100.445,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36987,Q#2738 - >seq9385,superfamily,333820,514,730,5.116480000000001e-24,100.445,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36988,Q#2738 - >seq9385,non-specific,238828,522,695,1.4519999999999999e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36989,Q#2738 - >seq9385,non-specific,238185,613,730,1.09698e-06,47.7308,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36990,Q#2738 - >seq9385,non-specific,275209,534,758,4.19682e-06,50.1488,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36991,Q#2738 - >seq9385,superfamily,275209,534,758,4.19682e-06,50.1488,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs5_gmonkey.pars.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
36992,Q#2739 - >seq9386,specific,197310,9,235,1.4178899999999998e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36993,Q#2739 - >seq9386,superfamily,351117,9,235,1.4178899999999998e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36994,Q#2739 - >seq9386,non-specific,197306,9,235,1.23015e-40,150.32399999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36995,Q#2739 - >seq9386,non-specific,197307,9,235,1.55457e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36996,Q#2739 - >seq9386,non-specific,223780,9,236,1.28177e-21,95.7431,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36997,Q#2739 - >seq9386,non-specific,197321,7,235,8.881e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
36998,Q#2739 - >seq9386,non-specific,197320,9,193,2.73859e-19,88.7261,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
36999,Q#2739 - >seq9386,specific,335306,10,228,1.80585e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37000,Q#2739 - >seq9386,non-specific,197319,13,235,1.86316e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37001,Q#2739 - >seq9386,non-specific,238827,507,555,6.1302e-12,66.1606,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37002,Q#2739 - >seq9386,superfamily,295487,507,555,6.1302e-12,66.1606,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37003,Q#2739 - >seq9386,non-specific,273186,9,236,1.04354e-11,66.1484,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37004,Q#2739 - >seq9386,non-specific,272954,9,193,6.46898e-11,63.9413,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37005,Q#2739 - >seq9386,non-specific,197336,9,193,6.165560000000001e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37006,Q#2739 - >seq9386,non-specific,197311,7,235,2.30515e-08,55.3757,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37007,Q#2739 - >seq9386,non-specific,197322,8,235,2.89737e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37008,Q#2739 - >seq9386,non-specific,339261,108,231,9.25583e-07,48.8727,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37009,Q#2739 - >seq9386,non-specific,223496,303,497,0.000253245,45.1363,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37010,Q#2739 - >seq9386,superfamily,223496,303,497,0.000253245,45.1363,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37011,Q#2739 - >seq9386,non-specific,235175,262,461,0.000551552,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37012,Q#2739 - >seq9386,superfamily,235175,262,461,0.000551552,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37013,Q#2739 - >seq9386,non-specific,274009,306,455,0.000562485,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37014,Q#2739 - >seq9386,superfamily,274009,306,455,0.000562485,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37015,Q#2739 - >seq9386,specific,311990,1204,1222,0.0006582239999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37016,Q#2739 - >seq9386,superfamily,311990,1204,1222,0.0006582239999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs5_gmonkey,pars,CompleteHit
37017,Q#2739 - >seq9386,non-specific,274475,254,425,0.00434533,41.2076,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37018,Q#2739 - >seq9386,superfamily,274475,254,425,0.00434533,41.2076,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37019,Q#2739 - >seq9386,non-specific,224117,262,445,0.00521773,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37020,Q#2739 - >seq9386,superfamily,224117,262,445,0.00521773,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37021,Q#2739 - >seq9386,non-specific,274008,266,461,0.0056667,40.8103,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37022,Q#2739 - >seq9386,superfamily,274008,266,461,0.0056667,40.8103,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37023,Q#2739 - >seq9386,non-specific,274008,262,433,0.00700053,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37024,Q#2739 - >seq9386,non-specific,333820,513,546,0.00879728,38.4274,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37025,Q#2739 - >seq9386,superfamily,333820,513,546,0.00879728,38.4274,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.pars.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37026,Q#2740 - >seq9387,non-specific,238827,476,507,1.3910499999999998e-06,50.3674,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs5_gmonkey.marg.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37027,Q#2740 - >seq9387,superfamily,295487,476,507,1.3910499999999998e-06,50.3674,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.marg.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37028,Q#2740 - >seq9387,specific,311990,1157,1175,0.00041580699999999997,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs5_gmonkey.marg.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37029,Q#2740 - >seq9387,superfamily,311990,1157,1175,0.00041580699999999997,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs5_gmonkey.marg.frame1,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37030,Q#2741 - >seq9388,non-specific,239242,1099,1164,0.00549892,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs5_gmonkey.marg.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37031,Q#2741 - >seq9388,superfamily,355772,1099,1164,0.00549892,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs5_gmonkey.marg.frame2,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37032,Q#2742 - >seq9389,specific,197310,9,235,3.0294099999999995e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37033,Q#2742 - >seq9389,superfamily,351117,9,235,3.0294099999999995e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37034,Q#2742 - >seq9389,specific,238827,507,769,2.89235e-47,168.238,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37035,Q#2742 - >seq9389,superfamily,295487,507,769,2.89235e-47,168.238,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37036,Q#2742 - >seq9389,non-specific,197306,9,235,2.0481599999999995e-40,149.554,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37037,Q#2742 - >seq9389,non-specific,333820,513,769,1.37704e-23,99.2889,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37038,Q#2742 - >seq9389,superfamily,333820,513,769,1.37704e-23,99.2889,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37039,Q#2742 - >seq9389,non-specific,197307,9,235,5.507840000000001e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37040,Q#2742 - >seq9389,non-specific,223780,9,236,7.32336e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37041,Q#2742 - >seq9389,non-specific,197321,7,235,1.4928700000000002e-20,92.23,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37042,Q#2742 - >seq9389,non-specific,197320,9,193,2.76448e-19,88.7261,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37043,Q#2742 - >seq9389,specific,335306,10,228,1.82245e-15,76.9001,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37044,Q#2742 - >seq9389,non-specific,197319,13,235,3.4151900000000003e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37045,Q#2742 - >seq9389,non-specific,273186,9,236,6.611969999999999e-12,66.9188,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37046,Q#2742 - >seq9389,non-specific,272954,9,193,3.31436e-11,64.7117,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37047,Q#2742 - >seq9389,non-specific,238828,561,734,6.83815e-11,63.373999999999995,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
37048,Q#2742 - >seq9389,non-specific,197336,9,193,6.2229e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37049,Q#2742 - >seq9389,non-specific,197311,7,235,4.8823e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37050,Q#2742 - >seq9389,non-specific,275209,466,797,6.67095e-08,55.9268,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37051,Q#2742 - >seq9389,superfamily,275209,466,797,6.67095e-08,55.9268,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37052,Q#2742 - >seq9389,non-specific,197322,8,235,2.92465e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37053,Q#2742 - >seq9389,non-specific,339261,108,231,2.68272e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37054,Q#2742 - >seq9389,non-specific,238185,652,769,2.97844e-06,46.5752,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs5_gmonkey,marg,CompleteHit
37055,Q#2742 - >seq9389,non-specific,235175,262,461,0.00020464799999999998,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37056,Q#2742 - >seq9389,superfamily,235175,262,461,0.00020464799999999998,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37057,Q#2742 - >seq9389,non-specific,223496,303,497,0.000290293,45.1363,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37058,Q#2742 - >seq9389,superfamily,223496,303,497,0.000290293,45.1363,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37059,Q#2742 - >seq9389,non-specific,274009,306,455,0.000597312,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37060,Q#2742 - >seq9389,superfamily,274009,306,455,0.000597312,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37061,Q#2742 - >seq9389,non-specific,274475,254,425,0.00677019,40.4372,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37062,Q#2742 - >seq9389,superfamily,274475,254,425,0.00677019,40.4372,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37063,Q#2742 - >seq9389,non-specific,224117,262,445,0.00867234,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37064,Q#2742 - >seq9389,superfamily,224117,262,445,0.00867234,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs5_gmonkey.marg.frame3,1909182253_L1PA15.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37065,Q#2743 - >seq9390,non-specific,173412,116,268,0.00272955,42.0503,PTZ00121,PTZ00121,NC,cl31754,MAEBL; Provisional,L1PA15.ORF2.hs0_human.marg.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37066,Q#2743 - >seq9390,superfamily,173412,116,268,0.00272955,42.0503,cl31754,PTZ00121 superfamily,NC, - ,MAEBL; Provisional,L1PA15.ORF2.hs0_human.marg.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37067,Q#2744 - >seq9391,non-specific,239242,1073,1137,0.00042683,43.6362,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs0_human.marg.frame1,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37068,Q#2744 - >seq9391,superfamily,355772,1073,1137,0.00042683,43.6362,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs0_human.marg.frame1,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37069,Q#2745 - >seq9392,specific,238827,510,772,1.5301699999999997e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37070,Q#2745 - >seq9392,superfamily,295487,510,772,1.5301699999999997e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37071,Q#2745 - >seq9392,specific,197310,9,236,6.053229999999999e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37072,Q#2745 - >seq9392,superfamily,351117,9,236,6.053229999999999e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37073,Q#2745 - >seq9392,non-specific,197306,9,236,1.7899500000000002e-41,152.636,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37074,Q#2745 - >seq9392,specific,333820,516,772,6.570469999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37075,Q#2745 - >seq9392,superfamily,333820,516,772,6.570469999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37076,Q#2745 - >seq9392,non-specific,197307,9,236,5.03633e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37077,Q#2745 - >seq9392,non-specific,223780,9,237,2.34872e-20,91.8911,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37078,Q#2745 - >seq9392,non-specific,197321,7,236,4.83349e-19,87.9928,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37079,Q#2745 - >seq9392,non-specific,197320,9,194,1.46021e-18,86.4149,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,marg,C-TerminusTruncated
37080,Q#2745 - >seq9392,specific,335306,10,229,1.1020799999999999e-17,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37081,Q#2745 - >seq9392,non-specific,273186,9,237,1.69819e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37082,Q#2745 - >seq9392,non-specific,197319,13,236,2.9430500000000003e-13,70.7685,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37083,Q#2745 - >seq9392,non-specific,272954,9,236,1.89466e-11,65.4821,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37084,Q#2745 - >seq9392,non-specific,238828,516,737,1.55829e-09,59.522,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37085,Q#2745 - >seq9392,non-specific,197336,9,194,3.13197e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37086,Q#2745 - >seq9392,non-specific,197311,7,236,1.5200799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37087,Q#2745 - >seq9392,non-specific,197322,8,236,4.7528499999999994e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,marg,CompleteHit
37088,Q#2745 - >seq9392,non-specific,339261,108,232,2.02941e-07,50.7987,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37089,Q#2745 - >seq9392,non-specific,275209,469,671,9.56597e-05,45.9116,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,C-TerminusTruncated
37090,Q#2745 - >seq9392,superfamily,275209,469,671,9.56597e-05,45.9116,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,C-TerminusTruncated
37091,Q#2745 - >seq9392,non-specific,238185,655,772,0.000395006,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs0_human,marg,CompleteHit
37092,Q#2745 - >seq9392,non-specific,274009,307,458,0.00121673,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,C-TerminusTruncated
37093,Q#2745 - >seq9392,superfamily,274009,307,458,0.00121673,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,C-TerminusTruncated
37094,Q#2745 - >seq9392,non-specific,235175,263,464,0.00212759,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37095,Q#2745 - >seq9392,superfamily,235175,263,464,0.00212759,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37096,Q#2745 - >seq9392,non-specific,274009,301,458,0.00552661,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37097,Q#2745 - >seq9392,specific,311990,1241,1259,0.00633676,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs0_human,marg,CompleteHit
37098,Q#2745 - >seq9392,superfamily,311990,1241,1259,0.00633676,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs0_human,marg,CompleteHit
37099,Q#2745 - >seq9392,non-specific,274009,263,447,0.00879822,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37100,Q#2745 - >seq9392,non-specific,274008,267,464,0.00950526,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37101,Q#2745 - >seq9392,superfamily,274008,267,464,0.00950526,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs0_human.marg.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs0_human,marg,BothTerminiTruncated
37102,Q#2746 - >seq9393,specific,238827,487,749,4.620079999999999e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37103,Q#2746 - >seq9393,superfamily,295487,487,749,4.620079999999999e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37104,Q#2746 - >seq9393,specific,333820,493,749,9.425729999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37105,Q#2746 - >seq9393,superfamily,333820,493,749,9.425729999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37106,Q#2746 - >seq9393,non-specific,238828,493,714,5.559660000000001e-10,60.6776,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37107,Q#2746 - >seq9393,non-specific,275209,446,648,8.363399999999999e-05,46.2968,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,C-TerminusTruncated
37108,Q#2746 - >seq9393,superfamily,275209,446,648,8.363399999999999e-05,46.2968,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,C-TerminusTruncated
37109,Q#2746 - >seq9393,non-specific,238185,632,749,0.00011575600000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37110,Q#2746 - >seq9393,non-specific,173412,116,268,0.0008692330000000001,43.5911,PTZ00121,PTZ00121,NC,cl31754,MAEBL; Provisional,L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,pars,BothTerminiTruncated
37111,Q#2746 - >seq9393,superfamily,173412,116,268,0.0008692330000000001,43.5911,cl31754,PTZ00121 superfamily,NC, - ,MAEBL; Provisional,L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,pars,BothTerminiTruncated
37112,Q#2746 - >seq9393,specific,311990,1218,1236,0.00298426,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA15,ORF2,hs0_human,pars,CompleteHit
37113,Q#2746 - >seq9393,superfamily,311990,1218,1236,0.00298426,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs0_human.pars.frame2,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA15,ORF2,hs0_human,pars,CompleteHit
37114,Q#2748 - >seq9395,specific,197310,9,236,4.986079999999999e-63,214.138,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37115,Q#2748 - >seq9395,superfamily,351117,9,236,4.986079999999999e-63,214.138,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37116,Q#2748 - >seq9395,non-specific,197306,9,236,8.113940000000001e-43,156.488,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37117,Q#2748 - >seq9395,non-specific,197307,9,236,5.31925e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37118,Q#2748 - >seq9395,non-specific,223780,9,237,1.8781099999999997e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37119,Q#2748 - >seq9395,non-specific,197321,7,236,1.67804e-20,92.23,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37120,Q#2748 - >seq9395,non-specific,197320,9,229,6.439509999999999e-19,87.5705,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37121,Q#2748 - >seq9395,specific,335306,10,229,1.01881e-17,83.4485,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37122,Q#2748 - >seq9395,non-specific,197319,13,236,2.71071e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37123,Q#2748 - >seq9395,non-specific,273186,9,237,3.63551e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37124,Q#2748 - >seq9395,non-specific,272954,9,236,1.03875e-12,69.3341,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37125,Q#2748 - >seq9395,non-specific,197336,9,194,2.8669699999999997e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37126,Q#2748 - >seq9395,non-specific,197311,7,236,7.35754e-09,56.9165,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37127,Q#2748 - >seq9395,non-specific,197322,8,236,4.38402e-08,56.1714,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs0_human,pars,CompleteHit
37128,Q#2748 - >seq9395,non-specific,339261,108,232,2.59823e-07,50.4135,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs0_human,pars,CompleteHit
37129,Q#2748 - >seq9395,non-specific,239242,1108,1172,0.00044169900000000004,43.6362,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,pars,BothTerminiTruncated
37130,Q#2748 - >seq9395,superfamily,355772,1108,1172,0.00044169900000000004,43.6362,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs0_human.pars.frame3,1909182259_L1PA15.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA15,ORF2,hs0_human,pars,BothTerminiTruncated
37131,Q#2751 - >seq9398,specific,238827,509,771,4.1954099999999994e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37132,Q#2751 - >seq9398,superfamily,295487,509,771,4.1954099999999994e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37133,Q#2751 - >seq9398,specific,197310,9,235,8.206439999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37134,Q#2751 - >seq9398,superfamily,351117,9,235,8.206439999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37135,Q#2751 - >seq9398,non-specific,197306,9,235,3.82125e-38,143.006,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37136,Q#2751 - >seq9398,specific,333820,515,771,3.3804e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37137,Q#2751 - >seq9398,superfamily,333820,515,771,3.3804e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37138,Q#2751 - >seq9398,non-specific,223780,9,236,7.37436e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37139,Q#2751 - >seq9398,non-specific,197307,9,235,1.8100000000000002e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37140,Q#2751 - >seq9398,non-specific,197321,7,235,2.07178e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37141,Q#2751 - >seq9398,non-specific,197320,9,228,7.236449999999999e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37142,Q#2751 - >seq9398,specific,335306,10,228,2.46705e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37143,Q#2751 - >seq9398,non-specific,273186,9,236,1.3738499999999999e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37144,Q#2751 - >seq9398,non-specific,272954,9,206,2.64781e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37145,Q#2751 - >seq9398,non-specific,197319,13,235,3.94298e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37146,Q#2751 - >seq9398,non-specific,238828,515,736,1.52803e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37147,Q#2751 - >seq9398,non-specific,197336,9,193,1.74583e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37148,Q#2751 - >seq9398,non-specific,236970,9,236,6.787919999999999e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37149,Q#2751 - >seq9398,non-specific,275209,466,799,8.44918e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37150,Q#2751 - >seq9398,superfamily,275209,466,799,8.44918e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37151,Q#2751 - >seq9398,non-specific,235175,290,468,5.26066e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37152,Q#2751 - >seq9398,superfamily,235175,290,468,5.26066e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37153,Q#2751 - >seq9398,non-specific,339261,108,231,6.813239999999999e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37154,Q#2751 - >seq9398,non-specific,238185,655,769,0.00011653399999999999,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37155,Q#2751 - >seq9398,non-specific,197311,30,235,0.00017919,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,pars,CompleteHit
37156,Q#2751 - >seq9398,non-specific,223496,262,445,0.000228612,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37157,Q#2751 - >seq9398,superfamily,223496,262,445,0.000228612,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37158,Q#2751 - >seq9398,non-specific,274009,293,407,0.000843552,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37159,Q#2751 - >seq9398,superfamily,274009,293,407,0.000843552,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37160,Q#2751 - >seq9398,non-specific,223496,315,499,0.0027161,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs1_chimp,pars,BothTerminiTruncated
37161,Q#2751 - >seq9398,non-specific,224117,262,466,0.00319187,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,N-TerminusTruncated
37162,Q#2751 - >seq9398,superfamily,224117,262,466,0.00319187,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs1_chimp,pars,N-TerminusTruncated
37163,Q#2751 - >seq9398,non-specific,274009,306,457,0.00675173,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.pars.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,pars,C-TerminusTruncated
37164,Q#2754 - >seq9401,specific,238827,509,771,3.818469999999999e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37165,Q#2754 - >seq9401,superfamily,295487,509,771,3.818469999999999e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37166,Q#2754 - >seq9401,specific,197310,9,235,7.836059999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37167,Q#2754 - >seq9401,superfamily,351117,9,235,7.836059999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37168,Q#2754 - >seq9401,non-specific,197306,9,235,3.7552699999999994e-38,143.006,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37169,Q#2754 - >seq9401,specific,333820,515,771,3.3215e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37170,Q#2754 - >seq9401,superfamily,333820,515,771,3.3215e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37171,Q#2754 - >seq9401,non-specific,223780,9,236,7.82015e-21,93.4319,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37172,Q#2754 - >seq9401,non-specific,197307,9,235,1.8306e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37173,Q#2754 - >seq9401,non-specific,197321,7,235,2.1354999999999998e-20,91.8448,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37174,Q#2754 - >seq9401,non-specific,197320,9,228,7.60155e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37175,Q#2754 - >seq9401,specific,335306,10,228,2.47145e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37176,Q#2754 - >seq9401,non-specific,273186,9,236,1.429e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37177,Q#2754 - >seq9401,non-specific,272954,9,206,2.67745e-12,68.1785,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37178,Q#2754 - >seq9401,non-specific,197319,13,235,4.02451e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37179,Q#2754 - >seq9401,non-specific,238828,515,736,1.50223e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37180,Q#2754 - >seq9401,non-specific,197336,9,193,1.74897e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37181,Q#2754 - >seq9401,non-specific,236970,9,236,6.92522e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37182,Q#2754 - >seq9401,non-specific,275209,466,799,8.53989e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37183,Q#2754 - >seq9401,superfamily,275209,466,799,8.53989e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37184,Q#2754 - >seq9401,non-specific,235175,290,468,4.6015e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37185,Q#2754 - >seq9401,superfamily,235175,290,468,4.6015e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37186,Q#2754 - >seq9401,non-specific,339261,108,231,6.758819999999999e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37187,Q#2754 - >seq9401,non-specific,238185,655,769,0.00011902200000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37188,Q#2754 - >seq9401,non-specific,197311,30,235,0.00018116400000000002,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs1_chimp,marg,CompleteHit
37189,Q#2754 - >seq9401,non-specific,223496,262,445,0.000201682,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37190,Q#2754 - >seq9401,superfamily,223496,262,445,0.000201682,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37191,Q#2754 - >seq9401,non-specific,274009,293,407,0.000757108,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37192,Q#2754 - >seq9401,superfamily,274009,293,407,0.000757108,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37193,Q#2754 - >seq9401,non-specific,223496,315,463,0.00233602,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs1_chimp,marg,BothTerminiTruncated
37194,Q#2754 - >seq9401,non-specific,224117,262,466,0.00309127,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,N-TerminusTruncated
37195,Q#2754 - >seq9401,superfamily,224117,262,466,0.00309127,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs1_chimp,marg,N-TerminusTruncated
37196,Q#2754 - >seq9401,non-specific,274009,306,457,0.00621547,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs1_chimp.marg.frame3,1909182301_L1PA16.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs1_chimp,marg,C-TerminusTruncated
37197,Q#2755 - >seq9402,specific,238827,509,771,5.12214e-66,222.166,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37198,Q#2755 - >seq9402,superfamily,295487,509,771,5.12214e-66,222.166,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37199,Q#2755 - >seq9402,specific,197310,9,235,1.39792e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37200,Q#2755 - >seq9402,superfamily,351117,9,235,1.39792e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37201,Q#2755 - >seq9402,non-specific,197306,9,235,5.839569999999999e-38,142.62,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37202,Q#2755 - >seq9402,specific,333820,515,771,4.85563e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37203,Q#2755 - >seq9402,superfamily,333820,515,771,4.85563e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37204,Q#2755 - >seq9402,non-specific,197307,9,235,5.86707e-22,96.5881,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37205,Q#2755 - >seq9402,non-specific,197320,9,220,1.55856e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37206,Q#2755 - >seq9402,non-specific,223780,9,236,3.55599e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37207,Q#2755 - >seq9402,non-specific,197321,7,235,1.3947899999999998e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37208,Q#2755 - >seq9402,specific,335306,10,228,8.097439999999999e-16,77.6705,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37209,Q#2755 - >seq9402,non-specific,273186,9,236,1.27563e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37210,Q#2755 - >seq9402,non-specific,238828,515,736,1.7219100000000002e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37211,Q#2755 - >seq9402,non-specific,197319,13,235,4.07616e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37212,Q#2755 - >seq9402,non-specific,272954,9,206,5.79866e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37213,Q#2755 - >seq9402,non-specific,275209,586,799,2.46086e-10,63.6308,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37214,Q#2755 - >seq9402,superfamily,275209,586,799,2.46086e-10,63.6308,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37215,Q#2755 - >seq9402,non-specific,197336,9,193,3.90136e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37216,Q#2755 - >seq9402,non-specific,197322,8,235,1.65955e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37217,Q#2755 - >seq9402,non-specific,339261,108,231,3.3302600000000003e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37218,Q#2755 - >seq9402,non-specific,236970,9,214,4.0658300000000005e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37219,Q#2755 - >seq9402,non-specific,197311,30,235,0.00012395,44.5901,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37220,Q#2755 - >seq9402,non-specific,235175,290,468,0.000309904,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37221,Q#2755 - >seq9402,superfamily,235175,290,468,0.000309904,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37222,Q#2755 - >seq9402,non-specific,238185,655,769,0.00036124599999999996,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs2_gorilla,marg,CompleteHit
37223,Q#2755 - >seq9402,non-specific,274009,306,457,0.00127774,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37224,Q#2755 - >seq9402,superfamily,274009,306,457,0.00127774,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs2_gorilla.marg.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37225,Q#2758 - >seq9405,specific,197310,9,133,8.810639999999999e-34,130.164,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37226,Q#2758 - >seq9405,superfamily,351117,9,133,8.810639999999999e-34,130.164,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37227,Q#2758 - >seq9405,non-specific,197306,9,132,5.007390000000001e-22,96.3964,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37228,Q#2758 - >seq9405,non-specific,197307,9,123,8.325330000000001e-12,66.5425,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37229,Q#2758 - >seq9405,non-specific,197321,7,130,1.6327000000000002e-10,62.5696,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37230,Q#2758 - >seq9405,non-specific,223780,9,123,1.8714299999999999e-10,62.6159,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37231,Q#2758 - >seq9405,non-specific,197320,9,123,8.08175e-09,57.525,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37232,Q#2758 - >seq9405,non-specific,273186,9,123,1.63514e-06,50.7404,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37233,Q#2758 - >seq9405,specific,335306,10,121,2.31253e-06,49.9362,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37234,Q#2758 - >seq9405,non-specific,272954,9,120,3.95372e-06,49.3037,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37235,Q#2758 - >seq9405,non-specific,197336,9,126,1.1536800000000001e-05,47.9923,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37236,Q#2758 - >seq9405,non-specific,197319,13,120,8.0258e-05,45.3453,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37237,Q#2758 - >seq9405,non-specific,197318,9,53,0.00860562,39.2019,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA16.ORF2.hs2_gorilla.pars.frame3,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37238,Q#2760 - >seq9407,specific,238827,503,765,2.620809999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37239,Q#2760 - >seq9407,superfamily,295487,503,765,2.620809999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37240,Q#2760 - >seq9407,specific,333820,509,765,3.96444e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37241,Q#2760 - >seq9407,superfamily,333820,509,765,3.96444e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37242,Q#2760 - >seq9407,non-specific,197310,132,230,5.73378e-18,84.3253,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37243,Q#2760 - >seq9407,superfamily,351117,132,230,5.73378e-18,84.3253,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37244,Q#2760 - >seq9407,non-specific,238828,509,730,1.4938099999999999e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37245,Q#2760 - >seq9407,non-specific,275209,580,793,2.56925e-10,63.6308,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37246,Q#2760 - >seq9407,superfamily,275209,580,793,2.56925e-10,63.6308,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37247,Q#2760 - >seq9407,non-specific,197306,127,230,6.71834e-09,57.8765,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37248,Q#2760 - >seq9407,non-specific,197320,128,215,3.80674e-05,46.3542,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37249,Q#2760 - >seq9407,non-specific,238185,649,763,0.000306317,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA16,ORF2,hs2_gorilla,pars,CompleteHit
37250,Q#2760 - >seq9407,non-specific,235175,285,462,0.000609783,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA16,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37251,Q#2760 - >seq9407,superfamily,235175,285,462,0.000609783,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA16,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37252,Q#2760 - >seq9407,non-specific,197307,126,230,0.00106156,41.8897,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37253,Q#2760 - >seq9407,non-specific,197321,126,230,0.0013247,41.7688,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37254,Q#2760 - >seq9407,non-specific,339261,130,226,0.00187534,39.2427,pfam14529,Exo_endo_phos_2,N,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37255,Q#2760 - >seq9407,non-specific,197322,131,230,0.00228233,41.5338,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37256,Q#2760 - >seq9407,non-specific,223780,127,231,0.00405704,40.2743,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37257,Q#2760 - >seq9407,non-specific,335306,127,223,0.00587869,39.5358,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37258,Q#2760 - >seq9407,non-specific,222878,298,457,0.00799068,39.9977,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37259,Q#2760 - >seq9407,superfamily,222878,298,457,0.00799068,39.9977,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37260,Q#2760 - >seq9407,non-specific,197319,126,230,0.00857159,39.1821,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs2_gorilla.pars.frame2,1909182311_L1PA16.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA16,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37261,Q#2761 - >seq9408,specific,238827,507,768,5.540369999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37262,Q#2761 - >seq9408,superfamily,295487,507,768,5.540369999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37263,Q#2761 - >seq9408,specific,197310,8,234,1.6230000000000002e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37264,Q#2761 - >seq9408,superfamily,351117,8,234,1.6230000000000002e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37265,Q#2761 - >seq9408,non-specific,197306,8,234,2.96497e-38,143.391,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37266,Q#2761 - >seq9408,specific,333820,513,768,8.8843e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37267,Q#2761 - >seq9408,superfamily,333820,513,768,8.8843e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37268,Q#2761 - >seq9408,non-specific,197307,8,234,1.93498e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37269,Q#2761 - >seq9408,non-specific,223780,8,235,6.0213400000000005e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37270,Q#2761 - >seq9408,non-specific,197321,6,234,6.42317e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37271,Q#2761 - >seq9408,non-specific,197320,8,219,1.62882e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37272,Q#2761 - >seq9408,specific,335306,9,227,4.51608e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37273,Q#2761 - >seq9408,non-specific,273186,8,235,7.094840000000001e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37274,Q#2761 - >seq9408,non-specific,197319,12,234,5.5183500000000005e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37275,Q#2761 - >seq9408,non-specific,238828,513,733,6.8671e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37276,Q#2761 - >seq9408,non-specific,272954,8,205,7.208340000000001e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37277,Q#2761 - >seq9408,non-specific,197336,8,192,1.27052e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37278,Q#2761 - >seq9408,non-specific,275209,464,796,1.40401e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37279,Q#2761 - >seq9408,superfamily,275209,464,796,1.40401e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37280,Q#2761 - >seq9408,non-specific,236970,8,213,2.39025e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37281,Q#2761 - >seq9408,non-specific,339261,107,230,2.84348e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37282,Q#2761 - >seq9408,non-specific,238185,653,766,0.000287528,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37283,Q#2761 - >seq9408,non-specific,197311,29,234,0.00034693,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs3_orang,pars,CompleteHit
37284,Q#2761 - >seq9408,non-specific,235175,289,466,0.000936851,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,BothTerminiTruncated
37285,Q#2761 - >seq9408,superfamily,235175,289,466,0.000936851,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,BothTerminiTruncated
37286,Q#2761 - >seq9408,non-specific,274009,305,455,0.000978677,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,C-TerminusTruncated
37287,Q#2761 - >seq9408,superfamily,274009,305,455,0.000978677,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,C-TerminusTruncated
37288,Q#2761 - >seq9408,non-specific,274008,261,380,0.00342517,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,N-TerminusTruncated
37289,Q#2761 - >seq9408,superfamily,274008,261,380,0.00342517,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,N-TerminusTruncated
37290,Q#2761 - >seq9408,non-specific,223496,224,443,0.00807495,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs3_orang,pars,BothTerminiTruncated
37291,Q#2761 - >seq9408,superfamily,223496,224,443,0.00807495,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1PA16,ORF2,hs3_orang,pars,BothTerminiTruncated
37292,Q#2761 - >seq9408,non-specific,274009,299,455,0.00959555,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.pars.frame1,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs3_orang,pars,BothTerminiTruncated
37293,Q#2766 - >seq9413,specific,238827,508,769,6.114739999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37294,Q#2766 - >seq9413,superfamily,295487,508,769,6.114739999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37295,Q#2766 - >seq9413,specific,197310,9,235,1.7553599999999995e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37296,Q#2766 - >seq9413,superfamily,351117,9,235,1.7553599999999995e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37297,Q#2766 - >seq9413,non-specific,197306,9,235,2.96767e-38,143.391,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37298,Q#2766 - >seq9413,specific,333820,514,769,9.153469999999998e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37299,Q#2766 - >seq9413,superfamily,333820,514,769,9.153469999999998e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37300,Q#2766 - >seq9413,non-specific,197307,9,235,1.9552499999999998e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37301,Q#2766 - >seq9413,non-specific,223780,9,236,5.97005e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37302,Q#2766 - >seq9413,non-specific,197321,7,235,6.429069999999999e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37303,Q#2766 - >seq9413,non-specific,197320,9,220,1.6614999999999998e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37304,Q#2766 - >seq9413,specific,335306,10,228,4.520109999999999e-16,78.4409,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37305,Q#2766 - >seq9413,non-specific,273186,9,236,7.1013099999999994e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37306,Q#2766 - >seq9413,non-specific,197319,13,235,5.5233800000000005e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37307,Q#2766 - >seq9413,non-specific,238828,514,734,7.07054e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37308,Q#2766 - >seq9413,non-specific,272954,9,206,7.2149e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37309,Q#2766 - >seq9413,non-specific,197336,9,193,1.27166e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37310,Q#2766 - >seq9413,non-specific,275209,465,797,1.41789e-09,61.3196,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37311,Q#2766 - >seq9413,superfamily,275209,465,797,1.41789e-09,61.3196,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37312,Q#2766 - >seq9413,non-specific,236970,9,214,2.39242e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37313,Q#2766 - >seq9413,non-specific,339261,108,231,2.8458400000000002e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37314,Q#2766 - >seq9413,non-specific,238185,654,767,0.000293428,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37315,Q#2766 - >seq9413,non-specific,197311,30,235,0.00035044599999999997,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs3_orang,marg,CompleteHit
37316,Q#2766 - >seq9413,non-specific,235175,290,467,0.0009377000000000001,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,BothTerminiTruncated
37317,Q#2766 - >seq9413,superfamily,235175,290,467,0.0009377000000000001,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,BothTerminiTruncated
37318,Q#2766 - >seq9413,non-specific,274009,306,456,0.000987883,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,C-TerminusTruncated
37319,Q#2766 - >seq9413,superfamily,274009,306,456,0.000987883,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,C-TerminusTruncated
37320,Q#2766 - >seq9413,non-specific,274008,262,381,0.00342826,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,N-TerminusTruncated
37321,Q#2766 - >seq9413,superfamily,274008,262,381,0.00342826,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,N-TerminusTruncated
37322,Q#2766 - >seq9413,non-specific,223496,225,444,0.00815095,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA16,ORF2,hs3_orang,marg,BothTerminiTruncated
37323,Q#2766 - >seq9413,superfamily,223496,225,444,0.00815095,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA16,ORF2,hs3_orang,marg,BothTerminiTruncated
37324,Q#2766 - >seq9413,non-specific,274009,300,456,0.00968567,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs3_orang.marg.frame3,1909182324_L1PA16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs3_orang,marg,BothTerminiTruncated
37325,Q#2768 - >seq9415,specific,238827,509,771,2.0663599999999997e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37326,Q#2768 - >seq9415,superfamily,295487,509,771,2.0663599999999997e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37327,Q#2768 - >seq9415,specific,197310,9,236,1.89701e-57,198.34400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37328,Q#2768 - >seq9415,superfamily,351117,9,236,1.89701e-57,198.34400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37329,Q#2768 - >seq9415,non-specific,197306,9,236,8.48935e-38,141.85,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37330,Q#2768 - >seq9415,specific,333820,515,771,2.38767e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37331,Q#2768 - >seq9415,superfamily,333820,515,771,2.38767e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37332,Q#2768 - >seq9415,non-specific,197321,7,236,1.1099999999999998e-19,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37333,Q#2768 - >seq9415,non-specific,197307,9,236,1.63494e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37334,Q#2768 - >seq9415,non-specific,223780,9,194,2.18519e-19,89.1947,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,C-TerminusTruncated
37335,Q#2768 - >seq9415,non-specific,197320,9,194,1.29994e-18,86.8001,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,C-TerminusTruncated
37336,Q#2768 - >seq9415,specific,335306,10,229,1.25543e-14,74.2037,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37337,Q#2768 - >seq9415,non-specific,273186,9,237,5.5046900000000005e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37338,Q#2768 - >seq9415,non-specific,197319,13,236,1.37304e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37339,Q#2768 - >seq9415,non-specific,272954,9,194,2.7742e-12,68.1785,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,C-TerminusTruncated
37340,Q#2768 - >seq9415,non-specific,238828,515,736,2.83444e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37341,Q#2768 - >seq9415,non-specific,197336,9,194,4.51775e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37342,Q#2768 - >seq9415,non-specific,275209,466,799,1.2734799999999999e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37343,Q#2768 - >seq9415,superfamily,275209,466,799,1.2734799999999999e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37344,Q#2768 - >seq9415,non-specific,236970,9,194,2.39891e-08,56.441,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs4_gibbon,marg,C-TerminusTruncated
37345,Q#2768 - >seq9415,non-specific,197322,8,236,1.28117e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37346,Q#2768 - >seq9415,non-specific,238185,655,769,0.00011207799999999999,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37347,Q#2768 - >seq9415,non-specific,235175,291,468,0.000514982,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37348,Q#2768 - >seq9415,superfamily,235175,291,468,0.000514982,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37349,Q#2768 - >seq9415,non-specific,339261,108,232,0.000706386,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37350,Q#2768 - >seq9415,non-specific,274008,263,382,0.0021411,42.3511,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37351,Q#2768 - >seq9415,superfamily,274008,263,382,0.0021411,42.3511,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37352,Q#2768 - >seq9415,non-specific,197311,30,236,0.00227127,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs4_gibbon,marg,CompleteHit
37353,Q#2768 - >seq9415,non-specific,274009,301,457,0.00259718,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37354,Q#2768 - >seq9415,superfamily,274009,301,457,0.00259718,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37355,Q#2768 - >seq9415,non-specific,274009,307,457,0.00594757,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.marg.frame3,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs4_gibbon,marg,C-TerminusTruncated
37356,Q#2771 - >seq9418,specific,238827,508,770,2.0834399999999997e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37357,Q#2771 - >seq9418,superfamily,295487,508,770,2.0834399999999997e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37358,Q#2771 - >seq9418,specific,197310,8,235,1.85881e-57,198.34400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37359,Q#2771 - >seq9418,superfamily,351117,8,235,1.85881e-57,198.34400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37360,Q#2771 - >seq9418,non-specific,197306,8,235,8.64633e-38,141.85,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37361,Q#2771 - >seq9418,specific,333820,514,770,2.47955e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37362,Q#2771 - >seq9418,superfamily,333820,514,770,2.47955e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37363,Q#2771 - >seq9418,non-specific,197321,6,235,1.11955e-19,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37364,Q#2771 - >seq9418,non-specific,197307,8,235,1.6647199999999999e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37365,Q#2771 - >seq9418,non-specific,223780,8,193,2.2673300000000003e-19,89.1947,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
37366,Q#2771 - >seq9418,non-specific,197320,8,193,1.3235600000000001e-18,86.8001,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
37367,Q#2771 - >seq9418,specific,335306,9,228,1.25431e-14,74.2037,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37368,Q#2771 - >seq9418,non-specific,273186,8,236,5.60374e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37369,Q#2771 - >seq9418,non-specific,197319,12,235,1.43739e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37370,Q#2771 - >seq9418,non-specific,272954,8,193,2.87702e-12,68.1785,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
37371,Q#2771 - >seq9418,non-specific,238828,514,735,2.9685e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37372,Q#2771 - >seq9418,non-specific,197336,8,193,4.5137e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37373,Q#2771 - >seq9418,non-specific,275209,465,798,1.2722899999999999e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37374,Q#2771 - >seq9418,superfamily,275209,465,798,1.2722899999999999e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37375,Q#2771 - >seq9418,non-specific,236970,8,193,2.37495e-08,56.441,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
37376,Q#2771 - >seq9418,non-specific,197322,7,235,1.28e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37377,Q#2771 - >seq9418,non-specific,238185,654,768,0.00011198700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37378,Q#2771 - >seq9418,non-specific,235175,290,467,0.000518896,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37379,Q#2771 - >seq9418,superfamily,235175,290,467,0.000518896,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37380,Q#2771 - >seq9418,non-specific,339261,107,231,0.000692302,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37381,Q#2771 - >seq9418,non-specific,274008,262,381,0.00215733,42.3511,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37382,Q#2771 - >seq9418,superfamily,274008,262,381,0.00215733,42.3511,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37383,Q#2771 - >seq9418,non-specific,197311,29,235,0.00226931,40.7381,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs4_gibbon,pars,CompleteHit
37384,Q#2771 - >seq9418,non-specific,274009,300,456,0.0026390999999999997,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37385,Q#2771 - >seq9418,superfamily,274009,300,456,0.0026390999999999997,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37386,Q#2771 - >seq9418,non-specific,274009,306,456,0.0060948999999999995,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs4_gibbon.pars.frame1,1909182327_L1PA16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
37387,Q#2775 - >seq9422,specific,238827,506,768,6.803839999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37388,Q#2775 - >seq9422,superfamily,295487,506,768,6.803839999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37389,Q#2775 - >seq9422,specific,197310,6,233,2.3963e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37390,Q#2775 - >seq9422,superfamily,351117,6,233,2.3963e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37391,Q#2775 - >seq9422,non-specific,197306,6,233,5.459739999999999e-39,145.317,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37392,Q#2775 - >seq9422,specific,333820,512,768,8.72193e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37393,Q#2775 - >seq9422,superfamily,333820,512,768,8.72193e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37394,Q#2775 - >seq9422,non-specific,197307,6,233,1.38371e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37395,Q#2775 - >seq9422,non-specific,197321,4,233,1.62978e-20,92.23,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37396,Q#2775 - >seq9422,non-specific,223780,6,234,1.0322700000000001e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37397,Q#2775 - >seq9422,non-specific,197320,6,218,2.59329e-19,88.7261,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37398,Q#2775 - >seq9422,specific,335306,7,226,1.6349100000000001e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37399,Q#2775 - >seq9422,non-specific,273186,6,234,1.65297e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37400,Q#2775 - >seq9422,non-specific,197319,10,233,6.2982e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37401,Q#2775 - >seq9422,non-specific,272954,6,204,2.96886e-13,70.8749,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37402,Q#2775 - >seq9422,non-specific,238828,512,733,8.91526e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37403,Q#2775 - >seq9422,non-specific,236970,6,212,3.3616599999999995e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37404,Q#2775 - >seq9422,non-specific,197336,6,191,3.92339e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37405,Q#2775 - >seq9422,non-specific,197322,5,233,7.76717e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37406,Q#2775 - >seq9422,non-specific,275209,583,796,2.10354e-08,57.4676,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
37407,Q#2775 - >seq9422,superfamily,275209,583,796,2.10354e-08,57.4676,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
37408,Q#2775 - >seq9422,non-specific,339261,105,229,1.80599e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37409,Q#2775 - >seq9422,non-specific,197311,27,233,2.3120100000000002e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37410,Q#2775 - >seq9422,non-specific,235175,288,465,2.4244099999999997e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37411,Q#2775 - >seq9422,superfamily,235175,288,465,2.4244099999999997e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37412,Q#2775 - >seq9422,non-specific,238185,652,766,0.00011853700000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs5_gmonkey,pars,CompleteHit
37413,Q#2775 - >seq9422,non-specific,224117,296,463,0.00396593,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
37414,Q#2775 - >seq9422,superfamily,224117,296,463,0.00396593,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
37415,Q#2775 - >seq9422,non-specific,274009,298,473,0.00412369,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37416,Q#2775 - >seq9422,superfamily,274009,298,473,0.00412369,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37417,Q#2775 - >seq9422,non-specific,274009,304,448,0.00838904,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
37418,Q#2775 - >seq9422,non-specific,274009,260,445,0.00985084,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.pars.frame3,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
37419,Q#2776 - >seq9423,specific,238827,508,770,6.272959999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37420,Q#2776 - >seq9423,superfamily,295487,508,770,6.272959999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37421,Q#2776 - >seq9423,specific,197310,8,235,2.1640899999999996e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37422,Q#2776 - >seq9423,superfamily,351117,8,235,2.1640899999999996e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37423,Q#2776 - >seq9423,non-specific,197306,8,235,5.1228000000000004e-39,145.702,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37424,Q#2776 - >seq9423,specific,333820,514,770,8.3397e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37425,Q#2776 - >seq9423,superfamily,333820,514,770,8.3397e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37426,Q#2776 - >seq9423,non-specific,197307,8,235,1.37565e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37427,Q#2776 - >seq9423,non-specific,197321,6,235,1.53063e-20,92.23,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37428,Q#2776 - >seq9423,non-specific,223780,8,236,9.161760000000001e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37429,Q#2776 - >seq9423,non-specific,197320,8,220,2.39012e-19,88.7261,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37430,Q#2776 - >seq9423,specific,335306,9,228,1.6407499999999998e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37431,Q#2776 - >seq9423,non-specific,273186,8,236,1.5390100000000002e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37432,Q#2776 - >seq9423,non-specific,197319,12,235,6.44076e-14,72.6945,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37433,Q#2776 - >seq9423,non-specific,272954,8,206,2.7648600000000003e-13,70.8749,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37434,Q#2776 - >seq9423,non-specific,238828,514,735,8.53588e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37435,Q#2776 - >seq9423,non-specific,236970,8,214,3.02091e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Exonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37436,Q#2776 - >seq9423,non-specific,197336,8,193,3.76001e-09,58.7779,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37437,Q#2776 - >seq9423,non-specific,197322,7,235,7.79582e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37438,Q#2776 - >seq9423,non-specific,275209,585,798,2.07436e-08,57.4676,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
37439,Q#2776 - >seq9423,superfamily,275209,585,798,2.07436e-08,57.4676,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
37440,Q#2776 - >seq9423,non-specific,339261,107,231,1.79453e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease_RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37441,Q#2776 - >seq9423,non-specific,197311,29,235,2.29862e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Endonuclease,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37442,Q#2776 - >seq9423,non-specific,235175,290,467,2.4333899999999998e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37443,Q#2776 - >seq9423,superfamily,235175,290,467,2.4333899999999998e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37444,Q#2776 - >seq9423,non-specific,238185,654,768,0.000114378,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA16,ORF2,hs5_gmonkey,marg,CompleteHit
37445,Q#2776 - >seq9423,non-specific,224117,298,465,0.00398018,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
37446,Q#2776 - >seq9423,superfamily,224117,298,465,0.00398018,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ATPase_ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
37447,Q#2776 - >seq9423,non-specific,274009,300,475,0.00403486,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37448,Q#2776 - >seq9423,superfamily,274009,300,475,0.00403486,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37449,Q#2776 - >seq9423,non-specific,274009,306,450,0.00834819,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
37450,Q#2776 - >seq9423,non-specific,274009,262,447,0.00980283,40.0511,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA16.ORF2.hs5_gmonkey.marg.frame1,1909182333_L1PA16.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,ChromSeg,L1PA16,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
37451,Q#2779 - >seq9426,non-specific,227489,32,385,0.0025964,41.8181,COG5160,ULP1,C,cl27325,"Protease, Ulp1 family  [Posttranslational modification, protein turnover, chaperones]; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].",L1PA16.ORF2.hs6_sqmonkey.marg.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
37452,Q#2779 - >seq9426,superfamily,227489,32,385,0.0025964,41.8181,cl27325,ULP1 superfamily,C, - ,"Protease, Ulp1 family  [Posttranslational modification, protein turnover, chaperones]; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].",L1PA16.ORF2.hs6_sqmonkey.marg.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
37453,Q#2780 - >seq9427,specific,238827,510,772,3.969679999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37454,Q#2780 - >seq9427,superfamily,295487,510,772,3.969679999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37455,Q#2780 - >seq9427,specific,197310,9,236,1.70276e-57,198.34400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37456,Q#2780 - >seq9427,superfamily,351117,9,236,1.70276e-57,198.34400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37457,Q#2780 - >seq9427,non-specific,197306,9,236,3.95754e-37,139.924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37458,Q#2780 - >seq9427,specific,333820,516,772,2.31013e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37459,Q#2780 - >seq9427,superfamily,333820,516,772,2.31013e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37460,Q#2780 - >seq9427,non-specific,223780,9,237,6.70086e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37461,Q#2780 - >seq9427,non-specific,197321,7,236,1.8703e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37462,Q#2780 - >seq9427,non-specific,197307,9,236,1.97732e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37463,Q#2780 - >seq9427,non-specific,197320,9,194,3.2966900000000003e-19,88.3409,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
37464,Q#2780 - >seq9427,non-specific,273186,9,237,3.90476e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37465,Q#2780 - >seq9427,specific,335306,10,229,1.3816299999999999e-14,74.2037,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37466,Q#2780 - >seq9427,non-specific,272954,9,194,3.49128e-13,70.8749,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
37467,Q#2780 - >seq9427,non-specific,197319,13,236,5.244859999999999e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37468,Q#2780 - >seq9427,non-specific,238828,516,737,1.26716e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37469,Q#2780 - >seq9427,non-specific,236970,9,194,1.5947800000000002e-09,59.9078,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
37470,Q#2780 - >seq9427,non-specific,275209,467,800,2.3784e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37471,Q#2780 - >seq9427,superfamily,275209,467,800,2.3784e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37472,Q#2780 - >seq9427,non-specific,197336,9,194,5.63869e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37473,Q#2780 - >seq9427,non-specific,238185,656,770,4.90957e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37474,Q#2780 - >seq9427,non-specific,235175,291,469,0.00034231699999999997,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
37475,Q#2780 - >seq9427,superfamily,235175,291,469,0.00034231699999999997,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
37476,Q#2780 - >seq9427,specific,225881,483,680,0.00225259,41.3629,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
37477,Q#2780 - >seq9427,superfamily,225881,483,680,0.00225259,41.3629,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
37478,Q#2780 - >seq9427,non-specific,339261,108,232,0.00234436,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37479,Q#2780 - >seq9427,non-specific,224117,301,467,0.00557045,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
37480,Q#2780 - >seq9427,superfamily,224117,301,467,0.00557045,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
37481,Q#2780 - >seq9427,non-specific,197311,30,203,0.00818927,38.8121,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs6_sqmonkey.marg.frame3,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,marg,CompleteHit
37482,Q#2782 - >seq9429,specific,238827,509,771,4.15929e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37483,Q#2782 - >seq9429,superfamily,295487,509,771,4.15929e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37484,Q#2782 - >seq9429,specific,197310,8,235,1.7009100000000002e-57,198.34400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37485,Q#2782 - >seq9429,superfamily,351117,8,235,1.7009100000000002e-57,198.34400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37486,Q#2782 - >seq9429,non-specific,197306,8,235,3.99207e-37,139.924,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37487,Q#2782 - >seq9429,specific,333820,515,771,2.44581e-34,130.105,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37488,Q#2782 - >seq9429,superfamily,333820,515,771,2.44581e-34,130.105,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37489,Q#2782 - >seq9429,non-specific,223780,8,236,7.01895e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37490,Q#2782 - >seq9429,non-specific,197321,6,235,1.90431e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37491,Q#2782 - >seq9429,non-specific,197307,8,235,2.0713699999999998e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37492,Q#2782 - >seq9429,non-specific,197320,8,193,3.29362e-19,88.3409,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
37493,Q#2782 - >seq9429,non-specific,273186,8,236,3.86466e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37494,Q#2782 - >seq9429,specific,335306,9,228,1.3803799999999998e-14,74.2037,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37495,Q#2782 - >seq9429,non-specific,272954,8,193,3.75896e-13,70.4897,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
37496,Q#2782 - >seq9429,non-specific,197319,12,235,5.19124e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37497,Q#2782 - >seq9429,non-specific,238828,515,736,1.26601e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37498,Q#2782 - >seq9429,non-specific,236970,8,193,1.6378099999999997e-09,59.9078,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
37499,Q#2782 - >seq9429,non-specific,275209,466,799,2.44032e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37500,Q#2782 - >seq9429,superfamily,275209,466,799,2.44032e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37501,Q#2782 - >seq9429,non-specific,197336,8,193,5.63354e-09,58.0075,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37502,Q#2782 - >seq9429,non-specific,238185,655,769,4.9055e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37503,Q#2782 - >seq9429,non-specific,235175,290,468,0.000353801,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
37504,Q#2782 - >seq9429,superfamily,235175,290,468,0.000353801,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
37505,Q#2782 - >seq9429,specific,225881,482,679,0.00231031,41.3629,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
37506,Q#2782 - >seq9429,superfamily,225881,482,679,0.00231031,41.3629,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA16,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
37507,Q#2782 - >seq9429,non-specific,339261,107,231,0.0023199,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37508,Q#2782 - >seq9429,non-specific,224117,300,466,0.00566029,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA16,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
37509,Q#2782 - >seq9429,superfamily,224117,300,466,0.00566029,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA16,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
37510,Q#2782 - >seq9429,non-specific,197311,29,202,0.00818212,38.8121,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs6_sqmonkey.pars.frame1,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA16,ORF2,hs6_sqmonkey,pars,CompleteHit
37511,Q#2783 - >seq9430,non-specific,227489,31,384,0.00263857,41.8181,COG5160,ULP1,C,cl27325,"Protease, Ulp1 family  [Posttranslational modification, protein turnover, chaperones]; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].",L1PA16.ORF2.hs6_sqmonkey.pars.frame2,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
37512,Q#2783 - >seq9430,superfamily,227489,31,384,0.00263857,41.8181,cl27325,ULP1 superfamily,C, - ,"Protease, Ulp1 family  [Posttranslational modification, protein turnover, chaperones]; Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].",L1PA16.ORF2.hs6_sqmonkey.pars.frame2,1909182337_L1PA16.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PA16,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
37513,Q#2786 - >seq9433,specific,238827,510,772,2.7457199999999994e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37514,Q#2786 - >seq9433,superfamily,295487,510,772,2.7457199999999994e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37515,Q#2786 - >seq9433,specific,197310,9,236,3.8231e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37516,Q#2786 - >seq9433,superfamily,351117,9,236,3.8231e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37517,Q#2786 - >seq9433,non-specific,197306,9,236,1.0561499999999999e-36,138.768,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37518,Q#2786 - >seq9433,specific,333820,516,772,1.3659999999999999e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37519,Q#2786 - >seq9433,superfamily,333820,516,772,1.3659999999999999e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37520,Q#2786 - >seq9433,non-specific,197321,7,236,1.8551100000000002e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37521,Q#2786 - >seq9433,non-specific,197307,9,236,3.00431e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37522,Q#2786 - >seq9433,non-specific,223780,9,237,8.143759999999999e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37523,Q#2786 - >seq9433,non-specific,197320,9,194,1.83689e-17,83.3333,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,marg,C-TerminusTruncated
37524,Q#2786 - >seq9433,non-specific,273186,9,237,1.0192399999999999e-14,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37525,Q#2786 - >seq9433,specific,335306,10,229,3.59975e-14,73.0481,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37526,Q#2786 - >seq9433,non-specific,272954,9,194,2.12055e-12,68.5637,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,C-TerminusTruncated
37527,Q#2786 - >seq9433,non-specific,197319,13,236,5.52627e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37528,Q#2786 - >seq9433,non-specific,238828,516,737,1.71358e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37529,Q#2786 - >seq9433,non-specific,197336,9,194,2.6747300000000003e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37530,Q#2786 - >seq9433,non-specific,236970,9,237,9.371870000000001e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,marg,CompleteHit
37531,Q#2786 - >seq9433,non-specific,275209,467,800,4.2107799999999995e-07,53.2304,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37532,Q#2786 - >seq9433,superfamily,275209,467,800,4.2107799999999995e-07,53.2304,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37533,Q#2786 - >seq9433,non-specific,238185,656,770,0.00011902200000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA16,ORF2,hs0_human,marg,CompleteHit
37534,Q#2786 - >seq9433,non-specific,235175,291,469,0.000174255,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,marg,BothTerminiTruncated
37535,Q#2786 - >seq9433,superfamily,235175,291,469,0.000174255,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,marg,BothTerminiTruncated
37536,Q#2786 - >seq9433,non-specific,224117,299,467,0.00165353,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,marg,N-TerminusTruncated
37537,Q#2786 - >seq9433,superfamily,224117,299,467,0.00165353,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs0_human.marg.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs0_human,marg,N-TerminusTruncated
37538,Q#2788 - >seq9435,specific,238827,508,770,2.6081499999999998e-64,217.15900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37539,Q#2788 - >seq9435,superfamily,295487,508,770,2.6081499999999998e-64,217.15900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37540,Q#2788 - >seq9435,specific,197310,8,235,3.81513e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37541,Q#2788 - >seq9435,superfamily,351117,8,235,3.81513e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37542,Q#2788 - >seq9435,non-specific,197306,8,235,1.05423e-36,138.768,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37543,Q#2788 - >seq9435,specific,333820,514,770,1.31195e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37544,Q#2788 - >seq9435,superfamily,333820,514,770,1.31195e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37545,Q#2788 - >seq9435,non-specific,197321,6,235,1.73289e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37546,Q#2788 - >seq9435,non-specific,197307,8,235,2.97055e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37547,Q#2788 - >seq9435,non-specific,223780,8,236,8.28387e-19,87.6539,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37548,Q#2788 - >seq9435,non-specific,197320,8,193,1.88622e-17,83.3333,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,pars,C-TerminusTruncated
37549,Q#2788 - >seq9435,non-specific,273186,8,236,1.0173899999999999e-14,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37550,Q#2788 - >seq9435,specific,335306,9,228,3.59336e-14,73.0481,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37551,Q#2788 - >seq9435,non-specific,272954,8,193,2.11672e-12,68.5637,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,C-TerminusTruncated
37552,Q#2788 - >seq9435,non-specific,197319,12,235,5.62014e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37553,Q#2788 - >seq9435,non-specific,238828,514,735,1.7267e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37554,Q#2788 - >seq9435,non-specific,197336,8,193,2.6454e-09,59.1631,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37555,Q#2788 - >seq9435,non-specific,236970,8,236,9.354969999999999e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA16,ORF2,hs0_human,pars,CompleteHit
37556,Q#2788 - >seq9435,non-specific,275209,465,798,4.2030299999999995e-07,53.2304,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37557,Q#2788 - >seq9435,superfamily,275209,465,798,4.2030299999999995e-07,53.2304,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37558,Q#2788 - >seq9435,non-specific,235175,290,467,6.28631e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,pars,BothTerminiTruncated
37559,Q#2788 - >seq9435,superfamily,235175,290,467,6.28631e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,pars,BothTerminiTruncated
37560,Q#2788 - >seq9435,non-specific,238185,654,768,0.000118828,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA16,ORF2,hs0_human,pars,CompleteHit
37561,Q#2788 - >seq9435,non-specific,224117,298,465,0.0026953000000000003,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA16,ORF2,hs0_human,pars,N-TerminusTruncated
37562,Q#2788 - >seq9435,superfamily,224117,298,465,0.0026953000000000003,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA16,ORF2,hs0_human,pars,N-TerminusTruncated
37563,Q#2788 - >seq9435,non-specific,130902,283,391,0.00545361,40.3782,TIGR01843,type_I_hlyD,NC,cl31145,"type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA16,ORF2,hs0_human,pars,BothTerminiTruncated
37564,Q#2788 - >seq9435,superfamily,130902,283,391,0.00545361,40.3782,cl31145,type_I_hlyD superfamily,NC, - ,"type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking]",L1PA16.ORF2.hs0_human.pars.frame3,1909182338_L1PA16.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA16,ORF2,hs0_human,pars,BothTerminiTruncated
37565,Q#2792 - >seq9439,specific,238827,509,766,1.3116599999999997e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37566,Q#2792 - >seq9439,superfamily,295487,509,766,1.3116599999999997e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37567,Q#2792 - >seq9439,specific,197310,9,236,1.4868399999999997e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37568,Q#2792 - >seq9439,superfamily,351117,9,236,1.4868399999999997e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37569,Q#2792 - >seq9439,non-specific,197306,9,236,1.1977799999999999e-33,129.909,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37570,Q#2792 - >seq9439,specific,333820,515,766,3.02088e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37571,Q#2792 - >seq9439,superfamily,333820,515,766,3.02088e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37572,Q#2792 - >seq9439,non-specific,197307,9,236,2.4798400000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37573,Q#2792 - >seq9439,non-specific,223780,9,237,1.02678e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37574,Q#2792 - >seq9439,non-specific,197321,7,236,3.6578e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37575,Q#2792 - >seq9439,non-specific,197320,9,229,1.7188499999999998e-17,83.3333,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37576,Q#2792 - >seq9439,specific,335306,10,229,3.02231e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37577,Q#2792 - >seq9439,non-specific,273186,9,237,7.23361e-14,72.6968,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37578,Q#2792 - >seq9439,non-specific,197319,13,236,1.0196600000000001e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37579,Q#2792 - >seq9439,non-specific,238828,580,732,1.40699e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37580,Q#2792 - >seq9439,non-specific,272954,9,207,4.77662e-10,61.2449,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37581,Q#2792 - >seq9439,non-specific,197322,8,236,1.1202400000000001e-07,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37582,Q#2792 - >seq9439,non-specific,275209,585,794,3.0057500000000003e-07,54.0008,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37583,Q#2792 - >seq9439,superfamily,275209,585,794,3.0057500000000003e-07,54.0008,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37584,Q#2792 - >seq9439,non-specific,197336,9,194,1.19488e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37585,Q#2792 - >seq9439,non-specific,236970,9,237,1.73834e-06,50.663000000000004,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37586,Q#2792 - >seq9439,non-specific,235175,291,468,3.0260500000000003e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37587,Q#2792 - >seq9439,superfamily,235175,291,468,3.0260500000000003e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37588,Q#2792 - >seq9439,non-specific,238185,654,736,0.000440964,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37589,Q#2792 - >seq9439,non-specific,223496,320,555,0.00122324,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37590,Q#2792 - >seq9439,superfamily,223496,320,555,0.00122324,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37591,Q#2792 - >seq9439,non-specific,339261,108,232,0.00125456,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37592,Q#2792 - >seq9439,specific,225881,481,679,0.0018927,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37593,Q#2792 - >seq9439,superfamily,225881,481,679,0.0018927,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37594,Q#2792 - >seq9439,non-specific,274009,294,455,0.0028474,41.9771,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37595,Q#2792 - >seq9439,superfamily,274009,294,455,0.0028474,41.9771,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37596,Q#2792 - >seq9439,non-specific,223266,211,464,0.00748436,40.333,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37597,Q#2792 - >seq9439,superfamily,223266,211,464,0.00748436,40.333,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs1_chimp,marg,BothTerminiTruncated
37598,Q#2792 - >seq9439,non-specific,224117,299,466,0.00981809,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37599,Q#2792 - >seq9439,superfamily,224117,299,466,0.00981809,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs1_chimp.marg.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs1_chimp,marg,N-TerminusTruncated
37600,Q#2793 - >seq9440,specific,311990,1140,1158,0.00237102,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs1_chimp.marg.frame1,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37601,Q#2793 - >seq9440,superfamily,311990,1140,1158,0.00237102,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs1_chimp.marg.frame1,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA17,ORF2,hs1_chimp,marg,CompleteHit
37602,Q#2794 - >seq9441,specific,311990,1119,1137,0.00161957,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs1_chimp.pars.frame1,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37603,Q#2794 - >seq9441,superfamily,311990,1119,1137,0.00161957,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs1_chimp.pars.frame1,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37604,Q#2796 - >seq9443,specific,238827,509,766,7.209929999999999e-63,213.30700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37605,Q#2796 - >seq9443,superfamily,295487,509,766,7.209929999999999e-63,213.30700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37606,Q#2796 - >seq9443,specific,197310,9,236,2.4319399999999997e-57,197.959,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37607,Q#2796 - >seq9443,superfamily,351117,9,236,2.4319399999999997e-57,197.959,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37608,Q#2796 - >seq9443,non-specific,197306,9,236,2.59815e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37609,Q#2796 - >seq9443,specific,333820,515,766,1.2201699999999999e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37610,Q#2796 - >seq9443,superfamily,333820,515,766,1.2201699999999999e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37611,Q#2796 - >seq9443,non-specific,197307,9,236,1.2283199999999999e-19,89.6545,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37612,Q#2796 - >seq9443,non-specific,223780,9,237,6.112580000000001e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37613,Q#2796 - >seq9443,non-specific,197321,7,236,2.1960500000000003e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37614,Q#2796 - >seq9443,specific,335306,10,229,3.28074e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37615,Q#2796 - >seq9443,non-specific,197320,9,229,3.85902e-17,82.5629,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37616,Q#2796 - >seq9443,non-specific,273186,9,237,2.90928e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37617,Q#2796 - >seq9443,non-specific,197319,13,236,7.084110000000001e-12,66.9165,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37618,Q#2796 - >seq9443,non-specific,238828,580,732,3.39237e-11,64.1444,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37619,Q#2796 - >seq9443,non-specific,272954,9,207,1.3414500000000002e-09,60.0893,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37620,Q#2796 - >seq9443,non-specific,197322,8,236,1.1690799999999999e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37621,Q#2796 - >seq9443,non-specific,275209,585,794,6.01527e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37622,Q#2796 - >seq9443,superfamily,275209,585,794,6.01527e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37623,Q#2796 - >seq9443,non-specific,197336,9,194,1.3786000000000002e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37624,Q#2796 - >seq9443,non-specific,236970,9,237,2.72504e-06,50.2778,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37625,Q#2796 - >seq9443,non-specific,235175,291,468,3.80117e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,pars,BothTerminiTruncated
37626,Q#2796 - >seq9443,superfamily,235175,291,468,3.80117e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,pars,BothTerminiTruncated
37627,Q#2796 - >seq9443,non-specific,223496,320,555,0.000747174,43.5955,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs1_chimp,pars,BothTerminiTruncated
37628,Q#2796 - >seq9443,superfamily,223496,320,555,0.000747174,43.5955,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs1_chimp,pars,BothTerminiTruncated
37629,Q#2796 - >seq9443,non-specific,238185,654,736,0.0008761089999999999,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37630,Q#2796 - >seq9443,non-specific,339261,108,232,0.00137477,39.6279,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs1_chimp,pars,CompleteHit
37631,Q#2796 - >seq9443,non-specific,274009,294,455,0.00228235,42.3623,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37632,Q#2796 - >seq9443,superfamily,274009,294,455,0.00228235,42.3623,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37633,Q#2796 - >seq9443,non-specific,224117,299,466,0.00754326,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37634,Q#2796 - >seq9443,superfamily,224117,299,466,0.00754326,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37635,Q#2796 - >seq9443,specific,225881,481,679,0.00790037,39.8221,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37636,Q#2796 - >seq9443,superfamily,225881,481,679,0.00790037,39.8221,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA17.ORF2.hs1_chimp.pars.frame3,1909182341_L1PA17.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs1_chimp,pars,N-TerminusTruncated
37637,Q#2799 - >seq9446,specific,238827,508,767,1.5668199999999996e-61,209.455,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37638,Q#2799 - >seq9446,superfamily,295487,508,767,1.5668199999999996e-61,209.455,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37639,Q#2799 - >seq9446,specific,197310,9,235,9.59994e-56,193.33700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37640,Q#2799 - >seq9446,superfamily,351117,9,235,9.59994e-56,193.33700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37641,Q#2799 - >seq9446,non-specific,197306,9,235,2.7684e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37642,Q#2799 - >seq9446,specific,333820,514,767,2.2302599999999996e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37643,Q#2799 - >seq9446,superfamily,333820,514,767,2.2302599999999996e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37644,Q#2799 - >seq9446,non-specific,223780,9,236,3.08687e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37645,Q#2799 - >seq9446,non-specific,197320,9,228,6.50641e-18,84.4889,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37646,Q#2799 - >seq9446,non-specific,197307,9,235,2.8233999999999997e-16,79.6393,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37647,Q#2799 - >seq9446,specific,335306,10,228,3.56837e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37648,Q#2799 - >seq9446,non-specific,197321,7,235,1.35829e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37649,Q#2799 - >seq9446,non-specific,273186,9,236,1.7146099999999998e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37650,Q#2799 - >seq9446,non-specific,272954,9,206,3.37261e-11,64.7117,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37651,Q#2799 - >seq9446,non-specific,197319,13,235,4.21234e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37652,Q#2799 - >seq9446,non-specific,238828,579,734,1.4467099999999999e-09,59.522,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37653,Q#2799 - >seq9446,non-specific,236970,9,193,3.02713e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37654,Q#2799 - >seq9446,non-specific,235175,290,467,8.29377e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37655,Q#2799 - >seq9446,superfamily,235175,290,467,8.29377e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37656,Q#2799 - >seq9446,non-specific,197336,9,193,2.42133e-05,47.2219,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37657,Q#2799 - >seq9446,non-specific,275209,584,795,4.92471e-05,46.681999999999995,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37658,Q#2799 - >seq9446,superfamily,275209,584,795,4.92471e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37659,Q#2799 - >seq9446,non-specific,223496,315,554,0.000553195,43.9807,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37660,Q#2799 - >seq9446,superfamily,223496,315,554,0.000553195,43.9807,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37661,Q#2799 - >seq9446,specific,311990,1231,1249,0.00647533,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37662,Q#2799 - >seq9446,superfamily,311990,1231,1249,0.00647533,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37663,Q#2799 - >seq9446,non-specific,238185,653,738,0.00707771,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs2_gorilla.pars.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,pars,CompleteHit
37664,Q#2802 - >seq9449,specific,238827,508,767,1.76865e-61,209.07,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37665,Q#2802 - >seq9449,superfamily,295487,508,767,1.76865e-61,209.07,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37666,Q#2802 - >seq9449,specific,197310,9,235,9.73137e-56,193.33700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37667,Q#2802 - >seq9449,superfamily,351117,9,235,9.73137e-56,193.33700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37668,Q#2802 - >seq9449,non-specific,197306,9,235,3.0292099999999997e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37669,Q#2802 - >seq9449,specific,333820,514,767,2.32616e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37670,Q#2802 - >seq9449,superfamily,333820,514,767,2.32616e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37671,Q#2802 - >seq9449,non-specific,223780,9,236,3.15731e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37672,Q#2802 - >seq9449,non-specific,197320,9,228,6.530319999999999e-18,84.4889,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37673,Q#2802 - >seq9449,non-specific,197307,9,235,2.9150299999999996e-16,79.6393,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37674,Q#2802 - >seq9449,specific,335306,10,228,3.6152900000000004e-15,75.7445,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37675,Q#2802 - >seq9449,non-specific,197321,7,235,1.3505200000000002e-14,74.896,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37676,Q#2802 - >seq9449,non-specific,273186,9,236,1.78652e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37677,Q#2802 - >seq9449,non-specific,272954,9,206,3.48056e-11,64.7117,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37678,Q#2802 - >seq9449,non-specific,197319,13,235,4.38783e-11,64.6053,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37679,Q#2802 - >seq9449,non-specific,238828,579,734,1.5071800000000002e-09,59.522,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37680,Q#2802 - >seq9449,non-specific,236970,9,193,3.3269399999999995e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37681,Q#2802 - >seq9449,non-specific,235175,290,467,8.75956e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37682,Q#2802 - >seq9449,superfamily,235175,290,467,8.75956e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37683,Q#2802 - >seq9449,non-specific,197336,9,193,2.42994e-05,47.2219,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37684,Q#2802 - >seq9449,non-specific,275209,584,795,5.0297200000000004e-05,46.681999999999995,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37685,Q#2802 - >seq9449,superfamily,275209,584,795,5.0297200000000004e-05,46.681999999999995,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37686,Q#2802 - >seq9449,non-specific,223496,315,554,0.000574359,43.9807,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37687,Q#2802 - >seq9449,superfamily,223496,315,554,0.000574359,43.9807,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37688,Q#2802 - >seq9449,specific,311990,1235,1253,0.00643219,34.9552,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37689,Q#2802 - >seq9449,superfamily,311990,1235,1253,0.00643219,34.9552,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37690,Q#2802 - >seq9449,non-specific,238185,653,738,0.00724063,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs2_gorilla.marg.frame3,1909182351_L1PA17.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs2_gorilla,marg,CompleteHit
37691,Q#2803 - >seq9450,specific,238827,510,772,4.001409999999999e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37692,Q#2803 - >seq9450,superfamily,295487,510,772,4.001409999999999e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37693,Q#2803 - >seq9450,specific,197310,9,236,7.526519999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37694,Q#2803 - >seq9450,superfamily,351117,9,236,7.526519999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37695,Q#2803 - >seq9450,non-specific,197306,9,236,5.7183199999999994e-36,136.842,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37696,Q#2803 - >seq9450,specific,333820,516,772,9.13237e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37697,Q#2803 - >seq9450,superfamily,333820,516,772,9.13237e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37698,Q#2803 - >seq9450,non-specific,223780,9,237,4.85536e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37699,Q#2803 - >seq9450,non-specific,197307,9,236,5.95368e-21,93.5065,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37700,Q#2803 - >seq9450,non-specific,197320,9,229,7.49187e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37701,Q#2803 - >seq9450,non-specific,197321,7,236,1.16024e-20,92.6152,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37702,Q#2803 - >seq9450,specific,335306,10,229,8.22184e-19,86.5301,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37703,Q#2803 - >seq9450,non-specific,273186,9,237,4.04891e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37704,Q#2803 - >seq9450,non-specific,272954,9,207,8.39319e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37705,Q#2803 - >seq9450,non-specific,197319,13,236,1.65357e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37706,Q#2803 - >seq9450,non-specific,238828,582,737,2.78616e-11,64.5296,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,N-TerminusTruncated
37707,Q#2803 - >seq9450,non-specific,236970,9,194,5.64873e-09,58.367,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,marg,C-TerminusTruncated
37708,Q#2803 - >seq9450,non-specific,197336,9,194,3.78389e-08,55.6963,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37709,Q#2803 - >seq9450,non-specific,275209,587,800,1.86726e-07,54.386,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,N-TerminusTruncated
37710,Q#2803 - >seq9450,superfamily,275209,587,800,1.86726e-07,54.386,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,N-TerminusTruncated
37711,Q#2803 - >seq9450,non-specific,339261,108,232,5.6104e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37712,Q#2803 - >seq9450,non-specific,197311,35,204,0.000139526,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37713,Q#2803 - >seq9450,non-specific,197314,7,192,0.000407243,43.4863,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA17,ORF2,hs3_orang,marg,C-TerminusTruncated
37714,Q#2803 - >seq9450,non-specific,238185,656,770,0.000892702,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37715,Q#2803 - >seq9450,non-specific,214017,261,414,0.00393595,39.2912,cd12924,iSH2_PIK3R1, - ,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37716,Q#2803 - >seq9450,superfamily,355389,261,414,0.00393595,39.2912,cl25402,iSH2_PI3K_IA_R superfamily, - , - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37717,Q#2803 - >seq9450,non-specific,224117,299,467,0.0039396,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs3_orang,marg,N-TerminusTruncated
37718,Q#2803 - >seq9450,superfamily,224117,299,467,0.0039396,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs3_orang,marg,N-TerminusTruncated
37719,Q#2803 - >seq9450,specific,311990,1237,1255,0.0054534,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37720,Q#2803 - >seq9450,superfamily,311990,1237,1255,0.0054534,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs3_orang.marg.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs3_orang,marg,CompleteHit
37721,Q#2808 - >seq9455,specific,238827,510,772,4.034149999999999e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37722,Q#2808 - >seq9455,superfamily,295487,510,772,4.034149999999999e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37723,Q#2808 - >seq9455,specific,197310,9,236,6.89133e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37724,Q#2808 - >seq9455,superfamily,351117,9,236,6.89133e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37725,Q#2808 - >seq9455,non-specific,197306,9,236,5.658459999999999e-36,136.842,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37726,Q#2808 - >seq9455,specific,333820,516,772,9.39263e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37727,Q#2808 - >seq9455,superfamily,333820,516,772,9.39263e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37728,Q#2808 - >seq9455,non-specific,223780,9,237,4.89709e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37729,Q#2808 - >seq9455,non-specific,197307,9,236,5.94823e-21,93.5065,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37730,Q#2808 - >seq9455,non-specific,197320,9,229,7.485009999999999e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37731,Q#2808 - >seq9455,non-specific,197321,7,236,1.1482299999999999e-20,92.6152,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37732,Q#2808 - >seq9455,specific,335306,10,229,8.2145e-19,86.5301,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37733,Q#2808 - >seq9455,non-specific,273186,9,237,3.96991e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37734,Q#2808 - >seq9455,non-specific,272954,9,207,8.23038e-13,69.7193,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37735,Q#2808 - >seq9455,non-specific,197319,13,236,1.6064200000000001e-12,68.8425,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37736,Q#2808 - >seq9455,non-specific,238828,582,737,2.80996e-11,64.5296,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,N-TerminusTruncated
37737,Q#2808 - >seq9455,non-specific,236970,9,194,5.74796e-09,58.367,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs3_orang,pars,C-TerminusTruncated
37738,Q#2808 - >seq9455,non-specific,197336,9,194,3.74594e-08,55.6963,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37739,Q#2808 - >seq9455,non-specific,275209,587,800,1.8987100000000002e-07,54.386,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,N-TerminusTruncated
37740,Q#2808 - >seq9455,superfamily,275209,587,800,1.8987100000000002e-07,54.386,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,N-TerminusTruncated
37741,Q#2808 - >seq9455,non-specific,339261,108,232,5.49837e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37742,Q#2808 - >seq9455,non-specific,197311,35,204,0.000135595,44.2049,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37743,Q#2808 - >seq9455,non-specific,197314,7,192,0.000406887,43.4863,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA17,ORF2,hs3_orang,pars,C-TerminusTruncated
37744,Q#2808 - >seq9455,non-specific,238185,656,770,0.0008919739999999999,39.6416,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37745,Q#2808 - >seq9455,non-specific,214017,261,414,0.00393263,39.2912,cd12924,iSH2_PIK3R1, - ,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37746,Q#2808 - >seq9455,superfamily,355389,261,414,0.00393263,39.2912,cl25402,iSH2_PI3K_IA_R superfamily, - , - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37747,Q#2808 - >seq9455,non-specific,224117,299,467,0.00393607,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs3_orang,pars,N-TerminusTruncated
37748,Q#2808 - >seq9455,superfamily,224117,299,467,0.00393607,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs3_orang,pars,N-TerminusTruncated
37749,Q#2808 - >seq9455,specific,311990,1236,1254,0.00550284,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37750,Q#2808 - >seq9455,superfamily,311990,1236,1254,0.00550284,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs3_orang.pars.frame3,1909182355_L1PA17.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs3_orang,pars,CompleteHit
37751,Q#2809 - >seq9456,specific,238827,510,772,2.9281899999999994e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37752,Q#2809 - >seq9456,superfamily,295487,510,772,2.9281899999999994e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37753,Q#2809 - >seq9456,specific,197310,9,236,6.018709999999998e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37754,Q#2809 - >seq9456,superfamily,351117,9,236,6.018709999999998e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37755,Q#2809 - >seq9456,non-specific,197306,9,236,2.6926299999999997e-34,131.835,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37756,Q#2809 - >seq9456,specific,333820,516,772,2.86585e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37757,Q#2809 - >seq9456,superfamily,333820,516,772,2.86585e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37758,Q#2809 - >seq9456,non-specific,197307,9,236,1.87661e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37759,Q#2809 - >seq9456,non-specific,223780,9,237,1.87492e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37760,Q#2809 - >seq9456,non-specific,197320,9,229,3.3838499999999997e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37761,Q#2809 - >seq9456,non-specific,197321,7,236,1.84499e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37762,Q#2809 - >seq9456,specific,335306,10,229,1.5457799999999998e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37763,Q#2809 - >seq9456,non-specific,273186,9,237,5.06846e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37764,Q#2809 - >seq9456,non-specific,197319,13,236,1.29725e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37765,Q#2809 - >seq9456,non-specific,272954,9,207,2.86604e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37766,Q#2809 - >seq9456,non-specific,238828,582,737,1.8533599999999997e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37767,Q#2809 - >seq9456,non-specific,197322,8,236,1.95741e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37768,Q#2809 - >seq9456,non-specific,275209,587,800,1.02409e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37769,Q#2809 - >seq9456,superfamily,275209,587,800,1.02409e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37770,Q#2809 - >seq9456,non-specific,236970,9,237,5.43647e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37771,Q#2809 - >seq9456,non-specific,197336,9,194,1.1912899999999999e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37772,Q#2809 - >seq9456,non-specific,238185,656,770,0.00035686800000000004,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37773,Q#2809 - >seq9456,non-specific,224117,263,467,0.00239011,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA17,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37774,Q#2809 - >seq9456,superfamily,224117,263,467,0.00239011,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs4_gibbon,marg,N-TerminusTruncated
37775,Q#2809 - >seq9456,non-specific,339261,108,232,0.00280391,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37776,Q#2809 - >seq9456,non-specific,223496,316,500,0.00474318,41.2843,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37777,Q#2809 - >seq9456,superfamily,223496,316,500,0.00474318,41.2843,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37778,Q#2809 - >seq9456,non-specific,214017,261,414,0.00546424,38.906,cd12924,iSH2_PIK3R1, - ,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37779,Q#2809 - >seq9456,superfamily,355389,261,414,0.00546424,38.906,cl25402,iSH2_PI3K_IA_R superfamily, - , - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37780,Q#2809 - >seq9456,specific,311990,1238,1256,0.00577924,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37781,Q#2809 - >seq9456,superfamily,311990,1238,1256,0.00577924,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA17,ORF2,hs4_gibbon,marg,CompleteHit
37782,Q#2809 - >seq9456,non-specific,223266,211,408,0.00786701,40.333,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA17,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37783,Q#2809 - >seq9456,superfamily,223266,211,408,0.00786701,40.333,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.marg.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,marg,BothTerminiTruncated
37784,Q#2814 - >seq9461,specific,238827,510,772,3.0689999999999994e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37785,Q#2814 - >seq9461,superfamily,295487,510,772,3.0689999999999994e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37786,Q#2814 - >seq9461,specific,197310,9,236,6.129249999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37787,Q#2814 - >seq9461,superfamily,351117,9,236,6.129249999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37788,Q#2814 - >seq9461,non-specific,197306,9,236,2.51524e-34,131.835,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37789,Q#2814 - >seq9461,specific,333820,516,772,2.89113e-31,121.245,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37790,Q#2814 - >seq9461,superfamily,333820,516,772,2.89113e-31,121.245,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37791,Q#2814 - >seq9461,non-specific,197307,9,236,1.73778e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37792,Q#2814 - >seq9461,non-specific,223780,9,237,1.8036599999999998e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37793,Q#2814 - >seq9461,non-specific,197320,9,229,3.41291e-19,88.3409,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37794,Q#2814 - >seq9461,non-specific,197321,7,236,1.8259500000000003e-18,86.45200000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37795,Q#2814 - >seq9461,specific,335306,10,229,1.5444000000000002e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37796,Q#2814 - >seq9461,non-specific,273186,9,237,4.83147e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37797,Q#2814 - >seq9461,non-specific,197319,13,236,1.27202e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37798,Q#2814 - >seq9461,non-specific,272954,9,207,2.8106999999999997e-11,65.0969,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37799,Q#2814 - >seq9461,non-specific,238828,582,737,1.83444e-10,62.2184,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37800,Q#2814 - >seq9461,non-specific,197322,8,236,1.9206099999999996e-09,60.4086,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37801,Q#2814 - >seq9461,non-specific,275209,587,800,1.0141500000000001e-07,55.1564,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37802,Q#2814 - >seq9461,superfamily,275209,587,800,1.0141500000000001e-07,55.1564,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37803,Q#2814 - >seq9461,non-specific,236970,9,237,5.38253e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37804,Q#2814 - >seq9461,non-specific,197336,9,194,1.16872e-06,51.0739,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37805,Q#2814 - >seq9461,non-specific,238185,656,770,0.000349694,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37806,Q#2814 - >seq9461,non-specific,224117,263,467,0.00249108,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA17,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37807,Q#2814 - >seq9461,superfamily,224117,263,467,0.00249108,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA17,ORF2,hs4_gibbon,pars,N-TerminusTruncated
37808,Q#2814 - >seq9461,non-specific,339261,108,232,0.00282875,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37809,Q#2814 - >seq9461,non-specific,223496,316,500,0.00486095,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA17,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37810,Q#2814 - >seq9461,superfamily,223496,316,500,0.00486095,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA17,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37811,Q#2814 - >seq9461,non-specific,214017,261,414,0.00540858,38.906,cd12924,iSH2_PIK3R1, - ,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37812,Q#2814 - >seq9461,superfamily,355389,261,414,0.00540858,38.906,cl25402,iSH2_PI3K_IA_R superfamily, - , - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37813,Q#2814 - >seq9461,specific,311990,1237,1255,0.00600565,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37814,Q#2814 - >seq9461,superfamily,311990,1237,1255,0.00600565,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA17,ORF2,hs4_gibbon,pars,CompleteHit
37815,Q#2814 - >seq9461,non-specific,223266,211,408,0.00779357,40.333,COG0188,GyrA,NC,cl33798,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PA17,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37816,Q#2814 - >seq9461,superfamily,223266,211,408,0.00779357,40.333,cl33798,GyrA superfamily,NC, - ,"DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]; Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair].",L1PA17.ORF2.hs4_gibbon.pars.frame3,1909182359_L1PA17.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA17,ORF2,hs4_gibbon,pars,BothTerminiTruncated
37817,Q#2817 - >seq9464,specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37818,Q#2817 - >seq9464,superfamily,295487,510,772,4.797929999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37819,Q#2817 - >seq9464,non-specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37820,Q#2817 - >seq9464,specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37821,Q#2817 - >seq9464,superfamily,351117,9,236,3.722229999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37822,Q#2817 - >seq9464,non-specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37823,Q#2817 - >seq9464,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37824,Q#2817 - >seq9464,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37825,Q#2817 - >seq9464,specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37826,Q#2817 - >seq9464,superfamily,333820,516,772,2.6306099999999997e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37827,Q#2817 - >seq9464,non-specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37828,Q#2817 - >seq9464,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37829,Q#2817 - >seq9464,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37830,Q#2817 - >seq9464,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37831,Q#2817 - >seq9464,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37832,Q#2817 - >seq9464,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37833,Q#2817 - >seq9464,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37834,Q#2817 - >seq9464,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37835,Q#2817 - >seq9464,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37836,Q#2817 - >seq9464,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37837,Q#2817 - >seq9464,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37838,Q#2817 - >seq9464,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37839,Q#2817 - >seq9464,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37840,Q#2817 - >seq9464,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37841,Q#2817 - >seq9464,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37842,Q#2817 - >seq9464,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37843,Q#2817 - >seq9464,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37844,Q#2817 - >seq9464,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37845,Q#2817 - >seq9464,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37846,Q#2817 - >seq9464,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37847,Q#2817 - >seq9464,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37848,Q#2817 - >seq9464,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37849,Q#2817 - >seq9464,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37850,Q#2817 - >seq9464,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37851,Q#2817 - >seq9464,superfamily,275209,467,800,4.2102600000000006e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37852,Q#2817 - >seq9464,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37853,Q#2817 - >seq9464,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37854,Q#2817 - >seq9464,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37855,Q#2817 - >seq9464,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37856,Q#2817 - >seq9464,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37857,Q#2817 - >seq9464,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37858,Q#2817 - >seq9464,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37859,Q#2817 - >seq9464,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37860,Q#2817 - >seq9464,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37861,Q#2817 - >seq9464,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37862,Q#2817 - >seq9464,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37863,Q#2817 - >seq9464,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37864,Q#2817 - >seq9464,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37865,Q#2817 - >seq9464,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37866,Q#2817 - >seq9464,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37867,Q#2817 - >seq9464,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37868,Q#2817 - >seq9464,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37869,Q#2817 - >seq9464,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37870,Q#2817 - >seq9464,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37871,Q#2817 - >seq9464,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37872,Q#2817 - >seq9464,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37873,Q#2817 - >seq9464,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37874,Q#2817 - >seq9464,superfamily,235175,295,464,0.00327835,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37875,Q#2817 - >seq9464,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
37876,Q#2817 - >seq9464,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37877,Q#2817 - >seq9464,superfamily,274008,263,500,0.00539502,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37878,Q#2817 - >seq9464,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,pars,N-TerminusTruncated
37879,Q#2817 - >seq9464,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37880,Q#2817 - >seq9464,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,pars,CompleteHit
37881,Q#2817 - >seq9464,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37882,Q#2817 - >seq9464,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37883,Q#2817 - >seq9464,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.pars.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
37884,Q#2820 - >seq9467,specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37885,Q#2820 - >seq9467,superfamily,295487,510,772,4.797929999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37886,Q#2820 - >seq9467,non-specific,238827,510,772,4.797929999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37887,Q#2820 - >seq9467,specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37888,Q#2820 - >seq9467,superfamily,351117,9,236,3.722229999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37889,Q#2820 - >seq9467,non-specific,197310,9,236,3.722229999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37890,Q#2820 - >seq9467,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37891,Q#2820 - >seq9467,non-specific,197306,9,236,1.2479299999999998e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37892,Q#2820 - >seq9467,specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37893,Q#2820 - >seq9467,superfamily,333820,516,772,2.6306099999999997e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37894,Q#2820 - >seq9467,non-specific,333820,516,772,2.6306099999999997e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37895,Q#2820 - >seq9467,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37896,Q#2820 - >seq9467,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37897,Q#2820 - >seq9467,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37898,Q#2820 - >seq9467,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37899,Q#2820 - >seq9467,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37900,Q#2820 - >seq9467,non-specific,197320,8,236,1.64575e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37901,Q#2820 - >seq9467,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37902,Q#2820 - >seq9467,non-specific,197321,7,236,6.908670000000001e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37903,Q#2820 - >seq9467,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37904,Q#2820 - >seq9467,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37905,Q#2820 - >seq9467,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37906,Q#2820 - >seq9467,non-specific,273186,9,237,7.187000000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37907,Q#2820 - >seq9467,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37908,Q#2820 - >seq9467,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37909,Q#2820 - >seq9467,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37910,Q#2820 - >seq9467,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37911,Q#2820 - >seq9467,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37912,Q#2820 - >seq9467,non-specific,197336,7,235,2.72945e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37913,Q#2820 - >seq9467,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37914,Q#2820 - >seq9467,non-specific,238828,516,737,2.16946e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37915,Q#2820 - >seq9467,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37916,Q#2820 - >seq9467,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37917,Q#2820 - >seq9467,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37918,Q#2820 - >seq9467,superfamily,275209,467,800,4.2102600000000006e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37919,Q#2820 - >seq9467,non-specific,275209,467,800,4.2102600000000006e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37920,Q#2820 - >seq9467,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37921,Q#2820 - >seq9467,non-specific,236970,9,238,4.11373e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37922,Q#2820 - >seq9467,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37923,Q#2820 - >seq9467,non-specific,339261,108,232,1.64828e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37924,Q#2820 - >seq9467,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37925,Q#2820 - >seq9467,non-specific,197311,7,236,1.8774200000000001e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37926,Q#2820 - >seq9467,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37927,Q#2820 - >seq9467,non-specific,197317,139,229,1.3442e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37928,Q#2820 - >seq9467,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37929,Q#2820 - >seq9467,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37930,Q#2820 - >seq9467,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37931,Q#2820 - >seq9467,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37932,Q#2820 - >seq9467,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37933,Q#2820 - >seq9467,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37934,Q#2820 - >seq9467,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37935,Q#2820 - >seq9467,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37936,Q#2820 - >seq9467,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37937,Q#2820 - >seq9467,specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37938,Q#2820 - >seq9467,superfamily,311990,1241,1259,0.00201331,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37939,Q#2820 - >seq9467,non-specific,311990,1241,1259,0.00201331,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37940,Q#2820 - >seq9467,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37941,Q#2820 - >seq9467,superfamily,235175,295,464,0.00327835,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37942,Q#2820 - >seq9467,non-specific,235175,295,464,0.00327835,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
37943,Q#2820 - >seq9467,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37944,Q#2820 - >seq9467,superfamily,274008,263,500,0.00539502,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37945,Q#2820 - >seq9467,non-specific,274008,263,500,0.00539502,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs2_gorilla,marg,N-TerminusTruncated
37946,Q#2820 - >seq9467,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37947,Q#2820 - >seq9467,non-specific,239569,525,748,0.00820342,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs2_gorilla,marg,CompleteHit
37948,Q#2820 - >seq9467,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37949,Q#2820 - >seq9467,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37950,Q#2820 - >seq9467,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs2_gorilla.marg.frame3,1909190003_L1PA4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
37951,Q#2821 - >seq9468,specific,238827,510,772,5.444349999999999e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37952,Q#2821 - >seq9468,superfamily,295487,510,772,5.444349999999999e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37953,Q#2821 - >seq9468,specific,197310,9,236,3.9069599999999994e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37954,Q#2821 - >seq9468,superfamily,351117,9,236,3.9069599999999994e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37955,Q#2821 - >seq9468,non-specific,197306,9,236,1.2722499999999997e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37956,Q#2821 - >seq9468,specific,333820,516,772,1.6705599999999998e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37957,Q#2821 - >seq9468,superfamily,333820,516,772,1.6705599999999998e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37958,Q#2821 - >seq9468,non-specific,197307,9,236,1.95109e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37959,Q#2821 - >seq9468,non-specific,223780,9,238,1.2191100000000002e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37960,Q#2821 - >seq9468,non-specific,197320,8,236,1.6614600000000001e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37961,Q#2821 - >seq9468,non-specific,197321,7,236,6.84339e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37962,Q#2821 - >seq9468,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37963,Q#2821 - >seq9468,non-specific,273186,9,237,7.119299999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37964,Q#2821 - >seq9468,non-specific,272954,9,236,1.44923e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37965,Q#2821 - >seq9468,non-specific,197319,8,236,4.43421e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37966,Q#2821 - >seq9468,non-specific,197336,7,235,2.83324e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37967,Q#2821 - >seq9468,non-specific,238828,516,737,2.5453000000000003e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37968,Q#2821 - >seq9468,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37969,Q#2821 - >seq9468,non-specific,275209,467,800,2.0259700000000003e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37970,Q#2821 - >seq9468,superfamily,275209,467,800,2.0259700000000003e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37971,Q#2821 - >seq9468,non-specific,236970,9,238,4.07619e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37972,Q#2821 - >seq9468,non-specific,339261,108,232,1.66434e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37973,Q#2821 - >seq9468,non-specific,197311,7,236,2.06164e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,marg,CompleteHit
37974,Q#2821 - >seq9468,non-specific,197317,139,229,1.3565100000000001e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,marg,N-TerminusTruncated
37975,Q#2821 - >seq9468,non-specific,238185,656,772,0.00017763400000000003,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37976,Q#2821 - >seq9468,non-specific,274009,305,453,0.000905039,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,C-TerminusTruncated
37977,Q#2821 - >seq9468,superfamily,274009,305,453,0.000905039,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,C-TerminusTruncated
37978,Q#2821 - >seq9468,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,marg,N-TerminusTruncated
37979,Q#2821 - >seq9468,specific,311990,1241,1259,0.00199368,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs0_human,marg,CompleteHit
37980,Q#2821 - >seq9468,superfamily,311990,1241,1259,0.00199368,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA4,ORF2,hs0_human,marg,CompleteHit
37981,Q#2821 - >seq9468,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs0_human,marg,C-TerminusTruncated
37982,Q#2821 - >seq9468,non-specific,235175,295,464,0.0031423,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,BothTerminiTruncated
37983,Q#2821 - >seq9468,superfamily,235175,295,464,0.0031423,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,BothTerminiTruncated
37984,Q#2821 - >seq9468,non-specific,239569,525,748,0.00381912,39.8635,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA4,ORF2,hs0_human,marg,CompleteHit
37985,Q#2821 - >seq9468,non-specific,274008,263,500,0.00512821,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,N-TerminusTruncated
37986,Q#2821 - >seq9468,superfamily,274008,263,500,0.00512821,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,marg,N-TerminusTruncated
37987,Q#2821 - >seq9468,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs0_human,marg,C-TerminusTruncated
37988,Q#2821 - >seq9468,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs0_human.marg.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs0_human,marg,C-TerminusTruncated
37989,Q#2825 - >seq9472,specific,311990,1173,1191,0.000114768,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs0_human.pars.frame2,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA4,ORF2,hs0_human,pars,CompleteHit
37990,Q#2825 - >seq9472,superfamily,311990,1173,1191,0.000114768,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA4.ORF2.hs0_human.pars.frame2,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA4,ORF2,hs0_human,pars,CompleteHit
37991,Q#2826 - >seq9473,specific,238827,510,772,6.206169999999999e-68,227.55900000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
37992,Q#2826 - >seq9473,superfamily,295487,510,772,6.206169999999999e-68,227.55900000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
37993,Q#2826 - >seq9473,specific,197310,9,236,3.0566499999999996e-63,214.908,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
37994,Q#2826 - >seq9473,superfamily,351117,9,236,3.0566499999999996e-63,214.908,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
37995,Q#2826 - >seq9473,non-specific,197306,9,236,1.5048699999999997e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
37996,Q#2826 - >seq9473,specific,333820,516,772,3.37816e-36,135.498,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
37997,Q#2826 - >seq9473,superfamily,333820,516,772,3.37816e-36,135.498,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
37998,Q#2826 - >seq9473,non-specific,197307,9,236,7.908379999999999e-27,110.455,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
37999,Q#2826 - >seq9473,non-specific,223780,9,238,3.4225100000000004e-24,103.06200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38000,Q#2826 - >seq9473,non-specific,197320,8,236,7.65572e-22,96.0449,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38001,Q#2826 - >seq9473,non-specific,197321,7,236,2.84173e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38002,Q#2826 - >seq9473,specific,335306,10,229,1.3662000000000002e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38003,Q#2826 - >seq9473,non-specific,273186,9,237,3.8641999999999993e-19,88.1048,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38004,Q#2826 - >seq9473,non-specific,272954,9,236,7.391880000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38005,Q#2826 - >seq9473,non-specific,197319,8,236,1.61605e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38006,Q#2826 - >seq9473,non-specific,197336,7,235,2.13027e-12,68.4079,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38007,Q#2826 - >seq9473,non-specific,238828,516,737,1.09702e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38008,Q#2826 - >seq9473,non-specific,197322,9,236,2.83609e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38009,Q#2826 - >seq9473,non-specific,275209,467,800,5.76128e-11,65.5568,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38010,Q#2826 - >seq9473,superfamily,275209,467,800,5.76128e-11,65.5568,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38011,Q#2826 - >seq9473,non-specific,236970,9,238,2.8878899999999996e-09,59.1374,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38012,Q#2826 - >seq9473,non-specific,339261,108,232,2.74559e-08,53.1099,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38013,Q#2826 - >seq9473,non-specific,197311,7,236,1.73389e-07,53.0645,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA4,ORF2,hs0_human,pars,CompleteHit
38014,Q#2826 - >seq9473,non-specific,197317,139,229,1.25457e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,pars,N-TerminusTruncated
38015,Q#2826 - >seq9473,non-specific,238185,656,772,8.44054e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38016,Q#2826 - >seq9473,non-specific,274009,305,453,0.00069211,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38017,Q#2826 - >seq9473,superfamily,274009,305,453,0.00069211,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38018,Q#2826 - >seq9473,non-specific,235175,295,464,0.00163996,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,BothTerminiTruncated
38019,Q#2826 - >seq9473,superfamily,235175,295,464,0.00163996,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,BothTerminiTruncated
38020,Q#2826 - >seq9473,non-specific,226098,138,239,0.00170816,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA4,ORF2,hs0_human,pars,N-TerminusTruncated
38021,Q#2826 - >seq9473,non-specific,197314,7,192,0.0019424,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38022,Q#2826 - >seq9473,non-specific,239569,525,748,0.0031967,40.2487,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA4,ORF2,hs0_human,pars,CompleteHit
38023,Q#2826 - >seq9473,non-specific,274008,263,500,0.00464517,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,N-TerminusTruncated
38024,Q#2826 - >seq9473,superfamily,274008,263,500,0.00464517,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,N-TerminusTruncated
38025,Q#2826 - >seq9473,non-specific,224117,311,428,0.00907711,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38026,Q#2826 - >seq9473,superfamily,224117,311,428,0.00907711,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38027,Q#2826 - >seq9473,non-specific,293702,337,451,0.00957582,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38028,Q#2826 - >seq9473,superfamily,293702,337,451,0.00957582,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA4.ORF2.hs0_human.pars.frame3,1909190007_L1PA4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA4,ORF2,hs0_human,pars,C-TerminusTruncated
38029,Q#2827 - >seq9474,specific,238827,510,772,5.8277699999999994e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38030,Q#2827 - >seq9474,superfamily,295487,510,772,5.8277699999999994e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38031,Q#2827 - >seq9474,non-specific,238827,510,772,5.8277699999999994e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38032,Q#2827 - >seq9474,specific,197310,9,236,4.651199999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38033,Q#2827 - >seq9474,superfamily,351117,9,236,4.651199999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38034,Q#2827 - >seq9474,non-specific,197310,9,236,4.651199999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38035,Q#2827 - >seq9474,non-specific,197306,9,236,1.2845900000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38036,Q#2827 - >seq9474,non-specific,197306,9,236,1.2845900000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38037,Q#2827 - >seq9474,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38038,Q#2827 - >seq9474,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38039,Q#2827 - >seq9474,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38040,Q#2827 - >seq9474,non-specific,197307,9,236,2.14662e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38041,Q#2827 - >seq9474,non-specific,197307,9,236,2.14662e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38042,Q#2827 - >seq9474,non-specific,223780,9,238,1.2307600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38043,Q#2827 - >seq9474,non-specific,223780,9,238,1.2307600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38044,Q#2827 - >seq9474,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38045,Q#2827 - >seq9474,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38046,Q#2827 - >seq9474,non-specific,197321,7,236,7.0411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38047,Q#2827 - >seq9474,non-specific,197321,7,236,7.0411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38048,Q#2827 - >seq9474,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38049,Q#2827 - >seq9474,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38050,Q#2827 - >seq9474,non-specific,273186,9,237,7.119299999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38051,Q#2827 - >seq9474,non-specific,273186,9,237,7.119299999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38052,Q#2827 - >seq9474,non-specific,272954,9,236,1.42222e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38053,Q#2827 - >seq9474,non-specific,272954,9,236,1.42222e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38054,Q#2827 - >seq9474,non-specific,197319,8,236,4.27092e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38055,Q#2827 - >seq9474,non-specific,197319,8,236,4.27092e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38056,Q#2827 - >seq9474,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38057,Q#2827 - >seq9474,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38058,Q#2827 - >seq9474,non-specific,238828,516,737,2.49791e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38059,Q#2827 - >seq9474,non-specific,238828,516,737,2.49791e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38060,Q#2827 - >seq9474,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38061,Q#2827 - >seq9474,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38062,Q#2827 - >seq9474,non-specific,275209,467,800,4.4021499999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38063,Q#2827 - >seq9474,superfamily,275209,467,800,4.4021499999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38064,Q#2827 - >seq9474,non-specific,275209,467,800,4.4021499999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38065,Q#2827 - >seq9474,non-specific,236970,9,238,4.42669e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38066,Q#2827 - >seq9474,non-specific,236970,9,238,4.42669e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38067,Q#2827 - >seq9474,non-specific,339261,108,232,1.66434e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38068,Q#2827 - >seq9474,non-specific,339261,108,232,1.66434e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38069,Q#2827 - >seq9474,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38070,Q#2827 - >seq9474,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38071,Q#2827 - >seq9474,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38072,Q#2827 - >seq9474,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38073,Q#2827 - >seq9474,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38074,Q#2827 - >seq9474,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38075,Q#2827 - >seq9474,non-specific,274009,305,453,0.000936172,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38076,Q#2827 - >seq9474,superfamily,274009,305,453,0.000936172,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38077,Q#2827 - >seq9474,non-specific,274009,305,453,0.000936172,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38078,Q#2827 - >seq9474,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38079,Q#2827 - >seq9474,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38080,Q#2827 - >seq9474,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38081,Q#2827 - >seq9474,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38082,Q#2827 - >seq9474,specific,311990,1241,1259,0.00213521,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38083,Q#2827 - >seq9474,superfamily,311990,1241,1259,0.00213521,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38084,Q#2827 - >seq9474,non-specific,311990,1241,1259,0.00213521,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38085,Q#2827 - >seq9474,non-specific,235175,295,464,0.00369146,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38086,Q#2827 - >seq9474,superfamily,235175,295,464,0.00369146,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38087,Q#2827 - >seq9474,non-specific,235175,295,464,0.00369146,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38088,Q#2827 - >seq9474,non-specific,274008,263,500,0.00577249,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38089,Q#2827 - >seq9474,superfamily,274008,263,500,0.00577249,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38090,Q#2827 - >seq9474,non-specific,274008,263,500,0.00577249,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38091,Q#2827 - >seq9474,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38092,Q#2827 - >seq9474,superfamily,293702,337,451,0.00898393,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38093,Q#2827 - >seq9474,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38094,Q#2827 - >seq9474,non-specific,239569,525,748,0.00898406,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38095,Q#2827 - >seq9474,non-specific,239569,525,748,0.00898406,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs2_gorilla.marg.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,marg,CompleteHit
38096,Q#2832 - >seq9479,specific,238827,510,772,5.8277699999999994e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38097,Q#2832 - >seq9479,superfamily,295487,510,772,5.8277699999999994e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38098,Q#2832 - >seq9479,non-specific,238827,510,772,5.8277699999999994e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38099,Q#2832 - >seq9479,specific,197310,9,236,4.651199999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38100,Q#2832 - >seq9479,superfamily,351117,9,236,4.651199999999999e-63,214.523,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38101,Q#2832 - >seq9479,non-specific,197310,9,236,4.651199999999999e-63,214.523,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38102,Q#2832 - >seq9479,non-specific,197306,9,236,1.2845900000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38103,Q#2832 - >seq9479,non-specific,197306,9,236,1.2845900000000001e-54,190.385,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38104,Q#2832 - >seq9479,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38105,Q#2832 - >seq9479,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38106,Q#2832 - >seq9479,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38107,Q#2832 - >seq9479,non-specific,197307,9,236,2.14662e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38108,Q#2832 - >seq9479,non-specific,197307,9,236,2.14662e-26,109.3,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38109,Q#2832 - >seq9479,non-specific,223780,9,238,1.2307600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38110,Q#2832 - >seq9479,non-specific,223780,9,238,1.2307600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38111,Q#2832 - >seq9479,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38112,Q#2832 - >seq9479,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38113,Q#2832 - >seq9479,non-specific,197321,7,236,7.0411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38114,Q#2832 - >seq9479,non-specific,197321,7,236,7.0411e-21,93.3856,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38115,Q#2832 - >seq9479,specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38116,Q#2832 - >seq9479,non-specific,335306,10,229,1.38594e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38117,Q#2832 - >seq9479,non-specific,273186,9,237,7.119299999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38118,Q#2832 - >seq9479,non-specific,273186,9,237,7.119299999999999e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38119,Q#2832 - >seq9479,non-specific,272954,9,236,1.42222e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38120,Q#2832 - >seq9479,non-specific,272954,9,236,1.42222e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38121,Q#2832 - >seq9479,non-specific,197319,8,236,4.27092e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38122,Q#2832 - >seq9479,non-specific,197319,8,236,4.27092e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38123,Q#2832 - >seq9479,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38124,Q#2832 - >seq9479,non-specific,197336,7,235,2.60503e-12,68.0227,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38125,Q#2832 - >seq9479,non-specific,238828,516,737,2.49791e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38126,Q#2832 - >seq9479,non-specific,238828,516,737,2.49791e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38127,Q#2832 - >seq9479,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38128,Q#2832 - >seq9479,non-specific,197322,9,236,2.87884e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38129,Q#2832 - >seq9479,non-specific,275209,467,800,4.4021499999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38130,Q#2832 - >seq9479,superfamily,275209,467,800,4.4021499999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38131,Q#2832 - >seq9479,non-specific,275209,467,800,4.4021499999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38132,Q#2832 - >seq9479,non-specific,236970,9,238,4.42669e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38133,Q#2832 - >seq9479,non-specific,236970,9,238,4.42669e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38134,Q#2832 - >seq9479,non-specific,339261,108,232,1.66434e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38135,Q#2832 - >seq9479,non-specific,339261,108,232,1.66434e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38136,Q#2832 - >seq9479,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38137,Q#2832 - >seq9479,non-specific,197311,7,236,1.89507e-07,52.6793,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38138,Q#2832 - >seq9479,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38139,Q#2832 - >seq9479,non-specific,197317,139,229,1.36894e-06,51.0636,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38140,Q#2832 - >seq9479,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38141,Q#2832 - >seq9479,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38142,Q#2832 - >seq9479,non-specific,274009,305,453,0.000936172,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38143,Q#2832 - >seq9479,superfamily,274009,305,453,0.000936172,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38144,Q#2832 - >seq9479,non-specific,274009,305,453,0.000936172,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38145,Q#2832 - >seq9479,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38146,Q#2832 - >seq9479,non-specific,226098,138,239,0.00173233,41.6172,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38147,Q#2832 - >seq9479,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38148,Q#2832 - >seq9479,non-specific,197314,7,192,0.00198755,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38149,Q#2832 - >seq9479,specific,311990,1241,1259,0.00213521,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38150,Q#2832 - >seq9479,superfamily,311990,1241,1259,0.00213521,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38151,Q#2832 - >seq9479,non-specific,311990,1241,1259,0.00213521,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38152,Q#2832 - >seq9479,non-specific,235175,295,464,0.00369146,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38153,Q#2832 - >seq9479,superfamily,235175,295,464,0.00369146,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38154,Q#2832 - >seq9479,non-specific,235175,295,464,0.00369146,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38155,Q#2832 - >seq9479,non-specific,274008,263,500,0.00577249,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38156,Q#2832 - >seq9479,superfamily,274008,263,500,0.00577249,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38157,Q#2832 - >seq9479,non-specific,274008,263,500,0.00577249,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38158,Q#2832 - >seq9479,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38159,Q#2832 - >seq9479,superfamily,293702,337,451,0.00898393,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38160,Q#2832 - >seq9479,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38161,Q#2832 - >seq9479,non-specific,239569,525,748,0.00898406,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38162,Q#2832 - >seq9479,non-specific,239569,525,748,0.00898406,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs2_gorilla.pars.frame3,1909190019_L1PA5.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs2_gorilla,pars,CompleteHit
38163,Q#2835 - >seq9482,specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38164,Q#2835 - >seq9482,superfamily,295487,510,772,1.6302099999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38165,Q#2835 - >seq9482,non-specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38166,Q#2835 - >seq9482,specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38167,Q#2835 - >seq9482,superfamily,351117,9,236,1.3895299999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38168,Q#2835 - >seq9482,non-specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38169,Q#2835 - >seq9482,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38170,Q#2835 - >seq9482,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38171,Q#2835 - >seq9482,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38172,Q#2835 - >seq9482,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38173,Q#2835 - >seq9482,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38174,Q#2835 - >seq9482,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38175,Q#2835 - >seq9482,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38176,Q#2835 - >seq9482,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38177,Q#2835 - >seq9482,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38178,Q#2835 - >seq9482,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38179,Q#2835 - >seq9482,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38180,Q#2835 - >seq9482,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38181,Q#2835 - >seq9482,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38182,Q#2835 - >seq9482,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38183,Q#2835 - >seq9482,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38184,Q#2835 - >seq9482,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38185,Q#2835 - >seq9482,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38186,Q#2835 - >seq9482,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38187,Q#2835 - >seq9482,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38188,Q#2835 - >seq9482,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38189,Q#2835 - >seq9482,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38190,Q#2835 - >seq9482,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38191,Q#2835 - >seq9482,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38192,Q#2835 - >seq9482,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38193,Q#2835 - >seq9482,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38194,Q#2835 - >seq9482,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38195,Q#2835 - >seq9482,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38196,Q#2835 - >seq9482,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38197,Q#2835 - >seq9482,superfamily,275209,467,800,1.02596e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38198,Q#2835 - >seq9482,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38199,Q#2835 - >seq9482,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38200,Q#2835 - >seq9482,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38201,Q#2835 - >seq9482,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38202,Q#2835 - >seq9482,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38203,Q#2835 - >seq9482,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38204,Q#2835 - >seq9482,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38205,Q#2835 - >seq9482,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38206,Q#2835 - >seq9482,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38207,Q#2835 - >seq9482,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38208,Q#2835 - >seq9482,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38209,Q#2835 - >seq9482,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38210,Q#2835 - >seq9482,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38211,Q#2835 - >seq9482,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38212,Q#2835 - >seq9482,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38213,Q#2835 - >seq9482,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38214,Q#2835 - >seq9482,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38215,Q#2835 - >seq9482,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38216,Q#2835 - >seq9482,specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38217,Q#2835 - >seq9482,superfamily,311990,1241,1259,0.00205315,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38218,Q#2835 - >seq9482,non-specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,pars,CompleteHit
38219,Q#2835 - >seq9482,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38220,Q#2835 - >seq9482,superfamily,274008,157,500,0.00350553,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38221,Q#2835 - >seq9482,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,N-TerminusTruncated
38222,Q#2835 - >seq9482,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,BothTerminiTruncated
38223,Q#2835 - >seq9482,superfamily,235175,295,464,0.00375458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,BothTerminiTruncated
38224,Q#2835 - >seq9482,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,pars,BothTerminiTruncated
38225,Q#2835 - >seq9482,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38226,Q#2835 - >seq9482,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38227,Q#2835 - >seq9482,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.pars.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,pars,C-TerminusTruncated
38228,Q#2838 - >seq9485,specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38229,Q#2838 - >seq9485,superfamily,295487,510,772,1.6302099999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38230,Q#2838 - >seq9485,non-specific,238827,510,772,1.6302099999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38231,Q#2838 - >seq9485,specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38232,Q#2838 - >seq9485,superfamily,351117,9,236,1.3895299999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38233,Q#2838 - >seq9485,non-specific,197310,9,236,1.3895299999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38234,Q#2838 - >seq9485,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38235,Q#2838 - >seq9485,non-specific,197306,9,236,2.1841e-54,189.615,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38236,Q#2838 - >seq9485,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38237,Q#2838 - >seq9485,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38238,Q#2838 - >seq9485,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38239,Q#2838 - >seq9485,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38240,Q#2838 - >seq9485,non-specific,197307,9,236,3.2366000000000004e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38241,Q#2838 - >seq9485,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38242,Q#2838 - >seq9485,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38243,Q#2838 - >seq9485,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38244,Q#2838 - >seq9485,non-specific,197320,8,236,1.82702e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38245,Q#2838 - >seq9485,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38246,Q#2838 - >seq9485,non-specific,197321,7,236,2.67281e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38247,Q#2838 - >seq9485,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38248,Q#2838 - >seq9485,non-specific,273186,9,237,9.651719999999999e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38249,Q#2838 - >seq9485,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38250,Q#2838 - >seq9485,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38251,Q#2838 - >seq9485,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38252,Q#2838 - >seq9485,non-specific,272954,9,236,1.96953e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38253,Q#2838 - >seq9485,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38254,Q#2838 - >seq9485,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38255,Q#2838 - >seq9485,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38256,Q#2838 - >seq9485,non-specific,197336,7,235,6.01137e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38257,Q#2838 - >seq9485,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38258,Q#2838 - >seq9485,non-specific,238828,516,737,2.40575e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38259,Q#2838 - >seq9485,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38260,Q#2838 - >seq9485,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38261,Q#2838 - >seq9485,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38262,Q#2838 - >seq9485,superfamily,275209,467,800,1.02596e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38263,Q#2838 - >seq9485,non-specific,275209,467,800,1.02596e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38264,Q#2838 - >seq9485,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38265,Q#2838 - >seq9485,non-specific,236970,9,238,1.2138699999999999e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38266,Q#2838 - >seq9485,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38267,Q#2838 - >seq9485,non-specific,339261,108,232,2.13005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38268,Q#2838 - >seq9485,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38269,Q#2838 - >seq9485,non-specific,197311,7,236,1.50586e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38270,Q#2838 - >seq9485,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38271,Q#2838 - >seq9485,non-specific,197317,139,229,2.49797e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38272,Q#2838 - >seq9485,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38273,Q#2838 - >seq9485,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38274,Q#2838 - >seq9485,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38275,Q#2838 - >seq9485,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38276,Q#2838 - >seq9485,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38277,Q#2838 - >seq9485,superfamily,274009,305,453,0.0009441219999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38278,Q#2838 - >seq9485,non-specific,274009,305,453,0.0009441219999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38279,Q#2838 - >seq9485,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38280,Q#2838 - >seq9485,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38281,Q#2838 - >seq9485,specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38282,Q#2838 - >seq9485,superfamily,311990,1241,1259,0.00205315,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38283,Q#2838 - >seq9485,non-specific,311990,1241,1259,0.00205315,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs3_orang,marg,CompleteHit
38284,Q#2838 - >seq9485,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38285,Q#2838 - >seq9485,superfamily,274008,157,500,0.00350553,41.5807,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38286,Q#2838 - >seq9485,non-specific,274008,157,500,0.00350553,41.5807,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,N-TerminusTruncated
38287,Q#2838 - >seq9485,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,BothTerminiTruncated
38288,Q#2838 - >seq9485,superfamily,235175,295,464,0.00375458,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,BothTerminiTruncated
38289,Q#2838 - >seq9485,non-specific,235175,295,464,0.00375458,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs3_orang,marg,BothTerminiTruncated
38290,Q#2838 - >seq9485,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38291,Q#2838 - >seq9485,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38292,Q#2838 - >seq9485,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs3_orang.marg.frame3,1909190025_L1PA5.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs3_orang,marg,C-TerminusTruncated
38293,Q#2842 - >seq9489,specific,238827,510,772,5.8847e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38294,Q#2842 - >seq9489,superfamily,295487,510,772,5.8847e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38295,Q#2842 - >seq9489,non-specific,238827,510,772,5.8847e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38296,Q#2842 - >seq9489,specific,197310,9,236,1.1786099999999999e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38297,Q#2842 - >seq9489,superfamily,351117,9,236,1.1786099999999999e-62,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38298,Q#2842 - >seq9489,non-specific,197310,9,236,1.1786099999999999e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38299,Q#2842 - >seq9489,non-specific,197306,9,236,1.96413e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38300,Q#2842 - >seq9489,non-specific,197306,9,236,1.96413e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38301,Q#2842 - >seq9489,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38302,Q#2842 - >seq9489,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38303,Q#2842 - >seq9489,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38304,Q#2842 - >seq9489,non-specific,197307,9,236,3.17538e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38305,Q#2842 - >seq9489,non-specific,197307,9,236,3.17538e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38306,Q#2842 - >seq9489,non-specific,223780,9,238,1.9256099999999998e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38307,Q#2842 - >seq9489,non-specific,223780,9,238,1.9256099999999998e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38308,Q#2842 - >seq9489,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38309,Q#2842 - >seq9489,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38310,Q#2842 - >seq9489,non-specific,197321,7,236,2.52474e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38311,Q#2842 - >seq9489,non-specific,197321,7,236,2.52474e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38312,Q#2842 - >seq9489,non-specific,273186,9,237,9.38119e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38313,Q#2842 - >seq9489,non-specific,273186,9,237,9.38119e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38314,Q#2842 - >seq9489,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38315,Q#2842 - >seq9489,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38316,Q#2842 - >seq9489,non-specific,272954,9,236,1.9881799999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38317,Q#2842 - >seq9489,non-specific,272954,9,236,1.9881799999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38318,Q#2842 - >seq9489,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38319,Q#2842 - >seq9489,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38320,Q#2842 - >seq9489,non-specific,197336,7,235,6.29902e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38321,Q#2842 - >seq9489,non-specific,197336,7,235,6.29902e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38322,Q#2842 - >seq9489,non-specific,238828,516,737,2.61807e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38323,Q#2842 - >seq9489,non-specific,238828,516,737,2.61807e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38324,Q#2842 - >seq9489,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38325,Q#2842 - >seq9489,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38326,Q#2842 - >seq9489,non-specific,275209,467,800,4.6027699999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38327,Q#2842 - >seq9489,superfamily,275209,467,800,4.6027699999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38328,Q#2842 - >seq9489,non-specific,275209,467,800,4.6027699999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38329,Q#2842 - >seq9489,non-specific,236970,9,238,1.17007e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38330,Q#2842 - >seq9489,non-specific,236970,9,238,1.17007e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38331,Q#2842 - >seq9489,non-specific,339261,108,232,2.0292199999999997e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38332,Q#2842 - >seq9489,non-specific,339261,108,232,2.0292199999999997e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38333,Q#2842 - >seq9489,non-specific,197311,7,236,1.4917799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38334,Q#2842 - >seq9489,non-specific,197311,7,236,1.4917799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38335,Q#2842 - >seq9489,non-specific,197317,139,229,2.3651400000000003e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38336,Q#2842 - >seq9489,non-specific,197317,139,229,2.3651400000000003e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38337,Q#2842 - >seq9489,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38338,Q#2842 - >seq9489,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38339,Q#2842 - >seq9489,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38340,Q#2842 - >seq9489,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38341,Q#2842 - >seq9489,non-specific,274009,305,453,0.0010102,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38342,Q#2842 - >seq9489,superfamily,274009,305,453,0.0010102,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38343,Q#2842 - >seq9489,non-specific,274009,305,453,0.0010102,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38344,Q#2842 - >seq9489,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38345,Q#2842 - >seq9489,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38346,Q#2842 - >seq9489,specific,311990,1241,1259,0.00211439,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38347,Q#2842 - >seq9489,superfamily,311990,1241,1259,0.00211439,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38348,Q#2842 - >seq9489,non-specific,311990,1241,1259,0.00211439,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38349,Q#2842 - >seq9489,non-specific,235175,295,464,0.00385128,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,BothTerminiTruncated
38350,Q#2842 - >seq9489,superfamily,235175,295,464,0.00385128,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,BothTerminiTruncated
38351,Q#2842 - >seq9489,non-specific,235175,295,464,0.00385128,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,BothTerminiTruncated
38352,Q#2842 - >seq9489,non-specific,274008,157,500,0.00429405,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38353,Q#2842 - >seq9489,superfamily,274008,157,500,0.00429405,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38354,Q#2842 - >seq9489,non-specific,274008,157,500,0.00429405,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,pars,N-TerminusTruncated
38355,Q#2842 - >seq9489,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38356,Q#2842 - >seq9489,superfamily,293702,337,451,0.00898393,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38357,Q#2842 - >seq9489,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,pars,C-TerminusTruncated
38358,Q#2842 - >seq9489,non-specific,239569,525,748,0.00906609,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38359,Q#2842 - >seq9489,non-specific,239569,525,748,0.00906609,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs4_gibbon.pars.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,pars,CompleteHit
38360,Q#2844 - >seq9491,specific,238827,510,772,5.8847e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38361,Q#2844 - >seq9491,superfamily,295487,510,772,5.8847e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38362,Q#2844 - >seq9491,non-specific,238827,510,772,5.8847e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38363,Q#2844 - >seq9491,specific,197310,9,236,1.1786099999999999e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38364,Q#2844 - >seq9491,superfamily,351117,9,236,1.1786099999999999e-62,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38365,Q#2844 - >seq9491,non-specific,197310,9,236,1.1786099999999999e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38366,Q#2844 - >seq9491,non-specific,197306,9,236,1.96413e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38367,Q#2844 - >seq9491,non-specific,197306,9,236,1.96413e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38368,Q#2844 - >seq9491,specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38369,Q#2844 - >seq9491,superfamily,333820,516,772,3.28513e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38370,Q#2844 - >seq9491,non-specific,333820,516,772,3.28513e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38371,Q#2844 - >seq9491,non-specific,197307,9,236,3.17538e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38372,Q#2844 - >seq9491,non-specific,197307,9,236,3.17538e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38373,Q#2844 - >seq9491,non-specific,223780,9,238,1.9256099999999998e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38374,Q#2844 - >seq9491,non-specific,223780,9,238,1.9256099999999998e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38375,Q#2844 - >seq9491,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38376,Q#2844 - >seq9491,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38377,Q#2844 - >seq9491,non-specific,197321,7,236,2.52474e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38378,Q#2844 - >seq9491,non-specific,197321,7,236,2.52474e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38379,Q#2844 - >seq9491,non-specific,273186,9,237,9.38119e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38380,Q#2844 - >seq9491,non-specific,273186,9,237,9.38119e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38381,Q#2844 - >seq9491,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38382,Q#2844 - >seq9491,non-specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38383,Q#2844 - >seq9491,non-specific,272954,9,236,1.9881799999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38384,Q#2844 - >seq9491,non-specific,272954,9,236,1.9881799999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38385,Q#2844 - >seq9491,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38386,Q#2844 - >seq9491,non-specific,197319,8,236,4.19856e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38387,Q#2844 - >seq9491,non-specific,197336,7,235,6.29902e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38388,Q#2844 - >seq9491,non-specific,197336,7,235,6.29902e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38389,Q#2844 - >seq9491,non-specific,238828,516,737,2.61807e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38390,Q#2844 - >seq9491,non-specific,238828,516,737,2.61807e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38391,Q#2844 - >seq9491,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38392,Q#2844 - >seq9491,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38393,Q#2844 - >seq9491,non-specific,275209,467,800,4.6027699999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38394,Q#2844 - >seq9491,superfamily,275209,467,800,4.6027699999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38395,Q#2844 - >seq9491,non-specific,275209,467,800,4.6027699999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38396,Q#2844 - >seq9491,non-specific,236970,9,238,1.17007e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38397,Q#2844 - >seq9491,non-specific,236970,9,238,1.17007e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38398,Q#2844 - >seq9491,non-specific,339261,108,232,2.0292199999999997e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38399,Q#2844 - >seq9491,non-specific,339261,108,232,2.0292199999999997e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38400,Q#2844 - >seq9491,non-specific,197311,7,236,1.4917799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38401,Q#2844 - >seq9491,non-specific,197311,7,236,1.4917799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38402,Q#2844 - >seq9491,non-specific,197317,139,229,2.3651400000000003e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38403,Q#2844 - >seq9491,non-specific,197317,139,229,2.3651400000000003e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38404,Q#2844 - >seq9491,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38405,Q#2844 - >seq9491,non-specific,238185,656,772,0.00018113,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38406,Q#2844 - >seq9491,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38407,Q#2844 - >seq9491,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38408,Q#2844 - >seq9491,non-specific,274009,305,453,0.0010102,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38409,Q#2844 - >seq9491,superfamily,274009,305,453,0.0010102,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38410,Q#2844 - >seq9491,non-specific,274009,305,453,0.0010102,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38411,Q#2844 - >seq9491,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38412,Q#2844 - >seq9491,non-specific,197314,7,192,0.00200545,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38413,Q#2844 - >seq9491,specific,311990,1241,1259,0.00211439,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38414,Q#2844 - >seq9491,superfamily,311990,1241,1259,0.00211439,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38415,Q#2844 - >seq9491,non-specific,311990,1241,1259,0.00211439,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38416,Q#2844 - >seq9491,non-specific,235175,295,464,0.00385128,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,BothTerminiTruncated
38417,Q#2844 - >seq9491,superfamily,235175,295,464,0.00385128,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,BothTerminiTruncated
38418,Q#2844 - >seq9491,non-specific,235175,295,464,0.00385128,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,BothTerminiTruncated
38419,Q#2844 - >seq9491,non-specific,274008,157,500,0.00429405,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38420,Q#2844 - >seq9491,superfamily,274008,157,500,0.00429405,41.1955,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38421,Q#2844 - >seq9491,non-specific,274008,157,500,0.00429405,41.1955,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs4_gibbon,marg,N-TerminusTruncated
38422,Q#2844 - >seq9491,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38423,Q#2844 - >seq9491,superfamily,293702,337,451,0.00898393,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38424,Q#2844 - >seq9491,non-specific,293702,337,451,0.00898393,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA5,ORF2,hs4_gibbon,marg,C-TerminusTruncated
38425,Q#2844 - >seq9491,non-specific,239569,525,748,0.00906609,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38426,Q#2844 - >seq9491,non-specific,239569,525,748,0.00906609,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs4_gibbon.marg.frame3,1909190028_L1PA5.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs4_gibbon,marg,CompleteHit
38427,Q#2846 - >seq9493,specific,238827,510,772,6.548899999999998e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38428,Q#2846 - >seq9493,superfamily,295487,510,772,6.548899999999998e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38429,Q#2846 - >seq9493,specific,197310,9,236,1.2016599999999997e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38430,Q#2846 - >seq9493,superfamily,351117,9,236,1.2016599999999997e-62,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38431,Q#2846 - >seq9493,non-specific,197306,9,236,1.9452700000000003e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38432,Q#2846 - >seq9493,specific,333820,516,772,3.3492199999999997e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38433,Q#2846 - >seq9493,superfamily,333820,516,772,3.3492199999999997e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38434,Q#2846 - >seq9493,non-specific,197307,9,236,3.2058499999999996e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38435,Q#2846 - >seq9493,non-specific,223780,9,238,2.00033e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38436,Q#2846 - >seq9493,non-specific,197320,8,236,1.7258e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38437,Q#2846 - >seq9493,non-specific,197321,7,236,2.52474e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38438,Q#2846 - >seq9493,non-specific,273186,9,237,9.292710000000001e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38439,Q#2846 - >seq9493,specific,335306,10,229,1.33402e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38440,Q#2846 - >seq9493,non-specific,272954,9,236,1.9881799999999998e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38441,Q#2846 - >seq9493,non-specific,197319,8,236,4.15927e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38442,Q#2846 - >seq9493,non-specific,197336,7,235,6.29902e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38443,Q#2846 - >seq9493,non-specific,238828,516,737,2.69293e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38444,Q#2846 - >seq9493,non-specific,197322,9,236,2.82692e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38445,Q#2846 - >seq9493,non-specific,275209,467,800,4.812519999999999e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38446,Q#2846 - >seq9493,superfamily,275209,467,800,4.812519999999999e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38447,Q#2846 - >seq9493,non-specific,236970,9,238,1.20277e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38448,Q#2846 - >seq9493,non-specific,339261,108,232,2.0096300000000002e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38449,Q#2846 - >seq9493,non-specific,197311,7,236,1.4917799999999997e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,marg,CompleteHit
38450,Q#2846 - >seq9493,non-specific,197317,139,229,2.3437e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,marg,N-TerminusTruncated
38451,Q#2846 - >seq9493,non-specific,238185,656,772,0.00018469599999999998,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38452,Q#2846 - >seq9493,non-specific,274009,305,453,0.000252426,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,C-TerminusTruncated
38453,Q#2846 - >seq9493,superfamily,274009,305,453,0.000252426,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,C-TerminusTruncated
38454,Q#2846 - >seq9493,non-specific,226098,138,239,0.0004954219999999999,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,marg,N-TerminusTruncated
38455,Q#2846 - >seq9493,non-specific,235175,295,464,0.0015286,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,BothTerminiTruncated
38456,Q#2846 - >seq9493,superfamily,235175,295,464,0.0015286,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,BothTerminiTruncated
38457,Q#2846 - >seq9493,non-specific,197314,7,192,0.00204175,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs0_human,marg,C-TerminusTruncated
38458,Q#2846 - >seq9493,specific,311990,1241,1259,0.00215624,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs0_human,marg,CompleteHit
38459,Q#2846 - >seq9493,superfamily,311990,1241,1259,0.00215624,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA5,ORF2,hs0_human,marg,CompleteHit
38460,Q#2846 - >seq9493,non-specific,224117,311,428,0.00476197,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,C-TerminusTruncated
38461,Q#2846 - >seq9493,superfamily,224117,311,428,0.00476197,41.2384,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA5,ORF2,hs0_human,marg,C-TerminusTruncated
38462,Q#2846 - >seq9493,non-specific,274008,157,500,0.00602171,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,N-TerminusTruncated
38463,Q#2846 - >seq9493,superfamily,274008,157,500,0.00602171,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,N-TerminusTruncated
38464,Q#2846 - >seq9493,non-specific,274009,305,504,0.00879822,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,marg,N-TerminusTruncated
38465,Q#2846 - >seq9493,non-specific,239569,525,748,0.00906609,38.7079,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs0_human.marg.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA5,ORF2,hs0_human,marg,CompleteHit
38466,Q#2850 - >seq9497,specific,238827,510,772,6.34951e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38467,Q#2850 - >seq9497,superfamily,295487,510,772,6.34951e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38468,Q#2850 - >seq9497,specific,197310,9,236,1.1885299999999998e-62,213.36700000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38469,Q#2850 - >seq9497,superfamily,351117,9,236,1.1885299999999998e-62,213.36700000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38470,Q#2850 - >seq9497,non-specific,197306,9,236,1.9434299999999998e-54,190.0,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38471,Q#2850 - >seq9497,specific,333820,516,772,3.28229e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38472,Q#2850 - >seq9497,superfamily,333820,516,772,3.28229e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38473,Q#2850 - >seq9497,non-specific,197307,9,236,2.99582e-26,108.914,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38474,Q#2850 - >seq9497,non-specific,223780,9,238,2.0563599999999996e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38475,Q#2850 - >seq9497,non-specific,197320,8,236,1.74068e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38476,Q#2850 - >seq9497,non-specific,197321,7,236,2.49859e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38477,Q#2850 - >seq9497,non-specific,273186,9,237,9.284230000000001e-20,90.0308,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38478,Q#2850 - >seq9497,specific,335306,10,229,1.33284e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38479,Q#2850 - >seq9497,non-specific,272954,9,236,1.96774e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38480,Q#2850 - >seq9497,non-specific,197319,8,236,4.19475e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38481,Q#2850 - >seq9497,non-specific,197336,7,235,6.29333e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38482,Q#2850 - >seq9497,non-specific,238828,516,737,2.61576e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38483,Q#2850 - >seq9497,non-specific,197322,9,236,2.82429e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38484,Q#2850 - >seq9497,non-specific,275209,467,800,4.68115e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38485,Q#2850 - >seq9497,superfamily,275209,467,800,4.68115e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38486,Q#2850 - >seq9497,non-specific,236970,9,238,1.1907e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38487,Q#2850 - >seq9497,non-specific,339261,108,232,2.02754e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38488,Q#2850 - >seq9497,non-specific,197311,7,236,1.51875e-08,56.1461,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA5,ORF2,hs0_human,pars,CompleteHit
38489,Q#2850 - >seq9497,non-specific,197317,139,229,2.36305e-06,50.2932,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,pars,N-TerminusTruncated
38490,Q#2850 - >seq9497,non-specific,238185,656,772,0.000184545,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38491,Q#2850 - >seq9497,non-specific,274009,305,453,0.00024380799999999998,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,C-TerminusTruncated
38492,Q#2850 - >seq9497,superfamily,274009,305,453,0.00024380799999999998,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,C-TerminusTruncated
38493,Q#2850 - >seq9497,non-specific,226098,138,239,0.000494988,43.158,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA5,ORF2,hs0_human,pars,N-TerminusTruncated
38494,Q#2850 - >seq9497,non-specific,235175,295,464,0.00143923,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,BothTerminiTruncated
38495,Q#2850 - >seq9497,superfamily,235175,295,464,0.00143923,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,BothTerminiTruncated
38496,Q#2850 - >seq9497,non-specific,197314,7,192,0.00207689,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA5,ORF2,hs0_human,pars,C-TerminusTruncated
38497,Q#2850 - >seq9497,specific,311990,1240,1258,0.00213356,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs0_human,pars,CompleteHit
38498,Q#2850 - >seq9497,superfamily,311990,1240,1258,0.00213356,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA5,ORF2,hs0_human,pars,CompleteHit
38499,Q#2850 - >seq9497,non-specific,224117,311,428,0.00471766,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,C-TerminusTruncated
38500,Q#2850 - >seq9497,superfamily,224117,311,428,0.00471766,41.2384,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA5,ORF2,hs0_human,pars,C-TerminusTruncated
38501,Q#2850 - >seq9497,non-specific,274008,157,500,0.0057188000000000004,40.8103,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,N-TerminusTruncated
38502,Q#2850 - >seq9497,superfamily,274008,157,500,0.0057188000000000004,40.8103,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,N-TerminusTruncated
38503,Q#2850 - >seq9497,non-specific,274009,305,504,0.00857026,40.4363,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA5,ORF2,hs0_human,pars,N-TerminusTruncated
38504,Q#2850 - >seq9497,non-specific,239569,525,748,0.008734899999999999,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA5.ORF2.hs0_human.pars.frame3,1909190036_L1PA5.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA5,ORF2,hs0_human,pars,CompleteHit
38505,Q#2852 - >seq9499,specific,238827,517,779,1.7843699999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38506,Q#2852 - >seq9499,superfamily,295487,517,779,1.7843699999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38507,Q#2852 - >seq9499,specific,197310,9,243,2.7293199999999995e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38508,Q#2852 - >seq9499,superfamily,351117,9,243,2.7293199999999995e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38509,Q#2852 - >seq9499,non-specific,197306,9,243,4.3573600000000003e-51,180.37,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38510,Q#2852 - >seq9499,specific,333820,523,779,2.64657e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38511,Q#2852 - >seq9499,superfamily,333820,523,779,2.64657e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38512,Q#2852 - >seq9499,non-specific,223780,9,245,7.71716e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38513,Q#2852 - >seq9499,non-specific,197307,9,243,9.426030000000001e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38514,Q#2852 - >seq9499,non-specific,197320,8,228,1.67762e-18,86.4149,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38515,Q#2852 - >seq9499,specific,335306,10,236,4.75055e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38516,Q#2852 - >seq9499,non-specific,273186,9,244,8.614630000000001e-18,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38517,Q#2852 - >seq9499,non-specific,197321,7,243,7.22232e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38518,Q#2852 - >seq9499,non-specific,272954,9,243,1.00505e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38519,Q#2852 - >seq9499,non-specific,197319,8,243,2.1489400000000003e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38520,Q#2852 - >seq9499,non-specific,197336,7,242,3.6337400000000002e-12,67.6375,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38521,Q#2852 - >seq9499,non-specific,238828,523,744,1.4006899999999998e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38522,Q#2852 - >seq9499,non-specific,275209,474,807,4.35284e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38523,Q#2852 - >seq9499,superfamily,275209,474,807,4.35284e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38524,Q#2852 - >seq9499,non-specific,339261,115,239,1.20882e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38525,Q#2852 - >seq9499,non-specific,197322,9,243,1.3422500000000002e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38526,Q#2852 - >seq9499,non-specific,236970,9,245,1.3116899999999998e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38527,Q#2852 - >seq9499,non-specific,197311,7,243,3.5439599999999996e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38528,Q#2852 - >seq9499,non-specific,238185,663,779,0.000133354,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38529,Q#2852 - >seq9499,non-specific,197317,146,236,0.00014830100000000002,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38530,Q#2852 - >seq9499,non-specific,226098,145,246,0.000606978,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38531,Q#2852 - >seq9499,specific,311990,1248,1266,0.000999827,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38532,Q#2852 - >seq9499,superfamily,311990,1248,1266,0.000999827,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38533,Q#2852 - >seq9499,non-specific,235175,302,471,0.00118271,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38534,Q#2852 - >seq9499,superfamily,235175,302,471,0.00118271,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38535,Q#2852 - >seq9499,non-specific,274009,312,460,0.00119373,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38536,Q#2852 - >seq9499,superfamily,274009,312,460,0.00119373,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38537,Q#2852 - >seq9499,non-specific,239569,532,755,0.00681801,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,marg,CompleteHit
38538,Q#2852 - >seq9499,non-specific,293702,344,458,0.00766751,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38539,Q#2852 - >seq9499,superfamily,293702,344,458,0.00766751,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38540,Q#2852 - >seq9499,non-specific,274008,164,507,0.00835455,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38541,Q#2852 - >seq9499,superfamily,274008,164,507,0.00835455,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.marg.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38542,Q#2857 - >seq9504,specific,238827,510,772,1.77935e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38543,Q#2857 - >seq9504,superfamily,295487,510,772,1.77935e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38544,Q#2857 - >seq9504,specific,197310,9,236,1.2370899999999999e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38545,Q#2857 - >seq9504,superfamily,351117,9,236,1.2370899999999999e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38546,Q#2857 - >seq9504,non-specific,197306,9,236,2.19178e-53,186.918,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38547,Q#2857 - >seq9504,specific,333820,516,772,3.0115699999999995e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38548,Q#2857 - >seq9504,superfamily,333820,516,772,3.0115699999999995e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38549,Q#2857 - >seq9504,non-specific,197307,9,236,1.034e-24,104.292,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38550,Q#2857 - >seq9504,non-specific,223780,9,238,5.86155e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38551,Q#2857 - >seq9504,non-specific,197320,8,221,7.959970000000001e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38552,Q#2857 - >seq9504,specific,335306,10,229,1.1234400000000001e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38553,Q#2857 - >seq9504,non-specific,197321,7,236,2.06077e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38554,Q#2857 - >seq9504,non-specific,273186,9,237,2.37397e-19,88.8752,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38555,Q#2857 - >seq9504,non-specific,272954,9,236,3.91746e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38556,Q#2857 - >seq9504,non-specific,197319,8,236,2.19375e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38557,Q#2857 - >seq9504,non-specific,197336,7,235,4.4518900000000005e-14,73.4155,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38558,Q#2857 - >seq9504,non-specific,197322,9,236,3.48501e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38559,Q#2857 - >seq9504,non-specific,238828,516,737,1.4184200000000002e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38560,Q#2857 - >seq9504,non-specific,275209,467,800,4.6027699999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38561,Q#2857 - >seq9504,superfamily,275209,467,800,4.6027699999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38562,Q#2857 - >seq9504,non-specific,339261,108,232,1.1339200000000002e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38563,Q#2857 - >seq9504,non-specific,236970,9,238,9.553580000000001e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38564,Q#2857 - >seq9504,non-specific,197311,7,236,1.23183e-07,53.4497,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38565,Q#2857 - >seq9504,non-specific,238185,656,772,0.00013004,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38566,Q#2857 - >seq9504,non-specific,197317,139,229,0.000143463,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38567,Q#2857 - >seq9504,non-specific,226098,138,239,0.000603284,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38568,Q#2857 - >seq9504,specific,311990,1241,1259,0.0010241,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38569,Q#2857 - >seq9504,superfamily,311990,1241,1259,0.0010241,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38570,Q#2857 - >seq9504,non-specific,274009,305,453,0.00129091,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38571,Q#2857 - >seq9504,superfamily,274009,305,453,0.00129091,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38572,Q#2857 - >seq9504,non-specific,235175,295,464,0.00135752,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38573,Q#2857 - >seq9504,superfamily,235175,295,464,0.00135752,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38574,Q#2857 - >seq9504,non-specific,197314,7,192,0.0019698,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA6,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38575,Q#2857 - >seq9504,non-specific,239569,525,748,0.00709264,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs2_gorilla,pars,CompleteHit
38576,Q#2857 - >seq9504,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38577,Q#2857 - >seq9504,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38578,Q#2857 - >seq9504,non-specific,274008,157,500,0.00888372,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38579,Q#2857 - >seq9504,superfamily,274008,157,500,0.00888372,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs2_gorilla.pars.frame3,1909190042_L1PA6.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs2_gorilla,pars,N-TerminusTruncated
38580,Q#2860 - >seq9507,specific,238827,510,772,1.77935e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38581,Q#2860 - >seq9507,superfamily,295487,510,772,1.77935e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38582,Q#2860 - >seq9507,specific,197310,9,236,2.0667499999999996e-62,212.597,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38583,Q#2860 - >seq9507,superfamily,351117,9,236,2.0667499999999996e-62,212.597,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38584,Q#2860 - >seq9507,non-specific,197306,9,236,4.788279999999999e-53,185.763,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38585,Q#2860 - >seq9507,specific,333820,516,772,3.04081e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38586,Q#2860 - >seq9507,superfamily,333820,516,772,3.04081e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38587,Q#2860 - >seq9507,non-specific,197307,9,236,1.40297e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38588,Q#2860 - >seq9507,non-specific,223780,9,238,5.80606e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38589,Q#2860 - >seq9507,non-specific,197320,8,221,7.10307e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38590,Q#2860 - >seq9507,specific,335306,10,229,1.1234400000000001e-19,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38591,Q#2860 - >seq9507,non-specific,197321,7,236,2.8710000000000005e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38592,Q#2860 - >seq9507,non-specific,273186,9,237,8.127890000000001e-19,87.3344,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38593,Q#2860 - >seq9507,non-specific,272954,9,236,1.46293e-15,77.8085,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38594,Q#2860 - >seq9507,non-specific,197319,8,236,2.11291e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38595,Q#2860 - >seq9507,non-specific,197336,7,235,6.239069999999999e-14,73.0303,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38596,Q#2860 - >seq9507,non-specific,197322,9,236,2.29291e-11,66.1866,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38597,Q#2860 - >seq9507,non-specific,238828,516,737,1.39207e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38598,Q#2860 - >seq9507,non-specific,275209,467,800,4.52145e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38599,Q#2860 - >seq9507,superfamily,275209,467,800,4.52145e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38600,Q#2860 - >seq9507,non-specific,339261,108,232,2.74098e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38601,Q#2860 - >seq9507,non-specific,236970,9,238,9.730040000000001e-09,57.5966,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38602,Q#2860 - >seq9507,non-specific,197311,7,236,3.02565e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38603,Q#2860 - >seq9507,non-specific,197314,7,192,0.000124244,45.0271,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
38604,Q#2860 - >seq9507,non-specific,238185,656,772,0.000132599,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38605,Q#2860 - >seq9507,non-specific,197317,139,229,0.000139634,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
38606,Q#2860 - >seq9507,non-specific,226098,138,239,0.00022712,44.3136,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
38607,Q#2860 - >seq9507,specific,311990,1241,1259,0.00106502,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38608,Q#2860 - >seq9507,superfamily,311990,1241,1259,0.00106502,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38609,Q#2860 - >seq9507,non-specific,274009,305,453,0.00129091,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
38610,Q#2860 - >seq9507,superfamily,274009,305,453,0.00129091,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
38611,Q#2860 - >seq9507,non-specific,235175,295,464,0.00135752,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
38612,Q#2860 - >seq9507,superfamily,235175,295,464,0.00135752,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,BothTerminiTruncated
38613,Q#2860 - >seq9507,non-specific,239569,525,748,0.00659484,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,pars,CompleteHit
38614,Q#2860 - >seq9507,non-specific,293702,337,451,0.00838248,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
38615,Q#2860 - >seq9507,superfamily,293702,337,451,0.00838248,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs1_chimp,pars,C-TerminusTruncated
38616,Q#2860 - >seq9507,non-specific,274008,157,500,0.00880894,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
38617,Q#2860 - >seq9507,superfamily,274008,157,500,0.00880894,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.pars.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,pars,N-TerminusTruncated
38618,Q#2862 - >seq9509,specific,238827,518,780,1.7530699999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38619,Q#2862 - >seq9509,superfamily,295487,518,780,1.7530699999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38620,Q#2862 - >seq9509,specific,197310,9,244,6.273179999999999e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38621,Q#2862 - >seq9509,superfamily,351117,9,244,6.273179999999999e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38622,Q#2862 - >seq9509,non-specific,197306,9,244,1.28434e-50,178.829,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38623,Q#2862 - >seq9509,specific,333820,524,780,2.72674e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38624,Q#2862 - >seq9509,superfamily,333820,524,780,2.72674e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38625,Q#2862 - >seq9509,non-specific,223780,9,246,7.12634e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38626,Q#2862 - >seq9509,non-specific,197307,9,244,1.6531400000000003e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38627,Q#2862 - >seq9509,non-specific,197320,8,229,2.0872099999999997e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38628,Q#2862 - >seq9509,specific,335306,10,237,6.4494099999999995e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38629,Q#2862 - >seq9509,non-specific,273186,9,245,3.86907e-17,82.3268,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38630,Q#2862 - >seq9509,non-specific,197321,7,244,1.2851399999999999e-16,80.67399999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38631,Q#2862 - >seq9509,non-specific,272954,9,244,5.028060000000001e-13,70.4897,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38632,Q#2862 - >seq9509,non-specific,197319,8,244,3.36657e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38633,Q#2862 - >seq9509,non-specific,197336,7,243,8.10802e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38634,Q#2862 - >seq9509,non-specific,238828,524,745,1.3252200000000002e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38635,Q#2862 - >seq9509,non-specific,275209,475,808,4.2799199999999995e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38636,Q#2862 - >seq9509,superfamily,275209,475,808,4.2799199999999995e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38637,Q#2862 - >seq9509,non-specific,197322,9,244,1.18385e-09,61.178999999999995,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38638,Q#2862 - >seq9509,non-specific,339261,116,240,3.09962e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38639,Q#2862 - >seq9509,non-specific,236970,9,246,3.07233e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38640,Q#2862 - >seq9509,non-specific,197311,7,244,1.15572e-05,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38641,Q#2862 - >seq9509,non-specific,238185,664,780,0.000137422,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38642,Q#2862 - >seq9509,non-specific,197317,147,237,0.000144469,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,marg,N-TerminusTruncated
38643,Q#2862 - >seq9509,non-specific,226098,146,247,0.000228715,44.3136,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs1_chimp,marg,N-TerminusTruncated
38644,Q#2862 - >seq9509,specific,311990,1249,1267,0.00104058,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38645,Q#2862 - >seq9509,superfamily,311990,1249,1267,0.00104058,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38646,Q#2862 - >seq9509,non-specific,235175,303,472,0.00116386,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
38647,Q#2862 - >seq9509,superfamily,235175,303,472,0.00116386,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,BothTerminiTruncated
38648,Q#2862 - >seq9509,non-specific,274009,313,461,0.0011948,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
38649,Q#2862 - >seq9509,superfamily,274009,313,461,0.0011948,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
38650,Q#2862 - >seq9509,non-specific,239569,533,756,0.00611807,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs1_chimp,marg,CompleteHit
38651,Q#2862 - >seq9509,non-specific,293702,345,459,0.00780832,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
38652,Q#2862 - >seq9509,superfamily,293702,345,459,0.00780832,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs1_chimp,marg,C-TerminusTruncated
38653,Q#2862 - >seq9509,non-specific,274008,165,508,0.00836194,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,N-TerminusTruncated
38654,Q#2862 - >seq9509,superfamily,274008,165,508,0.00836194,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs1_chimp.marg.frame3,1909190042_L1PA6.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs1_chimp,marg,N-TerminusTruncated
38655,Q#2863 - >seq9510,specific,238827,510,772,1.7967399999999996e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38656,Q#2863 - >seq9510,superfamily,295487,510,772,1.7967399999999996e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38657,Q#2863 - >seq9510,specific,197310,9,236,2.5083399999999995e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38658,Q#2863 - >seq9510,superfamily,351117,9,236,2.5083399999999995e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38659,Q#2863 - >seq9510,non-specific,197306,9,236,1.08371e-53,187.68900000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38660,Q#2863 - >seq9510,specific,333820,516,772,3.0703299999999996e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38661,Q#2863 - >seq9510,superfamily,333820,516,772,3.0703299999999996e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38662,Q#2863 - >seq9510,non-specific,197307,9,236,5.27871e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38663,Q#2863 - >seq9510,non-specific,223780,9,238,5.80606e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38664,Q#2863 - >seq9510,non-specific,197320,8,221,8.11251e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38665,Q#2863 - >seq9510,non-specific,273186,9,237,2.8690299999999997e-19,88.49,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38666,Q#2863 - >seq9510,specific,335306,10,229,2.88967e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38667,Q#2863 - >seq9510,non-specific,197321,7,236,3.4698200000000004e-19,88.37799999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38668,Q#2863 - >seq9510,non-specific,272954,9,236,6.827130000000001e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38669,Q#2863 - >seq9510,non-specific,197319,8,236,3.1045099999999996e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38670,Q#2863 - >seq9510,non-specific,197336,7,235,1.39653e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38671,Q#2863 - >seq9510,non-specific,238828,516,737,1.4184200000000002e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38672,Q#2863 - >seq9510,non-specific,197322,9,236,4.15272e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38673,Q#2863 - >seq9510,non-specific,275209,467,800,4.727499999999999e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38674,Q#2863 - >seq9510,superfamily,275209,467,800,4.727499999999999e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38675,Q#2863 - >seq9510,non-specific,339261,108,232,1.01917e-09,57.3471,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38676,Q#2863 - >seq9510,non-specific,236970,9,238,1.53718e-08,57.2114,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38677,Q#2863 - >seq9510,non-specific,197311,7,236,2.58078e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38678,Q#2863 - >seq9510,non-specific,197317,23,229,2.4855700000000003e-05,47.2116,cd09083,EEP-1, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,pars,CompleteHit
38679,Q#2863 - >seq9510,non-specific,238185,656,772,0.000132599,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38680,Q#2863 - >seq9510,non-specific,226098,138,239,0.000603284,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,pars,N-TerminusTruncated
38681,Q#2863 - >seq9510,specific,311990,1241,1259,0.00103418,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs0_human,pars,CompleteHit
38682,Q#2863 - >seq9510,superfamily,311990,1241,1259,0.00103418,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA6,ORF2,hs0_human,pars,CompleteHit
38683,Q#2863 - >seq9510,non-specific,274009,305,453,0.00131293,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,C-TerminusTruncated
38684,Q#2863 - >seq9510,superfamily,274009,305,453,0.00131293,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,C-TerminusTruncated
38685,Q#2863 - >seq9510,non-specific,235175,295,464,0.00135752,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,BothTerminiTruncated
38686,Q#2863 - >seq9510,superfamily,235175,295,464,0.00135752,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,BothTerminiTruncated
38687,Q#2863 - >seq9510,non-specific,197314,7,192,0.00284471,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA6,ORF2,hs0_human,pars,C-TerminusTruncated
38688,Q#2863 - >seq9510,non-specific,239569,525,748,0.00690172,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA6,ORF2,hs0_human,pars,CompleteHit
38689,Q#2863 - >seq9510,non-specific,293702,337,451,0.00831019,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs0_human,pars,C-TerminusTruncated
38690,Q#2863 - >seq9510,superfamily,293702,337,451,0.00831019,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs0_human,pars,C-TerminusTruncated
38691,Q#2863 - >seq9510,non-specific,274008,157,500,0.00873479,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,N-TerminusTruncated
38692,Q#2863 - >seq9510,superfamily,274008,157,500,0.00873479,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.pars.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,pars,N-TerminusTruncated
38693,Q#2864 - >seq9511,specific,238827,513,775,1.7890499999999995e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38694,Q#2864 - >seq9511,superfamily,295487,513,775,1.7890499999999995e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38695,Q#2864 - >seq9511,specific,197310,9,239,1.6124699999999997e-59,204.122,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38696,Q#2864 - >seq9511,superfamily,351117,9,239,1.6124699999999997e-59,204.122,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38697,Q#2864 - >seq9511,non-specific,197306,9,239,6.308539999999999e-52,182.68099999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38698,Q#2864 - >seq9511,specific,333820,519,775,2.7679699999999996e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38699,Q#2864 - >seq9511,superfamily,333820,519,775,2.7679699999999996e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38700,Q#2864 - >seq9511,non-specific,223780,9,241,3.13308e-23,100.365,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38701,Q#2864 - >seq9511,non-specific,197307,9,239,1.40011e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38702,Q#2864 - >seq9511,specific,335306,10,232,1.25114e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38703,Q#2864 - >seq9511,non-specific,197320,8,224,5.073229999999999e-19,87.9557,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38704,Q#2864 - >seq9511,non-specific,273186,9,240,2.20064e-18,86.1788,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38705,Q#2864 - >seq9511,non-specific,197321,7,239,3.6133699999999994e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38706,Q#2864 - >seq9511,non-specific,272954,9,239,5.247e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38707,Q#2864 - >seq9511,non-specific,197319,8,239,2.86932e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38708,Q#2864 - >seq9511,non-specific,197336,7,238,1.32137e-12,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38709,Q#2864 - >seq9511,non-specific,238828,519,740,1.4355899999999998e-10,62.6036,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38710,Q#2864 - >seq9511,non-specific,275209,470,803,4.6157599999999994e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38711,Q#2864 - >seq9511,superfamily,275209,470,803,4.6157599999999994e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38712,Q#2864 - >seq9511,non-specific,339261,111,235,1.14781e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38713,Q#2864 - >seq9511,non-specific,197322,9,239,4.9474799999999995e-09,59.253,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38714,Q#2864 - >seq9511,non-specific,197311,7,239,3.39384e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38715,Q#2864 - >seq9511,non-specific,236970,9,241,1.21571e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38716,Q#2864 - >seq9511,non-specific,238185,659,775,0.000135539,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38717,Q#2864 - >seq9511,non-specific,197317,142,232,0.00014384,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,N-TerminusTruncated
38718,Q#2864 - >seq9511,non-specific,226098,141,242,0.0006048669999999999,42.7728,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,N-TerminusTruncated
38719,Q#2864 - >seq9511,specific,311990,1244,1262,0.00103658,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs0_human,marg,CompleteHit
38720,Q#2864 - >seq9511,superfamily,311990,1244,1262,0.00103658,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs0_human,marg,CompleteHit
38721,Q#2864 - >seq9511,non-specific,235175,298,467,0.00117848,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,BothTerminiTruncated
38722,Q#2864 - >seq9511,superfamily,235175,298,467,0.00117848,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,BothTerminiTruncated
38723,Q#2864 - >seq9511,non-specific,274009,308,456,0.00119955,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,C-TerminusTruncated
38724,Q#2864 - >seq9511,superfamily,274009,308,456,0.00119955,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,C-TerminusTruncated
38725,Q#2864 - >seq9511,non-specific,239569,528,751,0.00661182,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs0_human,marg,CompleteHit
38726,Q#2864 - >seq9511,non-specific,293702,340,454,0.00731683,40.1827,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs0_human,marg,C-TerminusTruncated
38727,Q#2864 - >seq9511,superfamily,293702,340,454,0.00731683,40.1827,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs0_human,marg,C-TerminusTruncated
38728,Q#2864 - >seq9511,non-specific,197318,9,239,0.00732644,39.5871,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs0_human,marg,CompleteHit
38729,Q#2864 - >seq9511,non-specific,274008,160,503,0.00832499,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,N-TerminusTruncated
38730,Q#2864 - >seq9511,superfamily,274008,160,503,0.00832499,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs0_human.marg.frame3,1909190048_L1PA6.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs0_human,marg,N-TerminusTruncated
38731,Q#2871 - >seq9518,non-specific,197310,9,73,7.763739999999999e-14,72.3841,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38732,Q#2871 - >seq9518,superfamily,351117,9,73,7.763739999999999e-14,72.3841,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38733,Q#2871 - >seq9518,non-specific,197306,9,70,3.12691e-12,67.5065,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38734,Q#2871 - >seq9518,non-specific,223780,9,43,2.84554e-05,46.8227,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38735,Q#2871 - >seq9518,non-specific,197321,7,49,4.6344700000000004e-05,46.3912,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38736,Q#2871 - >seq9518,non-specific,197307,9,49,0.000211292,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38737,Q#2871 - >seq9518,non-specific,197336,7,43,0.00023366400000000002,44.1403,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38738,Q#2871 - >seq9518,specific,335306,10,74,0.00029716599999999997,43.3878,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38739,Q#2871 - >seq9518,non-specific,197320,8,43,0.0008089719999999999,42.5022,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38740,Q#2871 - >seq9518,non-specific,273186,9,43,0.00145452,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38741,Q#2871 - >seq9518,non-specific,272954,9,43,0.00982568,38.9033,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.pars.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38742,Q#2873 - >seq9520,specific,238827,503,765,8.714769999999998e-68,227.174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38743,Q#2873 - >seq9520,superfamily,295487,503,765,8.714769999999998e-68,227.174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38744,Q#2873 - >seq9520,specific,197310,59,229,9.61845e-40,147.498,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38745,Q#2873 - >seq9520,superfamily,351117,59,229,9.61845e-40,147.498,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38746,Q#2873 - >seq9520,specific,333820,509,765,2.19732e-35,133.186,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38747,Q#2873 - >seq9520,superfamily,333820,509,765,2.19732e-35,133.186,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38748,Q#2873 - >seq9520,non-specific,197306,60,229,1.8657799999999997e-34,132.22,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38749,Q#2873 - >seq9520,non-specific,223780,65,231,6.92439e-14,73.0163,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38750,Q#2873 - >seq9520,non-specific,197307,60,229,1.75476e-13,71.5501,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38751,Q#2873 - >seq9520,non-specific,197320,65,214,5.81723e-12,67.155,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38752,Q#2873 - >seq9520,non-specific,238828,509,730,2.4134e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38753,Q#2873 - >seq9520,non-specific,273186,64,230,1.77727e-10,62.6816,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38754,Q#2873 - >seq9520,non-specific,275209,460,793,3.22952e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38755,Q#2873 - >seq9520,superfamily,275209,460,793,3.22952e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38756,Q#2873 - >seq9520,non-specific,339261,101,225,1.7785e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38757,Q#2873 - >seq9520,non-specific,335306,33,222,7.017220000000001e-09,57.255,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38758,Q#2873 - >seq9520,non-specific,197321,60,229,1.40501e-08,56.7916,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38759,Q#2873 - >seq9520,non-specific,272954,60,229,1.09754e-07,54.3113,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38760,Q#2873 - >seq9520,non-specific,197319,59,229,1.00189e-06,51.5085,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38761,Q#2873 - >seq9520,non-specific,197322,84,229,1.7133199999999999e-06,51.1638,cd09088,Ape2-like_AP-endo,N,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38762,Q#2873 - >seq9520,non-specific,236970,61,231,3.834219999999999e-06,49.8926,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38763,Q#2873 - >seq9520,non-specific,197311,65,229,2.3100000000000002e-05,46.5161,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38764,Q#2873 - >seq9520,non-specific,197317,132,222,0.000114832,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38765,Q#2873 - >seq9520,non-specific,238185,649,765,0.000124355,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38766,Q#2873 - >seq9520,specific,311990,1234,1252,0.000989053,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38767,Q#2873 - >seq9520,superfamily,311990,1234,1252,0.000989053,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38768,Q#2873 - >seq9520,non-specific,226098,131,232,0.00119381,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
38769,Q#2873 - >seq9520,non-specific,235175,288,457,0.00158477,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA6,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
38770,Q#2873 - >seq9520,superfamily,235175,288,457,0.00158477,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA6,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
38771,Q#2873 - >seq9520,non-specific,274009,298,446,0.00175397,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38772,Q#2873 - >seq9520,superfamily,274009,298,446,0.00175397,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38773,Q#2873 - >seq9520,non-specific,239569,518,741,0.00566707,39.4783,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA6,ORF2,hs5_gmonkey,pars,CompleteHit
38774,Q#2873 - >seq9520,non-specific,293702,330,444,0.00908472,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38775,Q#2873 - >seq9520,superfamily,293702,330,444,0.00908472,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs5_gmonkey.pars.frame1,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_CellDiv,L1PA6,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
38776,Q#2874 - >seq9521,specific,238827,517,779,1.7500099999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38777,Q#2874 - >seq9521,superfamily,295487,517,779,1.7500099999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38778,Q#2874 - >seq9521,specific,197310,9,243,6.576879999999999e-59,202.582,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38779,Q#2874 - >seq9521,superfamily,351117,9,243,6.576879999999999e-59,202.582,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38780,Q#2874 - >seq9521,non-specific,197306,9,243,2.76933e-51,180.755,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38781,Q#2874 - >seq9521,specific,333820,523,779,2.47351e-35,132.80100000000002,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38782,Q#2874 - >seq9521,superfamily,333820,523,779,2.47351e-35,132.80100000000002,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38783,Q#2874 - >seq9521,non-specific,223780,9,245,7.153039999999999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38784,Q#2874 - >seq9521,non-specific,197307,9,243,1.11854e-21,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38785,Q#2874 - >seq9521,non-specific,197320,8,228,2.31394e-18,86.0297,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38786,Q#2874 - >seq9521,specific,335306,10,236,3.12369e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38787,Q#2874 - >seq9521,non-specific,273186,9,244,7.912419999999999e-18,84.63799999999999,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38788,Q#2874 - >seq9521,non-specific,197321,7,243,6.57206e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38789,Q#2874 - >seq9521,non-specific,272954,9,243,1.2582799999999999e-13,72.0305,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38790,Q#2874 - >seq9521,non-specific,197319,8,243,4.61904e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38791,Q#2874 - >seq9521,non-specific,197336,7,242,7.2438e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38792,Q#2874 - >seq9521,non-specific,238828,523,744,2.70963e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38793,Q#2874 - >seq9521,non-specific,275209,474,807,2.94021e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38794,Q#2874 - >seq9521,superfamily,275209,474,807,2.94021e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38795,Q#2874 - >seq9521,non-specific,339261,115,239,3.0375799999999998e-09,55.8063,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38796,Q#2874 - >seq9521,non-specific,197322,9,243,3.5896999999999997e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38797,Q#2874 - >seq9521,non-specific,236970,9,245,1.88387e-06,50.663000000000004,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38798,Q#2874 - >seq9521,non-specific,197311,7,243,5.5919100000000005e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38799,Q#2874 - >seq9521,non-specific,197317,146,236,0.000119441,44.9004,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
38800,Q#2874 - >seq9521,non-specific,238185,663,779,0.00013078,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38801,Q#2874 - >seq9521,specific,311990,1248,1266,0.00098043,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38802,Q#2874 - >seq9521,superfamily,311990,1248,1266,0.00098043,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38803,Q#2874 - >seq9521,non-specific,226098,145,246,0.00120849,42.0024,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA6,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
38804,Q#2874 - >seq9521,non-specific,235175,302,471,0.00128735,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
38805,Q#2874 - >seq9521,superfamily,235175,302,471,0.00128735,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
38806,Q#2874 - >seq9521,non-specific,274009,312,460,0.00133242,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
38807,Q#2874 - >seq9521,superfamily,274009,312,460,0.00133242,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
38808,Q#2874 - >seq9521,non-specific,239569,532,755,0.00681801,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA6,ORF2,hs5_gmonkey,marg,CompleteHit
38809,Q#2874 - >seq9521,non-specific,293702,344,458,0.00843403,39.7975,pfam17097,Kre28,C,cl25921,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
38810,Q#2874 - >seq9521,superfamily,293702,344,458,0.00843403,39.7975,cl25921,Kre28 superfamily,C, - ,"Spindle pole body component; In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA6,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
38811,Q#2874 - >seq9521,non-specific,274008,164,507,0.00909145,40.4251,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
38812,Q#2874 - >seq9521,superfamily,274008,164,507,0.00909145,40.4251,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA6.ORF2.hs5_gmonkey.marg.frame3,1909190048_L1PA6.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA6,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
38813,Q#2875 - >seq9522,specific,238827,510,772,3.4970999999999994e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38814,Q#2875 - >seq9522,superfamily,295487,510,772,3.4970999999999994e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38815,Q#2875 - >seq9522,specific,197310,9,236,3.1935899999999995e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38816,Q#2875 - >seq9522,superfamily,351117,9,236,3.1935899999999995e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38817,Q#2875 - >seq9522,non-specific,197306,9,236,2.6301399999999996e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38818,Q#2875 - >seq9522,specific,333820,516,772,1.0632499999999998e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38819,Q#2875 - >seq9522,superfamily,333820,516,772,1.0632499999999998e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38820,Q#2875 - >seq9522,non-specific,223780,9,238,6.141399999999999e-24,102.291,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38821,Q#2875 - >seq9522,non-specific,197307,9,236,3.44504e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38822,Q#2875 - >seq9522,non-specific,197320,8,236,3.33179e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38823,Q#2875 - >seq9522,non-specific,197321,7,236,8.0520100000000005e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38824,Q#2875 - >seq9522,specific,335306,10,229,2.03925e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38825,Q#2875 - >seq9522,non-specific,273186,9,237,4.70984e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38826,Q#2875 - >seq9522,non-specific,272954,9,236,8.393600000000001e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38827,Q#2875 - >seq9522,non-specific,197336,7,235,3.33201e-13,70.7191,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38828,Q#2875 - >seq9522,non-specific,197319,8,236,4.0042199999999997e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38829,Q#2875 - >seq9522,non-specific,238828,516,737,7.0115e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38830,Q#2875 - >seq9522,non-specific,197322,9,236,2.31173e-11,66.1866,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38831,Q#2875 - >seq9522,non-specific,275209,467,800,2.3768099999999996e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38832,Q#2875 - >seq9522,superfamily,275209,467,800,2.3768099999999996e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38833,Q#2875 - >seq9522,non-specific,339261,108,232,1.3360999999999998e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38834,Q#2875 - >seq9522,non-specific,236970,9,238,7.9131e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38835,Q#2875 - >seq9522,non-specific,197311,7,236,8.14093e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38836,Q#2875 - >seq9522,non-specific,238185,656,772,3.31976e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38837,Q#2875 - >seq9522,non-specific,197317,139,229,0.000362389,43.3596,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,marg,N-TerminusTruncated
38838,Q#2875 - >seq9522,non-specific,274009,305,458,0.00042243900000000004,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,C-TerminusTruncated
38839,Q#2875 - >seq9522,superfamily,274009,305,458,0.00042243900000000004,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,C-TerminusTruncated
38840,Q#2875 - >seq9522,specific,311990,1240,1258,0.00067157,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38841,Q#2875 - >seq9522,superfamily,311990,1240,1258,0.00067157,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs1_chimp,marg,CompleteHit
38842,Q#2875 - >seq9522,non-specific,235175,295,469,0.00221773,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,BothTerminiTruncated
38843,Q#2875 - >seq9522,superfamily,235175,295,469,0.00221773,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,BothTerminiTruncated
38844,Q#2875 - >seq9522,non-specific,274009,303,478,0.00605981,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,BothTerminiTruncated
38845,Q#2875 - >seq9522,non-specific,224117,123,433,0.00656028,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,N-TerminusTruncated
38846,Q#2875 - >seq9522,superfamily,224117,123,433,0.00656028,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs1_chimp,marg,N-TerminusTruncated
38847,Q#2875 - >seq9522,non-specific,224117,311,459,0.00927805,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs1_chimp,marg,C-TerminusTruncated
38848,Q#2875 - >seq9522,superfamily,224117,311,459,0.00927805,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.marg.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs1_chimp,marg,C-TerminusTruncated
38849,Q#2878 - >seq9525,specific,238827,498,760,4.4077899999999993e-69,231.02599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38850,Q#2878 - >seq9525,superfamily,295487,498,760,4.4077899999999993e-69,231.02599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38851,Q#2878 - >seq9525,specific,333820,504,760,3.2683199999999996e-37,138.194,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38852,Q#2878 - >seq9525,superfamily,333820,504,760,3.2683199999999996e-37,138.194,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38853,Q#2878 - >seq9525,non-specific,238828,504,725,3.62274e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38854,Q#2878 - >seq9525,non-specific,275209,455,788,2.0190900000000002e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38855,Q#2878 - >seq9525,superfamily,275209,455,788,2.0190900000000002e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38856,Q#2878 - >seq9525,non-specific,238185,644,760,1.53696e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38857,Q#2878 - >seq9525,non-specific,274009,293,446,0.000276086,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,C-TerminusTruncated
38858,Q#2878 - >seq9525,superfamily,274009,293,446,0.000276086,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,C-TerminusTruncated
38859,Q#2878 - >seq9525,specific,311990,1228,1246,0.000505761,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38860,Q#2878 - >seq9525,superfamily,311990,1228,1246,0.000505761,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38861,Q#2878 - >seq9525,non-specific,235175,251,457,0.00156288,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,BothTerminiTruncated
38862,Q#2878 - >seq9525,superfamily,235175,251,457,0.00156288,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,BothTerminiTruncated
38863,Q#2878 - >seq9525,non-specific,274009,291,466,0.00396148,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,BothTerminiTruncated
38864,Q#2878 - >seq9525,non-specific,224117,299,447,0.00706265,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs1_chimp,pars,C-TerminusTruncated
38865,Q#2878 - >seq9525,superfamily,224117,299,447,0.00706265,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs1_chimp.pars.frame2,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA7,ORF2,hs1_chimp,pars,C-TerminusTruncated
38866,Q#2880 - >seq9527,specific,197310,9,222,1.80155e-56,195.263,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38867,Q#2880 - >seq9527,superfamily,351117,9,222,1.80155e-56,195.263,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38868,Q#2880 - >seq9527,non-specific,197306,9,223,3.6470499999999997e-47,168.81400000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38869,Q#2880 - >seq9527,non-specific,223780,9,221,1.8241800000000002e-23,101.13600000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38870,Q#2880 - >seq9527,non-specific,197307,9,223,6.075369999999999e-22,96.2029,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38871,Q#2880 - >seq9527,non-specific,197320,8,221,2.42573e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38872,Q#2880 - >seq9527,non-specific,197321,7,223,8.13558e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38873,Q#2880 - >seq9527,specific,335306,10,212,1.4766399999999999e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38874,Q#2880 - >seq9527,non-specific,272954,9,221,5.4749e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38875,Q#2880 - >seq9527,non-specific,273186,9,221,9.06377e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38876,Q#2880 - >seq9527,non-specific,197336,7,221,1.34762e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38877,Q#2880 - >seq9527,non-specific,197319,8,223,1.07605e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38878,Q#2880 - >seq9527,non-specific,197322,9,222,1.3441199999999997e-09,60.7938,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38879,Q#2880 - >seq9527,non-specific,236970,9,217,4.64724e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38880,Q#2880 - >seq9527,non-specific,197311,7,204,3.00653e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38881,Q#2880 - >seq9527,non-specific,339261,108,217,0.000128753,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs1_chimp.pars.frame3,1909190051_L1PA7.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs1_chimp,pars,CompleteHit
38882,Q#2882 - >seq9529,specific,238827,498,760,4.4077899999999993e-69,231.02599999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38883,Q#2882 - >seq9529,superfamily,295487,498,760,4.4077899999999993e-69,231.02599999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38884,Q#2882 - >seq9529,specific,333820,504,760,3.3321e-37,138.194,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38885,Q#2882 - >seq9529,superfamily,333820,504,760,3.3321e-37,138.194,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38886,Q#2882 - >seq9529,non-specific,238828,504,725,3.6916199999999996e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38887,Q#2882 - >seq9529,non-specific,275209,455,788,2.03719e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38888,Q#2882 - >seq9529,superfamily,275209,455,788,2.03719e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38889,Q#2882 - >seq9529,non-specific,238185,644,760,1.53696e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38890,Q#2882 - >seq9529,non-specific,274009,293,446,0.000264655,45.4439,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38891,Q#2882 - >seq9529,superfamily,274009,293,446,0.000264655,45.4439,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38892,Q#2882 - >seq9529,specific,311990,1228,1246,0.000500832,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38893,Q#2882 - >seq9529,superfamily,311990,1228,1246,0.000500832,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38894,Q#2882 - >seq9529,non-specific,235175,251,457,0.00148536,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38895,Q#2882 - >seq9529,superfamily,235175,251,457,0.00148536,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38896,Q#2882 - >seq9529,non-specific,274009,291,466,0.00386226,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,BothTerminiTruncated
38897,Q#2882 - >seq9529,non-specific,224117,299,447,0.00694422,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38898,Q#2882 - >seq9529,superfamily,224117,299,447,0.00694422,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs2_gorilla.pars.frame2,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA7,ORF2,hs2_gorilla,pars,C-TerminusTruncated
38899,Q#2883 - >seq9530,specific,197310,9,222,1.07641e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38900,Q#2883 - >seq9530,superfamily,351117,9,222,1.07641e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38901,Q#2883 - >seq9530,non-specific,197306,9,223,5.054899999999999e-48,171.51,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38902,Q#2883 - >seq9530,non-specific,223780,9,221,1.38461e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38903,Q#2883 - >seq9530,non-specific,197307,9,223,7.93077e-23,98.8993,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38904,Q#2883 - >seq9530,non-specific,197320,8,221,2.35767e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38905,Q#2883 - >seq9530,non-specific,197321,7,223,1.0548999999999999e-18,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38906,Q#2883 - >seq9530,specific,335306,10,212,1.4766399999999999e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38907,Q#2883 - >seq9530,non-specific,272954,9,221,4.44483e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38908,Q#2883 - >seq9530,non-specific,273186,9,221,4.77724e-16,79.2452,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38909,Q#2883 - >seq9530,non-specific,197336,7,221,7.62209e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38910,Q#2883 - >seq9530,non-specific,197319,8,223,3.93165e-12,67.3017,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38911,Q#2883 - >seq9530,non-specific,197322,9,222,4.18525e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38912,Q#2883 - >seq9530,non-specific,236970,9,221,1.1358299999999999e-07,54.1298,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38913,Q#2883 - >seq9530,non-specific,197311,7,204,1.13477e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38914,Q#2883 - >seq9530,non-specific,339261,108,217,2.51155e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs2_gorilla.pars.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs2_gorilla,pars,CompleteHit
38915,Q#2886 - >seq9533,specific,238827,510,772,3.4632199999999993e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38916,Q#2886 - >seq9533,superfamily,295487,510,772,3.4632199999999993e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38917,Q#2886 - >seq9533,specific,197310,9,236,2.0075499999999996e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38918,Q#2886 - >seq9533,superfamily,351117,9,236,2.0075499999999996e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38919,Q#2886 - >seq9533,non-specific,197306,9,236,4.37668e-50,177.28799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38920,Q#2886 - >seq9533,specific,333820,516,772,1.03287e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38921,Q#2886 - >seq9533,superfamily,333820,516,772,1.03287e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38922,Q#2886 - >seq9533,non-specific,223780,9,238,4.4868300000000005e-24,103.06200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38923,Q#2886 - >seq9533,non-specific,197307,9,236,4.8403800000000004e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38924,Q#2886 - >seq9533,non-specific,197320,8,236,3.1177900000000006e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38925,Q#2886 - >seq9533,non-specific,197321,7,236,9.55547e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38926,Q#2886 - >seq9533,specific,335306,10,229,1.73419e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38927,Q#2886 - >seq9533,non-specific,273186,9,237,2.4861e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38928,Q#2886 - >seq9533,non-specific,272954,9,236,6.82092e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38929,Q#2886 - >seq9533,non-specific,197319,8,236,1.45687e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38930,Q#2886 - >seq9533,non-specific,197336,7,235,1.71444e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38931,Q#2886 - >seq9533,non-specific,238828,516,737,7.0115e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38932,Q#2886 - >seq9533,non-specific,197322,9,236,7.13397e-12,67.7274,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38933,Q#2886 - >seq9533,non-specific,275209,467,800,2.0976400000000002e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38934,Q#2886 - >seq9533,superfamily,275209,467,800,2.0976400000000002e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38935,Q#2886 - >seq9533,non-specific,339261,108,232,2.9419e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38936,Q#2886 - >seq9533,non-specific,236970,9,238,1.93726e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38937,Q#2886 - >seq9533,non-specific,197311,7,236,4.4771299999999995e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38938,Q#2886 - >seq9533,non-specific,238185,656,772,3.25567e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38939,Q#2886 - >seq9533,non-specific,197317,139,229,0.000259768,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs2_gorilla,marg,N-TerminusTruncated
38940,Q#2886 - >seq9533,non-specific,274009,305,458,0.00042243900000000004,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38941,Q#2886 - >seq9533,superfamily,274009,305,458,0.00042243900000000004,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38942,Q#2886 - >seq9533,specific,311990,1240,1258,0.000627072,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38943,Q#2886 - >seq9533,superfamily,311990,1240,1258,0.000627072,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs2_gorilla,marg,CompleteHit
38944,Q#2886 - >seq9533,non-specific,235175,295,469,0.00221773,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38945,Q#2886 - >seq9533,superfamily,235175,295,469,0.00221773,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38946,Q#2886 - >seq9533,non-specific,338612,158,360,0.00374451,41.1875,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38947,Q#2886 - >seq9533,superfamily,338612,158,360,0.00374451,41.1875,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38948,Q#2886 - >seq9533,non-specific,274009,303,478,0.00605981,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,BothTerminiTruncated
38949,Q#2886 - >seq9533,non-specific,224117,311,459,0.00889404,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38950,Q#2886 - >seq9533,superfamily,224117,311,459,0.00889404,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs2_gorilla.marg.frame3,1909190052_L1PA7.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs2_gorilla,marg,C-TerminusTruncated
38951,Q#2888 - >seq9535,specific,238827,510,772,3.2413899999999996e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38952,Q#2888 - >seq9535,superfamily,295487,510,772,3.2413899999999996e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38953,Q#2888 - >seq9535,specific,197310,9,236,1.8602499999999995e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38954,Q#2888 - >seq9535,superfamily,351117,9,236,1.8602499999999995e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38955,Q#2888 - >seq9535,non-specific,197306,9,236,4.01656e-50,177.28799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38956,Q#2888 - >seq9535,specific,333820,516,772,9.661559999999999e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38957,Q#2888 - >seq9535,superfamily,333820,516,772,9.661559999999999e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38958,Q#2888 - >seq9535,non-specific,223780,9,238,4.2823400000000004e-24,103.06200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38959,Q#2888 - >seq9535,non-specific,197307,9,236,4.75333e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38960,Q#2888 - >seq9535,non-specific,197320,8,236,3.0620099999999995e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38961,Q#2888 - >seq9535,non-specific,197321,7,236,8.865700000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38962,Q#2888 - >seq9535,specific,335306,10,229,1.73573e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38963,Q#2888 - >seq9535,non-specific,273186,9,237,2.39616e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38964,Q#2888 - >seq9535,non-specific,272954,9,236,6.76317e-16,78.9641,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38965,Q#2888 - >seq9535,non-specific,197319,8,236,1.41778e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38966,Q#2888 - >seq9535,non-specific,197336,7,235,1.6841600000000002e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38967,Q#2888 - >seq9535,non-specific,238828,516,737,6.886869999999999e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38968,Q#2888 - >seq9535,non-specific,197322,9,236,7.14062e-12,67.7274,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38969,Q#2888 - >seq9535,non-specific,275209,467,800,1.97243e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38970,Q#2888 - >seq9535,superfamily,275209,467,800,1.97243e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38971,Q#2888 - >seq9535,non-specific,339261,108,232,2.91591e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38972,Q#2888 - >seq9535,non-specific,236970,9,238,1.92145e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38973,Q#2888 - >seq9535,non-specific,197311,7,236,4.39803e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38974,Q#2888 - >seq9535,non-specific,238185,656,772,3.25833e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38975,Q#2888 - >seq9535,non-specific,197317,139,229,0.000255356,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,marg,N-TerminusTruncated
38976,Q#2888 - >seq9535,specific,311990,1241,1259,0.000639971,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38977,Q#2888 - >seq9535,superfamily,311990,1241,1259,0.000639971,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs3_orang,marg,CompleteHit
38978,Q#2888 - >seq9535,non-specific,274009,305,458,0.0008675730000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,C-TerminusTruncated
38979,Q#2888 - >seq9535,superfamily,274009,305,458,0.0008675730000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,C-TerminusTruncated
38980,Q#2888 - >seq9535,non-specific,274009,303,478,0.00193711,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,BothTerminiTruncated
38981,Q#2888 - >seq9535,non-specific,338612,158,360,0.00344235,41.5727,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF2,hs3_orang,marg,BothTerminiTruncated
38982,Q#2888 - >seq9535,superfamily,338612,158,360,0.00344235,41.5727,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF2,hs3_orang,marg,BothTerminiTruncated
38983,Q#2888 - >seq9535,non-specific,235175,305,469,0.00578515,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,BothTerminiTruncated
38984,Q#2888 - >seq9535,superfamily,235175,305,469,0.00578515,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,BothTerminiTruncated
38985,Q#2888 - >seq9535,non-specific,224117,311,459,0.00882702,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,marg,C-TerminusTruncated
38986,Q#2888 - >seq9535,superfamily,224117,311,459,0.00882702,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs3_orang.marg.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs3_orang,marg,C-TerminusTruncated
38987,Q#2892 - >seq9539,specific,238827,510,772,3.3309599999999995e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38988,Q#2892 - >seq9539,superfamily,295487,510,772,3.3309599999999995e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38989,Q#2892 - >seq9539,specific,197310,9,236,1.8400999999999996e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38990,Q#2892 - >seq9539,superfamily,351117,9,236,1.8400999999999996e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38991,Q#2892 - >seq9539,non-specific,197306,9,236,4.09103e-50,177.28799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38992,Q#2892 - >seq9539,specific,333820,516,772,9.9371e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38993,Q#2892 - >seq9539,superfamily,333820,516,772,9.9371e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38994,Q#2892 - >seq9539,non-specific,223780,9,238,4.402269999999999e-24,103.06200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38995,Q#2892 - >seq9539,non-specific,197307,9,236,4.8403800000000004e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38996,Q#2892 - >seq9539,non-specific,197320,8,236,3.0592099999999996e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38997,Q#2892 - >seq9539,non-specific,197321,7,236,8.857610000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38998,Q#2892 - >seq9539,specific,335306,10,229,1.73419e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
38999,Q#2892 - >seq9539,non-specific,273186,9,237,2.41668e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39000,Q#2892 - >seq9539,non-specific,272954,9,236,6.88543e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39001,Q#2892 - >seq9539,non-specific,197319,8,236,1.45687e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39002,Q#2892 - >seq9539,non-specific,197336,7,235,1.76328e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39003,Q#2892 - >seq9539,non-specific,238828,516,737,6.880760000000001e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39004,Q#2892 - >seq9539,non-specific,197322,9,236,7.13397e-12,67.7274,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39005,Q#2892 - >seq9539,non-specific,275209,467,800,1.9882400000000003e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39006,Q#2892 - >seq9539,superfamily,275209,467,800,1.9882400000000003e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39007,Q#2892 - >seq9539,non-specific,339261,108,232,2.9135000000000003e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39008,Q#2892 - >seq9539,non-specific,236970,9,238,1.93726e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39009,Q#2892 - >seq9539,non-specific,197311,7,236,4.3942100000000003e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39010,Q#2892 - >seq9539,non-specific,238185,656,772,3.25567e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39011,Q#2892 - >seq9539,non-specific,197317,139,229,0.000252846,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs3_orang,pars,N-TerminusTruncated
39012,Q#2892 - >seq9539,specific,311990,1240,1258,0.0006394759999999999,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39013,Q#2892 - >seq9539,superfamily,311990,1240,1258,0.0006394759999999999,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs3_orang,pars,CompleteHit
39014,Q#2892 - >seq9539,non-specific,274009,305,458,0.0008815730000000001,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,C-TerminusTruncated
39015,Q#2892 - >seq9539,superfamily,274009,305,458,0.0008815730000000001,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,C-TerminusTruncated
39016,Q#2892 - >seq9539,non-specific,274009,303,478,0.00200195,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,BothTerminiTruncated
39017,Q#2892 - >seq9539,non-specific,338612,158,360,0.00352814,41.5727,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF2,hs3_orang,pars,BothTerminiTruncated
39018,Q#2892 - >seq9539,superfamily,338612,158,360,0.00352814,41.5727,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF2,hs3_orang,pars,BothTerminiTruncated
39019,Q#2892 - >seq9539,non-specific,235175,305,469,0.00603023,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,BothTerminiTruncated
39020,Q#2892 - >seq9539,superfamily,235175,305,469,0.00603023,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,BothTerminiTruncated
39021,Q#2892 - >seq9539,non-specific,224117,311,459,0.0090457,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs3_orang,pars,C-TerminusTruncated
39022,Q#2892 - >seq9539,superfamily,224117,311,459,0.0090457,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs3_orang.pars.frame3,1909190056_L1PA7.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs3_orang,pars,C-TerminusTruncated
39023,Q#2894 - >seq9541,specific,311990,1175,1193,2.9496e-05,41.5036,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs4_gibbon.pars.frame2,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39024,Q#2894 - >seq9541,superfamily,311990,1175,1193,2.9496e-05,41.5036,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs4_gibbon.pars.frame2,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39025,Q#2895 - >seq9542,specific,238827,510,772,5.641799999999999e-69,230.641,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39026,Q#2895 - >seq9542,superfamily,295487,510,772,5.641799999999999e-69,230.641,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39027,Q#2895 - >seq9542,specific,197310,9,236,3.663159999999999e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39028,Q#2895 - >seq9542,superfamily,351117,9,236,3.663159999999999e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39029,Q#2895 - >seq9542,non-specific,197306,9,236,1.2466899999999998e-49,176.13299999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39030,Q#2895 - >seq9542,specific,333820,516,772,2.0698699999999996e-37,138.964,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39031,Q#2895 - >seq9542,superfamily,333820,516,772,2.0698699999999996e-37,138.964,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39032,Q#2895 - >seq9542,non-specific,223780,9,238,1.82641e-24,103.83200000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39033,Q#2895 - >seq9542,non-specific,197307,9,236,8.70212e-24,101.596,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39034,Q#2895 - >seq9542,non-specific,197320,8,236,4.7426899999999995e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39035,Q#2895 - >seq9542,non-specific,197321,7,236,1.44378e-19,89.5336,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39036,Q#2895 - >seq9542,specific,335306,10,229,2.01203e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39037,Q#2895 - >seq9542,non-specific,273186,9,237,7.18931e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39038,Q#2895 - >seq9542,non-specific,272954,9,236,9.35249e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39039,Q#2895 - >seq9542,non-specific,197319,8,236,1.23705e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39040,Q#2895 - >seq9542,non-specific,197336,7,235,1.49734e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39041,Q#2895 - >seq9542,non-specific,238828,516,737,3.0209599999999997e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39042,Q#2895 - >seq9542,non-specific,197322,9,236,1.06039e-11,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39043,Q#2895 - >seq9542,non-specific,275209,467,800,8.3882e-11,64.7864,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39044,Q#2895 - >seq9542,superfamily,275209,467,800,8.3882e-11,64.7864,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39045,Q#2895 - >seq9542,non-specific,339261,108,232,4.90594e-10,58.1175,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39046,Q#2895 - >seq9542,non-specific,197311,7,236,3.7694699999999997e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39047,Q#2895 - >seq9542,non-specific,236970,9,238,5.190930000000001e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39048,Q#2895 - >seq9542,non-specific,238185,656,772,1.37729e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,pars,CompleteHit
39049,Q#2895 - >seq9542,non-specific,274009,303,478,0.000348887,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39050,Q#2895 - >seq9542,superfamily,274009,303,478,0.000348887,44.6735,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39051,Q#2895 - >seq9542,non-specific,197317,139,229,0.00035762900000000004,43.3596,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
39052,Q#2895 - >seq9542,non-specific,274009,305,458,0.000686282,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39053,Q#2895 - >seq9542,non-specific,235175,263,469,0.00121886,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39054,Q#2895 - >seq9542,superfamily,235175,263,469,0.00121886,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39055,Q#2895 - >seq9542,non-specific,224117,123,433,0.00406549,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
39056,Q#2895 - >seq9542,superfamily,224117,123,433,0.00406549,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,N-TerminusTruncated
39057,Q#2895 - >seq9542,non-specific,224117,311,459,0.00923191,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39058,Q#2895 - >seq9542,superfamily,224117,311,459,0.00923191,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.pars.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39059,Q#2898 - >seq9545,specific,238827,510,772,3.4632199999999993e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39060,Q#2898 - >seq9545,superfamily,295487,510,772,3.4632199999999993e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39061,Q#2898 - >seq9545,specific,197310,9,236,1.7031399999999999e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39062,Q#2898 - >seq9545,superfamily,351117,9,236,1.7031399999999999e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39063,Q#2898 - >seq9545,non-specific,197306,9,236,1.23989e-49,176.13299999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39064,Q#2898 - >seq9545,specific,333820,516,772,1.0131e-36,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39065,Q#2898 - >seq9545,superfamily,333820,516,772,1.0131e-36,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39066,Q#2898 - >seq9545,non-specific,223780,9,238,5.80072e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39067,Q#2898 - >seq9545,non-specific,197307,9,236,2.39897e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39068,Q#2898 - >seq9545,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39069,Q#2898 - >seq9545,non-specific,197321,7,236,3.3377699999999997e-19,88.37799999999999,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39070,Q#2898 - >seq9545,specific,335306,10,229,2.03925e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39071,Q#2898 - >seq9545,non-specific,273186,9,237,1.3078100000000002e-16,80.786,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39072,Q#2898 - >seq9545,non-specific,272954,9,236,2.18997e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39073,Q#2898 - >seq9545,non-specific,197336,7,235,2.1868899999999998e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39074,Q#2898 - >seq9545,non-specific,197319,8,236,4.0042199999999997e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39075,Q#2898 - >seq9545,non-specific,238828,516,737,6.94583e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39076,Q#2898 - >seq9545,non-specific,197322,9,236,1.0754000000000002e-11,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39077,Q#2898 - >seq9545,non-specific,275209,467,800,2.0976400000000002e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39078,Q#2898 - >seq9545,superfamily,275209,467,800,2.0976400000000002e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39079,Q#2898 - >seq9545,non-specific,339261,108,232,2.35354e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39080,Q#2898 - >seq9545,non-specific,197311,7,236,3.22757e-07,52.2941,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39081,Q#2898 - >seq9545,non-specific,236970,9,238,6.844620000000001e-07,52.2038,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39082,Q#2898 - >seq9545,non-specific,238185,656,772,3.25567e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39083,Q#2898 - >seq9545,non-specific,197317,139,229,0.00037230000000000005,43.3596,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
39084,Q#2898 - >seq9545,non-specific,274009,303,478,0.000459715,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39085,Q#2898 - >seq9545,superfamily,274009,303,478,0.000459715,44.6735,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39086,Q#2898 - >seq9545,specific,311990,1240,1258,0.000627072,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39087,Q#2898 - >seq9545,superfamily,311990,1240,1258,0.000627072,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs4_gibbon,marg,CompleteHit
39088,Q#2898 - >seq9545,non-specific,274009,305,458,0.00086679,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39089,Q#2898 - >seq9545,non-specific,235175,263,469,0.00322036,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39090,Q#2898 - >seq9545,superfamily,235175,263,469,0.00322036,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39091,Q#2898 - >seq9545,non-specific,224117,123,433,0.00607963,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
39092,Q#2898 - >seq9545,superfamily,224117,123,433,0.00607963,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs4_gibbon.marg.frame3,1909190119_L1PA7.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs4_gibbon,marg,N-TerminusTruncated
39093,Q#2899 - >seq9546,specific,238827,510,772,3.6786299999999995e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39094,Q#2899 - >seq9546,superfamily,295487,510,772,3.6786299999999995e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39095,Q#2899 - >seq9546,specific,197310,9,236,3.323319999999999e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39096,Q#2899 - >seq9546,superfamily,351117,9,236,3.323319999999999e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39097,Q#2899 - >seq9546,non-specific,197306,9,236,2.8163299999999994e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39098,Q#2899 - >seq9546,specific,333820,516,772,1.11684e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39099,Q#2899 - >seq9546,superfamily,333820,516,772,1.11684e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39100,Q#2899 - >seq9546,non-specific,223780,9,238,1.5027499999999998e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39101,Q#2899 - >seq9546,non-specific,197307,9,236,5.44606e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39102,Q#2899 - >seq9546,non-specific,197320,8,236,6.354490000000001e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39103,Q#2899 - >seq9546,specific,335306,10,229,6.465159999999999e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39104,Q#2899 - >seq9546,non-specific,197321,7,236,8.49429e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39105,Q#2899 - >seq9546,non-specific,273186,9,237,1.5000999999999999e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39106,Q#2899 - >seq9546,non-specific,272954,9,236,9.671720000000001e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39107,Q#2899 - >seq9546,non-specific,197336,7,235,2.01203e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39108,Q#2899 - >seq9546,non-specific,197319,8,236,1.12097e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39109,Q#2899 - >seq9546,non-specific,238828,516,737,1.34986e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39110,Q#2899 - >seq9546,non-specific,197322,9,236,3.42217e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39111,Q#2899 - >seq9546,non-specific,275209,467,800,1.69467e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39112,Q#2899 - >seq9546,superfamily,275209,467,800,1.69467e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39113,Q#2899 - >seq9546,non-specific,339261,108,232,2.6623800000000005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39114,Q#2899 - >seq9546,non-specific,197311,7,236,8.537409999999999e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39115,Q#2899 - >seq9546,non-specific,236970,9,238,9.49406e-07,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,marg,CompleteHit
39116,Q#2899 - >seq9546,non-specific,238185,656,772,3.25833e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs0_human,marg,CompleteHit
39117,Q#2899 - >seq9546,non-specific,274009,305,458,0.00042282199999999994,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,C-TerminusTruncated
39118,Q#2899 - >seq9546,superfamily,274009,305,458,0.00042282199999999994,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,C-TerminusTruncated
39119,Q#2899 - >seq9546,specific,311990,1241,1259,0.000678705,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs0_human,marg,CompleteHit
39120,Q#2899 - >seq9546,superfamily,311990,1241,1259,0.000678705,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs0_human,marg,CompleteHit
39121,Q#2899 - >seq9546,non-specific,197317,139,229,0.00139457,41.8188,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,marg,N-TerminusTruncated
39122,Q#2899 - >seq9546,non-specific,235175,295,469,0.00239571,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,BothTerminiTruncated
39123,Q#2899 - >seq9546,superfamily,235175,295,469,0.00239571,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,BothTerminiTruncated
39124,Q#2899 - >seq9546,non-specific,274009,303,478,0.0063271,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,BothTerminiTruncated
39125,Q#2899 - >seq9546,non-specific,224117,311,459,0.00952484,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,marg,C-TerminusTruncated
39126,Q#2899 - >seq9546,superfamily,224117,311,459,0.00952484,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs0_human.marg.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs0_human,marg,C-TerminusTruncated
39127,Q#2902 - >seq9549,specific,238827,510,772,3.6786299999999995e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39128,Q#2902 - >seq9549,superfamily,295487,510,772,3.6786299999999995e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39129,Q#2902 - >seq9549,specific,197310,9,236,3.323319999999999e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39130,Q#2902 - >seq9549,superfamily,351117,9,236,3.323319999999999e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39131,Q#2902 - >seq9549,non-specific,197306,9,236,2.8163299999999994e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39132,Q#2902 - >seq9549,specific,333820,516,772,1.11684e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39133,Q#2902 - >seq9549,superfamily,333820,516,772,1.11684e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39134,Q#2902 - >seq9549,non-specific,223780,9,238,1.5027499999999998e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39135,Q#2902 - >seq9549,non-specific,197307,9,236,5.44606e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39136,Q#2902 - >seq9549,non-specific,197320,8,236,6.354490000000001e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39137,Q#2902 - >seq9549,specific,335306,10,229,6.465159999999999e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39138,Q#2902 - >seq9549,non-specific,197321,7,236,8.49429e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39139,Q#2902 - >seq9549,non-specific,273186,9,237,1.5000999999999999e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39140,Q#2902 - >seq9549,non-specific,272954,9,236,9.671720000000001e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39141,Q#2902 - >seq9549,non-specific,197336,7,235,2.01203e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39142,Q#2902 - >seq9549,non-specific,197319,8,236,1.12097e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39143,Q#2902 - >seq9549,non-specific,238828,516,737,1.34986e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39144,Q#2902 - >seq9549,non-specific,197322,9,236,3.42217e-11,65.8014,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39145,Q#2902 - >seq9549,non-specific,275209,467,800,1.69467e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39146,Q#2902 - >seq9549,superfamily,275209,467,800,1.69467e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39147,Q#2902 - >seq9549,non-specific,339261,108,232,2.6623800000000005e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39148,Q#2902 - >seq9549,non-specific,197311,7,236,8.537409999999999e-07,50.7533,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39149,Q#2902 - >seq9549,non-specific,236970,9,238,9.49406e-07,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs0_human,pars,CompleteHit
39150,Q#2902 - >seq9549,non-specific,238185,656,772,3.25833e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs0_human,pars,CompleteHit
39151,Q#2902 - >seq9549,non-specific,274009,305,458,0.00042282199999999994,44.6735,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,C-TerminusTruncated
39152,Q#2902 - >seq9549,superfamily,274009,305,458,0.00042282199999999994,44.6735,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,C-TerminusTruncated
39153,Q#2902 - >seq9549,specific,311990,1241,1259,0.000678705,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs0_human,pars,CompleteHit
39154,Q#2902 - >seq9549,superfamily,311990,1241,1259,0.000678705,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs0_human,pars,CompleteHit
39155,Q#2902 - >seq9549,non-specific,197317,139,229,0.00139457,41.8188,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs0_human,pars,N-TerminusTruncated
39156,Q#2902 - >seq9549,non-specific,235175,295,469,0.00239571,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,BothTerminiTruncated
39157,Q#2902 - >seq9549,superfamily,235175,295,469,0.00239571,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,BothTerminiTruncated
39158,Q#2902 - >seq9549,non-specific,274009,303,478,0.0063271,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,BothTerminiTruncated
39159,Q#2902 - >seq9549,non-specific,224117,311,459,0.00952484,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs0_human,pars,C-TerminusTruncated
39160,Q#2902 - >seq9549,superfamily,224117,311,459,0.00952484,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs0_human.pars.frame3,1909190120_L1PA7.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs0_human,pars,C-TerminusTruncated
39161,Q#2905 - >seq9552,specific,238827,516,778,3.2468999999999993e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39162,Q#2905 - >seq9552,superfamily,295487,516,778,3.2468999999999993e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39163,Q#2905 - >seq9552,specific,197310,9,241,2.64178e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39164,Q#2905 - >seq9552,superfamily,351117,9,241,2.64178e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39165,Q#2905 - >seq9552,non-specific,197306,9,241,5.10514e-48,171.51,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39166,Q#2905 - >seq9552,specific,333820,522,778,9.618399999999999e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39167,Q#2905 - >seq9552,superfamily,333820,522,778,9.618399999999999e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39168,Q#2905 - >seq9552,non-specific,223780,9,243,3.6085000000000003e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39169,Q#2905 - >seq9552,non-specific,197307,9,241,2.53082e-21,94.6621,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39170,Q#2905 - >seq9552,non-specific,197320,8,241,7.3948e-18,84.4889,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39171,Q#2905 - >seq9552,specific,335306,10,234,1.9804199999999998e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39172,Q#2905 - >seq9552,non-specific,197321,7,241,5.1375800000000007e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39173,Q#2905 - >seq9552,non-specific,273186,9,242,6.52797e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39174,Q#2905 - >seq9552,non-specific,272954,9,241,1.01359e-13,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39175,Q#2905 - >seq9552,non-specific,238828,522,743,1.30682e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39176,Q#2905 - >seq9552,non-specific,197319,8,241,1.74939e-11,65.7609,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39177,Q#2905 - >seq9552,non-specific,197336,7,240,2.2329e-11,65.3263,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39178,Q#2905 - >seq9552,non-specific,275209,473,806,1.33908e-10,64.4012,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39179,Q#2905 - >seq9552,superfamily,275209,473,806,1.33908e-10,64.4012,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39180,Q#2905 - >seq9552,non-specific,197322,9,241,1.7336299999999998e-10,63.4902,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39181,Q#2905 - >seq9552,non-specific,339261,113,237,3.77105e-10,58.5027,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39182,Q#2905 - >seq9552,non-specific,197311,7,241,2.1611e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39183,Q#2905 - >seq9552,non-specific,235175,268,475,2.8556999999999998e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39184,Q#2905 - >seq9552,superfamily,235175,268,475,2.8556999999999998e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39185,Q#2905 - >seq9552,non-specific,238185,662,778,3.27423e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39186,Q#2905 - >seq9552,non-specific,236970,9,243,5.0473500000000004e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39187,Q#2905 - >seq9552,non-specific,274009,310,464,0.00012903,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
39188,Q#2905 - >seq9552,superfamily,274009,310,464,0.00012903,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
39189,Q#2905 - >seq9552,non-specific,197317,144,234,0.00030732400000000004,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
39190,Q#2905 - >seq9552,specific,311990,1247,1265,0.000606249,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39191,Q#2905 - >seq9552,superfamily,311990,1247,1265,0.000606249,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs6_sqmonkey,marg,CompleteHit
39192,Q#2905 - >seq9552,non-specific,274009,308,484,0.00217381,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39193,Q#2905 - >seq9552,non-specific,224117,268,475,0.00507935,41.2384,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39194,Q#2905 - >seq9552,superfamily,224117,268,475,0.00507935,41.2384,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs6_sqmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39195,Q#2910 - >seq9557,specific,238827,519,781,3.4951299999999998e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39196,Q#2910 - >seq9557,superfamily,295487,519,781,3.4951299999999998e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39197,Q#2910 - >seq9557,specific,197310,9,245,1.5375299999999999e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39198,Q#2910 - >seq9557,superfamily,351117,9,245,1.5375299999999999e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39199,Q#2910 - >seq9557,non-specific,197306,9,245,3.19508e-47,169.199,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39200,Q#2910 - >seq9557,specific,333820,525,781,9.73691e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39201,Q#2910 - >seq9557,superfamily,333820,525,781,9.73691e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39202,Q#2910 - >seq9557,non-specific,223780,9,247,1.29045e-21,95.7431,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39203,Q#2910 - >seq9557,non-specific,197307,9,245,1.2281200000000001e-20,92.7361,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39204,Q#2910 - >seq9557,specific,335306,10,238,2.33446e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39205,Q#2910 - >seq9557,non-specific,197320,8,245,8.07922e-17,81.4073,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39206,Q#2910 - >seq9557,non-specific,197321,7,245,3.42836e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39207,Q#2910 - >seq9557,non-specific,273186,9,246,7.334959999999999e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39208,Q#2910 - >seq9557,non-specific,272954,9,245,1.2927200000000002e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39209,Q#2910 - >seq9557,non-specific,238828,525,746,1.31028e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39210,Q#2910 - >seq9557,non-specific,197319,8,245,2.47639e-12,68.0721,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39211,Q#2910 - >seq9557,non-specific,197336,7,244,6.4288e-12,66.8671,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39212,Q#2910 - >seq9557,non-specific,275209,476,809,1.5082e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39213,Q#2910 - >seq9557,superfamily,275209,476,809,1.5082e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39214,Q#2910 - >seq9557,non-specific,339261,117,241,1.8196800000000003e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39215,Q#2910 - >seq9557,non-specific,197322,9,245,8.46256e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39216,Q#2910 - >seq9557,non-specific,197311,7,245,1.7243800000000003e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39217,Q#2910 - >seq9557,non-specific,238185,665,781,3.3468e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39218,Q#2910 - >seq9557,non-specific,236970,9,247,0.000192322,44.4998,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39219,Q#2910 - >seq9557,non-specific,197317,148,238,0.000262044,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39220,Q#2910 - >seq9557,non-specific,274009,312,487,0.000459977,44.6735,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39221,Q#2910 - >seq9557,superfamily,274009,312,487,0.000459977,44.6735,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39222,Q#2910 - >seq9557,specific,311990,1250,1268,0.000663643,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39223,Q#2910 - >seq9557,superfamily,311990,1250,1268,0.000663643,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA7,ORF2,hs5_gmonkey,marg,CompleteHit
39224,Q#2910 - >seq9557,non-specific,274009,314,467,0.000889535,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
39225,Q#2910 - >seq9557,non-specific,226098,147,248,0.00194331,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39226,Q#2910 - >seq9557,non-specific,235175,304,478,0.00286121,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39227,Q#2910 - >seq9557,superfamily,235175,304,478,0.00286121,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39228,Q#2910 - >seq9557,non-specific,338612,167,369,0.00696774,40.4171,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39229,Q#2910 - >seq9557,superfamily,338612,167,369,0.00696774,40.4171,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA7,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39230,Q#2910 - >seq9557,non-specific,224117,132,442,0.0092037,40.0828,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39231,Q#2910 - >seq9557,superfamily,224117,132,442,0.0092037,40.0828,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA7.ORF2.hs5_gmonkey.marg.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA7,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39232,Q#2913 - >seq9560,specific,238827,510,772,3.4699399999999992e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39233,Q#2913 - >seq9560,superfamily,295487,510,772,3.4699399999999992e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39234,Q#2913 - >seq9560,specific,197310,9,236,3.733739999999999e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39235,Q#2913 - >seq9560,superfamily,351117,9,236,3.733739999999999e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39236,Q#2913 - >seq9560,non-specific,197306,9,236,8.941549999999999e-50,176.518,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39237,Q#2913 - >seq9560,specific,333820,516,772,1.0849299999999998e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39238,Q#2913 - >seq9560,superfamily,333820,516,772,1.0849299999999998e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39239,Q#2913 - >seq9560,non-specific,223780,9,238,5.3806300000000004e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39240,Q#2913 - >seq9560,non-specific,197307,9,236,7.229480000000001e-24,101.98100000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39241,Q#2913 - >seq9560,non-specific,197320,8,236,1.06013e-19,89.8817,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39242,Q#2913 - >seq9560,non-specific,197321,7,236,2.35307e-19,88.7632,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39243,Q#2913 - >seq9560,specific,335306,10,229,1.73573e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39244,Q#2913 - >seq9560,non-specific,273186,9,237,9.06257e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39245,Q#2913 - >seq9560,non-specific,272954,9,236,2.85199e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39246,Q#2913 - >seq9560,non-specific,197319,8,236,1.49974e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39247,Q#2913 - >seq9560,non-specific,197336,7,235,2.8713499999999997e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39248,Q#2913 - >seq9560,non-specific,238828,516,737,1.3122100000000001e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39249,Q#2913 - >seq9560,non-specific,197322,9,236,1.53584e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39250,Q#2913 - >seq9560,non-specific,275209,467,800,1.7098699999999997e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39251,Q#2913 - >seq9560,superfamily,275209,467,800,1.7098699999999997e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39252,Q#2913 - >seq9560,non-specific,339261,108,232,1.6078e-09,56.5767,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39253,Q#2913 - >seq9560,non-specific,236970,9,238,2.57018e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39254,Q#2913 - >seq9560,non-specific,197311,7,236,1.1191500000000001e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39255,Q#2913 - >seq9560,non-specific,238185,656,772,3.25833e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39256,Q#2913 - >seq9560,non-specific,197317,139,229,0.000253068,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
39257,Q#2913 - >seq9560,non-specific,274009,303,478,0.0005092730000000001,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39258,Q#2913 - >seq9560,superfamily,274009,303,478,0.0005092730000000001,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39259,Q#2913 - >seq9560,specific,311990,1241,1259,0.000678705,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39260,Q#2913 - >seq9560,superfamily,311990,1241,1259,0.000678705,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs5_gmonkey,pars,CompleteHit
39261,Q#2913 - >seq9560,non-specific,274009,305,458,0.000897418,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
39262,Q#2913 - >seq9560,non-specific,226098,138,239,0.00192818,41.232,COG3568,ElsH,N,cl00490,"Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]; Metal-dependent hydrolase [General function prediction only].",L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
39263,Q#2913 - >seq9560,non-specific,235175,295,469,0.0036294000000000005,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39264,Q#2913 - >seq9560,superfamily,235175,295,469,0.0036294000000000005,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39265,Q#2913 - >seq9560,non-specific,338612,158,360,0.00709104,40.4171,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39266,Q#2913 - >seq9560,superfamily,338612,158,360,0.00709104,40.4171,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA7.ORF2.hs5_gmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA7,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39267,Q#2916 - >seq9563,specific,238827,510,772,3.4632199999999993e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39268,Q#2916 - >seq9563,superfamily,295487,510,772,3.4632199999999993e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39269,Q#2916 - >seq9563,specific,197310,9,236,2.41278e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39270,Q#2916 - >seq9563,superfamily,351117,9,236,2.41278e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39271,Q#2916 - >seq9563,non-specific,197306,9,236,5.057759999999999e-50,177.28799999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39272,Q#2916 - >seq9563,specific,333820,516,772,1.09452e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39273,Q#2916 - >seq9563,superfamily,333820,516,772,1.09452e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39274,Q#2916 - >seq9563,non-specific,197307,9,236,5.3244e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39275,Q#2916 - >seq9563,non-specific,223780,9,238,5.37568e-24,102.677,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39276,Q#2916 - >seq9563,non-specific,197320,8,236,3.59439e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39277,Q#2916 - >seq9563,non-specific,197321,7,236,1.1226199999999999e-19,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39278,Q#2916 - >seq9563,specific,335306,10,229,1.73419e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39279,Q#2916 - >seq9563,non-specific,273186,9,237,2.73219e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39280,Q#2916 - >seq9563,non-specific,272954,9,236,7.78157e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39281,Q#2916 - >seq9563,non-specific,197319,8,236,1.7244000000000002e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39282,Q#2916 - >seq9563,non-specific,197336,7,235,2.0291099999999999e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39283,Q#2916 - >seq9563,non-specific,238828,516,737,1.42714e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39284,Q#2916 - >seq9563,non-specific,197322,9,236,7.13397e-12,67.7274,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39285,Q#2916 - >seq9563,non-specific,275209,467,800,1.60474e-10,64.016,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39286,Q#2916 - >seq9563,superfamily,275209,467,800,1.60474e-10,64.016,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39287,Q#2916 - >seq9563,non-specific,339261,108,232,2.99954e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39288,Q#2916 - >seq9563,non-specific,236970,9,238,2.06457e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39289,Q#2916 - >seq9563,non-specific,197311,7,236,4.4771299999999995e-07,51.5237,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39290,Q#2916 - >seq9563,non-specific,238185,656,772,3.25567e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39291,Q#2916 - >seq9563,non-specific,197317,139,229,0.000294652,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA7,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
39292,Q#2916 - >seq9563,specific,311990,1240,1258,0.000627072,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39293,Q#2916 - >seq9563,superfamily,311990,1240,1258,0.000627072,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA7,ORF2,hs6_sqmonkey,pars,CompleteHit
39294,Q#2916 - >seq9563,non-specific,274009,305,458,0.00162051,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39295,Q#2916 - >seq9563,superfamily,274009,305,458,0.00162051,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39296,Q#2916 - >seq9563,non-specific,274009,303,478,0.00273725,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA7,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39297,Q#2916 - >seq9563,non-specific,236270,273,404,0.00826223,40.0326,PRK08471,flgK,NC,cl35700,flagellar hook-associated protein FlgK; Validated,L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA7,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39298,Q#2916 - >seq9563,superfamily,236270,273,404,0.00826223,40.0326,cl35700,flgK superfamily,NC, - ,flagellar hook-associated protein FlgK; Validated,L1PA7.ORF2.hs6_sqmonkey.pars.frame3,1909190120_L1PA7.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PA7,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39299,Q#2919 - >seq9566,specific,238827,510,772,3.0030999999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39300,Q#2919 - >seq9566,superfamily,295487,510,772,3.0030999999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39301,Q#2919 - >seq9566,non-specific,238827,510,772,3.0030999999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39302,Q#2919 - >seq9566,specific,197310,9,236,2.1481499999999996e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39303,Q#2919 - >seq9566,superfamily,351117,9,236,2.1481499999999996e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39304,Q#2919 - >seq9566,non-specific,197310,9,236,2.1481499999999996e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39305,Q#2919 - >seq9566,non-specific,197306,9,236,1.4607199999999999e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39306,Q#2919 - >seq9566,non-specific,197306,9,236,1.4607199999999999e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39307,Q#2919 - >seq9566,specific,333820,516,772,1.3669e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39308,Q#2919 - >seq9566,superfamily,333820,516,772,1.3669e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39309,Q#2919 - >seq9566,non-specific,333820,516,772,1.3669e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39310,Q#2919 - >seq9566,non-specific,223780,9,238,1.00704e-23,101.906,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39311,Q#2919 - >seq9566,non-specific,223780,9,238,1.00704e-23,101.906,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39312,Q#2919 - >seq9566,non-specific,197307,9,236,2.05988e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39313,Q#2919 - >seq9566,non-specific,197307,9,236,2.05988e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39314,Q#2919 - >seq9566,non-specific,197320,8,236,9.43424e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39315,Q#2919 - >seq9566,non-specific,197320,8,236,9.43424e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39316,Q#2919 - >seq9566,non-specific,197321,7,236,7.25572e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39317,Q#2919 - >seq9566,non-specific,197321,7,236,7.25572e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39318,Q#2919 - >seq9566,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39319,Q#2919 - >seq9566,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39320,Q#2919 - >seq9566,non-specific,273186,9,237,6.73558e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39321,Q#2919 - >seq9566,non-specific,273186,9,237,6.73558e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39322,Q#2919 - >seq9566,non-specific,272954,9,236,1.4065799999999999e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39323,Q#2919 - >seq9566,non-specific,272954,9,236,1.4065799999999999e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39324,Q#2919 - >seq9566,non-specific,197336,7,235,4.2098400000000003e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39325,Q#2919 - >seq9566,non-specific,197336,7,235,4.2098400000000003e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39326,Q#2919 - >seq9566,non-specific,238828,516,737,2.08068e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39327,Q#2919 - >seq9566,non-specific,238828,516,737,2.08068e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39328,Q#2919 - >seq9566,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39329,Q#2919 - >seq9566,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39330,Q#2919 - >seq9566,non-specific,197319,8,236,3.1872099999999997e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39331,Q#2919 - >seq9566,non-specific,197319,8,236,3.1872099999999997e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39332,Q#2919 - >seq9566,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39333,Q#2919 - >seq9566,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39334,Q#2919 - >seq9566,non-specific,275209,467,800,8.204969999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39335,Q#2919 - >seq9566,superfamily,275209,467,800,8.204969999999999e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39336,Q#2919 - >seq9566,non-specific,275209,467,800,8.204969999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39337,Q#2919 - >seq9566,non-specific,197311,7,236,1.38584e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39338,Q#2919 - >seq9566,non-specific,197311,7,236,1.38584e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39339,Q#2919 - >seq9566,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39340,Q#2919 - >seq9566,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39341,Q#2919 - >seq9566,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39342,Q#2919 - >seq9566,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39343,Q#2919 - >seq9566,non-specific,197317,139,229,0.000264487,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,N-TerminusTruncated
39344,Q#2919 - >seq9566,non-specific,197317,139,229,0.000264487,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,N-TerminusTruncated
39345,Q#2919 - >seq9566,specific,311990,1240,1258,0.000755325,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39346,Q#2919 - >seq9566,superfamily,311990,1240,1258,0.000755325,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39347,Q#2919 - >seq9566,non-specific,311990,1240,1258,0.000755325,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,pars,CompleteHit
39348,Q#2919 - >seq9566,non-specific,235175,263,464,0.000775057,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39349,Q#2919 - >seq9566,superfamily,235175,263,464,0.000775057,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39350,Q#2919 - >seq9566,non-specific,235175,263,464,0.000775057,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39351,Q#2919 - >seq9566,non-specific,274009,307,458,0.00122595,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39352,Q#2919 - >seq9566,superfamily,274009,307,458,0.00122595,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39353,Q#2919 - >seq9566,non-specific,274009,307,458,0.00122595,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39354,Q#2919 - >seq9566,non-specific,224117,306,459,0.00330759,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39355,Q#2919 - >seq9566,superfamily,224117,306,459,0.00330759,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39356,Q#2919 - >seq9566,non-specific,224117,306,459,0.00330759,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,C-TerminusTruncated
39357,Q#2919 - >seq9566,non-specific,223496,291,427,0.00593342,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39358,Q#2919 - >seq9566,superfamily,223496,291,427,0.00593342,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39359,Q#2919 - >seq9566,non-specific,223496,291,427,0.00593342,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39360,Q#2919 - >seq9566,non-specific,274009,301,478,0.0060088,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39361,Q#2919 - >seq9566,non-specific,274009,301,478,0.0060088,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.pars.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,pars,BothTerminiTruncated
39362,Q#2922 - >seq9569,specific,238827,510,772,3.0030999999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39363,Q#2922 - >seq9569,superfamily,295487,510,772,3.0030999999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39364,Q#2922 - >seq9569,non-specific,238827,510,772,3.0030999999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39365,Q#2922 - >seq9569,specific,197310,9,236,2.1481499999999996e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39366,Q#2922 - >seq9569,superfamily,351117,9,236,2.1481499999999996e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39367,Q#2922 - >seq9569,non-specific,197310,9,236,2.1481499999999996e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39368,Q#2922 - >seq9569,non-specific,197306,9,236,1.4607199999999999e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39369,Q#2922 - >seq9569,non-specific,197306,9,236,1.4607199999999999e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39370,Q#2922 - >seq9569,specific,333820,516,772,1.3669e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39371,Q#2922 - >seq9569,superfamily,333820,516,772,1.3669e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39372,Q#2922 - >seq9569,non-specific,333820,516,772,1.3669e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39373,Q#2922 - >seq9569,non-specific,223780,9,238,1.00704e-23,101.906,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39374,Q#2922 - >seq9569,non-specific,223780,9,238,1.00704e-23,101.906,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39375,Q#2922 - >seq9569,non-specific,197307,9,236,2.05988e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39376,Q#2922 - >seq9569,non-specific,197307,9,236,2.05988e-23,100.825,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39377,Q#2922 - >seq9569,non-specific,197320,8,236,9.43424e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39378,Q#2922 - >seq9569,non-specific,197320,8,236,9.43424e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39379,Q#2922 - >seq9569,non-specific,197321,7,236,7.25572e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39380,Q#2922 - >seq9569,non-specific,197321,7,236,7.25572e-19,87.6076,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39381,Q#2922 - >seq9569,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39382,Q#2922 - >seq9569,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39383,Q#2922 - >seq9569,non-specific,273186,9,237,6.73558e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39384,Q#2922 - >seq9569,non-specific,273186,9,237,6.73558e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39385,Q#2922 - >seq9569,non-specific,272954,9,236,1.4065799999999999e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39386,Q#2922 - >seq9569,non-specific,272954,9,236,1.4065799999999999e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39387,Q#2922 - >seq9569,non-specific,197336,7,235,4.2098400000000003e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39388,Q#2922 - >seq9569,non-specific,197336,7,235,4.2098400000000003e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39389,Q#2922 - >seq9569,non-specific,238828,516,737,2.08068e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39390,Q#2922 - >seq9569,non-specific,238828,516,737,2.08068e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39391,Q#2922 - >seq9569,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39392,Q#2922 - >seq9569,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39393,Q#2922 - >seq9569,non-specific,197319,8,236,3.1872099999999997e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39394,Q#2922 - >seq9569,non-specific,197319,8,236,3.1872099999999997e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39395,Q#2922 - >seq9569,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39396,Q#2922 - >seq9569,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39397,Q#2922 - >seq9569,non-specific,275209,467,800,8.204969999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39398,Q#2922 - >seq9569,superfamily,275209,467,800,8.204969999999999e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39399,Q#2922 - >seq9569,non-specific,275209,467,800,8.204969999999999e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39400,Q#2922 - >seq9569,non-specific,197311,7,236,1.38584e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39401,Q#2922 - >seq9569,non-specific,197311,7,236,1.38584e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39402,Q#2922 - >seq9569,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39403,Q#2922 - >seq9569,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39404,Q#2922 - >seq9569,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39405,Q#2922 - >seq9569,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39406,Q#2922 - >seq9569,non-specific,197317,139,229,0.000264487,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,N-TerminusTruncated
39407,Q#2922 - >seq9569,non-specific,197317,139,229,0.000264487,44.13,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,N-TerminusTruncated
39408,Q#2922 - >seq9569,specific,311990,1240,1258,0.000755325,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39409,Q#2922 - >seq9569,superfamily,311990,1240,1258,0.000755325,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39410,Q#2922 - >seq9569,non-specific,311990,1240,1258,0.000755325,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs1_chimp,marg,CompleteHit
39411,Q#2922 - >seq9569,non-specific,235175,263,464,0.000775057,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39412,Q#2922 - >seq9569,superfamily,235175,263,464,0.000775057,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39413,Q#2922 - >seq9569,non-specific,235175,263,464,0.000775057,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39414,Q#2922 - >seq9569,non-specific,274009,307,458,0.00122595,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39415,Q#2922 - >seq9569,superfamily,274009,307,458,0.00122595,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39416,Q#2922 - >seq9569,non-specific,274009,307,458,0.00122595,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39417,Q#2922 - >seq9569,non-specific,224117,306,459,0.00330759,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39418,Q#2922 - >seq9569,superfamily,224117,306,459,0.00330759,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39419,Q#2922 - >seq9569,non-specific,224117,306,459,0.00330759,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,C-TerminusTruncated
39420,Q#2922 - >seq9569,non-specific,223496,291,427,0.00593342,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39421,Q#2922 - >seq9569,superfamily,223496,291,427,0.00593342,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39422,Q#2922 - >seq9569,non-specific,223496,291,427,0.00593342,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39423,Q#2922 - >seq9569,non-specific,274009,301,478,0.0060088,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39424,Q#2922 - >seq9569,non-specific,274009,301,478,0.0060088,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs1_chimp.marg.frame3,1909190123_L1PA8.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs1_chimp,marg,BothTerminiTruncated
39425,Q#2925 - >seq9572,specific,238827,510,772,2.9167399999999996e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39426,Q#2925 - >seq9572,superfamily,295487,510,772,2.9167399999999996e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39427,Q#2925 - >seq9572,non-specific,238827,510,772,2.9167399999999996e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39428,Q#2925 - >seq9572,specific,197310,9,236,4.7937799999999995e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39429,Q#2925 - >seq9572,superfamily,351117,9,236,4.7937799999999995e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39430,Q#2925 - >seq9572,non-specific,197310,9,236,4.7937799999999995e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39431,Q#2925 - >seq9572,non-specific,197306,9,236,3.4121399999999992e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39432,Q#2925 - >seq9572,non-specific,197306,9,236,3.4121399999999992e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39433,Q#2925 - >seq9572,specific,333820,516,772,1.50556e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39434,Q#2925 - >seq9572,superfamily,333820,516,772,1.50556e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39435,Q#2925 - >seq9572,non-specific,333820,516,772,1.50556e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39436,Q#2925 - >seq9572,non-specific,223780,9,238,1.2064600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39437,Q#2925 - >seq9572,non-specific,223780,9,238,1.2064600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39438,Q#2925 - >seq9572,non-specific,197307,9,236,3.2537100000000003e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39439,Q#2925 - >seq9572,non-specific,197307,9,236,3.2537100000000003e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39440,Q#2925 - >seq9572,non-specific,197320,8,236,3.1177900000000006e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39441,Q#2925 - >seq9572,non-specific,197320,8,236,3.1177900000000006e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39442,Q#2925 - >seq9572,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39443,Q#2925 - >seq9572,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39444,Q#2925 - >seq9572,non-specific,197321,7,236,2.15436e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39445,Q#2925 - >seq9572,non-specific,197321,7,236,2.15436e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39446,Q#2925 - >seq9572,non-specific,273186,9,237,2.68486e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39447,Q#2925 - >seq9572,non-specific,273186,9,237,2.68486e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39448,Q#2925 - >seq9572,non-specific,272954,9,236,5.68807e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39449,Q#2925 - >seq9572,non-specific,272954,9,236,5.68807e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39450,Q#2925 - >seq9572,non-specific,197336,7,235,6.59446e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39451,Q#2925 - >seq9572,non-specific,197336,7,235,6.59446e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39452,Q#2925 - >seq9572,non-specific,238828,516,737,2.2648400000000003e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39453,Q#2925 - >seq9572,non-specific,238828,516,737,2.2648400000000003e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39454,Q#2925 - >seq9572,non-specific,197319,8,236,3.6319800000000004e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39455,Q#2925 - >seq9572,non-specific,197319,8,236,3.6319800000000004e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39456,Q#2925 - >seq9572,non-specific,197322,9,236,4.9975e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39457,Q#2925 - >seq9572,non-specific,197322,9,236,4.9975e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39458,Q#2925 - >seq9572,non-specific,275209,467,800,1.0249999999999999e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39459,Q#2925 - >seq9572,superfamily,275209,467,800,1.0249999999999999e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39460,Q#2925 - >seq9572,non-specific,275209,467,800,1.0249999999999999e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39461,Q#2925 - >seq9572,non-specific,339261,108,232,1.20088e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39462,Q#2925 - >seq9572,non-specific,339261,108,232,1.20088e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39463,Q#2925 - >seq9572,non-specific,197311,7,236,3.45461e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39464,Q#2925 - >seq9572,non-specific,197311,7,236,3.45461e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39465,Q#2925 - >seq9572,non-specific,236970,9,238,3.85482e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39466,Q#2925 - >seq9572,non-specific,236970,9,238,3.85482e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39467,Q#2925 - >seq9572,non-specific,238185,656,772,2.8403899999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39468,Q#2925 - >seq9572,non-specific,238185,656,772,2.8403899999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39469,Q#2925 - >seq9572,non-specific,197317,139,229,0.000276662,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
39470,Q#2925 - >seq9572,non-specific,197317,139,229,0.000276662,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,marg,N-TerminusTruncated
39471,Q#2925 - >seq9572,specific,311990,1240,1258,0.0007334539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39472,Q#2925 - >seq9572,superfamily,311990,1240,1258,0.0007334539999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39473,Q#2925 - >seq9572,non-specific,311990,1240,1258,0.0007334539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,marg,CompleteHit
39474,Q#2925 - >seq9572,non-specific,274009,307,458,0.00295366,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,marg,C-TerminusTruncated
39475,Q#2925 - >seq9572,superfamily,274009,307,458,0.00295366,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,marg,C-TerminusTruncated
39476,Q#2925 - >seq9572,non-specific,274009,307,458,0.00295366,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,marg,C-TerminusTruncated
39477,Q#2925 - >seq9572,non-specific,274009,306,478,0.00595821,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,marg,BothTerminiTruncated
39478,Q#2925 - >seq9572,non-specific,274009,306,478,0.00595821,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.marg.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,marg,BothTerminiTruncated
39479,Q#2926 - >seq9573,specific,238827,510,772,2.9167399999999996e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39480,Q#2926 - >seq9573,superfamily,295487,510,772,2.9167399999999996e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39481,Q#2926 - >seq9573,non-specific,238827,510,772,2.9167399999999996e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39482,Q#2926 - >seq9573,specific,197310,9,236,4.7937799999999995e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39483,Q#2926 - >seq9573,superfamily,351117,9,236,4.7937799999999995e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39484,Q#2926 - >seq9573,non-specific,197310,9,236,4.7937799999999995e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39485,Q#2926 - >seq9573,non-specific,197306,9,236,3.4121399999999992e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39486,Q#2926 - >seq9573,non-specific,197306,9,236,3.4121399999999992e-49,174.977,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39487,Q#2926 - >seq9573,specific,333820,516,772,1.50556e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39488,Q#2926 - >seq9573,superfamily,333820,516,772,1.50556e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39489,Q#2926 - >seq9573,non-specific,333820,516,772,1.50556e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39490,Q#2926 - >seq9573,non-specific,223780,9,238,1.2064600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39491,Q#2926 - >seq9573,non-specific,223780,9,238,1.2064600000000001e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39492,Q#2926 - >seq9573,non-specific,197307,9,236,3.2537100000000003e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39493,Q#2926 - >seq9573,non-specific,197307,9,236,3.2537100000000003e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39494,Q#2926 - >seq9573,non-specific,197320,8,236,3.1177900000000006e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39495,Q#2926 - >seq9573,non-specific,197320,8,236,3.1177900000000006e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39496,Q#2926 - >seq9573,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39497,Q#2926 - >seq9573,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39498,Q#2926 - >seq9573,non-specific,197321,7,236,2.15436e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39499,Q#2926 - >seq9573,non-specific,197321,7,236,2.15436e-18,86.0668,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39500,Q#2926 - >seq9573,non-specific,273186,9,237,2.68486e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39501,Q#2926 - >seq9573,non-specific,273186,9,237,2.68486e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39502,Q#2926 - >seq9573,non-specific,272954,9,236,5.68807e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39503,Q#2926 - >seq9573,non-specific,272954,9,236,5.68807e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39504,Q#2926 - >seq9573,non-specific,197336,7,235,6.59446e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39505,Q#2926 - >seq9573,non-specific,197336,7,235,6.59446e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39506,Q#2926 - >seq9573,non-specific,238828,516,737,2.2648400000000003e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39507,Q#2926 - >seq9573,non-specific,238828,516,737,2.2648400000000003e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39508,Q#2926 - >seq9573,non-specific,197319,8,236,3.6319800000000004e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39509,Q#2926 - >seq9573,non-specific,197319,8,236,3.6319800000000004e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39510,Q#2926 - >seq9573,non-specific,197322,9,236,4.9975e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39511,Q#2926 - >seq9573,non-specific,197322,9,236,4.9975e-12,68.1126,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39512,Q#2926 - >seq9573,non-specific,275209,467,800,1.0249999999999999e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39513,Q#2926 - >seq9573,superfamily,275209,467,800,1.0249999999999999e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39514,Q#2926 - >seq9573,non-specific,275209,467,800,1.0249999999999999e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39515,Q#2926 - >seq9573,non-specific,339261,108,232,1.20088e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39516,Q#2926 - >seq9573,non-specific,339261,108,232,1.20088e-09,56.9619,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39517,Q#2926 - >seq9573,non-specific,197311,7,236,3.45461e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39518,Q#2926 - >seq9573,non-specific,197311,7,236,3.45461e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39519,Q#2926 - >seq9573,non-specific,236970,9,238,3.85482e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39520,Q#2926 - >seq9573,non-specific,236970,9,238,3.85482e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39521,Q#2926 - >seq9573,non-specific,238185,656,772,2.8403899999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39522,Q#2926 - >seq9573,non-specific,238185,656,772,2.8403899999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39523,Q#2926 - >seq9573,non-specific,197317,139,229,0.000276662,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
39524,Q#2926 - >seq9573,non-specific,197317,139,229,0.000276662,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs2_gorilla,pars,N-TerminusTruncated
39525,Q#2926 - >seq9573,specific,311990,1240,1258,0.0007334539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39526,Q#2926 - >seq9573,superfamily,311990,1240,1258,0.0007334539999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39527,Q#2926 - >seq9573,non-specific,311990,1240,1258,0.0007334539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs2_gorilla,pars,CompleteHit
39528,Q#2926 - >seq9573,non-specific,274009,307,458,0.00295366,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,pars,C-TerminusTruncated
39529,Q#2926 - >seq9573,superfamily,274009,307,458,0.00295366,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,pars,C-TerminusTruncated
39530,Q#2926 - >seq9573,non-specific,274009,307,458,0.00295366,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,pars,C-TerminusTruncated
39531,Q#2926 - >seq9573,non-specific,274009,306,478,0.00595821,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,pars,BothTerminiTruncated
39532,Q#2926 - >seq9573,non-specific,274009,306,478,0.00595821,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs2_gorilla.pars.frame3,1909190124_L1PA8.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs2_gorilla,pars,BothTerminiTruncated
39533,Q#2931 - >seq9578,specific,238827,510,772,2.7514099999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39534,Q#2931 - >seq9578,superfamily,295487,510,772,2.7514099999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39535,Q#2931 - >seq9578,non-specific,238827,510,772,2.7514099999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39536,Q#2931 - >seq9578,specific,197310,9,236,2.60659e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39537,Q#2931 - >seq9578,superfamily,351117,9,236,2.60659e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39538,Q#2931 - >seq9578,non-specific,197310,9,236,2.60659e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39539,Q#2931 - >seq9578,non-specific,197306,9,236,1.62415e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39540,Q#2931 - >seq9578,non-specific,197306,9,236,1.62415e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39541,Q#2931 - >seq9578,specific,333820,516,772,1.34074e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39542,Q#2931 - >seq9578,superfamily,333820,516,772,1.34074e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39543,Q#2931 - >seq9578,non-specific,333820,516,772,1.34074e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39544,Q#2931 - >seq9578,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39545,Q#2931 - >seq9578,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39546,Q#2931 - >seq9578,non-specific,197307,9,236,2.39897e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39547,Q#2931 - >seq9578,non-specific,197307,9,236,2.39897e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39548,Q#2931 - >seq9578,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39549,Q#2931 - >seq9578,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39550,Q#2931 - >seq9578,non-specific,197321,7,236,8.603629999999999e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39551,Q#2931 - >seq9578,non-specific,197321,7,236,8.603629999999999e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39552,Q#2931 - >seq9578,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39553,Q#2931 - >seq9578,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39554,Q#2931 - >seq9578,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39555,Q#2931 - >seq9578,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39556,Q#2931 - >seq9578,non-specific,272954,9,236,1.57423e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39557,Q#2931 - >seq9578,non-specific,272954,9,236,1.57423e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39558,Q#2931 - >seq9578,non-specific,238828,516,737,4.14753e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39559,Q#2931 - >seq9578,non-specific,238828,516,737,4.14753e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39560,Q#2931 - >seq9578,non-specific,197336,7,235,4.843819999999999e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39561,Q#2931 - >seq9578,non-specific,197336,7,235,4.843819999999999e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39562,Q#2931 - >seq9578,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39563,Q#2931 - >seq9578,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39564,Q#2931 - >seq9578,non-specific,197319,8,236,3.805419999999999e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39565,Q#2931 - >seq9578,non-specific,197319,8,236,3.805419999999999e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39566,Q#2931 - >seq9578,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39567,Q#2931 - >seq9578,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39568,Q#2931 - >seq9578,non-specific,275209,467,800,7.24333e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39569,Q#2931 - >seq9578,superfamily,275209,467,800,7.24333e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39570,Q#2931 - >seq9578,non-specific,275209,467,800,7.24333e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39571,Q#2931 - >seq9578,non-specific,197311,7,236,1.42517e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39572,Q#2931 - >seq9578,non-specific,197311,7,236,1.42517e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39573,Q#2931 - >seq9578,non-specific,236970,9,238,3.5861099999999997e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39574,Q#2931 - >seq9578,non-specific,236970,9,238,3.5861099999999997e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39575,Q#2931 - >seq9578,non-specific,238185,656,772,2.60184e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39576,Q#2931 - >seq9578,non-specific,238185,656,772,2.60184e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39577,Q#2931 - >seq9578,non-specific,235175,263,469,0.000264027,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,BothTerminiTruncated
39578,Q#2931 - >seq9578,superfamily,235175,263,469,0.000264027,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,BothTerminiTruncated
39579,Q#2931 - >seq9578,non-specific,235175,263,469,0.000264027,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,BothTerminiTruncated
39580,Q#2931 - >seq9578,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,N-TerminusTruncated
39581,Q#2931 - >seq9578,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,pars,N-TerminusTruncated
39582,Q#2931 - >seq9578,specific,311990,1240,1258,0.000712217,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39583,Q#2931 - >seq9578,superfamily,311990,1240,1258,0.000712217,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39584,Q#2931 - >seq9578,non-specific,311990,1240,1258,0.000712217,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,pars,CompleteHit
39585,Q#2931 - >seq9578,non-specific,274009,307,458,0.000837963,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,C-TerminusTruncated
39586,Q#2931 - >seq9578,superfamily,274009,307,458,0.000837963,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,C-TerminusTruncated
39587,Q#2931 - >seq9578,non-specific,274009,307,458,0.000837963,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,C-TerminusTruncated
39588,Q#2931 - >seq9578,non-specific,274009,306,478,0.00355747,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,BothTerminiTruncated
39589,Q#2931 - >seq9578,non-specific,274009,306,478,0.00355747,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.pars.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,pars,BothTerminiTruncated
39590,Q#2934 - >seq9581,specific,238827,510,772,2.7514099999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39591,Q#2934 - >seq9581,superfamily,295487,510,772,2.7514099999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39592,Q#2934 - >seq9581,non-specific,238827,510,772,2.7514099999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39593,Q#2934 - >seq9581,specific,197310,9,236,2.60659e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39594,Q#2934 - >seq9581,superfamily,351117,9,236,2.60659e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39595,Q#2934 - >seq9581,non-specific,197310,9,236,2.60659e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39596,Q#2934 - >seq9581,non-specific,197306,9,236,1.62415e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39597,Q#2934 - >seq9581,non-specific,197306,9,236,1.62415e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39598,Q#2934 - >seq9581,specific,333820,516,772,1.34074e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39599,Q#2934 - >seq9581,superfamily,333820,516,772,1.34074e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39600,Q#2934 - >seq9581,non-specific,333820,516,772,1.34074e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39601,Q#2934 - >seq9581,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39602,Q#2934 - >seq9581,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39603,Q#2934 - >seq9581,non-specific,197307,9,236,2.39897e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39604,Q#2934 - >seq9581,non-specific,197307,9,236,2.39897e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39605,Q#2934 - >seq9581,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39606,Q#2934 - >seq9581,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39607,Q#2934 - >seq9581,non-specific,197321,7,236,8.603629999999999e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39608,Q#2934 - >seq9581,non-specific,197321,7,236,8.603629999999999e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39609,Q#2934 - >seq9581,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39610,Q#2934 - >seq9581,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39611,Q#2934 - >seq9581,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39612,Q#2934 - >seq9581,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39613,Q#2934 - >seq9581,non-specific,272954,9,236,1.57423e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39614,Q#2934 - >seq9581,non-specific,272954,9,236,1.57423e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39615,Q#2934 - >seq9581,non-specific,238828,516,737,4.14753e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39616,Q#2934 - >seq9581,non-specific,238828,516,737,4.14753e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39617,Q#2934 - >seq9581,non-specific,197336,7,235,4.843819999999999e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39618,Q#2934 - >seq9581,non-specific,197336,7,235,4.843819999999999e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39619,Q#2934 - >seq9581,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39620,Q#2934 - >seq9581,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39621,Q#2934 - >seq9581,non-specific,197319,8,236,3.805419999999999e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39622,Q#2934 - >seq9581,non-specific,197319,8,236,3.805419999999999e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39623,Q#2934 - >seq9581,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39624,Q#2934 - >seq9581,non-specific,339261,108,232,2.0948899999999998e-10,59.2731,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39625,Q#2934 - >seq9581,non-specific,275209,467,800,7.24333e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39626,Q#2934 - >seq9581,superfamily,275209,467,800,7.24333e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39627,Q#2934 - >seq9581,non-specific,275209,467,800,7.24333e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39628,Q#2934 - >seq9581,non-specific,197311,7,236,1.42517e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39629,Q#2934 - >seq9581,non-specific,197311,7,236,1.42517e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39630,Q#2934 - >seq9581,non-specific,236970,9,238,3.5861099999999997e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39631,Q#2934 - >seq9581,non-specific,236970,9,238,3.5861099999999997e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39632,Q#2934 - >seq9581,non-specific,238185,656,772,2.60184e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39633,Q#2934 - >seq9581,non-specific,238185,656,772,2.60184e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39634,Q#2934 - >seq9581,non-specific,235175,263,469,0.000264027,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,BothTerminiTruncated
39635,Q#2934 - >seq9581,superfamily,235175,263,469,0.000264027,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,BothTerminiTruncated
39636,Q#2934 - >seq9581,non-specific,235175,263,469,0.000264027,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,BothTerminiTruncated
39637,Q#2934 - >seq9581,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,N-TerminusTruncated
39638,Q#2934 - >seq9581,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs3_orang,marg,N-TerminusTruncated
39639,Q#2934 - >seq9581,specific,311990,1240,1258,0.000712217,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39640,Q#2934 - >seq9581,superfamily,311990,1240,1258,0.000712217,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39641,Q#2934 - >seq9581,non-specific,311990,1240,1258,0.000712217,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs3_orang,marg,CompleteHit
39642,Q#2934 - >seq9581,non-specific,274009,307,458,0.000837963,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,C-TerminusTruncated
39643,Q#2934 - >seq9581,superfamily,274009,307,458,0.000837963,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,C-TerminusTruncated
39644,Q#2934 - >seq9581,non-specific,274009,307,458,0.000837963,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,C-TerminusTruncated
39645,Q#2934 - >seq9581,non-specific,274009,306,478,0.00355747,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,BothTerminiTruncated
39646,Q#2934 - >seq9581,non-specific,274009,306,478,0.00355747,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs3_orang.marg.frame3,1909190127_L1PA8.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs3_orang,marg,BothTerminiTruncated
39647,Q#2935 - >seq9582,specific,238827,510,772,2.6464299999999994e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39648,Q#2935 - >seq9582,superfamily,295487,510,772,2.6464299999999994e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39649,Q#2935 - >seq9582,specific,197310,9,236,2.20876e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39650,Q#2935 - >seq9582,superfamily,351117,9,236,2.20876e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39651,Q#2935 - >seq9582,non-specific,197306,9,236,1.07461e-48,173.43599999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39652,Q#2935 - >seq9582,specific,333820,516,772,5.18556e-36,134.727,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39653,Q#2935 - >seq9582,superfamily,333820,516,772,5.18556e-36,134.727,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39654,Q#2935 - >seq9582,non-specific,223780,9,238,7.77222e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39655,Q#2935 - >seq9582,non-specific,197307,9,236,9.272740000000001e-23,98.8993,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39656,Q#2935 - >seq9582,non-specific,197320,8,236,5.829500000000001e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39657,Q#2935 - >seq9582,specific,335306,10,229,1.5366e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39658,Q#2935 - >seq9582,non-specific,197321,7,236,2.56287e-17,82.9852,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39659,Q#2935 - >seq9582,non-specific,273186,9,237,8.44744e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39660,Q#2935 - >seq9582,non-specific,272954,9,236,4.94219e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39661,Q#2935 - >seq9582,non-specific,197336,7,235,8.09988e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39662,Q#2935 - >seq9582,non-specific,238828,516,737,2.37409e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39663,Q#2935 - >seq9582,non-specific,197322,9,236,1.92683e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39664,Q#2935 - >seq9582,non-specific,197319,8,236,2.8469000000000004e-11,64.9905,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39665,Q#2935 - >seq9582,non-specific,339261,108,232,4.3789300000000005e-10,58.1175,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39666,Q#2935 - >seq9582,non-specific,275209,467,800,1.0716300000000002e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39667,Q#2935 - >seq9582,superfamily,275209,467,800,1.0716300000000002e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39668,Q#2935 - >seq9582,non-specific,197311,7,236,9.52312e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39669,Q#2935 - >seq9582,non-specific,238185,656,772,2.89631e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39670,Q#2935 - >seq9582,non-specific,274009,307,458,0.00019240400000000002,45.8291,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39671,Q#2935 - >seq9582,superfamily,274009,307,458,0.00019240400000000002,45.8291,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39672,Q#2935 - >seq9582,non-specific,235175,295,469,0.000257395,45.0548,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39673,Q#2935 - >seq9582,superfamily,235175,295,469,0.000257395,45.0548,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39674,Q#2935 - >seq9582,specific,311990,1240,1258,0.000719227,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39675,Q#2935 - >seq9582,superfamily,311990,1240,1258,0.000719227,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs4_gibbon,marg,CompleteHit
39676,Q#2935 - >seq9582,non-specific,197317,139,229,0.0009734069999999999,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,N-TerminusTruncated
39677,Q#2935 - >seq9582,non-specific,224117,311,459,0.00395021,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39678,Q#2935 - >seq9582,superfamily,224117,311,459,0.00395021,41.2384,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39679,Q#2935 - >seq9582,non-specific,274009,306,478,0.00421285,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39680,Q#2935 - >seq9582,non-specific,223496,263,450,0.00668075,40.5139,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39681,Q#2935 - >seq9582,superfamily,223496,263,450,0.00668075,40.5139,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA8,ORF2,hs4_gibbon,marg,C-TerminusTruncated
39682,Q#2935 - >seq9582,non-specific,223496,291,427,0.00702919,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.marg.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs4_gibbon,marg,BothTerminiTruncated
39683,Q#2939 - >seq9586,specific,311990,1175,1193,2.9496e-05,41.5036,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs4_gibbon.pars.frame2,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39684,Q#2939 - >seq9586,superfamily,311990,1175,1193,2.9496e-05,41.5036,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs4_gibbon.pars.frame2,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39685,Q#2940 - >seq9587,specific,238827,510,772,4.7244499999999995e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39686,Q#2940 - >seq9587,superfamily,295487,510,772,4.7244499999999995e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39687,Q#2940 - >seq9587,specific,197310,9,236,4.5289299999999995e-59,202.967,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39688,Q#2940 - >seq9587,superfamily,351117,9,236,4.5289299999999995e-59,202.967,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39689,Q#2940 - >seq9587,non-specific,197306,9,236,1.0599e-48,173.43599999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39690,Q#2940 - >seq9587,specific,333820,516,772,9.99919e-37,137.03799999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39691,Q#2940 - >seq9587,superfamily,333820,516,772,9.99919e-37,137.03799999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39692,Q#2940 - >seq9587,non-specific,223780,9,238,2.56987e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39693,Q#2940 - >seq9587,non-specific,197307,9,236,3.4632e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39694,Q#2940 - >seq9587,non-specific,197320,8,236,2.90498e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39695,Q#2940 - >seq9587,non-specific,197321,7,236,1.19867e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39696,Q#2940 - >seq9587,specific,335306,10,229,1.5160999999999998e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39697,Q#2940 - >seq9587,non-specific,273186,9,237,4.97072e-15,76.1636,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39698,Q#2940 - >seq9587,non-specific,272954,9,236,2.43597e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39699,Q#2940 - >seq9587,non-specific,197336,7,235,5.65389e-13,69.9487,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39700,Q#2940 - >seq9587,non-specific,238828,516,737,1.13361e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39701,Q#2940 - >seq9587,non-specific,197319,8,236,9.360839999999999e-12,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39702,Q#2940 - >seq9587,non-specific,197322,9,236,1.89996e-11,66.5718,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39703,Q#2940 - >seq9587,non-specific,275209,467,800,4.5741199999999994e-10,62.4752,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39704,Q#2940 - >seq9587,superfamily,275209,467,800,4.5741199999999994e-10,62.4752,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39705,Q#2940 - >seq9587,non-specific,339261,108,232,9.39687e-10,57.3471,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39706,Q#2940 - >seq9587,non-specific,197311,7,236,1.0906099999999999e-05,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39707,Q#2940 - >seq9587,non-specific,238185,656,772,1.31178e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs4_gibbon,pars,CompleteHit
39708,Q#2940 - >seq9587,non-specific,235175,263,469,0.00010689,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39709,Q#2940 - >seq9587,superfamily,235175,263,469,0.00010689,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39710,Q#2940 - >seq9587,non-specific,274009,307,458,0.00015231200000000001,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39711,Q#2940 - >seq9587,superfamily,274009,307,458,0.00015231200000000001,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39712,Q#2940 - >seq9587,non-specific,197317,139,229,0.000960658,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,N-TerminusTruncated
39713,Q#2940 - >seq9587,non-specific,224117,311,459,0.00307562,41.6236,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39714,Q#2940 - >seq9587,superfamily,224117,311,459,0.00307562,41.6236,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39715,Q#2940 - >seq9587,non-specific,274009,306,478,0.00339297,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39716,Q#2940 - >seq9587,non-specific,223496,263,450,0.00413583,41.2843,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39717,Q#2940 - >seq9587,superfamily,223496,263,450,0.00413583,41.2843,cl33865,SbcC superfamily,C, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA8,ORF2,hs4_gibbon,pars,C-TerminusTruncated
39718,Q#2940 - >seq9587,non-specific,223496,299,427,0.0051118000000000005,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8.ORF2.hs4_gibbon.pars.frame3,1909190132_L1PA8.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8,ORF2,hs4_gibbon,pars,BothTerminiTruncated
39719,Q#2942 - >seq9589,specific,238827,510,772,2.8328699999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39720,Q#2942 - >seq9589,superfamily,295487,510,772,2.8328699999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39721,Q#2942 - >seq9589,non-specific,238827,510,772,2.8328699999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39722,Q#2942 - >seq9589,specific,197310,9,236,2.6833299999999996e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39723,Q#2942 - >seq9589,superfamily,351117,9,236,2.6833299999999996e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39724,Q#2942 - >seq9589,non-specific,197310,9,236,2.6833299999999996e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39725,Q#2942 - >seq9589,non-specific,197306,9,236,1.73754e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39726,Q#2942 - >seq9589,non-specific,197306,9,236,1.73754e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39727,Q#2942 - >seq9589,specific,333820,516,772,1.26522e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39728,Q#2942 - >seq9589,superfamily,333820,516,772,1.26522e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39729,Q#2942 - >seq9589,non-specific,333820,516,772,1.26522e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39730,Q#2942 - >seq9589,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39731,Q#2942 - >seq9589,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39732,Q#2942 - >seq9589,non-specific,197307,9,236,2.2019000000000003e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39733,Q#2942 - >seq9589,non-specific,197307,9,236,2.2019000000000003e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39734,Q#2942 - >seq9589,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39735,Q#2942 - >seq9589,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39736,Q#2942 - >seq9589,non-specific,197321,7,236,8.76806e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39737,Q#2942 - >seq9589,non-specific,197321,7,236,8.76806e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39738,Q#2942 - >seq9589,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39739,Q#2942 - >seq9589,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39740,Q#2942 - >seq9589,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39741,Q#2942 - >seq9589,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39742,Q#2942 - >seq9589,non-specific,272954,9,236,1.53053e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39743,Q#2942 - >seq9589,non-specific,272954,9,236,1.53053e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39744,Q#2942 - >seq9589,non-specific,197336,7,235,4.5368900000000004e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39745,Q#2942 - >seq9589,non-specific,197336,7,235,4.5368900000000004e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39746,Q#2942 - >seq9589,non-specific,238828,516,737,2.2436e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39747,Q#2942 - >seq9589,non-specific,238828,516,737,2.2436e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39748,Q#2942 - >seq9589,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39749,Q#2942 - >seq9589,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39750,Q#2942 - >seq9589,non-specific,197319,8,236,3.70039e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39751,Q#2942 - >seq9589,non-specific,197319,8,236,3.70039e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39752,Q#2942 - >seq9589,non-specific,339261,108,232,2.37649e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39753,Q#2942 - >seq9589,non-specific,339261,108,232,2.37649e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39754,Q#2942 - >seq9589,non-specific,275209,467,800,9.294019999999998e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39755,Q#2942 - >seq9589,superfamily,275209,467,800,9.294019999999998e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39756,Q#2942 - >seq9589,non-specific,275209,467,800,9.294019999999998e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39757,Q#2942 - >seq9589,non-specific,197311,7,236,1.47935e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39758,Q#2942 - >seq9589,non-specific,197311,7,236,1.47935e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39759,Q#2942 - >seq9589,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39760,Q#2942 - >seq9589,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39761,Q#2942 - >seq9589,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39762,Q#2942 - >seq9589,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39763,Q#2942 - >seq9589,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39764,Q#2942 - >seq9589,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
39765,Q#2942 - >seq9589,specific,311990,1240,1258,0.0006848539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39766,Q#2942 - >seq9589,superfamily,311990,1240,1258,0.0006848539999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39767,Q#2942 - >seq9589,non-specific,311990,1240,1258,0.0006848539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,marg,CompleteHit
39768,Q#2942 - >seq9589,non-specific,274009,307,458,0.0007831530000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
39769,Q#2942 - >seq9589,superfamily,274009,307,458,0.0007831530000000001,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
39770,Q#2942 - >seq9589,non-specific,274009,307,458,0.0007831530000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
39771,Q#2942 - >seq9589,non-specific,274009,306,478,0.00318719,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39772,Q#2942 - >seq9589,non-specific,274009,306,478,0.00318719,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.marg.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
39773,Q#2944 - >seq9591,specific,238827,510,772,2.8328699999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39774,Q#2944 - >seq9591,superfamily,295487,510,772,2.8328699999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39775,Q#2944 - >seq9591,non-specific,238827,510,772,2.8328699999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39776,Q#2944 - >seq9591,specific,197310,9,236,2.6833299999999996e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39777,Q#2944 - >seq9591,superfamily,351117,9,236,2.6833299999999996e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39778,Q#2944 - >seq9591,non-specific,197310,9,236,2.6833299999999996e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39779,Q#2944 - >seq9591,non-specific,197306,9,236,1.73754e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39780,Q#2944 - >seq9591,non-specific,197306,9,236,1.73754e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39781,Q#2944 - >seq9591,specific,333820,516,772,1.26522e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39782,Q#2944 - >seq9591,superfamily,333820,516,772,1.26522e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39783,Q#2944 - >seq9591,non-specific,333820,516,772,1.26522e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39784,Q#2944 - >seq9591,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39785,Q#2944 - >seq9591,non-specific,223780,9,238,1.2179899999999999e-23,101.521,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39786,Q#2944 - >seq9591,non-specific,197307,9,236,2.2019000000000003e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39787,Q#2944 - >seq9591,non-specific,197307,9,236,2.2019000000000003e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39788,Q#2944 - >seq9591,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39789,Q#2944 - >seq9591,non-specific,197320,8,236,1.03734e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39790,Q#2944 - >seq9591,non-specific,197321,7,236,8.76806e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39791,Q#2944 - >seq9591,non-specific,197321,7,236,8.76806e-19,87.2224,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39792,Q#2944 - >seq9591,specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39793,Q#2944 - >seq9591,non-specific,335306,10,229,1.6534799999999998e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39794,Q#2944 - >seq9591,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39795,Q#2944 - >seq9591,non-specific,273186,9,237,8.130699999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39796,Q#2944 - >seq9591,non-specific,272954,9,236,1.53053e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39797,Q#2944 - >seq9591,non-specific,272954,9,236,1.53053e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39798,Q#2944 - >seq9591,non-specific,197336,7,235,4.5368900000000004e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39799,Q#2944 - >seq9591,non-specific,197336,7,235,4.5368900000000004e-13,70.3339,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39800,Q#2944 - >seq9591,non-specific,238828,516,737,2.2436e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39801,Q#2944 - >seq9591,non-specific,238828,516,737,2.2436e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39802,Q#2944 - >seq9591,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39803,Q#2944 - >seq9591,non-specific,197322,9,236,2.32001e-12,69.2682,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39804,Q#2944 - >seq9591,non-specific,197319,8,236,3.70039e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39805,Q#2944 - >seq9591,non-specific,197319,8,236,3.70039e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39806,Q#2944 - >seq9591,non-specific,339261,108,232,2.37649e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39807,Q#2944 - >seq9591,non-specific,339261,108,232,2.37649e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39808,Q#2944 - >seq9591,non-specific,275209,467,800,9.294019999999998e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39809,Q#2944 - >seq9591,superfamily,275209,467,800,9.294019999999998e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39810,Q#2944 - >seq9591,non-specific,275209,467,800,9.294019999999998e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39811,Q#2944 - >seq9591,non-specific,197311,7,236,1.47935e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39812,Q#2944 - >seq9591,non-specific,197311,7,236,1.47935e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39813,Q#2944 - >seq9591,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39814,Q#2944 - >seq9591,non-specific,236970,9,238,3.3361e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39815,Q#2944 - >seq9591,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39816,Q#2944 - >seq9591,non-specific,238185,656,772,2.81284e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39817,Q#2944 - >seq9591,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
39818,Q#2944 - >seq9591,non-specific,197317,139,229,0.000289396,43.7448,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
39819,Q#2944 - >seq9591,specific,311990,1240,1258,0.0006848539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39820,Q#2944 - >seq9591,superfamily,311990,1240,1258,0.0006848539999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39821,Q#2944 - >seq9591,non-specific,311990,1240,1258,0.0006848539999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs5_gmonkey,pars,CompleteHit
39822,Q#2944 - >seq9591,non-specific,274009,307,458,0.0007831530000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
39823,Q#2944 - >seq9591,superfamily,274009,307,458,0.0007831530000000001,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
39824,Q#2944 - >seq9591,non-specific,274009,307,458,0.0007831530000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
39825,Q#2944 - >seq9591,non-specific,274009,306,478,0.00318719,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39826,Q#2944 - >seq9591,non-specific,274009,306,478,0.00318719,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs5_gmonkey.pars.frame3,1909190136_L1PA8.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
39827,Q#2948 - >seq9595,specific,311990,1178,1196,2.95681e-05,41.5036,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs6_sqmonkey.pars.frame2,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39828,Q#2948 - >seq9595,superfamily,311990,1178,1196,2.95681e-05,41.5036,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs6_sqmonkey.pars.frame2,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39829,Q#2949 - >seq9596,specific,238827,510,772,5.41489e-68,227.94400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39830,Q#2949 - >seq9596,superfamily,295487,510,772,5.41489e-68,227.94400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39831,Q#2949 - >seq9596,specific,197310,9,236,6.606819999999999e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39832,Q#2949 - >seq9596,superfamily,351117,9,236,6.606819999999999e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39833,Q#2949 - >seq9596,non-specific,197306,9,236,5.70919e-50,176.903,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39834,Q#2949 - >seq9596,specific,333820,516,772,2.66105e-37,138.579,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39835,Q#2949 - >seq9596,superfamily,333820,516,772,2.66105e-37,138.579,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39836,Q#2949 - >seq9596,non-specific,197307,9,236,1.61034e-24,103.90700000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39837,Q#2949 - >seq9596,non-specific,223780,9,238,3.08243e-24,103.447,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39838,Q#2949 - >seq9596,non-specific,197320,8,236,1.55327e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39839,Q#2949 - >seq9596,non-specific,197321,7,236,1.1500499999999998e-19,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39840,Q#2949 - >seq9596,specific,335306,10,229,1.38733e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39841,Q#2949 - >seq9596,non-specific,273186,9,237,8.76385e-17,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39842,Q#2949 - >seq9596,non-specific,272954,9,236,2.11989e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39843,Q#2949 - >seq9596,non-specific,197336,7,235,2.75148e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39844,Q#2949 - >seq9596,non-specific,197319,8,236,4.3780600000000004e-13,70.3833,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39845,Q#2949 - >seq9596,non-specific,238828,516,737,1.04137e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39846,Q#2949 - >seq9596,non-specific,197322,9,236,1.51584e-12,69.6534,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39847,Q#2949 - >seq9596,non-specific,275209,467,800,4.0016199999999996e-10,62.8604,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39848,Q#2949 - >seq9596,superfamily,275209,467,800,4.0016199999999996e-10,62.8604,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39849,Q#2949 - >seq9596,non-specific,339261,108,232,6.13226e-10,57.7323,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39850,Q#2949 - >seq9596,non-specific,236970,9,238,7.52898e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39851,Q#2949 - >seq9596,non-specific,197311,7,236,2.24206e-06,49.5977,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39852,Q#2949 - >seq9596,non-specific,238185,656,772,1.16698e-05,45.0344,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,pars,CompleteHit
39853,Q#2949 - >seq9596,non-specific,197317,139,229,0.000190445,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
39854,Q#2949 - >seq9596,non-specific,274009,307,458,0.000641389,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39855,Q#2949 - >seq9596,superfamily,274009,307,458,0.000641389,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39856,Q#2949 - >seq9596,non-specific,274009,306,478,0.00272335,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39857,Q#2949 - >seq9596,non-specific,338612,158,360,0.00532515,40.8023,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA8,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39858,Q#2949 - >seq9596,superfamily,338612,158,360,0.00532515,40.8023,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
39859,Q#2949 - >seq9596,non-specific,224117,311,459,0.00931029,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39860,Q#2949 - >seq9596,superfamily,224117,311,459,0.00931029,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs6_sqmonkey.pars.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
39861,Q#2952 - >seq9599,specific,238827,511,773,3.10311e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39862,Q#2952 - >seq9599,superfamily,295487,511,773,3.10311e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39863,Q#2952 - >seq9599,specific,197310,9,237,8.75016e-60,204.893,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39864,Q#2952 - >seq9599,superfamily,351117,9,237,8.75016e-60,204.893,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39865,Q#2952 - >seq9599,non-specific,197306,9,237,2.95289e-50,177.674,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39866,Q#2952 - >seq9599,specific,333820,517,773,1.33015e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39867,Q#2952 - >seq9599,superfamily,333820,517,773,1.33015e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39868,Q#2952 - >seq9599,non-specific,223780,9,239,1.3682600000000001e-24,104.21700000000001,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39869,Q#2952 - >seq9599,non-specific,197307,9,237,1.2816900000000001e-23,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39870,Q#2952 - >seq9599,non-specific,197320,8,237,3.6928000000000005e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39871,Q#2952 - >seq9599,non-specific,197321,7,237,3.40541e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39872,Q#2952 - >seq9599,specific,335306,10,230,1.51159e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39873,Q#2952 - >seq9599,non-specific,273186,9,238,2.24498e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39874,Q#2952 - >seq9599,non-specific,272954,9,237,4.31638e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39875,Q#2952 - >seq9599,non-specific,197336,7,236,5.7395e-14,73.0303,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39876,Q#2952 - >seq9599,non-specific,197319,8,237,9.847050000000001e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39877,Q#2952 - >seq9599,non-specific,197322,9,237,4.1199099999999997e-13,71.5794,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39878,Q#2952 - >seq9599,non-specific,238828,517,738,2.2688599999999997e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39879,Q#2952 - >seq9599,non-specific,339261,109,233,2.89014e-10,58.8879,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39880,Q#2952 - >seq9599,non-specific,275209,468,801,9.64897e-10,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39881,Q#2952 - >seq9599,superfamily,275209,468,801,9.64897e-10,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39882,Q#2952 - >seq9599,non-specific,236970,9,239,1.3611e-07,54.1298,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39883,Q#2952 - >seq9599,non-specific,197311,7,237,2.6911e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39884,Q#2952 - >seq9599,non-specific,238185,657,773,2.65738e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39885,Q#2952 - >seq9599,non-specific,197318,9,237,0.000146289,44.5947,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39886,Q#2952 - >seq9599,non-specific,197317,140,230,0.00020041599999999997,44.5152,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
39887,Q#2952 - >seq9599,specific,311990,1242,1260,0.000685915,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39888,Q#2952 - >seq9599,superfamily,311990,1242,1260,0.000685915,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs6_sqmonkey,marg,CompleteHit
39889,Q#2952 - >seq9599,non-specific,274009,308,459,0.0008115589999999999,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
39890,Q#2952 - >seq9599,superfamily,274009,308,459,0.0008115589999999999,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
39891,Q#2952 - >seq9599,non-specific,274009,307,479,0.00341632,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39892,Q#2952 - >seq9599,non-specific,338612,159,361,0.00624759,40.8023,pfam13166,AAA_13,NC,cl38390,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other,L1PA8,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39893,Q#2952 - >seq9599,superfamily,338612,159,361,0.00624759,40.8023,cl38390,AAA_13 superfamily,NC, - ,AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.,L1PA8.ORF2.hs6_sqmonkey.marg.frame3,1909190140_L1PA8.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA8,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
39894,Q#2955 - >seq9602,specific,238827,509,771,3.8601099999999994e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39895,Q#2955 - >seq9602,superfamily,295487,509,771,3.8601099999999994e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39896,Q#2955 - >seq9602,specific,197310,9,236,2.3408299999999995e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39897,Q#2955 - >seq9602,superfamily,351117,9,236,2.3408299999999995e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39898,Q#2955 - >seq9602,non-specific,197306,9,236,1.6226600000000001e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39899,Q#2955 - >seq9602,specific,333820,515,771,1.44723e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39900,Q#2955 - >seq9602,superfamily,333820,515,771,1.44723e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39901,Q#2955 - >seq9602,non-specific,223780,9,238,2.4358499999999998e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39902,Q#2955 - >seq9602,non-specific,197307,9,236,3.3769599999999995e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39903,Q#2955 - >seq9602,non-specific,197320,8,236,1.77994e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39904,Q#2955 - >seq9602,specific,335306,10,229,5.23346e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39905,Q#2955 - >seq9602,non-specific,197321,7,236,8.24182e-18,84.52600000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39906,Q#2955 - >seq9602,non-specific,273186,9,237,2.53531e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39907,Q#2955 - >seq9602,non-specific,272954,9,236,1.58762e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39908,Q#2955 - >seq9602,non-specific,197336,7,235,2.4676e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39909,Q#2955 - >seq9602,non-specific,238828,515,736,1.20331e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39910,Q#2955 - >seq9602,non-specific,197322,9,236,2.96656e-12,68.883,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39911,Q#2955 - >seq9602,non-specific,197319,8,236,9.480630000000001e-12,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39912,Q#2955 - >seq9602,non-specific,339261,108,232,4.0485900000000003e-10,58.5027,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39913,Q#2955 - >seq9602,non-specific,275209,466,799,1.48795e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39914,Q#2955 - >seq9602,superfamily,275209,466,799,1.48795e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39915,Q#2955 - >seq9602,non-specific,197311,7,236,1.37178e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39916,Q#2955 - >seq9602,non-specific,236970,9,238,3.5829199999999997e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,pars,CompleteHit
39917,Q#2955 - >seq9602,non-specific,238185,655,771,2.81055e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8,ORF2,hs0_human,pars,CompleteHit
39918,Q#2955 - >seq9602,specific,311990,1239,1257,0.00071867,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs0_human,pars,CompleteHit
39919,Q#2955 - >seq9602,superfamily,311990,1239,1257,0.00071867,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8,ORF2,hs0_human,pars,CompleteHit
39920,Q#2955 - >seq9602,non-specific,197317,139,229,0.000963871,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,pars,N-TerminusTruncated
39921,Q#2955 - >seq9602,non-specific,274009,307,457,0.00174707,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,pars,C-TerminusTruncated
39922,Q#2955 - >seq9602,superfamily,274009,307,457,0.00174707,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,pars,C-TerminusTruncated
39923,Q#2955 - >seq9602,non-specific,224117,263,500,0.0075675,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,pars,N-TerminusTruncated
39924,Q#2955 - >seq9602,superfamily,224117,263,500,0.0075675,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs0_human.pars.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs0_human,pars,N-TerminusTruncated
39925,Q#2958 - >seq9605,specific,238827,510,772,3.8670399999999995e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39926,Q#2958 - >seq9605,superfamily,295487,510,772,3.8670399999999995e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39927,Q#2958 - >seq9605,specific,197310,9,236,2.3435199999999996e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39928,Q#2958 - >seq9605,superfamily,351117,9,236,2.3435199999999996e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39929,Q#2958 - >seq9605,non-specific,197306,9,236,1.6718099999999999e-49,175.748,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39930,Q#2958 - >seq9605,specific,333820,516,772,1.3669e-36,136.653,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39931,Q#2958 - >seq9605,superfamily,333820,516,772,1.3669e-36,136.653,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39932,Q#2958 - >seq9605,non-specific,223780,9,238,2.5811800000000005e-23,100.751,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39933,Q#2958 - >seq9605,non-specific,197307,9,236,3.44504e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39934,Q#2958 - >seq9605,non-specific,197320,8,236,1.78157e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39935,Q#2958 - >seq9605,specific,335306,10,229,5.23812e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39936,Q#2958 - >seq9605,non-specific,197321,7,236,8.48656e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39937,Q#2958 - >seq9605,non-specific,273186,9,237,2.6101999999999997e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39938,Q#2958 - >seq9605,non-specific,272954,9,236,1.61917e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39939,Q#2958 - >seq9605,non-specific,197336,7,235,2.49306e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39940,Q#2958 - >seq9605,non-specific,238828,516,737,1.20438e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39941,Q#2958 - >seq9605,non-specific,197322,9,236,2.96933e-12,68.883,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39942,Q#2958 - >seq9605,non-specific,197319,8,236,9.57802e-12,66.5313,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39943,Q#2958 - >seq9605,non-specific,339261,108,232,4.21226e-10,58.5027,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39944,Q#2958 - >seq9605,non-specific,275209,467,800,1.47616e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39945,Q#2958 - >seq9605,superfamily,275209,467,800,1.47616e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39946,Q#2958 - >seq9605,non-specific,197311,7,236,1.38584e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39947,Q#2958 - >seq9605,non-specific,236970,9,238,3.7517800000000005e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8,ORF2,hs0_human,marg,CompleteHit
39948,Q#2958 - >seq9605,non-specific,238185,656,772,2.8403899999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8,ORF2,hs0_human,marg,CompleteHit
39949,Q#2958 - >seq9605,specific,311990,1240,1258,0.000719227,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs0_human,marg,CompleteHit
39950,Q#2958 - >seq9605,superfamily,311990,1240,1258,0.000719227,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8,ORF2,hs0_human,marg,CompleteHit
39951,Q#2958 - >seq9605,non-specific,274009,307,458,0.0007831530000000001,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,marg,C-TerminusTruncated
39952,Q#2958 - >seq9605,superfamily,274009,307,458,0.0007831530000000001,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,marg,C-TerminusTruncated
39953,Q#2958 - >seq9605,non-specific,197317,139,229,0.0009734069999999999,42.20399999999999,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8,ORF2,hs0_human,marg,N-TerminusTruncated
39954,Q#2958 - >seq9605,non-specific,235175,263,464,0.00335979,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,marg,BothTerminiTruncated
39955,Q#2958 - >seq9605,superfamily,235175,263,464,0.00335979,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,marg,BothTerminiTruncated
39956,Q#2958 - >seq9605,non-specific,224117,311,459,0.00951637,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8,ORF2,hs0_human,marg,C-TerminusTruncated
39957,Q#2958 - >seq9605,superfamily,224117,311,459,0.00951637,40.0828,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8.ORF2.hs0_human.marg.frame3,1909190141_L1PA8.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8,ORF2,hs0_human,marg,C-TerminusTruncated
39958,Q#2959 - >seq9606,specific,238827,489,751,6.779359999999999e-69,230.25599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39959,Q#2959 - >seq9606,superfamily,295487,489,751,6.779359999999999e-69,230.25599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39960,Q#2959 - >seq9606,specific,333820,495,751,1.81225e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39961,Q#2959 - >seq9606,superfamily,333820,495,751,1.81225e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39962,Q#2959 - >seq9606,non-specific,238828,495,716,1.40178e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39963,Q#2959 - >seq9606,non-specific,275209,446,779,4.39779e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39964,Q#2959 - >seq9606,superfamily,275209,446,779,4.39779e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39965,Q#2959 - >seq9606,non-specific,238185,635,751,2.1061399999999998e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39966,Q#2959 - >seq9606,specific,311990,1220,1238,0.00101737,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39967,Q#2959 - >seq9606,superfamily,311990,1220,1238,0.00101737,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs1_chimp.marg.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39968,Q#2961 - >seq9608,specific,197310,9,236,1.3224599999999998e-63,215.678,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39969,Q#2961 - >seq9608,superfamily,351117,9,236,1.3224599999999998e-63,215.678,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39970,Q#2961 - >seq9608,non-specific,197306,9,236,2.69922e-50,178.05900000000003,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39971,Q#2961 - >seq9608,non-specific,197307,9,236,2.13937e-25,106.21799999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39972,Q#2961 - >seq9608,non-specific,223780,9,238,1.12413e-22,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39973,Q#2961 - >seq9608,non-specific,197321,7,236,2.14442e-21,94.9264,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39974,Q#2961 - >seq9608,non-specific,197320,8,236,1.0970600000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39975,Q#2961 - >seq9608,specific,335306,10,229,2.60326e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39976,Q#2961 - >seq9608,non-specific,273186,9,237,1.78456e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39977,Q#2961 - >seq9608,non-specific,272954,9,236,1.50961e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39978,Q#2961 - >seq9608,non-specific,197319,8,236,4.22976e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39979,Q#2961 - >seq9608,non-specific,197336,7,235,1.3173699999999999e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39980,Q#2961 - >seq9608,non-specific,197322,9,236,5.71027e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39981,Q#2961 - >seq9608,non-specific,236970,9,238,3.74022e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39982,Q#2961 - >seq9608,non-specific,339261,108,232,5.605760000000001e-09,55.0359,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39983,Q#2961 - >seq9608,non-specific,197311,7,236,6.71589e-09,56.9165,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,marg,CompleteHit
39984,Q#2961 - >seq9608,non-specific,224117,233,363,0.00284276,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs1_chimp,marg,BothTerminiTruncated
39985,Q#2961 - >seq9608,superfamily,224117,233,363,0.00284276,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs1_chimp,marg,BothTerminiTruncated
39986,Q#2961 - >seq9608,non-specific,197317,139,229,0.00365804,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs1_chimp.marg.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,marg,N-TerminusTruncated
39987,Q#2962 - >seq9609,specific,238827,489,751,6.763669999999998e-69,230.25599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39988,Q#2962 - >seq9609,superfamily,295487,489,751,6.763669999999998e-69,230.25599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39989,Q#2962 - >seq9609,specific,333820,495,751,1.8459799999999996e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39990,Q#2962 - >seq9609,superfamily,333820,495,751,1.8459799999999996e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39991,Q#2962 - >seq9609,non-specific,238828,495,716,1.4137799999999999e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39992,Q#2962 - >seq9609,non-specific,275209,566,779,4.59297e-09,59.3936,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,N-TerminusTruncated
39993,Q#2962 - >seq9609,superfamily,275209,566,779,4.59297e-09,59.3936,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,N-TerminusTruncated
39994,Q#2962 - >seq9609,non-specific,238185,635,751,2.14582e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39995,Q#2962 - >seq9609,specific,311990,1219,1237,0.00102658,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39996,Q#2962 - >seq9609,superfamily,311990,1219,1237,0.00102658,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs1_chimp.pars.frame2,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39997,Q#2964 - >seq9611,specific,197310,9,236,1.3719699999999996e-63,215.678,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39998,Q#2964 - >seq9611,superfamily,351117,9,236,1.3719699999999996e-63,215.678,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
39999,Q#2964 - >seq9611,non-specific,197306,9,236,2.6964299999999995e-50,178.05900000000003,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40000,Q#2964 - >seq9611,non-specific,197307,9,236,2.13726e-25,106.21799999999999,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40001,Q#2964 - >seq9611,non-specific,223780,9,238,1.12301e-22,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40002,Q#2964 - >seq9611,non-specific,197321,7,236,2.14231e-21,94.9264,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40003,Q#2964 - >seq9611,non-specific,197320,8,236,1.09598e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40004,Q#2964 - >seq9611,specific,335306,10,229,2.6007600000000003e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40005,Q#2964 - >seq9611,non-specific,273186,9,237,1.7828099999999998e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40006,Q#2964 - >seq9611,non-specific,272954,9,236,1.50813e-16,80.5049,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40007,Q#2964 - >seq9611,non-specific,197319,8,236,4.22562e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40008,Q#2964 - >seq9611,non-specific,197336,7,235,1.31608e-13,71.8747,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40009,Q#2964 - >seq9611,non-specific,197322,9,236,5.70454e-11,65.031,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40010,Q#2964 - >seq9611,non-specific,236970,9,238,3.73658e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40011,Q#2964 - >seq9611,non-specific,339261,108,232,5.6553799999999996e-09,55.0359,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40012,Q#2964 - >seq9611,non-specific,197311,7,236,6.709589999999999e-09,56.9165,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs1_chimp,pars,CompleteHit
40013,Q#2964 - >seq9611,non-specific,224117,233,363,0.00284002,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs1_chimp,pars,BothTerminiTruncated
40014,Q#2964 - >seq9611,superfamily,224117,233,363,0.00284002,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs1_chimp,pars,BothTerminiTruncated
40015,Q#2964 - >seq9611,non-specific,197317,139,229,0.00365462,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs1_chimp.pars.frame3,1909190149_L1PA8A.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs1_chimp,pars,N-TerminusTruncated
40016,Q#2966 - >seq9613,specific,238827,473,735,3.3952099999999994e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40017,Q#2966 - >seq9613,superfamily,295487,473,735,3.3952099999999994e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40018,Q#2966 - >seq9613,specific,333820,479,735,3.7112899999999997e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40019,Q#2966 - >seq9613,superfamily,333820,479,735,3.7112899999999997e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40020,Q#2966 - >seq9613,non-specific,238828,545,700,3.04881e-12,67.226,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40021,Q#2966 - >seq9613,non-specific,275209,547,763,3.25972e-09,60.163999999999994,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40022,Q#2966 - >seq9613,superfamily,275209,547,763,3.25972e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40023,Q#2966 - >seq9613,non-specific,238185,619,735,3.28588e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40024,Q#2966 - >seq9613,specific,311990,1204,1222,0.00159197,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40025,Q#2966 - >seq9613,superfamily,311990,1204,1222,0.00159197,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs2_gorilla.marg.frame1,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40026,Q#2967 - >seq9614,specific,197310,9,236,1.4056299999999998e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40027,Q#2967 - >seq9614,superfamily,351117,9,236,1.4056299999999998e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40028,Q#2967 - >seq9614,non-specific,197306,9,236,4.11125e-49,174.592,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40029,Q#2967 - >seq9614,non-specific,197307,9,236,4.8302899999999995e-25,105.448,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40030,Q#2967 - >seq9614,non-specific,223780,9,238,1.22908e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40031,Q#2967 - >seq9614,non-specific,197321,7,236,2.36646e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40032,Q#2967 - >seq9614,non-specific,197320,8,236,1.594e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40033,Q#2967 - >seq9614,specific,335306,10,229,2.68571e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40034,Q#2967 - >seq9614,non-specific,273186,9,237,5.4031899999999997e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40035,Q#2967 - >seq9614,non-specific,272954,9,236,7.58339e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40036,Q#2967 - >seq9614,non-specific,197319,8,236,4.366399999999999e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40037,Q#2967 - >seq9614,non-specific,197336,7,235,1.97762e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40038,Q#2967 - >seq9614,non-specific,197322,9,236,1.46281e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40039,Q#2967 - >seq9614,non-specific,197311,7,236,3.4853800000000005e-08,54.9905,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40040,Q#2967 - >seq9614,non-specific,236970,9,238,4.1243300000000004e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40041,Q#2967 - >seq9614,non-specific,339261,108,232,1.04731e-07,51.5691,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs2_gorilla,marg,CompleteHit
40042,Q#2967 - >seq9614,non-specific,197314,7,192,0.00114083,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40043,Q#2967 - >seq9614,non-specific,274008,263,417,0.00117457,43.1215,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40044,Q#2967 - >seq9614,superfamily,274008,263,417,0.00117457,43.1215,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40045,Q#2967 - >seq9614,non-specific,197317,139,229,0.00431196,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs2_gorilla.marg.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40046,Q#2970 - >seq9617,specific,238827,510,772,4.708759999999999e-66,222.166,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40047,Q#2970 - >seq9617,superfamily,295487,510,772,4.708759999999999e-66,222.166,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40048,Q#2970 - >seq9617,specific,197310,9,236,1.6067599999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40049,Q#2970 - >seq9617,superfamily,351117,9,236,1.6067599999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40050,Q#2970 - >seq9617,non-specific,197306,9,236,1.1396299999999998e-48,173.43599999999998,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40051,Q#2970 - >seq9617,specific,333820,516,772,9.415579999999999e-35,131.26,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40052,Q#2970 - >seq9617,superfamily,333820,516,772,9.415579999999999e-35,131.26,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40053,Q#2970 - >seq9617,non-specific,197307,9,236,2.66637e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40054,Q#2970 - >seq9617,non-specific,223780,9,238,1.6534499999999999e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40055,Q#2970 - >seq9617,non-specific,197320,8,236,4.0312599999999994e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40056,Q#2970 - >seq9617,non-specific,197321,7,236,7.987750000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40057,Q#2970 - >seq9617,specific,335306,10,229,2.80813e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40058,Q#2970 - >seq9617,non-specific,273186,9,237,2.8082500000000003e-16,80.0156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40059,Q#2970 - >seq9617,non-specific,272954,9,236,1.02321e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40060,Q#2970 - >seq9617,non-specific,197336,7,235,2.08879e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40061,Q#2970 - >seq9617,non-specific,197319,8,236,5.30626e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40062,Q#2970 - >seq9617,non-specific,238828,582,737,8.00597e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40063,Q#2970 - >seq9617,non-specific,197322,9,236,1.5322799999999998e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40064,Q#2970 - >seq9617,non-specific,275209,587,800,4.446100000000001e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40065,Q#2970 - >seq9617,superfamily,275209,587,800,4.446100000000001e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40066,Q#2970 - >seq9617,non-specific,339261,108,232,1.54012e-08,53.8803,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40067,Q#2970 - >seq9617,non-specific,197311,7,236,3.34568e-08,54.9905,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40068,Q#2970 - >seq9617,non-specific,236970,9,238,5.56942e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40069,Q#2970 - >seq9617,non-specific,238185,656,772,5.51541e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40070,Q#2970 - >seq9617,non-specific,224117,233,501,0.000461631,44.32,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40071,Q#2970 - >seq9617,superfamily,224117,233,501,0.000461631,44.32,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40072,Q#2970 - >seq9617,non-specific,197314,7,192,0.00123526,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40073,Q#2970 - >seq9617,specific,311990,1241,1259,0.00170441,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40074,Q#2970 - >seq9617,superfamily,311990,1241,1259,0.00170441,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs2_gorilla,pars,CompleteHit
40075,Q#2970 - >seq9617,non-specific,197317,139,229,0.00470933,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs2_gorilla.pars.frame3,1909190157_L1PA8A.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40076,Q#2972 - >seq9619,non-specific,224117,202,381,0.00313577,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs3_orang.pars.frame2,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA8A,ORF2,hs3_orang,pars,BothTerminiTruncated
40077,Q#2972 - >seq9619,superfamily,224117,202,381,0.00313577,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs3_orang.pars.frame2,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA8A,ORF2,hs3_orang,pars,BothTerminiTruncated
40078,Q#2972 - >seq9619,non-specific,274008,253,408,0.00358306,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs3_orang.pars.frame2,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA8A,ORF2,hs3_orang,pars,BothTerminiTruncated
40079,Q#2972 - >seq9619,superfamily,274008,253,408,0.00358306,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs3_orang.pars.frame2,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA8A,ORF2,hs3_orang,pars,BothTerminiTruncated
40080,Q#2973 - >seq9620,specific,238827,495,757,1.6826499999999995e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40081,Q#2973 - >seq9620,superfamily,295487,495,757,1.6826499999999995e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40082,Q#2973 - >seq9620,specific,197310,9,222,7.12041e-58,199.5,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40083,Q#2973 - >seq9620,superfamily,351117,9,222,7.12041e-58,199.5,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40084,Q#2973 - >seq9620,non-specific,197306,9,223,3.34344e-45,163.421,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40085,Q#2973 - >seq9620,specific,333820,501,757,8.110519999999999e-35,131.26,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40086,Q#2973 - >seq9620,superfamily,333820,501,757,8.110519999999999e-35,131.26,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40087,Q#2973 - >seq9620,non-specific,197307,9,223,1.58087e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40088,Q#2973 - >seq9620,non-specific,197320,8,221,3.44572e-20,91.4225,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40089,Q#2973 - >seq9620,non-specific,223780,9,221,3.7507400000000005e-20,91.5059,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40090,Q#2973 - >seq9620,non-specific,197321,7,223,1.85103e-17,83.3704,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40091,Q#2973 - >seq9620,specific,335306,10,212,2.58373e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40092,Q#2973 - >seq9620,non-specific,273186,9,221,1.7490900000000002e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40093,Q#2973 - >seq9620,non-specific,272954,9,221,6.10437e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40094,Q#2973 - >seq9620,non-specific,197336,7,221,1.36085e-12,68.7931,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40095,Q#2973 - >seq9620,non-specific,238828,567,722,6.1793e-12,66.4556,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,N-TerminusTruncated
40096,Q#2973 - >seq9620,non-specific,197319,8,223,8.461189999999999e-10,60.7533,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40097,Q#2973 - >seq9620,non-specific,275209,572,785,4.07947e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,N-TerminusTruncated
40098,Q#2973 - >seq9620,superfamily,275209,572,785,4.07947e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,N-TerminusTruncated
40099,Q#2973 - >seq9620,non-specific,197322,9,222,9.46536e-09,58.0974,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40100,Q#2973 - >seq9620,non-specific,236970,9,221,2.4429200000000003e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40101,Q#2973 - >seq9620,non-specific,197311,7,204,1.17813e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40102,Q#2973 - >seq9620,non-specific,238185,641,757,4.2664e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40103,Q#2973 - >seq9620,non-specific,339261,108,217,0.000769652,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40104,Q#2973 - >seq9620,specific,311990,1225,1243,0.00109386,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40105,Q#2973 - >seq9620,superfamily,311990,1225,1243,0.00109386,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs3_orang,pars,CompleteHit
40106,Q#2973 - >seq9620,non-specific,197314,7,192,0.00117507,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.pars.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs3_orang,pars,C-TerminusTruncated
40107,Q#2974 - >seq9621,specific,238827,473,735,2.5341999999999995e-67,225.63299999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40108,Q#2974 - >seq9621,superfamily,295487,473,735,2.5341999999999995e-67,225.63299999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40109,Q#2974 - >seq9621,specific,333820,479,735,3.93276e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40110,Q#2974 - >seq9621,superfamily,333820,479,735,3.93276e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40111,Q#2974 - >seq9621,non-specific,238828,545,700,3.1067900000000003e-12,67.226,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,N-TerminusTruncated
40112,Q#2974 - >seq9621,non-specific,275209,547,763,3.56242e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,N-TerminusTruncated
40113,Q#2974 - >seq9621,superfamily,275209,547,763,3.56242e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,N-TerminusTruncated
40114,Q#2974 - >seq9621,non-specific,238185,619,735,3.19118e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40115,Q#2974 - >seq9621,specific,311990,1204,1222,0.00159197,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40116,Q#2974 - >seq9621,superfamily,311990,1204,1222,0.00159197,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs3_orang.marg.frame1,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40117,Q#2976 - >seq9623,specific,197310,9,236,1.2901599999999998e-61,210.28599999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40118,Q#2976 - >seq9623,superfamily,351117,9,236,1.2901599999999998e-61,210.28599999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40119,Q#2976 - >seq9623,non-specific,197306,9,236,4.80162e-49,174.207,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40120,Q#2976 - >seq9623,non-specific,197307,9,236,4.975270000000001e-25,105.448,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40121,Q#2976 - >seq9623,non-specific,223780,9,238,1.23026e-22,98.4395,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40122,Q#2976 - >seq9623,non-specific,197321,7,236,2.30217e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40123,Q#2976 - >seq9623,non-specific,197320,8,236,1.59553e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40124,Q#2976 - >seq9623,specific,335306,10,229,2.6882099999999997e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40125,Q#2976 - >seq9623,non-specific,273186,9,237,5.40833e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40126,Q#2976 - >seq9623,non-specific,272954,9,236,7.80795e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40127,Q#2976 - >seq9623,non-specific,197319,8,236,4.3705399999999994e-15,76.1613,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40128,Q#2976 - >seq9623,non-specific,197336,7,235,1.97949e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40129,Q#2976 - >seq9623,non-specific,197322,9,236,1.46422e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40130,Q#2976 - >seq9623,non-specific,197311,7,236,3.48855e-08,54.9905,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40131,Q#2976 - >seq9623,non-specific,236970,9,238,4.1282100000000004e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40132,Q#2976 - >seq9623,non-specific,339261,108,232,1.16614e-07,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs3_orang,marg,CompleteHit
40133,Q#2976 - >seq9623,non-specific,197314,7,192,0.00114187,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs3_orang,marg,C-TerminusTruncated
40134,Q#2976 - >seq9623,non-specific,274008,263,418,0.00371329,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs3_orang,marg,BothTerminiTruncated
40135,Q#2976 - >seq9623,superfamily,274008,263,418,0.00371329,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs3_orang,marg,BothTerminiTruncated
40136,Q#2976 - >seq9623,non-specific,197317,139,229,0.00431587,40.278,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs3_orang.marg.frame3,1909190203_L1PA8A.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs3_orang,marg,N-TerminusTruncated
40137,Q#2979 - >seq9626,specific,238827,509,771,1.1896799999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40138,Q#2979 - >seq9626,superfamily,295487,509,771,1.1896799999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40139,Q#2979 - >seq9626,specific,197310,9,236,2.7034099999999998e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40140,Q#2979 - >seq9626,superfamily,351117,9,236,2.7034099999999998e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40141,Q#2979 - >seq9626,non-specific,197306,9,236,1.49003e-48,173.051,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40142,Q#2979 - >seq9626,specific,333820,515,771,9.993930000000001e-36,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40143,Q#2979 - >seq9626,superfamily,333820,515,771,9.993930000000001e-36,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40144,Q#2979 - >seq9626,non-specific,197307,9,236,2.8996900000000004e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40145,Q#2979 - >seq9626,non-specific,223780,9,238,2.4347600000000005e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40146,Q#2979 - >seq9626,non-specific,197320,8,236,5.148840000000001e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40147,Q#2979 - >seq9626,non-specific,197321,7,236,8.36022e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40148,Q#2979 - >seq9626,specific,335306,10,229,2.80313e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40149,Q#2979 - >seq9626,non-specific,273186,9,237,3.58101e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40150,Q#2979 - >seq9626,non-specific,272954,9,236,1.14313e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40151,Q#2979 - >seq9626,non-specific,197336,7,235,2.73515e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40152,Q#2979 - >seq9626,non-specific,197319,8,236,6.38605e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40153,Q#2979 - >seq9626,non-specific,238828,515,736,7.342789999999999e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40154,Q#2979 - >seq9626,non-specific,197322,9,236,1.52944e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40155,Q#2979 - >seq9626,non-specific,275209,466,799,3.37015e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40156,Q#2979 - >seq9626,superfamily,275209,466,799,3.37015e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40157,Q#2979 - >seq9626,non-specific,339261,108,232,1.90316e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40158,Q#2979 - >seq9626,non-specific,197311,7,236,4.1835699999999995e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40159,Q#2979 - >seq9626,non-specific,236970,9,238,6.49136e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40160,Q#2979 - >seq9626,non-specific,235175,263,468,3.913e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40161,Q#2979 - >seq9626,superfamily,235175,263,468,3.913e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40162,Q#2979 - >seq9626,non-specific,238185,655,771,5.61483e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40163,Q#2979 - >seq9626,non-specific,224117,233,500,9.63947e-05,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
40164,Q#2979 - >seq9626,superfamily,224117,233,500,9.63947e-05,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
40165,Q#2979 - >seq9626,non-specific,223496,264,499,0.000232733,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40166,Q#2979 - >seq9626,superfamily,223496,264,499,0.000232733,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40167,Q#2979 - >seq9626,non-specific,224117,306,458,0.0008987210000000001,43.5496,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40168,Q#2979 - >seq9626,non-specific,197314,7,192,0.00134895,41.5603,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40169,Q#2979 - >seq9626,specific,311990,1239,1257,0.00173545,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40170,Q#2979 - >seq9626,superfamily,311990,1239,1257,0.00173545,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs4_gibbon,marg,CompleteHit
40171,Q#2979 - >seq9626,non-specific,197317,139,229,0.00528003,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,marg,N-TerminusTruncated
40172,Q#2979 - >seq9626,non-specific,274009,263,426,0.0054703,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40173,Q#2979 - >seq9626,superfamily,274009,263,426,0.0054703,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40174,Q#2979 - >seq9626,non-specific,224495,263,385,0.00955953,38.8859,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA8A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40175,Q#2979 - >seq9626,superfamily,224495,263,385,0.00955953,38.8859,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PA8A.ORF2.hs4_gibbon.marg.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA8A,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40176,Q#2982 - >seq9629,specific,238827,509,771,1.1759499999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40177,Q#2982 - >seq9629,superfamily,295487,509,771,1.1759499999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40178,Q#2982 - >seq9629,specific,197310,9,236,2.7261899999999997e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40179,Q#2982 - >seq9629,superfamily,351117,9,236,2.7261899999999997e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40180,Q#2982 - >seq9629,non-specific,197306,9,236,1.48867e-48,173.051,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40181,Q#2982 - >seq9629,specific,333820,515,771,1.00822e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40182,Q#2982 - >seq9629,superfamily,333820,515,771,1.00822e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40183,Q#2982 - >seq9629,non-specific,197307,9,236,3.00953e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40184,Q#2982 - >seq9629,non-specific,223780,9,238,2.55063e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40185,Q#2982 - >seq9629,non-specific,197320,8,236,5.39386e-20,90.6521,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40186,Q#2982 - >seq9629,non-specific,197321,7,236,8.432150000000001e-20,90.304,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40187,Q#2982 - >seq9629,specific,335306,10,229,2.80063e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40188,Q#2982 - >seq9629,non-specific,273186,9,237,3.6116099999999995e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40189,Q#2982 - >seq9629,non-specific,272954,9,236,1.1857899999999999e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40190,Q#2982 - >seq9629,non-specific,197336,7,235,2.78429e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40191,Q#2982 - >seq9629,non-specific,197319,8,236,6.56179e-13,69.9981,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40192,Q#2982 - >seq9629,non-specific,238828,515,736,7.405639999999999e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40193,Q#2982 - >seq9629,non-specific,197322,9,236,1.5280200000000002e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40194,Q#2982 - >seq9629,non-specific,275209,466,799,3.367e-09,60.163999999999994,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40195,Q#2982 - >seq9629,superfamily,275209,466,799,3.367e-09,60.163999999999994,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40196,Q#2982 - >seq9629,non-specific,339261,108,232,1.88324e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40197,Q#2982 - >seq9629,non-specific,197311,7,236,4.0259400000000005e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40198,Q#2982 - >seq9629,non-specific,236970,9,238,6.5449e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40199,Q#2982 - >seq9629,non-specific,235175,263,468,3.9762800000000005e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40200,Q#2982 - >seq9629,superfamily,235175,263,468,3.9762800000000005e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40201,Q#2982 - >seq9629,non-specific,238185,655,771,5.61025e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40202,Q#2982 - >seq9629,non-specific,224117,233,500,9.54953e-05,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
40203,Q#2982 - >seq9629,superfamily,224117,233,500,9.54953e-05,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
40204,Q#2982 - >seq9629,non-specific,223496,264,499,0.000232521,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40205,Q#2982 - >seq9629,superfamily,223496,264,499,0.000232521,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40206,Q#2982 - >seq9629,non-specific,224117,306,458,0.000920978,43.5496,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40207,Q#2982 - >seq9629,non-specific,197314,7,192,0.00138456,41.5603,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40208,Q#2982 - >seq9629,specific,311990,1239,1257,0.0017340999999999997,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40209,Q#2982 - >seq9629,superfamily,311990,1239,1257,0.0017340999999999997,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs4_gibbon,pars,CompleteHit
40210,Q#2982 - >seq9629,non-specific,197317,139,229,0.00527544,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs4_gibbon,pars,N-TerminusTruncated
40211,Q#2982 - >seq9629,non-specific,274009,263,426,0.00528367,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40212,Q#2982 - >seq9629,superfamily,274009,263,426,0.00528367,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40213,Q#2982 - >seq9629,non-specific,224495,263,385,0.00963729,38.8859,COG1579,COG1579,C,cl34310,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40214,Q#2982 - >seq9629,superfamily,224495,263,385,0.00963729,38.8859,cl34310,COG1579 superfamily,C, - ,"Predicted  nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]; Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only].",L1PA8A.ORF2.hs4_gibbon.pars.frame3,1909190213_L1PA8A.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8A,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40215,Q#2984 - >seq9631,specific,311990,1180,1198,7.80306e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs5_gmonkey.pars.frame2,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40216,Q#2984 - >seq9631,superfamily,311990,1180,1198,7.80306e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs5_gmonkey.pars.frame2,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40217,Q#2985 - >seq9632,specific,238827,510,772,1.3672399999999997e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40218,Q#2985 - >seq9632,superfamily,295487,510,772,1.3672399999999997e-68,229.485,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40219,Q#2985 - >seq9632,specific,197310,9,236,4.647509999999999e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40220,Q#2985 - >seq9632,superfamily,351117,9,236,4.647509999999999e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40221,Q#2985 - >seq9632,non-specific,197306,9,236,1.51275e-48,173.051,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40222,Q#2985 - >seq9632,specific,333820,516,772,1.68337e-36,136.268,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40223,Q#2985 - >seq9632,superfamily,333820,516,772,1.68337e-36,136.268,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40224,Q#2985 - >seq9632,non-specific,197307,9,236,1.0519199999999999e-23,101.596,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40225,Q#2985 - >seq9632,non-specific,223780,9,238,7.13043e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40226,Q#2985 - >seq9632,non-specific,197320,8,236,2.06275e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40227,Q#2985 - >seq9632,non-specific,197321,7,236,3.51226e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40228,Q#2985 - >seq9632,specific,335306,10,229,2.76566e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40229,Q#2985 - >seq9632,non-specific,273186,9,237,1.84382e-16,80.4008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40230,Q#2985 - >seq9632,non-specific,272954,9,236,4.79753e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40231,Q#2985 - >seq9632,non-specific,197336,7,235,2.0375099999999999e-13,71.4895,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40232,Q#2985 - >seq9632,non-specific,197319,8,236,2.04948e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40233,Q#2985 - >seq9632,non-specific,238828,516,737,2.69562e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40234,Q#2985 - >seq9632,non-specific,197322,9,236,1.5081799999999999e-10,63.8754,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40235,Q#2985 - >seq9632,non-specific,275209,467,800,1.03692e-09,61.7048,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40236,Q#2985 - >seq9632,superfamily,275209,467,800,1.03692e-09,61.7048,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40237,Q#2985 - >seq9632,non-specific,339261,108,232,3.56411e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40238,Q#2985 - >seq9632,non-specific,197311,7,236,4.40918e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40239,Q#2985 - >seq9632,non-specific,236970,9,238,4.5285000000000005e-08,55.6706,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40240,Q#2985 - >seq9632,non-specific,235175,263,469,1.3825099999999999e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40241,Q#2985 - >seq9632,superfamily,235175,263,469,1.3825099999999999e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40242,Q#2985 - >seq9632,non-specific,238185,656,772,2.30686e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,pars,CompleteHit
40243,Q#2985 - >seq9632,non-specific,224117,233,501,3.19275e-05,48.172,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
40244,Q#2985 - >seq9632,superfamily,224117,233,501,3.19275e-05,48.172,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
40245,Q#2985 - >seq9632,non-specific,224117,306,459,0.00037418,44.7052,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40246,Q#2985 - >seq9632,non-specific,274009,263,427,0.00051432,44.2883,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40247,Q#2985 - >seq9632,superfamily,274009,263,427,0.00051432,44.2883,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40248,Q#2985 - >seq9632,non-specific,274009,301,478,0.00112924,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40249,Q#2985 - >seq9632,non-specific,197314,7,192,0.00117404,41.9455,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40250,Q#2985 - >seq9632,non-specific,197317,139,229,0.00502827,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
40251,Q#2985 - >seq9632,non-specific,274009,297,458,0.00683855,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.pars.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40252,Q#2988 - >seq9635,specific,238827,527,789,1.3803899999999997e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40253,Q#2988 - >seq9635,superfamily,295487,527,789,1.3803899999999997e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40254,Q#2988 - >seq9635,specific,197310,9,253,1.3654699999999997e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40255,Q#2988 - >seq9635,superfamily,351117,9,253,1.3654699999999997e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40256,Q#2988 - >seq9635,non-specific,197306,9,253,6.438069999999999e-45,162.651,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40257,Q#2988 - >seq9635,specific,333820,533,789,1.0150099999999999e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40258,Q#2988 - >seq9635,superfamily,333820,533,789,1.0150099999999999e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40259,Q#2988 - >seq9635,non-specific,197307,9,253,8.40694e-19,87.3433,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40260,Q#2988 - >seq9635,non-specific,223780,9,255,5.21204e-18,85.3427,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40261,Q#2988 - >seq9635,non-specific,197320,8,253,2.29329e-16,80.2517,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40262,Q#2988 - >seq9635,specific,335306,10,246,2.5087900000000003e-16,79.2113,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40263,Q#2988 - >seq9635,non-specific,197321,7,253,6.30422e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40264,Q#2988 - >seq9635,non-specific,273186,9,254,2.4815e-13,71.156,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40265,Q#2988 - >seq9635,non-specific,238828,533,754,7.67382e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40266,Q#2988 - >seq9635,non-specific,272954,9,253,5.97199e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40267,Q#2988 - >seq9635,non-specific,197336,7,252,5.908e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40268,Q#2988 - >seq9635,non-specific,275209,484,817,3.5825100000000003e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40269,Q#2988 - >seq9635,superfamily,275209,484,817,3.5825100000000003e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40270,Q#2988 - >seq9635,non-specific,339261,125,249,2.14886e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40271,Q#2988 - >seq9635,non-specific,197322,9,253,1.67441e-07,54.2454,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40272,Q#2988 - >seq9635,non-specific,197311,89,253,1.65606e-05,46.9013,cd09077,R1-I-EN,N,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40273,Q#2988 - >seq9635,non-specific,235175,280,486,3.74849e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40274,Q#2988 - >seq9635,superfamily,235175,280,486,3.74849e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40275,Q#2988 - >seq9635,non-specific,238185,673,789,6.0403100000000004e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40276,Q#2988 - >seq9635,non-specific,224117,250,518,6.365779999999999e-05,47.4016,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40277,Q#2988 - >seq9635,superfamily,224117,250,518,6.365779999999999e-05,47.4016,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40278,Q#2988 - >seq9635,non-specific,236970,89,255,9.453790000000002e-05,45.6554,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40279,Q#2988 - >seq9635,non-specific,224117,323,476,0.000564066,44.32,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40280,Q#2988 - >seq9635,non-specific,274009,280,444,0.000706417,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40281,Q#2988 - >seq9635,superfamily,274009,280,444,0.000706417,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40282,Q#2988 - >seq9635,non-specific,274009,318,495,0.0015772,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40283,Q#2988 - >seq9635,specific,311990,1257,1275,0.00175966,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40284,Q#2988 - >seq9635,superfamily,311990,1257,1275,0.00175966,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs5_gmonkey,marg,CompleteHit
40285,Q#2988 - >seq9635,non-specific,197317,156,246,0.00536266,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40286,Q#2988 - >seq9635,non-specific,274009,314,475,0.00923035,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs5_gmonkey.marg.frame3,1909190216_L1PA8A.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40287,Q#2989 - >seq9636,specific,238827,515,777,1.35182e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40288,Q#2989 - >seq9636,superfamily,295487,515,777,1.35182e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40289,Q#2989 - >seq9636,specific,197310,9,241,2.8758799999999997e-58,200.65599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40290,Q#2989 - >seq9636,superfamily,351117,9,241,2.8758799999999997e-58,200.65599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40291,Q#2989 - >seq9636,non-specific,197306,9,241,7.077949999999999e-47,168.044,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40292,Q#2989 - >seq9636,specific,333820,521,777,1.0242e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40293,Q#2989 - >seq9636,superfamily,333820,521,777,1.0242e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40294,Q#2989 - >seq9636,non-specific,197307,9,241,1.77042e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40295,Q#2989 - >seq9636,non-specific,223780,9,243,2.60727e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40296,Q#2989 - >seq9636,specific,335306,10,234,3.39439e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40297,Q#2989 - >seq9636,non-specific,197320,8,241,8.749850000000001e-18,84.4889,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40298,Q#2989 - >seq9636,non-specific,197321,7,241,1.2331e-16,81.0592,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40299,Q#2989 - >seq9636,non-specific,273186,9,242,3.31665e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40300,Q#2989 - >seq9636,non-specific,272954,9,241,2.53167e-13,71.2601,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40301,Q#2989 - >seq9636,non-specific,238828,521,742,1.31687e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40302,Q#2989 - >seq9636,non-specific,197336,7,240,1.0292999999999999e-11,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40303,Q#2989 - >seq9636,non-specific,197319,8,241,6.18705e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40304,Q#2989 - >seq9636,non-specific,339261,113,237,2.37769e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40305,Q#2989 - >seq9636,non-specific,275209,472,805,3.51162e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40306,Q#2989 - >seq9636,superfamily,275209,472,805,3.51162e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40307,Q#2989 - >seq9636,non-specific,197322,9,241,4.44448e-09,59.253,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40308,Q#2989 - >seq9636,non-specific,197311,7,241,1.40489e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40309,Q#2989 - >seq9636,non-specific,236970,9,243,7.482139999999999e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40310,Q#2989 - >seq9636,non-specific,235175,268,474,4.46842e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
40311,Q#2989 - >seq9636,superfamily,235175,268,474,4.46842e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
40312,Q#2989 - >seq9636,non-specific,238185,661,777,5.64228e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40313,Q#2989 - >seq9636,non-specific,224117,238,506,0.00010818899999999999,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
40314,Q#2989 - >seq9636,superfamily,224117,238,506,0.00010818899999999999,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
40315,Q#2989 - >seq9636,non-specific,224117,311,464,0.000607267,43.9348,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
40316,Q#2989 - >seq9636,non-specific,274009,268,432,0.000664295,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
40317,Q#2989 - >seq9636,superfamily,274009,268,432,0.000664295,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
40318,Q#2989 - >seq9636,non-specific,274009,306,483,0.00135151,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
40319,Q#2989 - >seq9636,specific,311990,1245,1263,0.00166017,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40320,Q#2989 - >seq9636,superfamily,311990,1245,1263,0.00166017,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs6_sqmonkey,marg,CompleteHit
40321,Q#2989 - >seq9636,non-specific,197317,144,234,0.0051213000000000005,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
40322,Q#2989 - >seq9636,non-specific,274009,302,463,0.00875521,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.marg.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
40323,Q#2992 - >seq9639,specific,238827,513,775,1.3600899999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40324,Q#2992 - >seq9639,superfamily,295487,513,775,1.3600899999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40325,Q#2992 - >seq9639,specific,197310,9,239,1.5764400000000002e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40326,Q#2992 - >seq9639,superfamily,351117,9,239,1.5764400000000002e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40327,Q#2992 - >seq9639,non-specific,197306,9,239,6.66821e-47,168.044,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40328,Q#2992 - >seq9639,specific,333820,519,775,1.07303e-35,133.957,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40329,Q#2992 - >seq9639,superfamily,333820,519,775,1.07303e-35,133.957,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40330,Q#2992 - >seq9639,non-specific,197307,9,239,1.3806700000000002e-20,92.3509,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40331,Q#2992 - >seq9639,non-specific,223780,9,241,1.4480000000000002e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40332,Q#2992 - >seq9639,specific,335306,10,232,1.61745e-19,88.4561,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40333,Q#2992 - >seq9639,non-specific,197320,8,239,4.8613999999999994e-18,84.8741,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40334,Q#2992 - >seq9639,non-specific,197321,7,239,8.361139999999999e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40335,Q#2992 - >seq9639,non-specific,273186,9,240,1.3550999999999999e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40336,Q#2992 - >seq9639,non-specific,272954,9,239,1.70594e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40337,Q#2992 - >seq9639,non-specific,238828,519,740,1.36506e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40338,Q#2992 - >seq9639,non-specific,197336,7,238,1.53337e-11,65.7115,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40339,Q#2992 - >seq9639,non-specific,197319,8,239,7.16587e-11,63.8349,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40340,Q#2992 - >seq9639,non-specific,339261,111,235,2.3508699999999998e-09,56.1915,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40341,Q#2992 - >seq9639,non-specific,275209,470,803,3.5363400000000002e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40342,Q#2992 - >seq9639,superfamily,275209,470,803,3.5363400000000002e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40343,Q#2992 - >seq9639,non-specific,197322,9,239,5.4089500000000004e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40344,Q#2992 - >seq9639,non-specific,197311,7,239,2.8571400000000003e-08,55.3757,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40345,Q#2992 - >seq9639,non-specific,236970,9,241,4.34654e-06,49.5074,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40346,Q#2992 - >seq9639,non-specific,235175,266,472,4.65347e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
40347,Q#2992 - >seq9639,superfamily,235175,266,472,4.65347e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
40348,Q#2992 - >seq9639,non-specific,238185,659,775,5.63313e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40349,Q#2992 - >seq9639,non-specific,224117,236,504,0.000111707,46.6312,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
40350,Q#2992 - >seq9639,superfamily,224117,236,504,0.000111707,46.6312,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
40351,Q#2992 - >seq9639,non-specific,224117,309,462,0.000621746,43.9348,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
40352,Q#2992 - >seq9639,non-specific,274009,266,430,0.000674408,43.9031,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
40353,Q#2992 - >seq9639,superfamily,274009,266,430,0.000674408,43.9031,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
40354,Q#2992 - >seq9639,non-specific,274009,304,481,0.00138374,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
40355,Q#2992 - >seq9639,specific,311990,1243,1261,0.00167393,36.8812,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40356,Q#2992 - >seq9639,superfamily,311990,1243,1261,0.00167393,36.8812,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs6_sqmonkey,pars,CompleteHit
40357,Q#2992 - >seq9639,non-specific,197317,142,232,0.00511244,39.8928,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
40358,Q#2992 - >seq9639,non-specific,274009,300,461,0.00873968,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs6_sqmonkey.pars.frame3,1909190225_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
40359,Q#2995 - >seq9642,specific,238827,471,733,3.750579999999999e-67,225.248,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40360,Q#2995 - >seq9642,superfamily,295487,471,733,3.750579999999999e-67,225.248,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40361,Q#2995 - >seq9642,specific,333820,477,733,3.5407099999999997e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40362,Q#2995 - >seq9642,superfamily,333820,477,733,3.5407099999999997e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40363,Q#2995 - >seq9642,non-specific,238828,543,698,1.28155e-12,68.3816,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,N-TerminusTruncated
40364,Q#2995 - >seq9642,non-specific,275209,545,761,1.41113e-09,60.9344,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,N-TerminusTruncated
40365,Q#2995 - >seq9642,superfamily,275209,545,761,1.41113e-09,60.9344,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,N-TerminusTruncated
40366,Q#2995 - >seq9642,non-specific,238185,617,733,1.45275e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40367,Q#2995 - >seq9642,specific,225881,367,697,0.00979359,39.4369,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40368,Q#2995 - >seq9642,superfamily,225881,367,697,0.00979359,39.4369,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs0_human.pars.frame1,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40369,Q#2997 - >seq9644,specific,197310,9,235,3.80682e-61,208.745,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40370,Q#2997 - >seq9644,superfamily,351117,9,235,3.80682e-61,208.745,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40371,Q#2997 - >seq9644,non-specific,197306,9,235,6.0167099999999986e-49,174.207,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40372,Q#2997 - >seq9644,non-specific,197307,9,235,2.3715999999999998e-23,100.44,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40373,Q#2997 - >seq9644,non-specific,223780,9,237,2.4236700000000003e-22,97.6691,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40374,Q#2997 - >seq9644,non-specific,197321,7,235,2.90269e-21,94.5412,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40375,Q#2997 - >seq9644,non-specific,197320,8,235,1.7443799999999997e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40376,Q#2997 - >seq9644,specific,335306,10,228,4.0279900000000004e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40377,Q#2997 - >seq9644,non-specific,273186,9,236,3.5763099999999997e-16,79.6304,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40378,Q#2997 - >seq9644,non-specific,272954,9,235,3.09396e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40379,Q#2997 - >seq9644,non-specific,197319,8,235,3.00898e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40380,Q#2997 - >seq9644,non-specific,197336,7,234,2.3516e-13,71.1043,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40381,Q#2997 - >seq9644,non-specific,197322,9,235,6.096589999999999e-10,61.9494,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40382,Q#2997 - >seq9644,non-specific,236970,9,237,1.71428e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40383,Q#2997 - >seq9644,non-specific,197311,7,235,6.76177e-09,56.9165,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40384,Q#2997 - >seq9644,non-specific,339261,108,231,3.70733e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40385,Q#2997 - >seq9644,specific,311990,1197,1215,0.00019852799999999998,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40386,Q#2997 - >seq9644,superfamily,311990,1197,1215,0.00019852799999999998,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA8A,ORF2,hs0_human,pars,CompleteHit
40387,Q#2997 - >seq9644,non-specific,274008,262,415,0.000481506,44.2771,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,pars,BothTerminiTruncated
40388,Q#2997 - >seq9644,superfamily,274008,262,415,0.000481506,44.2771,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,pars,BothTerminiTruncated
40389,Q#2997 - >seq9644,non-specific,224259,293,380,0.000740604,42.746,COG1340,COG1340,C,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8A,ORF2,hs0_human,pars,C-TerminusTruncated
40390,Q#2997 - >seq9644,superfamily,224259,293,380,0.000740604,42.746,cl34231,COG1340 superfamily,C, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA8A,ORF2,hs0_human,pars,C-TerminusTruncated
40391,Q#2997 - >seq9644,non-specific,197314,7,192,0.00194611,41.1751,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs0_human,pars,C-TerminusTruncated
40392,Q#2997 - >seq9644,non-specific,224117,232,388,0.00264031,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,pars,BothTerminiTruncated
40393,Q#2997 - >seq9644,superfamily,224117,232,388,0.00264031,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs0_human.pars.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs0_human,pars,BothTerminiTruncated
40394,Q#3000 - >seq9647,specific,238827,510,772,3.1232699999999997e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40395,Q#3000 - >seq9647,superfamily,295487,510,772,3.1232699999999997e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40396,Q#3000 - >seq9647,specific,197310,9,236,2.7598099999999995e-62,212.21200000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40397,Q#3000 - >seq9647,superfamily,351117,9,236,2.7598099999999995e-62,212.21200000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40398,Q#3000 - >seq9647,non-specific,197306,9,236,7.168220000000001e-49,173.822,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40399,Q#3000 - >seq9647,specific,333820,516,772,4.49847e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40400,Q#3000 - >seq9647,superfamily,333820,516,772,4.49847e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40401,Q#3000 - >seq9647,non-specific,197307,9,236,5.38953e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40402,Q#3000 - >seq9647,non-specific,223780,9,238,3.39607e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40403,Q#3000 - >seq9647,non-specific,197321,7,236,3.4316e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40404,Q#3000 - >seq9647,non-specific,197320,8,236,7.11355e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40405,Q#3000 - >seq9647,specific,335306,10,229,3.39545e-19,87.6857,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40406,Q#3000 - >seq9647,non-specific,273186,9,237,1.18465e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40407,Q#3000 - >seq9647,non-specific,272954,9,236,2.5639799999999997e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40408,Q#3000 - >seq9647,non-specific,197319,8,236,1.00115e-12,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40409,Q#3000 - >seq9647,non-specific,197336,7,235,1.25654e-12,69.1783,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40410,Q#3000 - >seq9647,non-specific,238828,582,737,7.28048e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40411,Q#3000 - >seq9647,non-specific,197322,9,236,2.2609799999999998e-10,63.105,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40412,Q#3000 - >seq9647,non-specific,275209,587,800,4.10092e-09,59.7788,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40413,Q#3000 - >seq9647,superfamily,275209,587,800,4.10092e-09,59.7788,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40414,Q#3000 - >seq9647,non-specific,339261,108,232,1.8863599999999998e-08,53.4951,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40415,Q#3000 - >seq9647,non-specific,197311,7,236,4.2266900000000005e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40416,Q#3000 - >seq9647,non-specific,236970,9,238,5.31643e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40417,Q#3000 - >seq9647,non-specific,238185,656,772,6.25537e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40418,Q#3000 - >seq9647,non-specific,224117,233,501,6.42904e-05,47.4016,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40419,Q#3000 - >seq9647,superfamily,224117,233,501,6.42904e-05,47.4016,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40420,Q#3000 - >seq9647,non-specific,235175,263,469,0.00038999,44.6696,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,marg,BothTerminiTruncated
40421,Q#3000 - >seq9647,superfamily,235175,263,469,0.00038999,44.6696,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,marg,BothTerminiTruncated
40422,Q#3000 - >seq9647,specific,311990,1240,1258,0.0018784000000000003,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40423,Q#3000 - >seq9647,superfamily,311990,1240,1258,0.0018784000000000003,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA8A,ORF2,hs0_human,marg,CompleteHit
40424,Q#3000 - >seq9647,non-specific,197314,7,192,0.00241883,40.7899,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PA8A,ORF2,hs0_human,marg,C-TerminusTruncated
40425,Q#3000 - >seq9647,non-specific,197317,139,229,0.00338034,40.6632,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA8A,ORF2,hs0_human,marg,N-TerminusTruncated
40426,Q#3000 - >seq9647,non-specific,274009,263,427,0.0065944,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,marg,BothTerminiTruncated
40427,Q#3000 - >seq9647,superfamily,274009,263,427,0.0065944,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF2.hs0_human.marg.frame3,1909190232_L1PA8A.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF2,hs0_human,marg,BothTerminiTruncated
40428,Q#3001 - >seq9648,specific,238827,469,731,6.296599999999998e-70,233.33700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40429,Q#3001 - >seq9648,superfamily,295487,469,731,6.296599999999998e-70,233.33700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40430,Q#3001 - >seq9648,specific,333820,475,731,4.443039999999999e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40431,Q#3001 - >seq9648,superfamily,333820,475,731,4.443039999999999e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40432,Q#3001 - >seq9648,non-specific,238828,475,696,5.0997e-14,72.6188,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40433,Q#3001 - >seq9648,non-specific,275209,426,696,1.0197799999999999e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40434,Q#3001 - >seq9648,superfamily,275209,426,696,1.0197799999999999e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40435,Q#3001 - >seq9648,non-specific,238185,615,729,1.57656e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40436,Q#3001 - >seq9648,non-specific,239569,484,744,0.0005026259999999999,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40437,Q#3001 - >seq9648,specific,311990,1201,1218,0.00540152,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40438,Q#3001 - >seq9648,superfamily,311990,1201,1218,0.00540152,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs1_chimp.marg.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40439,Q#3003 - >seq9650,specific,197310,3,230,6.818779999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40440,Q#3003 - >seq9650,superfamily,351117,3,230,6.818779999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40441,Q#3003 - >seq9650,non-specific,197306,3,230,2.5210999999999998e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40442,Q#3003 - >seq9650,non-specific,223780,3,231,8.8595e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40443,Q#3003 - >seq9650,non-specific,197320,3,200,2.9454499999999997e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40444,Q#3003 - >seq9650,non-specific,197307,3,230,4.116980000000001e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40445,Q#3003 - >seq9650,specific,335306,4,223,5.32076e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40446,Q#3003 - >seq9650,non-specific,197319,7,230,1.90037e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40447,Q#3003 - >seq9650,non-specific,273186,3,231,5.391200000000001e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40448,Q#3003 - >seq9650,non-specific,272954,3,230,8.740510000000001e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40449,Q#3003 - >seq9650,non-specific,197321,1,230,1.45335e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40450,Q#3003 - >seq9650,non-specific,197336,3,188,1.4946799999999998e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40451,Q#3003 - >seq9650,non-specific,197322,2,230,2.1337299999999997e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40452,Q#3003 - >seq9650,non-specific,236970,3,183,3.6323300000000003e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40453,Q#3003 - >seq9650,non-specific,197311,24,230,3.71074e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40454,Q#3003 - >seq9650,non-specific,235175,300,438,9.84438e-06,49.6772,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40455,Q#3003 - >seq9650,superfamily,235175,300,438,9.84438e-06,49.6772,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40456,Q#3003 - >seq9650,non-specific,223496,225,423,1.329e-05,49.3735,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40457,Q#3003 - >seq9650,superfamily,223496,225,423,1.329e-05,49.3735,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40458,Q#3003 - >seq9650,non-specific,334125,206,405,0.000338107,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
40459,Q#3003 - >seq9650,superfamily,334125,206,405,0.000338107,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs1_chimp,marg,N-TerminusTruncated
40460,Q#3003 - >seq9650,non-specific,339261,102,226,0.0007672380000000001,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs1_chimp,marg,CompleteHit
40461,Q#3003 - >seq9650,non-specific,338310,987,1049,0.00126844,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40462,Q#3003 - >seq9650,superfamily,338310,987,1049,0.00126844,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40463,Q#3003 - >seq9650,non-specific,274009,301,451,0.00150783,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40464,Q#3003 - >seq9650,superfamily,274009,301,451,0.00150783,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40465,Q#3003 - >seq9650,non-specific,274009,288,466,0.0016134,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,BothTerminiTruncated
40466,Q#3003 - >seq9650,non-specific,224117,277,471,0.00659171,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40467,Q#3003 - >seq9650,superfamily,224117,277,471,0.00659171,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40468,Q#3003 - >seq9650,non-specific,235175,277,430,0.00942002,40.0472,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.marg.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,marg,C-TerminusTruncated
40469,Q#3004 - >seq9651,specific,238827,469,731,6.097239999999999e-70,233.33700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40470,Q#3004 - >seq9651,superfamily,295487,469,731,6.097239999999999e-70,233.33700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40471,Q#3004 - >seq9651,specific,333820,475,731,4.27079e-35,132.031,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40472,Q#3004 - >seq9651,superfamily,333820,475,731,4.27079e-35,132.031,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40473,Q#3004 - >seq9651,non-specific,238828,475,696,4.7686300000000007e-14,72.6188,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40474,Q#3004 - >seq9651,non-specific,275209,426,696,9.575110000000002e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40475,Q#3004 - >seq9651,superfamily,275209,426,696,9.575110000000002e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40476,Q#3004 - >seq9651,non-specific,238185,615,729,1.57523e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40477,Q#3004 - >seq9651,non-specific,239569,484,744,0.0004885590000000001,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40478,Q#3004 - >seq9651,specific,311990,1200,1217,0.0053972000000000004,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40479,Q#3004 - >seq9651,superfamily,311990,1200,1217,0.0053972000000000004,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs1_chimp.pars.frame2,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40480,Q#3006 - >seq9653,specific,197310,3,230,6.808139999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40481,Q#3006 - >seq9653,superfamily,351117,3,230,6.808139999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40482,Q#3006 - >seq9653,non-specific,197306,3,230,2.5922199999999995e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40483,Q#3006 - >seq9653,non-specific,223780,3,231,8.85065e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40484,Q#3006 - >seq9653,non-specific,197320,3,200,2.94253e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40485,Q#3006 - >seq9653,non-specific,197307,3,230,4.11291e-20,90.8101,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40486,Q#3006 - >seq9653,specific,335306,4,223,5.31563e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40487,Q#3006 - >seq9653,non-specific,197319,7,230,1.8985000000000002e-16,80.3985,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40488,Q#3006 - >seq9653,non-specific,273186,3,231,5.38589e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40489,Q#3006 - >seq9653,non-specific,272954,3,230,8.73189e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40490,Q#3006 - >seq9653,non-specific,197321,1,230,1.4115e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40491,Q#3006 - >seq9653,non-specific,197336,3,188,1.49322e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40492,Q#3006 - >seq9653,non-specific,197322,2,230,2.13161e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40493,Q#3006 - >seq9653,non-specific,236970,3,183,3.62881e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40494,Q#3006 - >seq9653,non-specific,197311,24,230,3.7072699999999997e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40495,Q#3006 - >seq9653,non-specific,235175,300,438,9.66892e-06,49.6772,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40496,Q#3006 - >seq9653,superfamily,235175,300,438,9.66892e-06,49.6772,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40497,Q#3006 - >seq9653,non-specific,223496,225,423,1.2093599999999999e-05,49.3735,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40498,Q#3006 - >seq9653,superfamily,223496,225,423,1.2093599999999999e-05,49.3735,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40499,Q#3006 - >seq9653,non-specific,334125,206,405,0.000337778,44.4476,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs1_chimp,pars,N-TerminusTruncated
40500,Q#3006 - >seq9653,superfamily,334125,206,405,0.000337778,44.4476,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs1_chimp,pars,N-TerminusTruncated
40501,Q#3006 - >seq9653,non-specific,339261,102,226,0.000781505,40.3983,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs1_chimp,pars,CompleteHit
40502,Q#3006 - >seq9653,non-specific,274009,301,451,0.00145624,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40503,Q#3006 - >seq9653,superfamily,274009,301,451,0.00145624,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40504,Q#3006 - >seq9653,non-specific,274009,288,466,0.00153206,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40505,Q#3006 - >seq9653,non-specific,338310,986,1048,0.00274173,40.2492,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40506,Q#3006 - >seq9653,superfamily,338310,986,1048,0.00274173,40.2492,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs1_chimp,pars,BothTerminiTruncated
40507,Q#3006 - >seq9653,non-specific,224117,277,471,0.00647487,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40508,Q#3006 - >seq9653,superfamily,224117,277,471,0.00647487,40.468,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40509,Q#3006 - >seq9653,non-specific,235175,277,430,0.00886856,40.0472,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs1_chimp.pars.frame3,1909190240_L1PB1.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs1_chimp,pars,C-TerminusTruncated
40510,Q#3007 - >seq9654,specific,238827,503,770,5.0028799999999994e-64,216.388,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40511,Q#3007 - >seq9654,superfamily,295487,503,770,5.0028799999999994e-64,216.388,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40512,Q#3007 - >seq9654,specific,197310,3,230,1.5249499999999998e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40513,Q#3007 - >seq9654,superfamily,351117,3,230,1.5249499999999998e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40514,Q#3007 - >seq9654,specific,333820,509,733,6.30238e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40515,Q#3007 - >seq9654,superfamily,333820,509,733,6.30238e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40516,Q#3007 - >seq9654,non-specific,197306,3,230,6.119949999999999e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40517,Q#3007 - >seq9654,non-specific,197320,3,223,2.0633699999999997e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40518,Q#3007 - >seq9654,non-specific,223780,3,231,2.88788e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40519,Q#3007 - >seq9654,non-specific,197307,3,230,3.33134e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40520,Q#3007 - >seq9654,specific,335306,4,223,2.4477e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40521,Q#3007 - >seq9654,non-specific,273186,3,231,8.51469e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40522,Q#3007 - >seq9654,non-specific,197321,1,230,3.99632e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40523,Q#3007 - >seq9654,non-specific,197319,7,230,7.094549999999999e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40524,Q#3007 - >seq9654,non-specific,272954,3,230,9.12539e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40525,Q#3007 - >seq9654,non-specific,238828,509,730,1.55196e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40526,Q#3007 - >seq9654,non-specific,197336,3,188,1.47518e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40527,Q#3007 - >seq9654,non-specific,275209,460,730,1.18746e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40528,Q#3007 - >seq9654,superfamily,275209,460,730,1.18746e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40529,Q#3007 - >seq9654,non-specific,197322,2,230,1.2115200000000002e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40530,Q#3007 - >seq9654,non-specific,236970,3,183,2.73221e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40531,Q#3007 - >seq9654,non-specific,197311,24,230,1.8742300000000002e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40532,Q#3007 - >seq9654,non-specific,334125,206,404,0.00039905400000000003,44.0624,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs3_orang,marg,N-TerminusTruncated
40533,Q#3007 - >seq9654,superfamily,334125,206,404,0.00039905400000000003,44.0624,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs3_orang,marg,N-TerminusTruncated
40534,Q#3007 - >seq9654,non-specific,339261,102,226,0.000599927,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40535,Q#3007 - >seq9654,non-specific,239569,518,731,0.0008221869999999999,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,CompleteHit
40536,Q#3007 - >seq9654,non-specific,274009,301,450,0.00155203,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40537,Q#3007 - >seq9654,superfamily,274009,301,450,0.00155203,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40538,Q#3007 - >seq9654,non-specific,238185,649,726,0.00251186,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs3_orang,marg,C-TerminusTruncated
40539,Q#3007 - >seq9654,non-specific,235175,304,456,0.00262515,41.9732,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,marg,BothTerminiTruncated
40540,Q#3007 - >seq9654,superfamily,235175,304,456,0.00262515,41.9732,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,marg,BothTerminiTruncated
40541,Q#3007 - >seq9654,non-specific,274009,288,428,0.00813912,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.marg.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,marg,BothTerminiTruncated
40542,Q#3008 - >seq9655,non-specific,338310,944,1006,0.0009412810000000001,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs3_orang.marg.frame1,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs3_orang,marg,BothTerminiTruncated
40543,Q#3008 - >seq9655,superfamily,338310,944,1006,0.0009412810000000001,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs3_orang.marg.frame1,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs3_orang,marg,BothTerminiTruncated
40544,Q#3009 - >seq9656,specific,238827,502,764,1.3909799999999997e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40545,Q#3009 - >seq9656,superfamily,295487,502,764,1.3909799999999997e-68,229.485,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40546,Q#3009 - >seq9656,specific,197310,3,230,1.5135499999999999e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40547,Q#3009 - >seq9656,superfamily,351117,3,230,1.5135499999999999e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40548,Q#3009 - >seq9656,specific,333820,508,764,1.47102e-34,130.49,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40549,Q#3009 - >seq9656,superfamily,333820,508,764,1.47102e-34,130.49,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40550,Q#3009 - >seq9656,non-specific,197306,3,230,5.9653799999999996e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40551,Q#3009 - >seq9656,non-specific,197320,3,223,2.06972e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40552,Q#3009 - >seq9656,non-specific,223780,3,231,2.92422e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40553,Q#3009 - >seq9656,non-specific,197307,3,230,3.4055399999999996e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40554,Q#3009 - >seq9656,specific,335306,4,223,2.4324400000000003e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40555,Q#3009 - >seq9656,non-specific,273186,3,231,8.46045e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40556,Q#3009 - >seq9656,non-specific,197321,1,230,3.93375e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40557,Q#3009 - >seq9656,non-specific,197319,7,230,7.04947e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40558,Q#3009 - >seq9656,non-specific,272954,3,230,8.815529999999999e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40559,Q#3009 - >seq9656,non-specific,238828,508,729,1.58662e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40560,Q#3009 - >seq9656,non-specific,197336,3,188,1.46588e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40561,Q#3009 - >seq9656,non-specific,197322,2,230,1.20374e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40562,Q#3009 - >seq9656,non-specific,275209,459,729,1.30046e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,C-TerminusTruncated
40563,Q#3009 - >seq9656,superfamily,275209,459,729,1.30046e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,C-TerminusTruncated
40564,Q#3009 - >seq9656,non-specific,236970,3,183,2.6665e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs3_orang,pars,C-TerminusTruncated
40565,Q#3009 - >seq9656,non-specific,197311,24,230,1.81172e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40566,Q#3009 - >seq9656,non-specific,238185,648,762,5.6374799999999994e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40567,Q#3009 - >seq9656,non-specific,339261,102,226,0.000531187,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40568,Q#3009 - >seq9656,non-specific,239569,517,777,0.000626676,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs3_orang,pars,CompleteHit
40569,Q#3009 - >seq9656,non-specific,274009,301,449,0.00124838,43.1327,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,pars,C-TerminusTruncated
40570,Q#3009 - >seq9656,superfamily,274009,301,449,0.00124838,43.1327,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,pars,C-TerminusTruncated
40571,Q#3009 - >seq9656,non-specific,334125,206,403,0.00354184,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs3_orang,pars,N-TerminusTruncated
40572,Q#3009 - >seq9656,superfamily,334125,206,403,0.00354184,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs3_orang,pars,N-TerminusTruncated
40573,Q#3009 - >seq9656,non-specific,235175,285,436,0.00619374,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,pars,BothTerminiTruncated
40574,Q#3009 - >seq9656,superfamily,235175,285,436,0.00619374,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,pars,BothTerminiTruncated
40575,Q#3009 - >seq9656,non-specific,274009,288,427,0.00743261,40.4363,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs3_orang.pars.frame3,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs3_orang,pars,BothTerminiTruncated
40576,Q#3011 - >seq9658,non-specific,338310,938,1000,0.000934916,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs3_orang.pars.frame1,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs3_orang,pars,BothTerminiTruncated
40577,Q#3011 - >seq9658,superfamily,338310,938,1000,0.000934916,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs3_orang.pars.frame1,1909190242_L1PB1.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs3_orang,pars,BothTerminiTruncated
40578,Q#3014 - >seq9661,non-specific,338310,946,1008,0.00474816,39.4788,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs2_gorilla.marg.frame1,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40579,Q#3014 - >seq9661,superfamily,338310,946,1008,0.00474816,39.4788,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs2_gorilla.marg.frame1,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40580,Q#3015 - >seq9662,specific,197310,3,229,9.92781e-58,199.115,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40581,Q#3015 - >seq9662,superfamily,351117,3,229,9.92781e-58,199.115,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40582,Q#3015 - >seq9662,non-specific,197306,3,229,2.8102199999999997e-33,128.753,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40583,Q#3015 - >seq9662,non-specific,197320,3,222,3.86718e-22,96.8153,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40584,Q#3015 - >seq9662,non-specific,223780,3,230,5.425209999999999e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40585,Q#3015 - >seq9662,non-specific,197307,3,229,1.5578e-19,89.2693,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40586,Q#3015 - >seq9662,non-specific,273186,3,230,1.7643200000000002e-17,83.4824,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40587,Q#3015 - >seq9662,specific,335306,4,222,4.50212e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40588,Q#3015 - >seq9662,non-specific,197319,7,229,9.307200000000001e-17,81.1689,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40589,Q#3015 - >seq9662,non-specific,272954,3,229,7.904319999999999e-16,78.5789,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40590,Q#3015 - >seq9662,non-specific,197321,1,229,1.23052e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40591,Q#3015 - >seq9662,non-specific,197336,3,187,1.37069e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40592,Q#3015 - >seq9662,non-specific,197322,2,229,1.4282299999999998e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40593,Q#3015 - >seq9662,non-specific,236970,3,242,1.10702e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40594,Q#3015 - >seq9662,non-specific,197311,24,229,3.89848e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40595,Q#3015 - >seq9662,non-specific,334125,205,402,0.000153236,45.218,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40596,Q#3015 - >seq9662,superfamily,334125,205,402,0.000153236,45.218,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
40597,Q#3015 - >seq9662,non-specific,339261,101,225,0.000198935,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40598,Q#3015 - >seq9662,non-specific,235175,284,465,0.00130944,42.7436,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
40599,Q#3015 - >seq9662,superfamily,235175,284,465,0.00130944,42.7436,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
40600,Q#3015 - >seq9662,non-specific,274009,300,461,0.0013208,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40601,Q#3015 - >seq9662,superfamily,274009,300,461,0.0013208,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40602,Q#3015 - >seq9662,non-specific,274009,287,462,0.00135475,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
40603,Q#3015 - >seq9662,non-specific,224117,276,468,0.00548831,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40604,Q#3015 - >seq9662,superfamily,224117,276,468,0.00548831,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40605,Q#3015 - >seq9662,non-specific,338310,990,1052,0.00627955,39.0936,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
40606,Q#3015 - >seq9662,superfamily,338310,990,1052,0.00627955,39.0936,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs2_gorilla.pars.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
40607,Q#3016 - >seq9663,specific,238827,467,733,3.8105999999999997e-63,214.077,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40608,Q#3016 - >seq9663,superfamily,295487,467,733,3.8105999999999997e-63,214.077,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40609,Q#3016 - >seq9663,specific,333820,473,696,1.32831e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40610,Q#3016 - >seq9663,superfamily,333820,473,696,1.32831e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40611,Q#3016 - >seq9663,non-specific,238828,473,693,1.6969500000000002e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40612,Q#3016 - >seq9663,non-specific,275209,423,693,8.788399999999999e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40613,Q#3016 - >seq9663,superfamily,275209,423,693,8.788399999999999e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40614,Q#3016 - >seq9663,non-specific,239569,497,694,8.09585e-05,44.8711,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40615,Q#3016 - >seq9663,non-specific,238185,612,689,0.0010037000000000002,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
40616,Q#3016 - >seq9663,specific,311990,1203,1220,0.00562649,35.3404,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40617,Q#3016 - >seq9663,superfamily,311990,1203,1220,0.00562649,35.3404,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB1.ORF2.hs2_gorilla.pars.frame2,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB1,ORF2,hs2_gorilla,pars,CompleteHit
40618,Q#3018 - >seq9665,specific,238827,503,769,6.60983e-62,210.61,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40619,Q#3018 - >seq9665,superfamily,295487,503,769,6.60983e-62,210.61,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40620,Q#3018 - >seq9665,specific,197310,3,229,3.7303699999999997e-57,197.574,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40621,Q#3018 - >seq9665,superfamily,351117,3,229,3.7303699999999997e-57,197.574,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40622,Q#3018 - >seq9665,non-specific,197306,3,229,1.2087899999999999e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40623,Q#3018 - >seq9665,specific,333820,509,732,3.4649599999999996e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40624,Q#3018 - >seq9665,superfamily,333820,509,732,3.4649599999999996e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40625,Q#3018 - >seq9665,non-specific,197320,3,222,5.50297e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40626,Q#3018 - >seq9665,non-specific,223780,3,230,5.0000100000000006e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40627,Q#3018 - >seq9665,non-specific,197307,3,229,1.48029e-17,83.4913,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40628,Q#3018 - >seq9665,specific,335306,4,222,4.8522500000000004e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40629,Q#3018 - >seq9665,non-specific,273186,3,230,6.558579999999999e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40630,Q#3018 - >seq9665,non-specific,197319,7,229,9.30833e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40631,Q#3018 - >seq9665,non-specific,272954,3,229,1.32715e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40632,Q#3018 - >seq9665,non-specific,197321,1,229,3.2719599999999995e-14,73.7404,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40633,Q#3018 - >seq9665,non-specific,238828,509,729,6.212279999999999e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40634,Q#3018 - >seq9665,non-specific,197336,3,187,1.47832e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40635,Q#3018 - >seq9665,non-specific,275209,459,729,1.02955e-08,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40636,Q#3018 - >seq9665,superfamily,275209,459,729,1.02955e-08,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40637,Q#3018 - >seq9665,non-specific,197322,2,229,1.5429899999999998e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40638,Q#3018 - >seq9665,non-specific,236970,3,182,5.85617e-07,52.2038,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40639,Q#3018 - >seq9665,non-specific,197311,24,229,8.11714e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40640,Q#3018 - >seq9665,non-specific,223496,224,422,6.46406e-05,47.0623,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40641,Q#3018 - >seq9665,superfamily,223496,224,422,6.46406e-05,47.0623,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40642,Q#3018 - >seq9665,non-specific,239569,533,730,0.00010232399999999999,44.8711,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40643,Q#3018 - >seq9665,non-specific,235175,299,456,0.000132597,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40644,Q#3018 - >seq9665,superfamily,235175,299,456,0.000132597,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
40645,Q#3018 - >seq9665,non-specific,339261,101,225,0.000147663,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs2_gorilla,marg,CompleteHit
40646,Q#3018 - >seq9665,non-specific,238185,648,725,0.00255921,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40647,Q#3018 - >seq9665,non-specific,334125,205,404,0.00434097,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40648,Q#3018 - >seq9665,superfamily,334125,205,404,0.00434097,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
40649,Q#3018 - >seq9665,non-specific,274009,300,450,0.00820091,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40650,Q#3018 - >seq9665,superfamily,274009,300,450,0.00820091,40.4363,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs2_gorilla.marg.frame3,1909190242_L1PB1.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
40651,Q#3019 - >seq9666,non-specific,338310,944,1006,0.0009412810000000001,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs4_gibbon.marg.frame3,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40652,Q#3019 - >seq9666,superfamily,338310,944,1006,0.0009412810000000001,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs4_gibbon.marg.frame3,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40653,Q#3020 - >seq9667,specific,238827,505,770,2.4404499999999994e-64,217.544,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40654,Q#3020 - >seq9667,superfamily,295487,505,770,2.4404499999999994e-64,217.544,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40655,Q#3020 - >seq9667,specific,197310,3,229,4.486399999999999e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40656,Q#3020 - >seq9667,superfamily,351117,3,229,4.486399999999999e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40657,Q#3020 - >seq9667,specific,333820,511,735,5.8337299999999995e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40658,Q#3020 - >seq9667,superfamily,333820,511,735,5.8337299999999995e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40659,Q#3020 - >seq9667,non-specific,197306,3,229,1.1868899999999999e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40660,Q#3020 - >seq9667,non-specific,197320,3,222,6.29193e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40661,Q#3020 - >seq9667,non-specific,223780,3,230,5.9355600000000006e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40662,Q#3020 - >seq9667,non-specific,197307,3,229,1.5242500000000002e-17,83.4913,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40663,Q#3020 - >seq9667,specific,335306,4,222,4.85658e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40664,Q#3020 - >seq9667,non-specific,273186,3,230,6.75296e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40665,Q#3020 - >seq9667,non-specific,197319,7,229,9.40473e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40666,Q#3020 - >seq9667,non-specific,272954,3,229,1.3036600000000002e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40667,Q#3020 - >seq9667,non-specific,197321,1,229,3.33695e-14,73.7404,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40668,Q#3020 - >seq9667,non-specific,238828,511,732,1.34688e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40669,Q#3020 - >seq9667,non-specific,197336,3,187,1.4796500000000002e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40670,Q#3020 - >seq9667,non-specific,275209,462,732,9.94625e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40671,Q#3020 - >seq9667,superfamily,275209,462,732,9.94625e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40672,Q#3020 - >seq9667,non-specific,197322,2,229,1.54441e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40673,Q#3020 - >seq9667,non-specific,236970,3,182,6.13336e-07,52.2038,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40674,Q#3020 - >seq9667,non-specific,197311,24,229,8.12418e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40675,Q#3020 - >seq9667,non-specific,339261,101,225,0.000146363,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40676,Q#3020 - >seq9667,non-specific,274009,300,452,0.000633353,43.9031,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40677,Q#3020 - >seq9667,superfamily,274009,300,452,0.000633353,43.9031,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40678,Q#3020 - >seq9667,non-specific,239569,520,733,0.000764142,42.1747,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,CompleteHit
40679,Q#3020 - >seq9667,non-specific,238185,651,728,0.0024395,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,marg,C-TerminusTruncated
40680,Q#3020 - >seq9667,non-specific,223496,224,424,0.00249765,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40681,Q#3020 - >seq9667,superfamily,223496,224,424,0.00249765,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40682,Q#3020 - >seq9667,non-specific,334125,205,406,0.00388458,40.9808,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1PB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
40683,Q#3020 - >seq9667,superfamily,334125,205,406,0.00388458,40.9808,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,Other_Chrom,L1PB1,ORF2,hs4_gibbon,marg,N-TerminusTruncated
40684,Q#3020 - >seq9667,non-specific,274009,287,431,0.00435386,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40685,Q#3020 - >seq9667,non-specific,235175,303,458,0.00440285,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40686,Q#3020 - >seq9667,superfamily,235175,303,458,0.00440285,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs4_gibbon.marg.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,marg,BothTerminiTruncated
40687,Q#3022 - >seq9669,non-specific,338310,938,1000,0.0009358260000000001,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs4_gibbon.pars.frame3,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40688,Q#3022 - >seq9669,superfamily,338310,938,1000,0.0009358260000000001,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs4_gibbon.pars.frame3,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40689,Q#3024 - >seq9671,specific,238827,502,764,1.3537499999999998e-68,229.485,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40690,Q#3024 - >seq9671,superfamily,295487,502,764,1.3537499999999998e-68,229.485,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40691,Q#3024 - >seq9671,specific,197310,3,229,4.459159999999999e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40692,Q#3024 - >seq9671,superfamily,351117,3,229,4.459159999999999e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40693,Q#3024 - >seq9671,specific,333820,508,764,1.4028899999999997e-34,130.875,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40694,Q#3024 - >seq9671,superfamily,333820,508,764,1.4028899999999997e-34,130.875,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40695,Q#3024 - >seq9671,non-specific,197306,3,229,1.18042e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40696,Q#3024 - >seq9671,non-specific,197320,3,222,6.62457e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40697,Q#3024 - >seq9671,non-specific,223780,3,230,6.0157700000000005e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40698,Q#3024 - >seq9671,non-specific,197307,3,229,1.74679e-17,83.4913,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40699,Q#3024 - >seq9671,specific,335306,4,222,4.8306400000000004e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40700,Q#3024 - >seq9671,non-specific,273186,3,230,6.716039999999999e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40701,Q#3024 - >seq9671,non-specific,197319,7,229,9.803369999999999e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40702,Q#3024 - >seq9671,non-specific,272954,3,229,1.3087799999999998e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40703,Q#3024 - >seq9671,non-specific,197321,1,229,3.5774099999999996e-14,73.7404,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40704,Q#3024 - >seq9671,non-specific,238828,508,729,1.54367e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40705,Q#3024 - >seq9671,non-specific,197336,3,187,1.47168e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40706,Q#3024 - >seq9671,non-specific,275209,459,729,1.13971e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40707,Q#3024 - >seq9671,superfamily,275209,459,729,1.13971e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40708,Q#3024 - >seq9671,non-specific,197322,2,229,1.5359000000000002e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40709,Q#3024 - >seq9671,non-specific,236970,3,182,6.156e-07,52.2038,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40710,Q#3024 - >seq9671,non-specific,197311,24,229,8.081939999999999e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40711,Q#3024 - >seq9671,non-specific,238185,648,762,5.6421e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40712,Q#3024 - >seq9671,non-specific,339261,101,225,0.00014285,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40713,Q#3024 - >seq9671,non-specific,239569,517,777,0.00060466,42.5599,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB1,ORF2,hs4_gibbon,pars,CompleteHit
40714,Q#3024 - >seq9671,non-specific,274009,300,449,0.00145493,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40715,Q#3024 - >seq9671,superfamily,274009,300,449,0.00145493,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,pars,C-TerminusTruncated
40716,Q#3024 - >seq9671,non-specific,334125,205,403,0.00504638,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
40717,Q#3024 - >seq9671,superfamily,334125,205,403,0.00504638,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB1,ORF2,hs4_gibbon,pars,N-TerminusTruncated
40718,Q#3024 - >seq9671,non-specific,235175,284,436,0.00604363,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40719,Q#3024 - >seq9671,superfamily,235175,284,436,0.00604363,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40720,Q#3024 - >seq9671,non-specific,274009,287,427,0.00677863,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs4_gibbon.pars.frame2,1909190245_L1PB1.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB1,ORF2,hs4_gibbon,pars,BothTerminiTruncated
40721,Q#3026 - >seq9673,specific,238827,503,765,3.155079999999999e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40722,Q#3026 - >seq9673,superfamily,295487,503,765,3.155079999999999e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40723,Q#3026 - >seq9673,specific,197310,3,230,1.9545499999999996e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40724,Q#3026 - >seq9673,superfamily,351117,3,230,1.9545499999999996e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40725,Q#3026 - >seq9673,specific,333820,509,765,5.130009999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40726,Q#3026 - >seq9673,superfamily,333820,509,765,5.130009999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40727,Q#3026 - >seq9673,non-specific,197306,3,230,1.98476e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40728,Q#3026 - >seq9673,non-specific,197320,3,223,9.74554e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40729,Q#3026 - >seq9673,non-specific,197307,3,230,3.96449e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40730,Q#3026 - >seq9673,non-specific,223780,3,231,1.55398e-18,86.4983,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40731,Q#3026 - >seq9673,specific,335306,4,223,7.92923e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40732,Q#3026 - >seq9673,non-specific,197321,1,230,4.611030000000001e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40733,Q#3026 - >seq9673,non-specific,273186,3,231,6.27165e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40734,Q#3026 - >seq9673,non-specific,272954,3,230,6.2983400000000005e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40735,Q#3026 - >seq9673,non-specific,197319,7,230,1.40881e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40736,Q#3026 - >seq9673,non-specific,238828,509,730,1.04521e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40737,Q#3026 - >seq9673,non-specific,197336,3,188,4.73063e-11,64.5559,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40738,Q#3026 - >seq9673,non-specific,236970,3,188,2.77173e-07,53.3594,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,marg,C-TerminusTruncated
40739,Q#3026 - >seq9673,non-specific,275209,459,664,2.86759e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,C-TerminusTruncated
40740,Q#3026 - >seq9673,superfamily,275209,459,664,2.86759e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,C-TerminusTruncated
40741,Q#3026 - >seq9673,non-specific,197322,2,230,5.88187e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40742,Q#3026 - >seq9673,non-specific,197311,1,230,1.5419e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,marg,CompleteHit
40743,Q#3026 - >seq9673,non-specific,235175,285,462,5.85233e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,marg,BothTerminiTruncated
40744,Q#3026 - >seq9673,superfamily,235175,285,462,5.85233e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,marg,BothTerminiTruncated
40745,Q#3026 - >seq9673,non-specific,238185,649,763,6.66433e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40746,Q#3026 - >seq9673,non-specific,274009,301,451,0.000138759,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,marg,C-TerminusTruncated
40747,Q#3026 - >seq9673,superfamily,274009,301,451,0.000138759,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,marg,C-TerminusTruncated
40748,Q#3026 - >seq9673,non-specific,339261,102,226,0.00015747799999999999,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs0_human,marg,CompleteHit
40749,Q#3026 - >seq9673,specific,311990,1235,1252,0.000649095,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs0_human,marg,CompleteHit
40750,Q#3026 - >seq9673,superfamily,311990,1235,1252,0.000649095,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs0_human.marg.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs0_human,marg,CompleteHit
40751,Q#3028 - >seq9675,non-specific,338310,935,996,0.00454649,39.4788,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs0_human.marg.frame1,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF2,hs0_human,marg,BothTerminiTruncated
40752,Q#3028 - >seq9675,superfamily,338310,935,996,0.00454649,39.4788,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs0_human.marg.frame1,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB2,ORF2,hs0_human,marg,BothTerminiTruncated
40753,Q#3029 - >seq9676,specific,238827,503,765,3.1803999999999993e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40754,Q#3029 - >seq9676,superfamily,295487,503,765,3.1803999999999993e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40755,Q#3029 - >seq9676,specific,197310,3,230,1.9902599999999996e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40756,Q#3029 - >seq9676,superfamily,351117,3,230,1.9902599999999996e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40757,Q#3029 - >seq9676,specific,333820,509,765,5.125539999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40758,Q#3029 - >seq9676,superfamily,333820,509,765,5.125539999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40759,Q#3029 - >seq9676,non-specific,197306,3,230,1.98295e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40760,Q#3029 - >seq9676,non-specific,197320,3,223,9.92315e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40761,Q#3029 - >seq9676,non-specific,197307,3,230,4.11407e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40762,Q#3029 - >seq9676,non-specific,223780,3,231,1.64305e-18,86.4983,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40763,Q#3029 - >seq9676,specific,335306,4,223,7.92214e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40764,Q#3029 - >seq9676,non-specific,197321,1,230,4.52084e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40765,Q#3029 - >seq9676,non-specific,273186,3,231,6.506350000000001e-16,78.86,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40766,Q#3029 - >seq9676,non-specific,272954,3,230,6.53348e-15,75.8825,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40767,Q#3029 - >seq9676,non-specific,197319,7,230,1.43414e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40768,Q#3029 - >seq9676,non-specific,238828,509,730,1.11536e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40769,Q#3029 - >seq9676,non-specific,197336,3,188,4.72635e-11,64.5559,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40770,Q#3029 - >seq9676,non-specific,236970,3,188,2.79451e-07,53.3594,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs0_human,pars,C-TerminusTruncated
40771,Q#3029 - >seq9676,non-specific,275209,459,664,2.94165e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,C-TerminusTruncated
40772,Q#3029 - >seq9676,superfamily,275209,459,664,2.94165e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,C-TerminusTruncated
40773,Q#3029 - >seq9676,non-specific,197322,2,230,5.876509999999999e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40774,Q#3029 - >seq9676,non-specific,197311,1,230,1.52625e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs0_human,pars,CompleteHit
40775,Q#3029 - >seq9676,non-specific,235175,285,462,6.04872e-05,47.36600000000001,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,pars,BothTerminiTruncated
40776,Q#3029 - >seq9676,superfamily,235175,285,462,6.04872e-05,47.36600000000001,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,pars,BothTerminiTruncated
40777,Q#3029 - >seq9676,non-specific,238185,649,763,6.7241e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40778,Q#3029 - >seq9676,non-specific,274009,301,451,0.000138632,46.2143,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,pars,C-TerminusTruncated
40779,Q#3029 - >seq9676,superfamily,274009,301,451,0.000138632,46.2143,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs0_human,pars,C-TerminusTruncated
40780,Q#3029 - >seq9676,non-specific,339261,102,226,0.000157348,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs0_human,pars,CompleteHit
40781,Q#3029 - >seq9676,specific,311990,1235,1252,0.00064859,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB2,ORF2,hs0_human,pars,CompleteHit
40782,Q#3029 - >seq9676,superfamily,311990,1235,1252,0.00064859,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs0_human.pars.frame3,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB2,ORF2,hs0_human,pars,CompleteHit
40783,Q#3030 - >seq9677,non-specific,338310,935,996,0.00454209,39.4788,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs0_human.pars.frame1,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB2,ORF2,hs0_human,pars,BothTerminiTruncated
40784,Q#3030 - >seq9677,superfamily,338310,935,996,0.00454209,39.4788,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB2.ORF2.hs0_human.pars.frame1,1909190248_L1PB2.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB2,ORF2,hs0_human,pars,BothTerminiTruncated
40785,Q#3031 - >seq9678,specific,238827,508,770,1.1896799999999998e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40786,Q#3031 - >seq9678,superfamily,295487,508,770,1.1896799999999998e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40787,Q#3031 - >seq9678,specific,197310,9,236,1.58506e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40788,Q#3031 - >seq9678,superfamily,351117,9,236,1.58506e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40789,Q#3031 - >seq9678,specific,333820,514,770,6.87475e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40790,Q#3031 - >seq9678,superfamily,333820,514,770,6.87475e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40791,Q#3031 - >seq9678,non-specific,197306,9,236,6.736589999999999e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40792,Q#3031 - >seq9678,non-specific,197320,9,229,2.08306e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40793,Q#3031 - >seq9678,non-specific,223780,9,237,2.7281799999999998e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40794,Q#3031 - >seq9678,non-specific,197307,9,236,3.17718e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40795,Q#3031 - >seq9678,specific,335306,10,229,2.4477e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40796,Q#3031 - >seq9678,non-specific,273186,9,237,8.27765e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40797,Q#3031 - >seq9678,non-specific,197321,7,236,3.88519e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40798,Q#3031 - >seq9678,non-specific,197319,13,236,6.519159999999999e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40799,Q#3031 - >seq9678,non-specific,272954,9,236,8.87196e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40800,Q#3031 - >seq9678,non-specific,238828,514,735,4.0540800000000004e-14,73.00399999999999,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40801,Q#3031 - >seq9678,non-specific,197336,9,194,1.47518e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40802,Q#3031 - >seq9678,non-specific,275209,465,722,7.10173e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40803,Q#3031 - >seq9678,superfamily,275209,465,722,7.10173e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40804,Q#3031 - >seq9678,non-specific,197322,8,236,1.2115200000000002e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40805,Q#3031 - >seq9678,non-specific,236970,9,189,2.73221e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40806,Q#3031 - >seq9678,non-specific,197311,30,236,2.05646e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40807,Q#3031 - >seq9678,non-specific,238185,654,768,0.000102749,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40808,Q#3031 - >seq9678,non-specific,334125,212,409,0.000442578,44.0624,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40809,Q#3031 - >seq9678,superfamily,334125,212,409,0.000442578,44.0624,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB1,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
40810,Q#3031 - >seq9678,non-specific,339261,108,232,0.000629609,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40811,Q#3031 - >seq9678,non-specific,239569,523,783,0.00243888,40.6339,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,marg,CompleteHit
40812,Q#3031 - >seq9678,non-specific,274009,306,455,0.00310458,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40813,Q#3031 - >seq9678,superfamily,274009,306,455,0.00310458,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
40814,Q#3031 - >seq9678,non-specific,274009,293,433,0.00332183,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40815,Q#3031 - >seq9678,non-specific,235175,305,461,0.00495764,41.2028,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40816,Q#3031 - >seq9678,superfamily,235175,305,461,0.00495764,41.2028,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs5_gmonkey.marg.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40817,Q#3033 - >seq9680,non-specific,338310,944,1006,0.0009412810000000001,41.4048,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs5_gmonkey.marg.frame1,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40818,Q#3033 - >seq9680,superfamily,338310,944,1006,0.0009412810000000001,41.4048,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs5_gmonkey.marg.frame1,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PB1,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
40819,Q#3034 - >seq9681,specific,238827,502,764,1.3322099999999996e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40820,Q#3034 - >seq9681,superfamily,295487,502,764,1.3322099999999996e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40821,Q#3034 - >seq9681,specific,197310,3,230,1.6352299999999997e-58,201.426,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40822,Q#3034 - >seq9681,superfamily,351117,3,230,1.6352299999999997e-58,201.426,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40823,Q#3034 - >seq9681,specific,333820,508,764,7.89822e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40824,Q#3034 - >seq9681,superfamily,333820,508,764,7.89822e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40825,Q#3034 - >seq9681,non-specific,197306,3,230,6.50371e-33,127.98299999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40826,Q#3034 - >seq9681,non-specific,197320,3,223,2.08947e-21,94.8893,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40827,Q#3034 - >seq9681,non-specific,223780,3,231,2.92422e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40828,Q#3034 - >seq9681,non-specific,197307,3,230,3.31009e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40829,Q#3034 - >seq9681,specific,335306,4,223,2.4324400000000003e-17,82.2929,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40830,Q#3034 - >seq9681,non-specific,273186,3,231,8.46045e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40831,Q#3034 - >seq9681,non-specific,197321,1,230,3.970900000000001e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40832,Q#3034 - >seq9681,non-specific,197319,7,230,7.11603e-15,75.7761,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40833,Q#3034 - >seq9681,non-specific,272954,3,230,8.815529999999999e-15,75.4973,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40834,Q#3034 - >seq9681,non-specific,238828,508,729,4.42847e-14,72.6188,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40835,Q#3034 - >seq9681,non-specific,197336,3,188,1.46588e-10,63.0151,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40836,Q#3034 - >seq9681,non-specific,275209,459,716,7.375149999999999e-09,59.0084,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40837,Q#3034 - >seq9681,superfamily,275209,459,716,7.375149999999999e-09,59.0084,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40838,Q#3034 - >seq9681,non-specific,197322,2,230,1.20374e-08,57.7122,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40839,Q#3034 - >seq9681,non-specific,236970,3,183,2.7397900000000006e-06,50.2778,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40840,Q#3034 - >seq9681,non-specific,197311,24,230,1.89777e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40841,Q#3034 - >seq9681,non-specific,238185,648,762,0.00011153,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40842,Q#3034 - >seq9681,non-specific,334125,206,403,0.00045132699999999996,44.0624,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
40843,Q#3034 - >seq9681,superfamily,334125,206,403,0.00045132699999999996,44.0624,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB1,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
40844,Q#3034 - >seq9681,non-specific,339261,102,226,0.000613998,40.7835,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40845,Q#3034 - >seq9681,non-specific,239569,517,777,0.00246881,40.6339,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB1,ORF2,hs5_gmonkey,pars,CompleteHit
40846,Q#3034 - >seq9681,non-specific,274009,300,449,0.00335728,41.5919,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40847,Q#3034 - >seq9681,superfamily,274009,300,449,0.00335728,41.5919,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
40848,Q#3034 - >seq9681,non-specific,274009,287,427,0.00350225,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40849,Q#3034 - >seq9681,non-specific,235175,299,455,0.00588659,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40850,Q#3034 - >seq9681,superfamily,235175,299,455,0.00588659,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB1.ORF2.hs5_gmonkey.pars.frame3,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40851,Q#3036 - >seq9683,non-specific,338310,938,1000,0.00303415,39.864000000000004,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs5_gmonkey.pars.frame1,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40852,Q#3036 - >seq9683,superfamily,338310,938,1000,0.00303415,39.864000000000004,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PB1.ORF2.hs5_gmonkey.pars.frame1,1909190248_L1PB1.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Unusual,L1PB1,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
40853,Q#3038 - >seq9685,non-specific,240274,203,525,0.000807069,43.4401,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1PB4.ORF2.hs3_orang.pars.frame2,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB4,ORF2,hs3_orang,pars,C-TerminusTruncated
40854,Q#3038 - >seq9685,superfamily,240274,203,525,0.000807069,43.4401,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1PB4.ORF2.hs3_orang.pars.frame2,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB4,ORF2,hs3_orang,pars,C-TerminusTruncated
40855,Q#3038 - >seq9685,specific,311990,1187,1202,0.009880400000000001,34.57,pfam08333,DUF1725,C,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs3_orang.pars.frame2,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs3_orang,pars,C-TerminusTruncated
40856,Q#3038 - >seq9685,superfamily,311990,1187,1202,0.009880400000000001,34.57,cl07081,DUF1725 superfamily,C, - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs3_orang.pars.frame2,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs3_orang,pars,C-TerminusTruncated
40857,Q#3039 - >seq9686,specific,238827,509,771,5.432189999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40858,Q#3039 - >seq9686,superfamily,295487,509,771,5.432189999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40859,Q#3039 - >seq9686,specific,197310,9,235,6.838279999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40860,Q#3039 - >seq9686,superfamily,351117,9,235,6.838279999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40861,Q#3039 - >seq9686,specific,333820,515,771,1.3657499999999998e-32,125.09700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40862,Q#3039 - >seq9686,superfamily,333820,515,771,1.3657499999999998e-32,125.09700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40863,Q#3039 - >seq9686,non-specific,197306,9,235,5.5182900000000005e-30,119.508,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40864,Q#3039 - >seq9686,non-specific,223780,9,236,1.14279e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40865,Q#3039 - >seq9686,non-specific,197320,9,228,6.918730000000001e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40866,Q#3039 - >seq9686,non-specific,197307,9,235,4.30982e-19,88.1137,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40867,Q#3039 - >seq9686,specific,335306,10,228,6.597610000000001e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40868,Q#3039 - >seq9686,non-specific,197319,13,235,2.38725e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40869,Q#3039 - >seq9686,non-specific,197321,7,235,5.8836799999999994e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40870,Q#3039 - >seq9686,non-specific,273186,9,236,1.2074600000000001e-14,75.008,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40871,Q#3039 - >seq9686,non-specific,272954,9,235,3.80316e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40872,Q#3039 - >seq9686,non-specific,238828,515,736,5.55435e-11,63.7592,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40873,Q#3039 - >seq9686,non-specific,236970,9,236,4.32849e-10,61.8338,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40874,Q#3039 - >seq9686,non-specific,275209,465,799,6.14679e-09,59.0084,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40875,Q#3039 - >seq9686,superfamily,275209,465,799,6.14679e-09,59.0084,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40876,Q#3039 - >seq9686,non-specific,197336,9,193,2.90353e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40877,Q#3039 - >seq9686,non-specific,238185,655,769,2.3541199999999997e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40878,Q#3039 - >seq9686,non-specific,197311,36,203,5.56033e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40879,Q#3039 - >seq9686,non-specific,224117,298,466,5.6843000000000004e-05,47.4016,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs3_orang,pars,N-TerminusTruncated
40880,Q#3039 - >seq9686,superfamily,224117,298,466,5.6843000000000004e-05,47.4016,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs3_orang,pars,N-TerminusTruncated
40881,Q#3039 - >seq9686,non-specific,214019,306,413,0.00315327,39.6802,cd12926,iSH2_PIK3R2,N,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,pars,N-TerminusTruncated
40882,Q#3039 - >seq9686,superfamily,355389,306,413,0.00315327,39.6802,cl25402,iSH2_PI3K_IA_R superfamily,N, - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,pars,N-TerminusTruncated
40883,Q#3039 - >seq9686,non-specific,274475,254,448,0.00448419,40.8224,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40884,Q#3039 - >seq9686,superfamily,274475,254,448,0.00448419,40.8224,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40885,Q#3039 - >seq9686,specific,225881,482,679,0.00481723,40.5925,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40886,Q#3039 - >seq9686,superfamily,225881,482,679,0.00481723,40.5925,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40887,Q#3039 - >seq9686,non-specific,223496,287,463,0.00743535,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40888,Q#3039 - >seq9686,superfamily,223496,287,463,0.00743535,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs3_orang,pars,BothTerminiTruncated
40889,Q#3039 - >seq9686,non-specific,339261,107,231,0.00801933,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs3_orang.pars.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs3_orang,pars,CompleteHit
40890,Q#3042 - >seq9689,specific,238827,510,772,1.1158099999999997e-63,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40891,Q#3042 - >seq9689,superfamily,295487,510,772,1.1158099999999997e-63,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40892,Q#3042 - >seq9689,specific,197310,9,236,1.5407199999999999e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40893,Q#3042 - >seq9689,superfamily,351117,9,236,1.5407199999999999e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40894,Q#3042 - >seq9689,specific,333820,516,772,1.3249299999999998e-31,122.016,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40895,Q#3042 - >seq9689,superfamily,333820,516,772,1.3249299999999998e-31,122.016,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40896,Q#3042 - >seq9689,non-specific,197306,9,236,3.78468e-31,122.975,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40897,Q#3042 - >seq9689,non-specific,197320,9,229,2.71268e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40898,Q#3042 - >seq9689,non-specific,223780,9,237,2.9939899999999998e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40899,Q#3042 - >seq9689,non-specific,197307,9,236,6.268269999999999e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40900,Q#3042 - >seq9689,specific,335306,10,229,8.56891e-20,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40901,Q#3042 - >seq9689,non-specific,197321,7,236,3.7582e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40902,Q#3042 - >seq9689,non-specific,197319,13,236,5.03306e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40903,Q#3042 - >seq9689,non-specific,273186,9,237,8.03256e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40904,Q#3042 - >seq9689,non-specific,272954,9,236,2.95051e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40905,Q#3042 - >seq9689,non-specific,236970,9,237,5.73224e-11,64.5302,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40906,Q#3042 - >seq9689,non-specific,238828,516,737,2.57513e-10,61.8332,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40907,Q#3042 - >seq9689,non-specific,197336,9,194,9.010559999999999e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40908,Q#3042 - >seq9689,non-specific,275209,466,800,3.67935e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40909,Q#3042 - >seq9689,superfamily,275209,466,800,3.67935e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40910,Q#3042 - >seq9689,non-specific,197311,30,204,4.5984799999999994e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40911,Q#3042 - >seq9689,non-specific,224117,299,467,7.92094e-05,47.0164,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs3_orang,marg,N-TerminusTruncated
40912,Q#3042 - >seq9689,superfamily,224117,299,467,7.92094e-05,47.0164,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs3_orang,marg,N-TerminusTruncated
40913,Q#3042 - >seq9689,non-specific,238185,656,770,0.00010060200000000001,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40914,Q#3042 - >seq9689,specific,311990,1240,1258,0.00101097,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40915,Q#3042 - >seq9689,superfamily,311990,1240,1258,0.00101097,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40916,Q#3042 - >seq9689,non-specific,214019,307,414,0.00139415,40.4506,cd12926,iSH2_PIK3R2,N,cl25402,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,marg,N-TerminusTruncated
40917,Q#3042 - >seq9689,superfamily,355389,307,414,0.00139415,40.4506,cl25402,iSH2_PI3K_IA_R superfamily,N, - ,"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,marg,N-TerminusTruncated
40918,Q#3042 - >seq9689,non-specific,274475,255,449,0.00240919,41.978,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,marg,BothTerminiTruncated
40919,Q#3042 - >seq9689,superfamily,274475,255,449,0.00240919,41.978,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs3_orang,marg,BothTerminiTruncated
40920,Q#3042 - >seq9689,non-specific,339261,108,232,0.00649363,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs3_orang,marg,CompleteHit
40921,Q#3042 - >seq9689,non-specific,223496,288,464,0.00816551,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs3_orang,marg,BothTerminiTruncated
40922,Q#3042 - >seq9689,superfamily,223496,288,464,0.00816551,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs3_orang.marg.frame3,1909190249_L1PB4.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs3_orang,marg,BothTerminiTruncated
40923,Q#3043 - >seq9690,specific,238827,503,765,1.4233699999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40924,Q#3043 - >seq9690,superfamily,295487,503,765,1.4233699999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40925,Q#3043 - >seq9690,specific,197310,3,230,1.1094899999999997e-59,204.50799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40926,Q#3043 - >seq9690,superfamily,351117,3,230,1.1094899999999997e-59,204.50799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40927,Q#3043 - >seq9690,specific,333820,509,765,3.18029e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40928,Q#3043 - >seq9690,superfamily,333820,509,765,3.18029e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40929,Q#3043 - >seq9690,non-specific,197306,3,230,1.73164e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40930,Q#3043 - >seq9690,non-specific,197320,3,243,1.57744e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40931,Q#3043 - >seq9690,non-specific,197307,3,230,3.15557e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40932,Q#3043 - >seq9690,non-specific,223780,3,231,4.24843e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40933,Q#3043 - >seq9690,specific,335306,4,223,2.1907299999999998e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40934,Q#3043 - >seq9690,non-specific,272954,3,243,2.4783e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40935,Q#3043 - >seq9690,non-specific,197321,1,230,2.64873e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40936,Q#3043 - >seq9690,non-specific,273186,3,231,2.6888000000000002e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40937,Q#3043 - >seq9690,non-specific,197319,7,230,5.4535900000000006e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40938,Q#3043 - >seq9690,non-specific,238828,509,730,3.5756e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40939,Q#3043 - >seq9690,non-specific,197336,3,188,6.90615e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40940,Q#3043 - >seq9690,non-specific,236970,3,243,1.7046e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40941,Q#3043 - >seq9690,non-specific,275209,460,789,2.6072199999999998e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40942,Q#3043 - >seq9690,superfamily,275209,460,789,2.6072199999999998e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40943,Q#3043 - >seq9690,non-specific,197322,2,230,1.06258e-07,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40944,Q#3043 - >seq9690,non-specific,197311,1,230,1.91691e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40945,Q#3043 - >seq9690,non-specific,238185,649,763,1.92001e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40946,Q#3043 - >seq9690,non-specific,339261,102,226,3.77337e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs1_chimp,marg,CompleteHit
40947,Q#3043 - >seq9690,non-specific,235175,285,462,7.06722e-05,46.9808,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs1_chimp,marg,BothTerminiTruncated
40948,Q#3043 - >seq9690,superfamily,235175,285,462,7.06722e-05,46.9808,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs1_chimp,marg,BothTerminiTruncated
40949,Q#3043 - >seq9690,non-specific,274009,301,451,0.00141146,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs1_chimp,marg,C-TerminusTruncated
40950,Q#3043 - >seq9690,superfamily,274009,301,451,0.00141146,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs1_chimp.marg.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs1_chimp,marg,C-TerminusTruncated
40951,Q#3045 - >seq9692,non-specific,338310,933,995,0.00159091,41.0196,pfam12317,IFT46_B_C,NC,cl13716,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs1_chimp.marg.frame1,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs1_chimp,marg,BothTerminiTruncated
40952,Q#3045 - >seq9692,superfamily,338310,933,995,0.00159091,41.0196,cl13716,IFT46_B_C superfamily,NC, - ,"Intraflagellar transport complex B protein 46 C terminal; This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.",L1PBa.ORF2.hs1_chimp.marg.frame1,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame1,Unusual,L1PBa,ORF2,hs1_chimp,marg,BothTerminiTruncated
40953,Q#3046 - >seq9693,specific,238827,481,743,1.2280999999999999e-68,229.1,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40954,Q#3046 - >seq9693,superfamily,295487,481,743,1.2280999999999999e-68,229.1,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40955,Q#3046 - >seq9693,specific,333820,487,743,1.60377e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40956,Q#3046 - >seq9693,superfamily,333820,487,743,1.60377e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40957,Q#3046 - >seq9693,non-specific,238828,487,708,1.29932e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40958,Q#3046 - >seq9693,non-specific,275209,438,767,2.16668e-08,57.4676,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40959,Q#3046 - >seq9693,superfamily,275209,438,767,2.16668e-08,57.4676,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40960,Q#3046 - >seq9693,non-specific,238185,627,741,8.02879e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs1_chimp.pars.frame2,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40961,Q#3048 - >seq9695,specific,197310,3,230,1.5418699999999998e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40962,Q#3048 - >seq9695,superfamily,351117,3,230,1.5418699999999998e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40963,Q#3048 - >seq9695,non-specific,197306,3,230,1.8016500000000002e-33,129.138,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40964,Q#3048 - >seq9695,non-specific,197307,3,230,4.33341e-21,93.5065,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40965,Q#3048 - >seq9695,non-specific,197320,3,243,7.96893e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40966,Q#3048 - >seq9695,non-specific,223780,3,231,3.87864e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40967,Q#3048 - >seq9695,non-specific,272954,3,243,9.3601e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40968,Q#3048 - >seq9695,specific,335306,4,223,1.9443999999999999e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40969,Q#3048 - >seq9695,non-specific,197321,1,230,2.24822e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40970,Q#3048 - >seq9695,non-specific,273186,3,231,6.620019999999999e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40971,Q#3048 - >seq9695,non-specific,197319,7,230,8.17421e-16,78.0873,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40972,Q#3048 - >seq9695,non-specific,197336,3,188,6.11895e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40973,Q#3048 - >seq9695,non-specific,236970,3,243,2.4651800000000003e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40974,Q#3048 - >seq9695,non-specific,197322,2,230,9.39888e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40975,Q#3048 - >seq9695,non-specific,197311,1,230,1.03413e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40976,Q#3048 - >seq9695,non-specific,339261,102,226,2.86819e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs1_chimp.pars.frame3,1909190250_L1PBa.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs1_chimp,pars,CompleteHit
40977,Q#3050 - >seq9697,specific,238827,481,743,7.475529999999999e-68,227.174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40978,Q#3050 - >seq9697,superfamily,295487,481,743,7.475529999999999e-68,227.174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40979,Q#3050 - >seq9697,specific,333820,487,711,3.52524e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40980,Q#3050 - >seq9697,superfamily,333820,487,711,3.52524e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40981,Q#3050 - >seq9697,non-specific,238828,487,708,9.57337e-14,71.8484,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40982,Q#3050 - >seq9697,non-specific,275209,438,767,2.4962400000000004e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40983,Q#3050 - >seq9697,superfamily,275209,438,767,2.4962400000000004e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40984,Q#3050 - >seq9697,non-specific,238185,627,741,0.000100584,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs2_gorilla.pars.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40985,Q#3051 - >seq9698,specific,197310,3,230,5.713249999999999e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40986,Q#3051 - >seq9698,superfamily,351117,3,230,5.713249999999999e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40987,Q#3051 - >seq9698,non-specific,197306,3,230,1.13341e-33,129.909,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40988,Q#3051 - >seq9698,non-specific,197307,3,230,6.88827e-21,93.1213,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40989,Q#3051 - >seq9698,non-specific,197320,3,243,8.261989999999999e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40990,Q#3051 - >seq9698,non-specific,223780,3,231,4.0220699999999996e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40991,Q#3051 - >seq9698,non-specific,272954,3,243,9.9811e-17,80.8901,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40992,Q#3051 - >seq9698,specific,335306,4,223,2.01361e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40993,Q#3051 - >seq9698,non-specific,197321,1,230,3.03409e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40994,Q#3051 - >seq9698,non-specific,273186,3,231,6.86207e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40995,Q#3051 - >seq9698,non-specific,197319,7,230,1.30644e-15,77.7021,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40996,Q#3051 - >seq9698,non-specific,197336,3,188,6.34015e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40997,Q#3051 - >seq9698,non-specific,236970,3,243,2.555e-10,62.218999999999994,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40998,Q#3051 - >seq9698,non-specific,197322,2,230,9.74364e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
40999,Q#3051 - >seq9698,non-specific,197311,1,230,1.06981e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
41000,Q#3051 - >seq9698,non-specific,339261,102,226,2.63713e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs2_gorilla.pars.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs2_gorilla,pars,CompleteHit
41001,Q#3053 - >seq9700,specific,238827,481,743,1.2079499999999997e-67,226.78900000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41002,Q#3053 - >seq9700,superfamily,295487,481,743,1.2079499999999997e-67,226.78900000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41003,Q#3053 - >seq9700,specific,333820,487,711,5.97747e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41004,Q#3053 - >seq9700,superfamily,333820,487,711,5.97747e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41005,Q#3053 - >seq9700,non-specific,238828,487,708,1.3053599999999998e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41006,Q#3053 - >seq9700,non-specific,275209,438,767,2.82898e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41007,Q#3053 - >seq9700,superfamily,275209,438,767,2.82898e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41008,Q#3053 - >seq9700,non-specific,238185,627,741,0.000150699,41.9528,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs2_gorilla.marg.frame2,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame2,RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41009,Q#3054 - >seq9701,specific,197310,3,230,2.4029199999999998e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41010,Q#3054 - >seq9701,superfamily,351117,3,230,2.4029199999999998e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41011,Q#3054 - >seq9701,non-specific,197306,3,230,4.289109999999999e-33,128.368,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41012,Q#3054 - >seq9701,non-specific,197307,3,230,4.96975e-21,93.5065,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41013,Q#3054 - >seq9701,non-specific,197320,3,243,8.391280000000001e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41014,Q#3054 - >seq9701,non-specific,223780,3,231,4.08534e-20,91.1207,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41015,Q#3054 - >seq9701,non-specific,272954,3,243,9.853930000000001e-17,81.2752,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41016,Q#3054 - >seq9701,specific,335306,4,223,2.0441500000000001e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41017,Q#3054 - >seq9701,non-specific,197321,1,230,2.1135799999999999e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41018,Q#3054 - >seq9701,non-specific,273186,3,231,6.96886e-16,78.4748,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41019,Q#3054 - >seq9701,non-specific,197319,7,230,7.40075e-16,78.4725,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41020,Q#3054 - >seq9701,non-specific,197336,3,188,6.43774e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41021,Q#3054 - >seq9701,non-specific,236970,3,243,3.3271800000000005e-10,61.8338,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41022,Q#3054 - >seq9701,non-specific,197322,2,230,9.89574e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41023,Q#3054 - >seq9701,non-specific,197311,1,230,1.08555e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41024,Q#3054 - >seq9701,non-specific,339261,102,226,3.03223e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs2_gorilla.marg.frame3,1909190252_L1PBa.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs2_gorilla,marg,CompleteHit
41025,Q#3055 - >seq9702,specific,238827,503,766,7.665989999999999e-67,224.47799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41026,Q#3055 - >seq9702,superfamily,295487,503,766,7.665989999999999e-67,224.47799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41027,Q#3055 - >seq9702,specific,197310,3,230,1.1130499999999999e-59,204.50799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41028,Q#3055 - >seq9702,superfamily,351117,3,230,1.1130499999999999e-59,204.50799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41029,Q#3055 - >seq9702,specific,333820,509,766,1.73605e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41030,Q#3055 - >seq9702,superfamily,333820,509,766,1.73605e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41031,Q#3055 - >seq9702,non-specific,197306,3,230,1.78987e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41032,Q#3055 - >seq9702,non-specific,197320,3,243,1.5999e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41033,Q#3055 - >seq9702,non-specific,197307,3,230,2.7241e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41034,Q#3055 - >seq9702,non-specific,223780,3,231,4.35042e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41035,Q#3055 - >seq9702,specific,335306,4,223,2.24162e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41036,Q#3055 - >seq9702,non-specific,272954,3,243,2.5611699999999998e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41037,Q#3055 - >seq9702,non-specific,197321,1,230,2.56288e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41038,Q#3055 - >seq9702,non-specific,273186,3,231,2.85819e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41039,Q#3055 - >seq9702,non-specific,197319,7,230,5.32706e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41040,Q#3055 - >seq9702,non-specific,238828,509,763,1.49172e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41041,Q#3055 - >seq9702,non-specific,197336,3,188,7.0688e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41042,Q#3055 - >seq9702,non-specific,236970,3,243,1.71317e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41043,Q#3055 - >seq9702,non-specific,275209,460,790,1.5843e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41044,Q#3055 - >seq9702,superfamily,275209,460,790,1.5843e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41045,Q#3055 - >seq9702,non-specific,197322,2,230,1.08793e-07,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41046,Q#3055 - >seq9702,non-specific,197311,1,230,2.449e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41047,Q#3055 - >seq9702,non-specific,235175,288,462,3.8628400000000004e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,marg,BothTerminiTruncated
41048,Q#3055 - >seq9702,superfamily,235175,288,462,3.8628400000000004e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,marg,BothTerminiTruncated
41049,Q#3055 - >seq9702,non-specific,339261,102,226,4.81483e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41050,Q#3055 - >seq9702,non-specific,238185,649,764,0.0007580810000000001,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs3_orang,marg,CompleteHit
41051,Q#3055 - >seq9702,non-specific,274009,288,440,0.00103007,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,marg,BothTerminiTruncated
41052,Q#3055 - >seq9702,superfamily,274009,288,440,0.00103007,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,marg,BothTerminiTruncated
41053,Q#3055 - >seq9702,non-specific,274009,301,451,0.00256745,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.marg.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,marg,C-TerminusTruncated
41054,Q#3060 - >seq9707,specific,238827,503,765,3.8747e-68,228.33,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41055,Q#3060 - >seq9707,superfamily,295487,503,765,3.8747e-68,228.33,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41056,Q#3060 - >seq9707,specific,197310,3,230,1.0781899999999998e-59,204.50799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41057,Q#3060 - >seq9707,superfamily,351117,3,230,1.0781899999999998e-59,204.50799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41058,Q#3060 - >seq9707,specific,333820,509,765,1.2878499999999998e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41059,Q#3060 - >seq9707,superfamily,333820,509,765,1.2878499999999998e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41060,Q#3060 - >seq9707,non-specific,197306,3,230,1.84267e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41061,Q#3060 - >seq9707,non-specific,197320,3,243,1.9161099999999997e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41062,Q#3060 - >seq9707,non-specific,197307,3,230,3.0816300000000003e-19,88.4989,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41063,Q#3060 - >seq9707,non-specific,223780,3,231,5.15727e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41064,Q#3060 - >seq9707,specific,335306,4,223,2.22127e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41065,Q#3060 - >seq9707,non-specific,197321,1,230,2.63643e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41066,Q#3060 - >seq9707,non-specific,273186,3,231,3.02423e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41067,Q#3060 - >seq9707,non-specific,272954,3,243,3.0335300000000002e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41068,Q#3060 - >seq9707,non-specific,197319,7,230,5.63582e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41069,Q#3060 - >seq9707,non-specific,238828,509,730,3.69456e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41070,Q#3060 - >seq9707,non-specific,197336,3,188,7.00374e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41071,Q#3060 - >seq9707,non-specific,236970,3,243,1.89501e-09,59.9078,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41072,Q#3060 - >seq9707,non-specific,275209,460,789,2.5988799999999998e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41073,Q#3060 - >seq9707,superfamily,275209,460,789,2.5988799999999998e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41074,Q#3060 - >seq9707,non-specific,197322,2,230,1.07779e-07,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41075,Q#3060 - >seq9707,non-specific,238185,649,763,1.79858e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41076,Q#3060 - >seq9707,non-specific,197311,1,230,2.38277e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41077,Q#3060 - >seq9707,non-specific,235175,288,462,4.45787e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,pars,BothTerminiTruncated
41078,Q#3060 - >seq9707,superfamily,235175,288,462,4.45787e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,pars,BothTerminiTruncated
41079,Q#3060 - >seq9707,non-specific,339261,102,226,4.63777e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs3_orang,pars,CompleteHit
41080,Q#3060 - >seq9707,non-specific,274009,288,440,0.00123971,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,pars,BothTerminiTruncated
41081,Q#3060 - >seq9707,superfamily,274009,288,440,0.00123971,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,pars,BothTerminiTruncated
41082,Q#3060 - >seq9707,non-specific,274009,301,451,0.0027684000000000003,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs3_orang.pars.frame3,1909190254_L1PBa.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round4large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs3_orang,pars,C-TerminusTruncated
41083,Q#3062 - >seq9709,specific,238827,507,768,3.1927599999999997e-66,222.937,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41084,Q#3062 - >seq9709,superfamily,295487,507,768,3.1927599999999997e-66,222.937,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41085,Q#3062 - >seq9709,specific,197310,9,236,8.980839999999998e-62,210.671,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41086,Q#3062 - >seq9709,superfamily,351117,9,236,8.980839999999998e-62,210.671,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41087,Q#3062 - >seq9709,non-specific,197306,9,236,7.62045e-32,124.90100000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41088,Q#3062 - >seq9709,specific,333820,513,768,7.93456e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41089,Q#3062 - >seq9709,superfamily,333820,513,768,7.93456e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41090,Q#3062 - >seq9709,non-specific,197307,9,236,9.78255e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41091,Q#3062 - >seq9709,non-specific,223780,9,237,1.1594100000000001e-21,95.7431,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41092,Q#3062 - >seq9709,non-specific,197320,9,206,1.0741200000000001e-20,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41093,Q#3062 - >seq9709,specific,335306,10,229,4.81658e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41094,Q#3062 - >seq9709,non-specific,197321,7,236,5.6883e-18,84.9112,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41095,Q#3062 - >seq9709,non-specific,197319,13,236,7.26474e-16,78.4725,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41096,Q#3062 - >seq9709,non-specific,273186,9,237,3.11108e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41097,Q#3062 - >seq9709,non-specific,272954,9,236,2.06017e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41098,Q#3062 - >seq9709,non-specific,238828,513,733,7.70649e-13,69.152,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41099,Q#3062 - >seq9709,non-specific,197336,9,153,6.60442e-10,61.0891,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41100,Q#3062 - >seq9709,non-specific,236970,9,194,1.50367e-08,57.2114,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41101,Q#3062 - >seq9709,non-specific,275209,458,792,2.0171099999999998e-08,57.4676,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41102,Q#3062 - >seq9709,superfamily,275209,458,792,2.0171099999999998e-08,57.4676,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41103,Q#3062 - >seq9709,non-specific,235175,290,466,1.55569e-06,52.3736,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41104,Q#3062 - >seq9709,superfamily,235175,290,466,1.55569e-06,52.3736,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41105,Q#3062 - >seq9709,non-specific,197314,7,192,3.7962599999999997e-06,49.6495,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41106,Q#3062 - >seq9709,non-specific,197311,7,146,6.13179e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41107,Q#3062 - >seq9709,non-specific,197322,8,236,2.0444e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41108,Q#3062 - >seq9709,non-specific,238185,652,766,2.4440900000000002e-05,44.263999999999996,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41109,Q#3062 - >seq9709,non-specific,223496,319,553,0.000208194,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41110,Q#3062 - >seq9709,superfamily,223496,319,553,0.000208194,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41111,Q#3062 - >seq9709,non-specific,334125,212,409,0.00082228,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
41112,Q#3062 - >seq9709,superfamily,334125,212,409,0.00082228,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs2_gorilla,pars,N-TerminusTruncated
41113,Q#3062 - >seq9709,non-specific,274009,310,466,0.000909937,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41114,Q#3062 - >seq9709,superfamily,274009,310,466,0.000909937,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41115,Q#3062 - >seq9709,non-specific,274009,293,432,0.00105952,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,BothTerminiTruncated
41116,Q#3062 - >seq9709,non-specific,339261,108,232,0.00396561,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41117,Q#3062 - >seq9709,non-specific,224117,282,430,0.00436234,41.2384,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41118,Q#3062 - >seq9709,superfamily,224117,282,430,0.00436234,41.2384,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB3,ORF2,hs2_gorilla,pars,C-TerminusTruncated
41119,Q#3065 - >seq9712,specific,197310,9,236,1.2734599999999997e-62,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41120,Q#3065 - >seq9712,superfamily,351117,9,236,1.2734599999999997e-62,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41121,Q#3065 - >seq9712,specific,238827,507,755,6.743389999999999e-62,206.75799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41122,Q#3065 - >seq9712,superfamily,295487,507,755,6.743389999999999e-62,206.75799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41123,Q#3065 - >seq9712,non-specific,197306,9,236,7.88702e-32,124.131,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41124,Q#3065 - >seq9712,specific,333820,513,736,1.1290999999999998e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41125,Q#3065 - >seq9712,superfamily,333820,513,736,1.1290999999999998e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41126,Q#3065 - >seq9712,non-specific,197307,9,236,1.92794e-22,96.9733,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41127,Q#3065 - >seq9712,non-specific,223780,9,237,2.02929e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41128,Q#3065 - >seq9712,non-specific,197320,9,206,2.9810000000000002e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41129,Q#3065 - >seq9712,specific,335306,10,229,2.58323e-19,87.3005,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41130,Q#3065 - >seq9712,non-specific,197321,7,236,6.580919999999999e-19,86.8372,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41131,Q#3065 - >seq9712,non-specific,197319,13,236,1.17877e-16,80.0133,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41132,Q#3065 - >seq9712,non-specific,273186,9,237,6.398640000000001e-16,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41133,Q#3065 - >seq9712,non-specific,272954,9,236,5.63301e-15,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41134,Q#3065 - >seq9712,non-specific,238828,513,733,4.95239e-13,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41135,Q#3065 - >seq9712,non-specific,197336,9,153,3.51548e-10,61.0891,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41136,Q#3065 - >seq9712,non-specific,275209,458,733,8.18863e-09,57.8528,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41137,Q#3065 - >seq9712,superfamily,275209,458,733,8.18863e-09,57.8528,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41138,Q#3065 - >seq9712,non-specific,236970,9,194,1.0699399999999999e-08,56.8262,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41139,Q#3065 - >seq9712,non-specific,197314,7,192,2.04916e-06,49.6495,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41140,Q#3065 - >seq9712,non-specific,235175,290,466,3.54601e-06,50.4476,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41141,Q#3065 - >seq9712,superfamily,235175,290,466,3.54601e-06,50.4476,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41142,Q#3065 - >seq9712,non-specific,197311,7,146,4.092130000000001e-06,48.0569,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41143,Q#3065 - >seq9712,non-specific,197322,8,236,1.08992e-05,47.696999999999996,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41144,Q#3065 - >seq9712,non-specific,238185,652,729,0.000877141,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41145,Q#3065 - >seq9712,non-specific,334125,212,409,0.00115891,41.7512,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
41146,Q#3065 - >seq9712,superfamily,334125,212,409,0.00115891,41.7512,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs2_gorilla,marg,N-TerminusTruncated
41147,Q#3065 - >seq9712,non-specific,274009,310,466,0.00222653,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41148,Q#3065 - >seq9712,superfamily,274009,310,466,0.00222653,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41149,Q#3065 - >seq9712,non-specific,223496,319,553,0.00276834,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41150,Q#3065 - >seq9712,superfamily,223496,319,553,0.00276834,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41151,Q#3065 - >seq9712,non-specific,274009,293,432,0.00304927,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs2_gorilla,marg,BothTerminiTruncated
41152,Q#3065 - >seq9712,non-specific,339261,108,232,0.00462111,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs2_gorilla,marg,CompleteHit
41153,Q#3065 - >seq9712,specific,225881,441,676,0.00689241,39.0517,COG3344,YkfC,C,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41154,Q#3065 - >seq9712,superfamily,225881,441,676,0.00689241,39.0517,cl34590,YkfC superfamily,C, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB3.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs2_gorilla,marg,C-TerminusTruncated
41155,Q#3067 - >seq9714,non-specific,340205,155,215,1.09902e-24,92.3992,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41156,Q#3067 - >seq9714,superfamily,340205,155,215,1.09902e-24,92.3992,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41157,Q#3068 - >seq9715,non-specific,335182,67,162,3.84886e-35,120.485,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41158,Q#3068 - >seq9715,superfamily,335182,67,162,3.84886e-35,120.485,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41159,Q#3068 - >seq9715,non-specific,340204,21,63,1.46997e-07,46.632,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41160,Q#3068 - >seq9715,superfamily,340204,21,63,1.46997e-07,46.632,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs3_orang,pars,CompleteHit
41161,Q#3068 - >seq9715,non-specific,334565,22,145,0.00955423,36.6988,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs3_orang,pars,C-TerminusTruncated
41162,Q#3068 - >seq9715,superfamily,334565,22,145,0.00955423,36.6988,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs3_orang,pars,C-TerminusTruncated
41163,Q#3071 - >seq9718,non-specific,335182,67,162,5.71586e-35,120.1,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41164,Q#3071 - >seq9718,superfamily,335182,67,162,5.71586e-35,120.1,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41165,Q#3071 - >seq9718,non-specific,340205,165,228,3.61626e-30,106.652,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41166,Q#3071 - >seq9718,superfamily,340205,165,228,3.61626e-30,106.652,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41167,Q#3071 - >seq9718,non-specific,340204,21,63,4.78747e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41168,Q#3071 - >seq9718,superfamily,340204,21,63,4.78747e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs3_orang,marg,CompleteHit
41169,Q#3073 - >seq9720,specific,238827,480,742,1.0759999999999998e-68,229.87,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41170,Q#3073 - >seq9720,superfamily,295487,480,742,1.0759999999999998e-68,229.87,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41171,Q#3073 - >seq9720,specific,333820,486,742,1.88196e-33,127.40799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41172,Q#3073 - >seq9720,superfamily,333820,486,742,1.88196e-33,127.40799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41173,Q#3073 - >seq9720,non-specific,238828,486,707,2.37492e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41174,Q#3073 - >seq9720,non-specific,275209,439,766,2.32805e-07,54.0008,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41175,Q#3073 - >seq9720,superfamily,275209,439,766,2.32805e-07,54.0008,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41176,Q#3073 - >seq9720,non-specific,238185,626,740,1.76829e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41177,Q#3073 - >seq9720,specific,311990,1210,1228,0.000333491,38.8072,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41178,Q#3073 - >seq9720,superfamily,311990,1210,1228,0.000333491,38.8072,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs3_orang.pars.frame2,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41179,Q#3077 - >seq9724,specific,238827,508,770,6.377549999999999e-68,227.55900000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41180,Q#3077 - >seq9724,superfamily,295487,508,770,6.377549999999999e-68,227.55900000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41181,Q#3077 - >seq9724,specific,197310,9,235,8.878419999999998e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41182,Q#3077 - >seq9724,superfamily,351117,9,235,8.878419999999998e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41183,Q#3077 - >seq9724,specific,333820,514,770,2.8141100000000002e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41184,Q#3077 - >seq9724,superfamily,333820,514,770,2.8141100000000002e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41185,Q#3077 - >seq9724,non-specific,197306,9,235,6.37018e-32,124.90100000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41186,Q#3077 - >seq9724,non-specific,197307,9,235,3.6785400000000004e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41187,Q#3077 - >seq9724,non-specific,197320,9,206,2.4605100000000002e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41188,Q#3077 - >seq9724,non-specific,223780,9,236,6.050660000000001e-20,90.7355,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41189,Q#3077 - >seq9724,specific,335306,10,228,3.54246e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41190,Q#3077 - >seq9724,non-specific,197321,7,235,6.34496e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41191,Q#3077 - >seq9724,non-specific,197319,13,235,1.74141e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41192,Q#3077 - >seq9724,non-specific,272954,9,207,4.06246e-13,70.4897,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41193,Q#3077 - >seq9724,non-specific,273186,9,236,4.8846e-13,70.3856,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41194,Q#3077 - >seq9724,non-specific,238828,514,735,4.0989e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41195,Q#3077 - >seq9724,non-specific,197336,9,194,1.12764e-08,57.2371,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41196,Q#3077 - >seq9724,non-specific,275209,467,794,1.12571e-07,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41197,Q#3077 - >seq9724,superfamily,275209,467,794,1.12571e-07,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41198,Q#3077 - >seq9724,non-specific,236970,9,248,3.4003500000000004e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41199,Q#3077 - >seq9724,non-specific,197311,7,146,9.78693e-06,47.6717,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,marg,C-TerminusTruncated
41200,Q#3077 - >seq9724,non-specific,197314,7,192,3.25433e-05,46.5679,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs3_orang,marg,C-TerminusTruncated
41201,Q#3077 - >seq9724,non-specific,238185,654,768,4.43171e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41202,Q#3077 - >seq9724,non-specific,235175,289,446,0.00019355299999999998,45.8252,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,marg,BothTerminiTruncated
41203,Q#3077 - >seq9724,superfamily,235175,289,446,0.00019355299999999998,45.8252,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,marg,BothTerminiTruncated
41204,Q#3077 - >seq9724,non-specific,334125,213,408,0.000600513,43.6772,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs3_orang,marg,N-TerminusTruncated
41205,Q#3077 - >seq9724,superfamily,334125,213,408,0.000600513,43.6772,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs3_orang,marg,N-TerminusTruncated
41206,Q#3077 - >seq9724,specific,311990,1273,1291,0.000722752,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41207,Q#3077 - >seq9724,superfamily,311990,1273,1291,0.000722752,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41208,Q#3077 - >seq9724,non-specific,274009,298,431,0.00298745,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,marg,BothTerminiTruncated
41209,Q#3077 - >seq9724,superfamily,274009,298,431,0.00298745,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,marg,BothTerminiTruncated
41210,Q#3077 - >seq9724,non-specific,339261,108,231,0.00343483,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs3_orang.marg.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs3_orang,marg,CompleteHit
41211,Q#3080 - >seq9727,specific,238827,510,772,1.4997899999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41212,Q#3080 - >seq9727,superfamily,295487,510,772,1.4997899999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41213,Q#3080 - >seq9727,specific,197310,9,239,8.626789999999998e-44,159.054,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41214,Q#3080 - >seq9727,superfamily,351117,9,239,8.626789999999998e-44,159.054,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41215,Q#3080 - >seq9727,specific,333820,516,772,8.879309999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41216,Q#3080 - >seq9727,superfamily,333820,516,772,8.879309999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41217,Q#3080 - >seq9727,non-specific,197306,9,239,4.0203100000000004e-24,102.56,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41218,Q#3080 - >seq9727,non-specific,197307,9,239,7.31387e-15,75.7873,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41219,Q#3080 - >seq9727,non-specific,197320,9,209,1.23917e-14,74.8589,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41220,Q#3080 - >seq9727,specific,335306,10,232,5.6074300000000003e-14,72.2777,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41221,Q#3080 - >seq9727,non-specific,223780,9,240,5.62515e-13,70.3199,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41222,Q#3080 - >seq9727,non-specific,238828,516,737,1.10443e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41223,Q#3080 - >seq9727,non-specific,197321,7,239,5.04326e-11,64.1104,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41224,Q#3080 - >seq9727,non-specific,197319,13,239,6.74692e-11,63.8349,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41225,Q#3080 - >seq9727,non-specific,273186,9,240,1.5548499999999999e-09,59.9852,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41226,Q#3080 - >seq9727,non-specific,272954,9,239,6.156119999999999e-09,58.1633,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41227,Q#3080 - >seq9727,non-specific,275209,461,796,2.68496e-06,50.9192,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41228,Q#3080 - >seq9727,superfamily,275209,461,796,2.68496e-06,50.9192,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41229,Q#3080 - >seq9727,non-specific,235175,312,470,4.01015e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41230,Q#3080 - >seq9727,superfamily,235175,312,470,4.01015e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41231,Q#3080 - >seq9727,non-specific,197314,7,195,7.46916e-05,45.7975,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41232,Q#3080 - >seq9727,non-specific,238185,656,770,0.000430165,40.412,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41233,Q#3080 - >seq9727,non-specific,197336,9,156,0.000768812,42.5995,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41234,Q#3080 - >seq9727,specific,311990,1239,1257,0.0007690739999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41235,Q#3080 - >seq9727,superfamily,311990,1239,1257,0.0007690739999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41236,Q#3080 - >seq9727,non-specific,223496,302,500,0.00174807,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41237,Q#3080 - >seq9727,superfamily,223496,302,500,0.00174807,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41238,Q#3080 - >seq9727,non-specific,274009,313,458,0.0018995000000000001,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41239,Q#3080 - >seq9727,superfamily,274009,313,458,0.0018995000000000001,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41240,Q#3080 - >seq9727,non-specific,334125,215,412,0.0032952,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
41241,Q#3080 - >seq9727,superfamily,334125,215,412,0.0032952,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
41242,Q#3080 - >seq9727,non-specific,274009,303,435,0.00403125,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41243,Q#3080 - >seq9727,non-specific,339261,111,235,0.00477373,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs5_gmonkey,pars,CompleteHit
41244,Q#3083 - >seq9730,specific,238827,509,772,1.5351899999999997e-66,223.707,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41245,Q#3083 - >seq9730,superfamily,295487,509,772,1.5351899999999997e-66,223.707,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41246,Q#3083 - >seq9730,specific,197310,9,238,4.35694e-43,157.128,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41247,Q#3083 - >seq9730,superfamily,351117,9,238,4.35694e-43,157.128,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41248,Q#3083 - >seq9730,specific,333820,515,739,2.62097e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41249,Q#3083 - >seq9730,superfamily,333820,515,739,2.62097e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41250,Q#3083 - >seq9730,non-specific,197306,9,238,6.61112e-24,101.789,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41251,Q#3083 - >seq9730,non-specific,197307,9,238,1.01719e-14,75.4021,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41252,Q#3083 - >seq9730,non-specific,197320,9,208,1.90992e-14,74.4737,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41253,Q#3083 - >seq9730,non-specific,223780,9,239,3.2310200000000005e-14,73.7867,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41254,Q#3083 - >seq9730,specific,335306,10,231,5.328869999999999e-13,69.5814,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41255,Q#3083 - >seq9730,non-specific,238828,515,736,1.0446e-12,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41256,Q#3083 - >seq9730,non-specific,197319,13,238,8.05667e-11,63.8349,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41257,Q#3083 - >seq9730,non-specific,197321,7,238,1.2776299999999998e-10,62.9548,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41258,Q#3083 - >seq9730,non-specific,273186,9,239,1.04601e-09,60.3704,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41259,Q#3083 - >seq9730,non-specific,272954,9,238,6.13242e-08,55.0817,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41260,Q#3083 - >seq9730,non-specific,275209,460,796,3.65332e-06,50.534,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41261,Q#3083 - >seq9730,superfamily,275209,460,796,3.65332e-06,50.534,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41262,Q#3083 - >seq9730,non-specific,235175,311,469,3.21945e-05,48.1364,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41263,Q#3083 - >seq9730,superfamily,235175,311,469,3.21945e-05,48.1364,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41264,Q#3083 - >seq9730,non-specific,197314,7,194,0.000189591,44.2567,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41265,Q#3083 - >seq9730,specific,311990,1239,1257,0.00075474,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41266,Q#3083 - >seq9730,superfamily,311990,1239,1257,0.00075474,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41267,Q#3083 - >seq9730,non-specific,197336,9,155,0.000962913,42.2143,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41268,Q#3083 - >seq9730,non-specific,223496,301,499,0.00145203,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41269,Q#3083 - >seq9730,superfamily,223496,301,499,0.00145203,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41270,Q#3083 - >seq9730,non-specific,238185,655,732,0.0017687000000000002,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41271,Q#3083 - >seq9730,non-specific,274009,312,457,0.00185359,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41272,Q#3083 - >seq9730,superfamily,274009,312,457,0.00185359,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41273,Q#3083 - >seq9730,non-specific,334125,214,411,0.00292341,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
41274,Q#3083 - >seq9730,superfamily,334125,214,411,0.00292341,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
41275,Q#3083 - >seq9730,non-specific,274009,302,434,0.00367654,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41276,Q#3083 - >seq9730,non-specific,339261,110,234,0.00536372,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB3.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs5_gmonkey,marg,CompleteHit
41277,Q#3085 - >seq9732,specific,238827,505,767,2.3116699999999996e-66,223.322,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41278,Q#3085 - >seq9732,superfamily,295487,505,767,2.3116699999999996e-66,223.322,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41279,Q#3085 - >seq9732,specific,197310,9,235,3.0511999999999997e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41280,Q#3085 - >seq9732,superfamily,351117,9,235,3.0511999999999997e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41281,Q#3085 - >seq9732,specific,333820,511,767,2.00151e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41282,Q#3085 - >seq9732,superfamily,333820,511,767,2.00151e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41283,Q#3085 - >seq9732,non-specific,197306,9,235,2.6721699999999997e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41284,Q#3085 - >seq9732,non-specific,197307,9,235,2.64775e-21,94.6621,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41285,Q#3085 - >seq9732,non-specific,197320,9,206,5.4104099999999995e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41286,Q#3085 - >seq9732,non-specific,223780,9,236,1.0733e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41287,Q#3085 - >seq9732,specific,335306,10,228,1.5982800000000001e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41288,Q#3085 - >seq9732,non-specific,197321,7,235,1.36657e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41289,Q#3085 - >seq9732,non-specific,273186,9,236,7.866939999999999e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41290,Q#3085 - >seq9732,non-specific,197319,13,235,2.58106e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41291,Q#3085 - >seq9732,non-specific,272954,9,207,3.60758e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41292,Q#3085 - >seq9732,non-specific,238828,511,732,4.0083000000000005e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41293,Q#3085 - >seq9732,non-specific,197336,9,194,1.70771e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41294,Q#3085 - >seq9732,non-specific,236970,9,194,3.57444e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41295,Q#3085 - >seq9732,non-specific,197311,7,146,2.98856e-06,49.2125,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41296,Q#3085 - >seq9732,non-specific,197314,7,192,4.93245e-06,49.2643,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41297,Q#3085 - >seq9732,non-specific,275209,462,666,9.536720000000001e-06,48.9932,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41298,Q#3085 - >seq9732,superfamily,275209,462,666,9.536720000000001e-06,48.9932,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41299,Q#3085 - >seq9732,non-specific,197322,8,235,6.493e-05,46.1562,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,pars,CompleteHit
41300,Q#3085 - >seq9732,non-specific,224117,281,428,0.000557188,44.32,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41301,Q#3085 - >seq9732,superfamily,224117,281,428,0.000557188,44.32,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41302,Q#3085 - >seq9732,specific,311990,1235,1253,0.000737232,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs0_human,pars,CompleteHit
41303,Q#3085 - >seq9732,superfamily,311990,1235,1253,0.000737232,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB3,ORF2,hs0_human,pars,CompleteHit
41304,Q#3085 - >seq9732,non-specific,274009,309,453,0.00124012,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,pars,BothTerminiTruncated
41305,Q#3085 - >seq9732,superfamily,274009,309,453,0.00124012,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,pars,BothTerminiTruncated
41306,Q#3085 - >seq9732,non-specific,334125,213,407,0.00130588,42.5216,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs0_human,pars,N-TerminusTruncated
41307,Q#3085 - >seq9732,superfamily,334125,213,407,0.00130588,42.5216,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs0_human,pars,N-TerminusTruncated
41308,Q#3085 - >seq9732,non-specific,238185,651,765,0.00156711,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41309,Q#3085 - >seq9732,non-specific,274009,304,459,0.00161176,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,pars,BothTerminiTruncated
41310,Q#3085 - >seq9732,non-specific,339261,108,231,0.00373868,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs0_human,pars,CompleteHit
41311,Q#3085 - >seq9732,non-specific,310273,307,458,0.00610411,40.499,pfam05557,MAD,C,cl37733,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41312,Q#3085 - >seq9732,superfamily,310273,307,458,0.00610411,40.499,cl37733,MAD superfamily,C, - ,"Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.",L1PB3.ORF2.hs0_human.pars.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PB3,ORF2,hs0_human,pars,C-TerminusTruncated
41313,Q#3086 - >seq9733,specific,197310,9,235,6.707399999999998e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41314,Q#3086 - >seq9733,superfamily,351117,9,235,6.707399999999998e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41315,Q#3086 - >seq9733,non-specific,197306,9,235,1.74945e-32,126.44200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41316,Q#3086 - >seq9733,non-specific,197307,9,235,6.40947e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41317,Q#3086 - >seq9733,non-specific,223780,9,236,5.15891e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41318,Q#3086 - >seq9733,non-specific,197320,9,206,1.7843900000000003e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41319,Q#3086 - >seq9733,specific,335306,10,228,3.1746200000000003e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41320,Q#3086 - >seq9733,non-specific,197321,7,235,4.9591799999999995e-18,84.9112,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41321,Q#3086 - >seq9733,non-specific,197319,13,235,2.6249300000000002e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41322,Q#3086 - >seq9733,non-specific,272954,9,235,2.2302e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41323,Q#3086 - >seq9733,non-specific,273186,9,236,9.77709e-14,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41324,Q#3086 - >seq9733,non-specific,197336,9,194,1.00993e-08,57.2371,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41325,Q#3086 - >seq9733,non-specific,236970,9,248,9.062319999999999e-07,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41326,Q#3086 - >seq9733,non-specific,197311,7,146,5.68288e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs3_orang,pars,C-TerminusTruncated
41327,Q#3086 - >seq9733,non-specific,197314,7,192,2.92021e-05,46.5679,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs3_orang,pars,C-TerminusTruncated
41328,Q#3086 - >seq9733,non-specific,334125,213,408,3.2187399999999996e-05,47.5292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs3_orang,pars,N-TerminusTruncated
41329,Q#3086 - >seq9733,superfamily,334125,213,408,3.2187399999999996e-05,47.5292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs3_orang,pars,N-TerminusTruncated
41330,Q#3086 - >seq9733,non-specific,274009,298,408,0.00356644,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,pars,BothTerminiTruncated
41331,Q#3086 - >seq9733,superfamily,274009,298,408,0.00356644,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs3_orang,pars,BothTerminiTruncated
41332,Q#3086 - >seq9733,non-specific,339261,108,231,0.00422625,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs3_orang.pars.frame3,1909201640_L1PB3.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs3_orang,pars,CompleteHit
41333,Q#3087 - >seq9734,specific,311990,1125,1143,0.00010594700000000001,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs2_gorilla.pars.frame1,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41334,Q#3087 - >seq9734,superfamily,311990,1125,1143,0.00010594700000000001,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs2_gorilla.pars.frame1,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB3,ORF2,hs2_gorilla,pars,CompleteHit
41335,Q#3091 - >seq9738,specific,311990,1166,1183,1.9942799999999998e-05,42.273999999999994,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41336,Q#3091 - >seq9738,superfamily,311990,1166,1183,1.9942799999999998e-05,42.273999999999994,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41337,Q#3092 - >seq9739,specific,238827,501,762,3.90048e-63,214.077,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41338,Q#3092 - >seq9739,superfamily,295487,501,762,3.90048e-63,214.077,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41339,Q#3092 - >seq9739,specific,197310,3,229,8.252299999999999e-59,202.196,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41340,Q#3092 - >seq9739,superfamily,351117,3,229,8.252299999999999e-59,202.196,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41341,Q#3092 - >seq9739,specific,333820,507,731,1.7561199999999998e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41342,Q#3092 - >seq9739,superfamily,333820,507,731,1.7561199999999998e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41343,Q#3092 - >seq9739,non-specific,197306,3,229,2.73129e-30,120.279,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41344,Q#3092 - >seq9739,non-specific,197320,3,222,1.18771e-21,95.6597,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41345,Q#3092 - >seq9739,non-specific,223780,3,230,2.87286e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41346,Q#3092 - >seq9739,non-specific,197307,3,229,5.92981e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41347,Q#3092 - >seq9739,non-specific,273186,3,230,6.6803e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41348,Q#3092 - >seq9739,specific,335306,4,222,3.7128900000000005e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41349,Q#3092 - >seq9739,non-specific,272954,3,229,2.78986e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41350,Q#3092 - >seq9739,non-specific,197321,1,229,4.86164e-15,76.0516,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41351,Q#3092 - >seq9739,non-specific,197319,7,229,8.846110000000001e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41352,Q#3092 - >seq9739,non-specific,238828,507,728,4.906770000000001e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41353,Q#3092 - >seq9739,non-specific,197336,3,187,5.6989e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41354,Q#3092 - >seq9739,non-specific,236970,3,187,3.2102699999999997e-08,56.0558,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41355,Q#3092 - >seq9739,non-specific,275209,458,662,8.06821e-08,55.5416,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41356,Q#3092 - >seq9739,superfamily,275209,458,662,8.06821e-08,55.5416,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41357,Q#3092 - >seq9739,non-specific,197322,2,229,3.9453e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41358,Q#3092 - >seq9739,non-specific,197311,1,229,1.7966700000000001e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41359,Q#3092 - >seq9739,non-specific,235175,283,460,7.39273e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41360,Q#3092 - >seq9739,superfamily,235175,283,460,7.39273e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41361,Q#3092 - >seq9739,non-specific,339261,101,225,0.00018655900000000001,42.3243,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs5_gmonkey,pars,CompleteHit
41362,Q#3092 - >seq9739,non-specific,274009,286,438,0.00129548,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41363,Q#3092 - >seq9739,superfamily,274009,286,438,0.00129548,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41364,Q#3092 - >seq9739,specific,225881,474,671,0.00146687,42.1333,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41365,Q#3092 - >seq9739,superfamily,225881,474,671,0.00146687,42.1333,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41366,Q#3092 - >seq9739,non-specific,238185,647,724,0.00147183,38.8712,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41367,Q#3092 - >seq9739,non-specific,274009,299,449,0.00496978,41.2067,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41368,Q#3094 - >seq9741,non-specific,335182,157,252,1.64669e-30,110.855,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41369,Q#3094 - >seq9741,superfamily,335182,157,252,1.64669e-30,110.855,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41370,Q#3094 - >seq9741,non-specific,340205,255,318,1.38228e-27,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41371,Q#3094 - >seq9741,superfamily,340205,255,318,1.38228e-27,102.029,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41372,Q#3094 - >seq9741,non-specific,340204,111,153,7.037720000000001e-05,39.3132,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41373,Q#3094 - >seq9741,superfamily,340204,111,153,7.037720000000001e-05,39.3132,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs5_gmonkey,marg,CompleteHit
41374,Q#3094 - >seq9741,non-specific,274009,33,150,0.00016838,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41375,Q#3094 - >seq9741,superfamily,274009,33,150,0.00016838,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41376,Q#3094 - >seq9741,non-specific,274008,28,149,0.000252134,42.7363,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41377,Q#3094 - >seq9741,superfamily,274008,28,149,0.000252134,42.7363,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41378,Q#3094 - >seq9741,non-specific,337766,42,139,0.000957658,40.2887,pfam10498,IFT57,N,cl26417,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PB2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
41379,Q#3094 - >seq9741,superfamily,337766,42,139,0.000957658,40.2887,cl26417,IFT57 superfamily,N, - ,"Intra-flagellar transport protein 57; Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Flagellar,L1PB2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
41380,Q#3094 - >seq9741,non-specific,224117,49,150,0.00147986,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41381,Q#3094 - >seq9741,superfamily,224117,49,150,0.00147986,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41382,Q#3094 - >seq9741,non-specific,112704,2,121,0.00157979,39.2263,pfam03904,DUF334,C,cl30944,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
41383,Q#3094 - >seq9741,superfamily,112704,2,121,0.00157979,39.2263,cl30944,DUF334 superfamily,C, - ,Domain of unknown function (DUF334); Staphylococcus aureus plasmid proteins with no characterized function.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs5_gmonkey,marg,C-TerminusTruncated
41384,Q#3094 - >seq9741,non-specific,224117,26,149,0.00179328,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41385,Q#3094 - >seq9741,non-specific,314569,93,142,0.00188875,38.9368,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41386,Q#3094 - >seq9741,superfamily,327698,93,142,0.00188875,38.9368,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41387,Q#3094 - >seq9741,non-specific,223571,61,123,0.00194049,39.5051,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41388,Q#3094 - >seq9741,superfamily,223571,61,123,0.00194049,39.5051,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41389,Q#3094 - >seq9741,non-specific,235175,53,243,0.0023928,39.2768,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41390,Q#3094 - >seq9741,superfamily,235175,53,243,0.0023928,39.2768,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41391,Q#3094 - >seq9741,non-specific,197874,46,162,0.00337541,38.4601,smart00787,Spc7,N,cl33249,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
41392,Q#3094 - >seq9741,superfamily,197874,46,162,0.00337541,38.4601,cl33249,Spc7 superfamily,N, - ,Spc7 kinetochore protein; This domain is found in cell division proteins which are required for kinetochore-spindle association.,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PB2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
41393,Q#3094 - >seq9741,non-specific,224117,43,150,0.00493371,38.542,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41394,Q#3094 - >seq9741,non-specific,274073,32,147,0.00532119,38.4222,TIGR02302,aProt_lowcomp,NC,cl37089,"TIGR02302 family protein; Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41395,Q#3094 - >seq9741,superfamily,274073,32,147,0.00532119,38.4222,cl37089,aProt_lowcomp superfamily,NC, - ,"TIGR02302 family protein; Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41396,Q#3094 - >seq9741,non-specific,274008,57,149,0.00595613,38.1139,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41397,Q#3094 - >seq9741,non-specific,274009,32,155,0.0063269,38.1251,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs5_gmonkey,marg,N-TerminusTruncated
41398,Q#3094 - >seq9741,non-specific,235943,36,132,0.00712249,37.875,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41399,Q#3094 - >seq9741,superfamily,235943,36,132,0.00712249,37.875,cl35548,PRK07133 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs5_gmonkey,marg,BothTerminiTruncated
41400,Q#3096 - >seq9743,specific,238827,501,762,5.62672e-63,213.30700000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41401,Q#3096 - >seq9743,superfamily,295487,501,762,5.62672e-63,213.30700000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41402,Q#3096 - >seq9743,specific,197310,3,229,3.5041599999999992e-59,203.352,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41403,Q#3096 - >seq9743,superfamily,351117,3,229,3.5041599999999992e-59,203.352,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41404,Q#3096 - >seq9743,specific,333820,507,731,2.0712499999999995e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41405,Q#3096 - >seq9743,superfamily,333820,507,731,2.0712499999999995e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41406,Q#3096 - >seq9743,non-specific,197306,3,229,1.2947399999999998e-30,121.434,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41407,Q#3096 - >seq9743,non-specific,197320,3,222,1.4802e-21,95.2745,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41408,Q#3096 - >seq9743,non-specific,223780,3,230,4.40345e-19,88.4243,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41409,Q#3096 - >seq9743,non-specific,197307,3,229,7.31548e-19,87.3433,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41410,Q#3096 - >seq9743,non-specific,273186,3,230,7.92949e-17,81.5564,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41411,Q#3096 - >seq9743,specific,335306,4,222,3.75331e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41412,Q#3096 - >seq9743,non-specific,272954,3,229,4.03169e-15,76.6529,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41413,Q#3096 - >seq9743,non-specific,197321,1,229,7.091679999999999e-15,75.6664,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41414,Q#3096 - >seq9743,non-specific,197319,7,229,1.64447e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41415,Q#3096 - >seq9743,non-specific,238828,507,728,5.45109e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41416,Q#3096 - >seq9743,non-specific,197336,3,187,5.76163e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41417,Q#3096 - >seq9743,non-specific,236970,3,187,2.58329e-08,56.441,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41418,Q#3096 - >seq9743,non-specific,275209,458,662,8.15972e-08,55.5416,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41419,Q#3096 - >seq9743,superfamily,275209,458,662,8.15972e-08,55.5416,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41420,Q#3096 - >seq9743,non-specific,197322,2,229,3.9892200000000003e-07,53.0898,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41421,Q#3096 - >seq9743,non-specific,197311,1,229,1.88475e-06,49.9829,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41422,Q#3096 - >seq9743,non-specific,235175,283,460,2.08715e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41423,Q#3096 - >seq9743,superfamily,235175,283,460,2.08715e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41424,Q#3096 - >seq9743,non-specific,339261,101,225,0.000130512,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41425,Q#3096 - >seq9743,specific,311990,1232,1249,0.00065936,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41426,Q#3096 - >seq9743,superfamily,311990,1232,1249,0.00065936,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs5_gmonkey,marg,CompleteHit
41427,Q#3096 - >seq9743,specific,225881,474,671,0.0012234000000000001,42.5185,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41428,Q#3096 - >seq9743,superfamily,225881,474,671,0.0012234000000000001,42.5185,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41429,Q#3096 - >seq9743,non-specific,238185,647,724,0.00215263,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41430,Q#3096 - >seq9743,non-specific,274009,286,438,0.00226931,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41431,Q#3096 - >seq9743,superfamily,274009,286,438,0.00226931,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41432,Q#3096 - >seq9743,non-specific,274009,299,449,0.00827377,40.4363,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41433,Q#3099 - >seq9746,non-specific,335182,67,162,5.63901e-37,125.493,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41434,Q#3099 - >seq9746,superfamily,335182,67,162,5.63901e-37,125.493,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41435,Q#3099 - >seq9746,non-specific,340205,165,228,1.8050099999999995e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41436,Q#3099 - >seq9746,superfamily,340205,165,228,1.8050099999999995e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41437,Q#3099 - >seq9746,non-specific,340204,21,63,8.19077e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41438,Q#3099 - >seq9746,superfamily,340204,21,63,8.19077e-09,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs1_chimp,pars,CompleteHit
41439,Q#3099 - >seq9746,non-specific,334565,22,145,0.0041278,37.8544,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs1_chimp,pars,C-TerminusTruncated
41440,Q#3099 - >seq9746,superfamily,334565,22,145,0.0041278,37.8544,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase,L1PB3,ORF1,hs1_chimp,pars,C-TerminusTruncated
41441,Q#3100 - >seq9747,non-specific,335182,67,162,9.44297e-36,122.02600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41442,Q#3100 - >seq9747,superfamily,335182,67,162,9.44297e-36,122.02600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41443,Q#3100 - >seq9747,non-specific,340205,165,228,4.0512399999999994e-29,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41444,Q#3100 - >seq9747,superfamily,340205,165,228,4.0512399999999994e-29,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41445,Q#3100 - >seq9747,non-specific,340204,21,63,3.39694e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41446,Q#3100 - >seq9747,superfamily,340204,21,63,3.39694e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs2_gorilla,marg,CompleteHit
41447,Q#3100 - >seq9747,non-specific,314569,3,50,0.00476215,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
41448,Q#3100 - >seq9747,superfamily,327698,3,50,0.00476215,37.0108,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB3.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB3,ORF1,hs2_gorilla,marg,BothTerminiTruncated
41449,Q#3102 - >seq9749,non-specific,335182,67,162,4.723239999999999e-37,125.493,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41450,Q#3102 - >seq9749,superfamily,335182,67,162,4.723239999999999e-37,125.493,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41451,Q#3102 - >seq9749,non-specific,340205,165,228,1.4565299999999998e-30,107.807,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41452,Q#3102 - >seq9749,superfamily,340205,165,228,1.4565299999999998e-30,107.807,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41453,Q#3102 - >seq9749,non-specific,340204,21,63,7.96847e-09,50.0988,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41454,Q#3102 - >seq9749,superfamily,340204,21,63,7.96847e-09,50.0988,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB3,ORF1,hs1_chimp,marg,CompleteHit
41455,Q#3102 - >seq9749,non-specific,334565,22,145,0.00423689,37.8544,pfam01496,V_ATPase_I,C,cl38044,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB3,ORF1,hs1_chimp,marg,C-TerminusTruncated
41456,Q#3102 - >seq9749,superfamily,334565,22,145,0.00423689,37.8544,cl38044,V_ATPase_I superfamily,C, - ,"V-type ATPase 116kDa subunit family; This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.",L1PB3.ORF1.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase,L1PB3,ORF1,hs1_chimp,marg,C-TerminusTruncated
41457,Q#3103 - >seq9750,specific,311990,1169,1187,0.00010681799999999999,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs1_chimp.pars.frame1,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41458,Q#3103 - >seq9750,superfamily,311990,1169,1187,0.00010681799999999999,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs1_chimp.pars.frame1,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41459,Q#3105 - >seq9752,specific,238827,507,769,7.880889999999998e-68,227.55900000000003,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41460,Q#3105 - >seq9752,superfamily,295487,507,769,7.880889999999998e-68,227.55900000000003,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41461,Q#3105 - >seq9752,specific,197310,9,235,7.081109999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41462,Q#3105 - >seq9752,superfamily,351117,9,235,7.081109999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41463,Q#3105 - >seq9752,specific,333820,513,769,2.7752899999999996e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41464,Q#3105 - >seq9752,superfamily,333820,513,769,2.7752899999999996e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41465,Q#3105 - >seq9752,non-specific,197306,9,235,6.226969999999999e-31,122.205,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41466,Q#3105 - >seq9752,non-specific,197307,9,235,4.10968e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41467,Q#3105 - >seq9752,non-specific,197320,9,206,5.96533e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41468,Q#3105 - >seq9752,non-specific,223780,9,236,1.47169e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41469,Q#3105 - >seq9752,specific,335306,10,228,2.1097999999999997e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41470,Q#3105 - >seq9752,non-specific,197321,7,235,9.84495e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41471,Q#3105 - >seq9752,non-specific,197319,13,235,9.30064e-15,75.3909,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41472,Q#3105 - >seq9752,non-specific,273186,9,236,2.3880200000000003e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41473,Q#3105 - >seq9752,non-specific,272954,9,207,4.40536e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41474,Q#3105 - >seq9752,non-specific,238828,513,734,4.8852099999999995e-12,66.8408,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41475,Q#3105 - >seq9752,non-specific,197336,9,194,1.1094000000000001e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41476,Q#3105 - >seq9752,non-specific,275209,466,793,1.09453e-07,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41477,Q#3105 - >seq9752,superfamily,275209,466,793,1.09453e-07,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41478,Q#3105 - >seq9752,non-specific,236970,9,194,3.13101e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
41479,Q#3105 - >seq9752,non-specific,197311,7,146,4.222440000000001e-06,48.8273,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
41480,Q#3105 - >seq9752,non-specific,197314,7,192,5.2250800000000005e-06,49.2643,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
41481,Q#3105 - >seq9752,non-specific,238185,653,767,4.07757e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41482,Q#3105 - >seq9752,non-specific,235175,308,446,0.000130894,46.2104,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
41483,Q#3105 - >seq9752,superfamily,235175,308,446,0.000130894,46.2104,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
41484,Q#3105 - >seq9752,non-specific,197322,8,235,0.000196558,45.0006,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41485,Q#3105 - >seq9752,non-specific,274009,309,454,0.000875813,43.5179,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
41486,Q#3105 - >seq9752,superfamily,274009,309,454,0.000875813,43.5179,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
41487,Q#3105 - >seq9752,non-specific,334125,213,408,0.00179139,42.1364,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
41488,Q#3105 - >seq9752,superfamily,334125,213,408,0.00179139,42.1364,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB3,ORF2,hs1_chimp,pars,N-TerminusTruncated
41489,Q#3105 - >seq9752,non-specific,274009,299,431,0.00205682,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,BothTerminiTruncated
41490,Q#3105 - >seq9752,non-specific,224117,281,429,0.00656927,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
41491,Q#3105 - >seq9752,superfamily,224117,281,429,0.00656927,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB3,ORF2,hs1_chimp,pars,C-TerminusTruncated
41492,Q#3105 - >seq9752,non-specific,339261,108,231,0.00677779,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs1_chimp.pars.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs1_chimp,pars,CompleteHit
41493,Q#3108 - >seq9755,specific,238827,500,762,8.849899999999999e-68,227.174,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41494,Q#3108 - >seq9755,superfamily,295487,500,762,8.849899999999999e-68,227.174,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41495,Q#3108 - >seq9755,specific,197310,3,229,3.0935599999999993e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41496,Q#3108 - >seq9755,superfamily,351117,3,229,3.0935599999999993e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41497,Q#3108 - >seq9755,specific,333820,506,762,3.4123e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41498,Q#3108 - >seq9755,superfamily,333820,506,762,3.4123e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41499,Q#3108 - >seq9755,non-specific,197306,3,229,4.4668199999999995e-31,122.59,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41500,Q#3108 - >seq9755,non-specific,197307,3,229,4.49168e-21,93.8917,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41501,Q#3108 - >seq9755,non-specific,197320,3,200,5.654e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41502,Q#3108 - >seq9755,non-specific,223780,3,230,1.80151e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41503,Q#3108 - >seq9755,specific,335306,4,222,2.09722e-18,85.3745,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41504,Q#3108 - >seq9755,non-specific,197321,1,229,9.6929e-18,84.1408,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41505,Q#3108 - >seq9755,non-specific,197319,7,229,1.13665e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41506,Q#3108 - >seq9755,non-specific,273186,3,230,2.3958799999999998e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41507,Q#3108 - >seq9755,non-specific,272954,3,201,4.8998199999999995e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41508,Q#3108 - >seq9755,non-specific,238828,506,727,5.5927e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41509,Q#3108 - >seq9755,non-specific,197336,3,188,1.2551099999999998e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41510,Q#3108 - >seq9755,non-specific,275209,459,786,1.30915e-07,55.1564,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41511,Q#3108 - >seq9755,superfamily,275209,459,786,1.30915e-07,55.1564,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41512,Q#3108 - >seq9755,non-specific,236970,3,188,2.92047e-07,53.3594,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
41513,Q#3108 - >seq9755,non-specific,197311,1,140,3.7541500000000003e-06,48.8273,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
41514,Q#3108 - >seq9755,non-specific,197314,1,186,5.19414e-06,49.2643,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs1_chimp,marg,C-TerminusTruncated
41515,Q#3108 - >seq9755,non-specific,238185,646,760,4.83292e-05,43.4936,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41516,Q#3108 - >seq9755,non-specific,235175,302,439,0.00010002399999999999,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41517,Q#3108 - >seq9755,superfamily,235175,302,439,0.00010002399999999999,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41518,Q#3108 - >seq9755,non-specific,197322,2,229,0.00019538700000000002,45.0006,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41519,Q#3108 - >seq9755,specific,311990,1284,1302,0.0007653369999999999,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41520,Q#3108 - >seq9755,superfamily,311990,1284,1302,0.0007653369999999999,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41521,Q#3108 - >seq9755,non-specific,274009,303,447,0.00138579,43.1327,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41522,Q#3108 - >seq9755,superfamily,274009,303,447,0.00138579,43.1327,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41523,Q#3108 - >seq9755,non-specific,223496,292,436,0.00160174,42.8251,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41524,Q#3108 - >seq9755,superfamily,223496,292,436,0.00160174,42.8251,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41525,Q#3108 - >seq9755,non-specific,274009,293,424,0.00172644,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs1_chimp,marg,BothTerminiTruncated
41526,Q#3108 - >seq9755,non-specific,339261,102,225,0.00445271,38.0871,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs1_chimp.marg.frame3,1909201640_L1PB3.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs1_chimp,marg,CompleteHit
41527,Q#3111 - >seq9758,non-specific,335182,67,162,9.44297e-36,122.02600000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41528,Q#3111 - >seq9758,superfamily,335182,67,162,9.44297e-36,122.02600000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41529,Q#3111 - >seq9758,non-specific,340205,165,228,4.0512399999999994e-29,103.955,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41530,Q#3111 - >seq9758,superfamily,340205,165,228,4.0512399999999994e-29,103.955,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41531,Q#3111 - >seq9758,non-specific,340204,21,63,3.39694e-07,45.4764,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41532,Q#3111 - >seq9758,superfamily,340204,21,63,3.39694e-07,45.4764,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB3,ORF1,hs2_gorilla,pars,CompleteHit
41533,Q#3111 - >seq9758,non-specific,314569,3,50,0.00476215,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
41534,Q#3111 - >seq9758,superfamily,327698,3,50,0.00476215,37.0108,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB3.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB3.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB3,ORF1,hs2_gorilla,pars,BothTerminiTruncated
41535,Q#3115 - >seq9762,specific,238827,503,767,2.4912499999999997e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41536,Q#3115 - >seq9762,superfamily,295487,503,767,2.4912499999999997e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41537,Q#3115 - >seq9762,specific,197310,3,230,2.4209e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41538,Q#3115 - >seq9762,superfamily,351117,3,230,2.4209e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41539,Q#3115 - >seq9762,specific,333820,509,733,1.5064099999999998e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41540,Q#3115 - >seq9762,superfamily,333820,509,733,1.5064099999999998e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41541,Q#3115 - >seq9762,non-specific,197306,3,230,2.88002e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41542,Q#3115 - >seq9762,non-specific,197320,3,243,1.60747e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41543,Q#3115 - >seq9762,non-specific,223780,3,231,5.58679e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41544,Q#3115 - >seq9762,non-specific,197307,3,230,9.20269e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41545,Q#3115 - >seq9762,specific,335306,4,223,1.63184e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41546,Q#3115 - >seq9762,non-specific,197321,1,230,1.76734e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41547,Q#3115 - >seq9762,non-specific,273186,3,231,3.2444099999999998e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41548,Q#3115 - >seq9762,non-specific,272954,3,243,4.19425e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41549,Q#3115 - >seq9762,non-specific,197319,7,230,1.50765e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41550,Q#3115 - >seq9762,non-specific,238828,509,730,3.60987e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41551,Q#3115 - >seq9762,non-specific,197336,3,188,2.5076499999999996e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41552,Q#3115 - >seq9762,non-specific,236970,3,243,1.4051800000000001e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41553,Q#3115 - >seq9762,non-specific,275209,460,730,5.0111e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41554,Q#3115 - >seq9762,superfamily,275209,460,730,5.0111e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41555,Q#3115 - >seq9762,non-specific,197322,2,230,5.69829e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41556,Q#3115 - >seq9762,non-specific,197311,1,230,2.2657699999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41557,Q#3115 - >seq9762,non-specific,235175,288,462,2.32281e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41558,Q#3115 - >seq9762,superfamily,235175,288,462,2.32281e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41559,Q#3115 - >seq9762,non-specific,339261,102,226,4.2834300000000004e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs5_gmonkey,pars,CompleteHit
41560,Q#3115 - >seq9762,non-specific,238185,649,726,0.000819335,39.6416,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41561,Q#3115 - >seq9762,non-specific,274009,301,451,0.00252746,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41562,Q#3115 - >seq9762,superfamily,274009,301,451,0.00252746,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41563,Q#3115 - >seq9762,non-specific,274009,288,440,0.0048474,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41564,Q#3116 - >seq9763,specific,311990,1146,1164,3.75072e-05,41.1184,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs4_gibbon.pars.frame1,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41565,Q#3116 - >seq9763,superfamily,311990,1146,1164,3.75072e-05,41.1184,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs4_gibbon.pars.frame1,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41566,Q#3119 - >seq9766,non-specific,335182,137,233,3.6170699999999995e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41567,Q#3119 - >seq9766,superfamily,335182,137,233,3.6170699999999995e-31,112.396,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41568,Q#3119 - >seq9766,non-specific,335182,137,233,3.6170699999999995e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41569,Q#3119 - >seq9766,non-specific,340205,236,299,1.2415e-25,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41570,Q#3119 - >seq9766,superfamily,340205,236,299,1.2415e-25,96.6364,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41571,Q#3119 - >seq9766,non-specific,340205,236,299,1.2415e-25,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41572,Q#3119 - >seq9766,non-specific,340204,92,134,1.85919e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41573,Q#3119 - >seq9766,superfamily,340204,92,134,1.85919e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41574,Q#3119 - >seq9766,non-specific,340204,92,134,1.85919e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,pars,CompleteHit
41575,Q#3119 - >seq9766,non-specific,274008,34,183,0.000214301,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41576,Q#3119 - >seq9766,superfamily,274008,34,183,0.000214301,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41577,Q#3119 - >seq9766,non-specific,274008,34,183,0.000214301,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41578,Q#3119 - >seq9766,non-specific,235175,23,137,0.0011818,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41579,Q#3119 - >seq9766,superfamily,235175,23,137,0.0011818,40.4324,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41580,Q#3119 - >seq9766,non-specific,235175,23,137,0.0011818,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41581,Q#3119 - >seq9766,non-specific,237177,25,130,0.00127526,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41582,Q#3119 - >seq9766,superfamily,237177,25,130,0.00127526,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41583,Q#3119 - >seq9766,non-specific,237177,25,130,0.00127526,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
41584,Q#3119 - >seq9766,non-specific,224117,22,131,0.00151058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41585,Q#3119 - >seq9766,superfamily,224117,22,131,0.00151058,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41586,Q#3119 - >seq9766,non-specific,224117,22,131,0.00151058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41587,Q#3119 - >seq9766,non-specific,224117,14,130,0.0022408000000000003,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41588,Q#3119 - >seq9766,non-specific,224117,14,130,0.0022408000000000003,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41589,Q#3119 - >seq9766,non-specific,274009,13,138,0.00348774,38.8955,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41590,Q#3119 - >seq9766,superfamily,274009,13,138,0.00348774,38.8955,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41591,Q#3119 - >seq9766,non-specific,274009,13,138,0.00348774,38.8955,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,N-TerminusTruncated
41592,Q#3119 - >seq9766,non-specific,224117,24,142,0.00607816,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41593,Q#3119 - >seq9766,non-specific,224117,24,142,0.00607816,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41594,Q#3119 - >seq9766,non-specific,274009,14,131,0.00632345,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41595,Q#3119 - >seq9766,non-specific,274009,14,131,0.00632345,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
41596,Q#3122 - >seq9769,non-specific,335182,137,233,3.6170699999999995e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41597,Q#3122 - >seq9769,superfamily,335182,137,233,3.6170699999999995e-31,112.396,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41598,Q#3122 - >seq9769,non-specific,335182,137,233,3.6170699999999995e-31,112.396,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41599,Q#3122 - >seq9769,non-specific,340205,236,299,1.2415e-25,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41600,Q#3122 - >seq9769,superfamily,340205,236,299,1.2415e-25,96.6364,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41601,Q#3122 - >seq9769,non-specific,340205,236,299,1.2415e-25,96.6364,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41602,Q#3122 - >seq9769,non-specific,340204,92,134,1.85919e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41603,Q#3122 - >seq9769,superfamily,340204,92,134,1.85919e-06,43.9356,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41604,Q#3122 - >seq9769,non-specific,340204,92,134,1.85919e-06,43.9356,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PBa,ORF1,hs6_sqmonkey,marg,CompleteHit
41605,Q#3122 - >seq9769,non-specific,274008,34,183,0.000214301,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41606,Q#3122 - >seq9769,superfamily,274008,34,183,0.000214301,42.7363,cl37069,SMC_prok_B superfamily,N, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41607,Q#3122 - >seq9769,non-specific,274008,34,183,0.000214301,42.7363,TIGR02168,SMC_prok_B,N,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41608,Q#3122 - >seq9769,non-specific,235175,23,137,0.0011818,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41609,Q#3122 - >seq9769,superfamily,235175,23,137,0.0011818,40.4324,cl35229,PRK03918 superfamily,C, - ,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41610,Q#3122 - >seq9769,non-specific,235175,23,137,0.0011818,40.4324,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41611,Q#3122 - >seq9769,non-specific,237177,25,130,0.00127526,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41612,Q#3122 - >seq9769,superfamily,237177,25,130,0.00127526,40.1466,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41613,Q#3122 - >seq9769,non-specific,237177,25,130,0.00127526,40.1466,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PBa,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
41614,Q#3122 - >seq9769,non-specific,224117,22,131,0.00151058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41615,Q#3122 - >seq9769,superfamily,224117,22,131,0.00151058,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41616,Q#3122 - >seq9769,non-specific,224117,22,131,0.00151058,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41617,Q#3122 - >seq9769,non-specific,224117,14,130,0.0022408000000000003,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41618,Q#3122 - >seq9769,non-specific,224117,14,130,0.0022408000000000003,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41619,Q#3122 - >seq9769,non-specific,274009,13,138,0.00348774,38.8955,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41620,Q#3122 - >seq9769,superfamily,274009,13,138,0.00348774,38.8955,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41621,Q#3122 - >seq9769,non-specific,274009,13,138,0.00348774,38.8955,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,N-TerminusTruncated
41622,Q#3122 - >seq9769,non-specific,224117,24,142,0.00607816,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41623,Q#3122 - >seq9769,non-specific,224117,24,142,0.00607816,38.1568,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41624,Q#3122 - >seq9769,non-specific,274009,14,131,0.00632345,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41625,Q#3122 - >seq9769,non-specific,274009,14,131,0.00632345,38.1251,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
41626,Q#3125 - >seq9772,specific,238827,502,759,1.7876999999999999e-62,211.766,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41627,Q#3125 - >seq9772,superfamily,295487,502,759,1.7876999999999999e-62,211.766,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41628,Q#3125 - >seq9772,specific,197310,3,230,4.12521e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41629,Q#3125 - >seq9772,superfamily,351117,3,230,4.12521e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41630,Q#3125 - >seq9772,specific,333820,508,732,1.65842e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41631,Q#3125 - >seq9772,superfamily,333820,508,732,1.65842e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41632,Q#3125 - >seq9772,non-specific,197306,3,230,1.8283e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41633,Q#3125 - >seq9772,non-specific,197320,3,223,1.98982e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41634,Q#3125 - >seq9772,non-specific,223780,3,231,8.50162e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41635,Q#3125 - >seq9772,non-specific,197307,3,230,2.90678e-18,85.4173,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41636,Q#3125 - >seq9772,specific,335306,4,223,1.11238e-16,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41637,Q#3125 - >seq9772,non-specific,273186,3,231,1.22563e-15,77.7044,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41638,Q#3125 - >seq9772,non-specific,197321,1,230,1.8784400000000002e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41639,Q#3125 - >seq9772,non-specific,272954,3,230,1.61317e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41640,Q#3125 - >seq9772,non-specific,197319,7,230,1.6635900000000002e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41641,Q#3125 - >seq9772,non-specific,238828,508,729,1.5672799999999999e-13,71.078,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41642,Q#3125 - >seq9772,non-specific,197336,3,188,2.3600200000000003e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41643,Q#3125 - >seq9772,non-specific,236970,3,243,5.04559e-09,58.367,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41644,Q#3125 - >seq9772,non-specific,275209,459,729,7.25652e-08,55.5416,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
41645,Q#3125 - >seq9772,superfamily,275209,459,729,7.25652e-08,55.5416,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
41646,Q#3125 - >seq9772,non-specific,197322,2,230,2.4866599999999996e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41647,Q#3125 - >seq9772,non-specific,235175,287,461,1.92151e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
41648,Q#3125 - >seq9772,superfamily,235175,287,461,1.92151e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
41649,Q#3125 - >seq9772,non-specific,197311,1,230,1.93037e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41650,Q#3125 - >seq9772,non-specific,339261,102,226,0.000126866,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs6_sqmonkey,pars,CompleteHit
41651,Q#3125 - >seq9772,non-specific,238185,648,725,0.000419915,40.412,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
41652,Q#3125 - >seq9772,non-specific,274009,300,450,0.00184571,42.3623,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
41653,Q#3125 - >seq9772,superfamily,274009,300,450,0.00184571,42.3623,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
41654,Q#3125 - >seq9772,non-specific,274009,287,402,0.0040885999999999995,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
41655,Q#3125 - >seq9772,non-specific,334125,206,402,0.00489939,40.5956,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41656,Q#3125 - >seq9772,superfamily,334125,206,402,0.00489939,40.5956,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PBa,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41657,Q#3128 - >seq9775,specific,238827,503,765,1.52622e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41658,Q#3128 - >seq9775,superfamily,295487,503,765,1.52622e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41659,Q#3128 - >seq9775,specific,197310,3,230,2.4245299999999994e-59,203.737,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41660,Q#3128 - >seq9775,superfamily,351117,3,230,2.4245299999999994e-59,203.737,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41661,Q#3128 - >seq9775,specific,333820,509,765,3.40972e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41662,Q#3128 - >seq9775,superfamily,333820,509,765,3.40972e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41663,Q#3128 - >seq9775,non-specific,197306,3,230,2.72602e-32,126.057,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41664,Q#3128 - >seq9775,non-specific,197320,3,243,1.7727299999999998e-20,92.1929,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41665,Q#3128 - >seq9775,non-specific,223780,3,231,5.82032e-19,88.0391,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41666,Q#3128 - >seq9775,non-specific,197307,3,230,9.40626e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41667,Q#3128 - >seq9775,specific,335306,4,223,1.66705e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41668,Q#3128 - >seq9775,non-specific,197321,1,230,1.94754e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41669,Q#3128 - >seq9775,non-specific,273186,3,231,3.3473500000000002e-15,76.5488,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41670,Q#3128 - >seq9775,non-specific,272954,3,243,4.2868200000000005e-15,76.2677,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41671,Q#3128 - >seq9775,non-specific,197319,7,230,1.49805e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41672,Q#3128 - >seq9775,non-specific,238828,509,730,3.79371e-13,69.9224,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41673,Q#3128 - >seq9775,non-specific,197336,3,188,2.5624200000000005e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41674,Q#3128 - >seq9775,non-specific,236970,3,243,1.3466300000000001e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41675,Q#3128 - >seq9775,non-specific,275209,460,789,2.6873299999999998e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41676,Q#3128 - >seq9775,superfamily,275209,460,789,2.6873299999999998e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41677,Q#3128 - >seq9775,non-specific,197322,2,230,5.8239e-07,52.7046,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41678,Q#3128 - >seq9775,non-specific,238185,649,763,1.74382e-05,44.6492,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41679,Q#3128 - >seq9775,non-specific,197311,1,230,2.2289899999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41680,Q#3128 - >seq9775,non-specific,235175,288,462,2.56333e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41681,Q#3128 - >seq9775,superfamily,235175,288,462,2.56333e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41682,Q#3128 - >seq9775,non-specific,339261,102,226,3.85262e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs5_gmonkey,marg,CompleteHit
41683,Q#3128 - >seq9775,non-specific,274009,301,451,0.00274001,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41684,Q#3128 - >seq9775,superfamily,274009,301,451,0.00274001,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41685,Q#3128 - >seq9775,non-specific,274009,288,440,0.00507979,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41686,Q#3129 - >seq9776,specific,238827,502,758,1.5936699999999996e-63,214.84799999999998,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41687,Q#3129 - >seq9776,superfamily,295487,502,758,1.5936699999999996e-63,214.84799999999998,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41688,Q#3129 - >seq9776,specific,197310,3,230,1.32342e-57,198.73,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41689,Q#3129 - >seq9776,superfamily,351117,3,230,1.32342e-57,198.73,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41690,Q#3129 - >seq9776,specific,333820,508,732,1.47812e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41691,Q#3129 - >seq9776,superfamily,333820,508,732,1.47812e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41692,Q#3129 - >seq9776,non-specific,197306,3,230,6.392999999999999e-32,124.90100000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41693,Q#3129 - >seq9776,non-specific,197320,3,223,2.2007299999999998e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41694,Q#3129 - >seq9776,non-specific,223780,3,231,9.05564e-19,87.2687,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41695,Q#3129 - >seq9776,non-specific,197307,3,230,2.4656599999999998e-18,85.8025,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41696,Q#3129 - >seq9776,specific,335306,4,223,1.19327e-16,80.3669,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41697,Q#3129 - >seq9776,non-specific,273186,3,231,1.25649e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41698,Q#3129 - >seq9776,non-specific,197321,1,230,1.8897099999999997e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41699,Q#3129 - >seq9776,non-specific,272954,3,230,1.42322e-14,74.7269,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41700,Q#3129 - >seq9776,non-specific,197319,7,230,1.59676e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41701,Q#3129 - >seq9776,non-specific,238828,508,729,1.2193800000000002e-13,71.4632,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41702,Q#3129 - >seq9776,non-specific,197336,3,188,2.53384e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41703,Q#3129 - >seq9776,non-specific,236970,3,243,4.04152e-09,58.7522,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41704,Q#3129 - >seq9776,non-specific,275209,459,729,7.6042e-08,55.5416,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
41705,Q#3129 - >seq9776,superfamily,275209,459,729,7.6042e-08,55.5416,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
41706,Q#3129 - >seq9776,non-specific,197322,2,230,2.67211e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41707,Q#3129 - >seq9776,non-specific,235175,287,461,1.82009e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
41708,Q#3129 - >seq9776,superfamily,235175,287,461,1.82009e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
41709,Q#3129 - >seq9776,non-specific,197311,1,230,1.83165e-05,46.9013,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41710,Q#3129 - >seq9776,non-specific,339261,102,226,0.000101275,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41711,Q#3129 - >seq9776,non-specific,238185,648,725,0.00045198300000000004,40.412,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
41712,Q#3129 - >seq9776,non-specific,274009,300,450,0.00168737,42.7475,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
41713,Q#3129 - >seq9776,superfamily,274009,300,450,0.00168737,42.7475,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
41714,Q#3129 - >seq9776,non-specific,334125,206,402,0.00287464,41.36600000000001,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
41715,Q#3129 - >seq9776,superfamily,334125,206,402,0.00287464,41.36600000000001,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PBa,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
41716,Q#3129 - >seq9776,non-specific,274009,287,402,0.00331928,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PBa,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
41717,Q#3129 - >seq9776,non-specific,239569,517,730,0.00661146,39.0931,cd03487,RT_Bac_retron_II, - ,cl02808,RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.,L1PBa.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PBa.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PBa,ORF2,hs6_sqmonkey,marg,CompleteHit
41718,Q#3131 - >seq9778,specific,238827,510,772,2.7849899999999993e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41719,Q#3131 - >seq9778,superfamily,295487,510,772,2.7849899999999993e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41720,Q#3131 - >seq9778,specific,197310,9,230,3.8903799999999997e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41721,Q#3131 - >seq9778,superfamily,351117,9,230,3.8903799999999997e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41722,Q#3131 - >seq9778,non-specific,197306,9,229,5.89213e-43,156.873,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41723,Q#3131 - >seq9778,specific,333820,516,772,3.21265e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41724,Q#3131 - >seq9778,superfamily,333820,516,772,3.21265e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41725,Q#3131 - >seq9778,non-specific,197307,9,229,2.36799e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41726,Q#3131 - >seq9778,non-specific,223780,9,229,1.6298200000000003e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41727,Q#3131 - >seq9778,non-specific,197320,9,229,8.64059e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41728,Q#3131 - >seq9778,specific,335306,10,229,2.86734e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41729,Q#3131 - >seq9778,non-specific,197321,7,229,3.7161699999999996e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41730,Q#3131 - >seq9778,non-specific,273186,9,229,1.6675400000000002e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41731,Q#3131 - >seq9778,non-specific,272954,9,221,4.01716e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41732,Q#3131 - >seq9778,non-specific,197319,13,229,1.07626e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41733,Q#3131 - >seq9778,non-specific,238828,516,737,1.85172e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41734,Q#3131 - >seq9778,non-specific,197336,9,194,1.3692599999999999e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41735,Q#3131 - >seq9778,non-specific,197322,8,229,2.5869000000000002e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41736,Q#3131 - >seq9778,non-specific,339261,108,229,1.50991e-07,51.1839,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41737,Q#3131 - >seq9778,non-specific,197311,7,229,1.13431e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41738,Q#3131 - >seq9778,non-specific,275209,467,737,1.2473000000000001e-06,52.0748,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
41739,Q#3131 - >seq9778,superfamily,275209,467,737,1.2473000000000001e-06,52.0748,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
41740,Q#3131 - >seq9778,non-specific,236970,9,229,6.89974e-06,49.1222,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41741,Q#3131 - >seq9778,non-specific,238185,656,772,3.30625e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41742,Q#3131 - >seq9778,specific,311990,1235,1253,0.000368104,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41743,Q#3131 - >seq9778,superfamily,311990,1235,1253,0.000368104,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41744,Q#3131 - >seq9778,non-specific,224117,263,467,0.00133245,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41745,Q#3131 - >seq9778,superfamily,224117,263,467,0.00133245,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41746,Q#3131 - >seq9778,non-specific,224117,266,391,0.00257677,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41747,Q#3131 - >seq9778,non-specific,274009,301,458,0.00270203,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41748,Q#3131 - >seq9778,superfamily,274009,301,458,0.00270203,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41749,Q#3131 - >seq9778,non-specific,274008,267,462,0.00791669,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41750,Q#3131 - >seq9778,superfamily,274008,267,462,0.00791669,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41751,Q#3131 - >seq9778,non-specific,235175,294,464,0.00821496,40.4324,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41752,Q#3131 - >seq9778,superfamily,235175,294,464,0.00821496,40.4324,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41753,Q#3131 - >seq9778,specific,316774,305,363,0.00960413,36.9828,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41754,Q#3131 - >seq9778,superfamily,316774,305,363,0.00960413,36.9828,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,pars,CompleteHit
41755,Q#3132 - >seq9779,non-specific,239242,1075,1138,0.00471861,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PREC2.ORF2.hs4_gibbon.marg.frame1,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41756,Q#3132 - >seq9779,superfamily,355772,1075,1138,0.00471861,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PREC2.ORF2.hs4_gibbon.marg.frame1,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41757,Q#3134 - >seq9781,specific,238827,510,772,3.3428899999999996e-65,219.855,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41758,Q#3134 - >seq9781,superfamily,295487,510,772,3.3428899999999996e-65,219.855,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41759,Q#3134 - >seq9781,specific,197310,9,230,4.310019999999999e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41760,Q#3134 - >seq9781,superfamily,351117,9,230,4.310019999999999e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41761,Q#3134 - >seq9781,non-specific,197306,9,229,5.75046e-43,156.873,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41762,Q#3134 - >seq9781,specific,333820,516,772,3.5883e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41763,Q#3134 - >seq9781,superfamily,333820,516,772,3.5883e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41764,Q#3134 - >seq9781,non-specific,197307,9,229,2.35632e-22,97.7437,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41765,Q#3134 - >seq9781,non-specific,223780,9,229,1.59147e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41766,Q#3134 - >seq9781,non-specific,197320,9,229,8.357300000000001e-20,90.2669,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41767,Q#3134 - >seq9781,specific,335306,10,229,2.88015e-17,81.9077,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41768,Q#3134 - >seq9781,non-specific,197321,7,229,3.73314e-16,79.5184,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41769,Q#3134 - >seq9781,non-specific,273186,9,229,1.6137299999999998e-12,68.8448,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41770,Q#3134 - >seq9781,non-specific,272954,9,221,3.71066e-12,67.7933,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41771,Q#3134 - >seq9781,non-specific,197319,13,229,1.07111e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41772,Q#3134 - >seq9781,non-specific,238828,516,737,1.9675499999999998e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41773,Q#3134 - >seq9781,non-specific,197336,9,194,1.3378199999999998e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41774,Q#3134 - >seq9781,non-specific,197322,8,229,2.59886e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41775,Q#3134 - >seq9781,non-specific,339261,108,229,1.5761e-07,50.7987,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41776,Q#3134 - >seq9781,non-specific,197311,7,229,1.11818e-06,50.3681,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41777,Q#3134 - >seq9781,non-specific,275209,467,737,1.3093000000000001e-06,51.6896,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
41778,Q#3134 - >seq9781,superfamily,275209,467,737,1.3093000000000001e-06,51.6896,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
41779,Q#3134 - >seq9781,non-specific,236970,9,229,6.684989999999999e-06,49.1222,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41780,Q#3134 - >seq9781,non-specific,238185,656,772,3.38511e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41781,Q#3134 - >seq9781,specific,311990,1240,1258,0.000384296,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41782,Q#3134 - >seq9781,superfamily,311990,1240,1258,0.000384296,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PREC2,ORF2,hs4_gibbon,marg,CompleteHit
41783,Q#3134 - >seq9781,non-specific,224117,263,467,0.00140813,42.7792,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41784,Q#3134 - >seq9781,superfamily,224117,263,467,0.00140813,42.7792,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41785,Q#3134 - >seq9781,non-specific,224117,266,391,0.00265487,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41786,Q#3134 - >seq9781,non-specific,274009,301,458,0.00287969,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41787,Q#3134 - >seq9781,superfamily,274009,301,458,0.00287969,41.9771,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41788,Q#3134 - >seq9781,non-specific,274008,267,462,0.00801963,40.4251,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41789,Q#3134 - >seq9781,superfamily,274008,267,462,0.00801963,40.4251,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41790,Q#3134 - >seq9781,non-specific,235175,263,464,0.00945018,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41791,Q#3134 - >seq9781,superfamily,235175,263,464,0.00945018,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PREC2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41792,Q#3136 - >seq9783,specific,311990,1172,1190,0.00016963599999999997,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41793,Q#3136 - >seq9783,superfamily,311990,1172,1190,0.00016963599999999997,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41794,Q#3137 - >seq9784,specific,238827,510,772,2.5107999999999997e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41795,Q#3137 - >seq9784,superfamily,295487,510,772,2.5107999999999997e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41796,Q#3137 - >seq9784,specific,197310,9,230,3.73818e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41797,Q#3137 - >seq9784,superfamily,351117,9,230,3.73818e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41798,Q#3137 - >seq9784,non-specific,197306,9,223,1.48535e-41,152.636,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41799,Q#3137 - >seq9784,specific,333820,516,772,2.9503299999999998e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41800,Q#3137 - >seq9784,superfamily,333820,516,772,2.9503299999999998e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41801,Q#3137 - >seq9784,non-specific,197307,9,229,1.72452e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41802,Q#3137 - >seq9784,non-specific,197320,9,221,1.21553e-18,86.8001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41803,Q#3137 - >seq9784,non-specific,223780,9,223,2.8244400000000003e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41804,Q#3137 - >seq9784,non-specific,197321,7,229,7.19813e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41805,Q#3137 - >seq9784,specific,335306,10,229,1.11634e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41806,Q#3137 - >seq9784,non-specific,272954,9,221,1.35126e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41807,Q#3137 - >seq9784,non-specific,273186,9,221,2.22677e-11,65.378,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41808,Q#3137 - >seq9784,non-specific,238828,516,737,1.9258799999999999e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41809,Q#3137 - >seq9784,non-specific,197336,9,194,2.2559499999999998e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41810,Q#3137 - >seq9784,non-specific,197319,13,223,1.4626e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41811,Q#3137 - >seq9784,non-specific,197322,8,223,2.45959e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41812,Q#3137 - >seq9784,non-specific,275209,467,737,7.182160000000001e-07,52.8452,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41813,Q#3137 - >seq9784,superfamily,275209,467,737,7.182160000000001e-07,52.8452,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41814,Q#3137 - >seq9784,non-specific,339261,108,229,3.19844e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41815,Q#3137 - >seq9784,non-specific,197311,7,207,6.548580000000001e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41816,Q#3137 - >seq9784,non-specific,236970,9,221,8.27801e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41817,Q#3137 - >seq9784,non-specific,238185,656,772,2.8334499999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41818,Q#3137 - >seq9784,non-specific,224117,266,391,0.00136915,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41819,Q#3137 - >seq9784,superfamily,224117,266,391,0.00136915,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41820,Q#3137 - >seq9784,non-specific,274009,307,452,0.00686072,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41821,Q#3137 - >seq9784,superfamily,274009,307,452,0.00686072,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41822,Q#3137 - >seq9784,specific,316774,305,363,0.00732618,36.9828,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41823,Q#3137 - >seq9784,superfamily,316774,305,363,0.00732618,36.9828,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs5_gmonkey,pars,CompleteHit
41824,Q#3139 - >seq9786,specific,311990,1172,1190,0.00016963599999999997,39.5776,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs5_gmonkey.marg.frame2,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41825,Q#3139 - >seq9786,superfamily,311990,1172,1190,0.00016963599999999997,39.5776,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PREC2.ORF2.hs5_gmonkey.marg.frame2,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41826,Q#3140 - >seq9787,specific,238827,510,772,2.5107999999999997e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41827,Q#3140 - >seq9787,superfamily,295487,510,772,2.5107999999999997e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41828,Q#3140 - >seq9787,specific,197310,9,230,3.73818e-58,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41829,Q#3140 - >seq9787,superfamily,351117,9,230,3.73818e-58,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41830,Q#3140 - >seq9787,non-specific,197306,9,223,1.48535e-41,152.636,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41831,Q#3140 - >seq9787,specific,333820,516,772,2.9503299999999998e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41832,Q#3140 - >seq9787,superfamily,333820,516,772,2.9503299999999998e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41833,Q#3140 - >seq9787,non-specific,197307,9,229,1.72452e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41834,Q#3140 - >seq9787,non-specific,197320,9,221,1.21553e-18,86.8001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41835,Q#3140 - >seq9787,non-specific,223780,9,223,2.8244400000000003e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41836,Q#3140 - >seq9787,non-specific,197321,7,229,7.19813e-16,78.748,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41837,Q#3140 - >seq9787,specific,335306,10,229,1.11634e-15,77.2853,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41838,Q#3140 - >seq9787,non-specific,272954,9,221,1.35126e-12,68.9489,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41839,Q#3140 - >seq9787,non-specific,273186,9,221,2.22677e-11,65.378,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41840,Q#3140 - >seq9787,non-specific,238828,516,737,1.9258799999999999e-10,62.2184,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41841,Q#3140 - >seq9787,non-specific,197336,9,194,2.2559499999999998e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41842,Q#3140 - >seq9787,non-specific,197319,13,223,1.4626e-09,59.9829,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41843,Q#3140 - >seq9787,non-specific,197322,8,223,2.45959e-08,56.9418,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41844,Q#3140 - >seq9787,non-specific,275209,467,737,7.182160000000001e-07,52.8452,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41845,Q#3140 - >seq9787,superfamily,275209,467,737,7.182160000000001e-07,52.8452,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41846,Q#3140 - >seq9787,non-specific,339261,108,229,3.19844e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41847,Q#3140 - >seq9787,non-specific,197311,7,207,6.548580000000001e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41848,Q#3140 - >seq9787,non-specific,236970,9,221,8.27801e-06,48.736999999999995,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41849,Q#3140 - >seq9787,non-specific,238185,656,772,2.8334499999999998e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41850,Q#3140 - >seq9787,non-specific,224117,266,391,0.00136915,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41851,Q#3140 - >seq9787,superfamily,224117,266,391,0.00136915,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PREC2,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41852,Q#3140 - >seq9787,non-specific,274009,307,452,0.00686072,40.8215,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41853,Q#3140 - >seq9787,superfamily,274009,307,452,0.00686072,40.8215,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PREC2,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41854,Q#3140 - >seq9787,specific,316774,305,363,0.00732618,36.9828,pfam14282,FlxA, - ,cl16771,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41855,Q#3140 - >seq9787,superfamily,316774,305,363,0.00732618,36.9828,cl16771,FlxA superfamily, - , - ,"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.",L1PREC2.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PREC2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PREC2,ORF2,hs5_gmonkey,marg,CompleteHit
41856,Q#3141 - >seq9788,non-specific,239242,1070,1133,0.00469546,40.1694,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PREC2.ORF2.hs4_gibbon.pars.frame1,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41857,Q#3141 - >seq9788,superfamily,355772,1070,1133,0.00469546,40.1694,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PREC2.ORF2.hs4_gibbon.pars.frame1,1909201640_L1PREC2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PREC2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41858,Q#3145 - >seq9792,specific,238827,507,768,6.452999999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41859,Q#3145 - >seq9792,superfamily,295487,507,768,6.452999999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41860,Q#3145 - >seq9792,specific,197310,9,234,4.57651e-42,154.046,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41861,Q#3145 - >seq9792,superfamily,351117,9,234,4.57651e-42,154.046,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41862,Q#3145 - >seq9792,specific,333820,513,737,3.84582e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41863,Q#3145 - >seq9792,superfamily,333820,513,737,3.84582e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41864,Q#3145 - >seq9792,non-specific,197306,9,234,1.43376e-19,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41865,Q#3145 - >seq9792,specific,335306,10,227,2.32614e-15,76.5149,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41866,Q#3145 - >seq9792,non-specific,238828,513,734,5.61184e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41867,Q#3145 - >seq9792,non-specific,223780,9,235,1.4432700000000002e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41868,Q#3145 - >seq9792,non-specific,197320,9,227,2.72184e-12,67.9254,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41869,Q#3145 - >seq9792,non-specific,197307,9,234,4.04411e-12,67.3129,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41870,Q#3145 - >seq9792,non-specific,273186,9,235,3.1398200000000004e-09,58.8296,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41871,Q#3145 - >seq9792,non-specific,197321,7,234,1.15303e-08,57.1768,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41872,Q#3145 - >seq9792,non-specific,275209,584,796,4.50945e-08,56.312,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41873,Q#3145 - >seq9792,superfamily,275209,584,796,4.50945e-08,56.312,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41874,Q#3145 - >seq9792,non-specific,197319,13,234,1.90702e-07,53.4345,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41875,Q#3145 - >seq9792,non-specific,235175,261,465,8.0756e-07,53.5291,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41876,Q#3145 - >seq9792,superfamily,235175,261,465,8.0756e-07,53.5291,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41877,Q#3145 - >seq9792,non-specific,272954,9,234,5.77127e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41878,Q#3145 - >seq9792,non-specific,197336,9,74,1.63761e-05,47.6071,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
41879,Q#3145 - >seq9792,non-specific,238185,653,738,0.000292843,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs4_gibbon,pars,CompleteHit
41880,Q#3145 - >seq9792,non-specific,224117,262,467,0.000689996,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41881,Q#3145 - >seq9792,superfamily,224117,262,467,0.000689996,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41882,Q#3145 - >seq9792,non-specific,334125,210,409,0.0007544510000000001,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41883,Q#3145 - >seq9792,superfamily,334125,210,409,0.0007544510000000001,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41884,Q#3145 - >seq9792,non-specific,274009,292,471,0.00180356,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41885,Q#3145 - >seq9792,superfamily,274009,292,471,0.00180356,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41886,Q#3145 - >seq9792,non-specific,224117,261,498,0.00404054,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,N-TerminusTruncated
41887,Q#3145 - >seq9792,non-specific,223496,318,497,0.00530067,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41888,Q#3145 - >seq9792,superfamily,223496,318,497,0.00530067,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41889,Q#3145 - >seq9792,non-specific,274475,253,446,0.00545715,40.8224,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41890,Q#3145 - >seq9792,superfamily,274475,253,446,0.00545715,40.8224,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB4,ORF2,hs4_gibbon,pars,BothTerminiTruncated
41891,Q#3145 - >seq9792,non-specific,223496,259,470,0.0070111999999999996,40.5139,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
41892,Q#3145 - >seq9792,non-specific,224117,220,484,0.00941167,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB4,ORF2,hs4_gibbon,pars,C-TerminusTruncated
41893,Q#3148 - >seq9795,specific,311990,1146,1164,3.75072e-05,41.1184,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41894,Q#3148 - >seq9795,superfamily,311990,1146,1164,3.75072e-05,41.1184,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41895,Q#3149 - >seq9796,specific,238827,507,768,6.452999999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41896,Q#3149 - >seq9796,superfamily,295487,507,768,6.452999999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41897,Q#3149 - >seq9796,specific,197310,9,234,4.57651e-42,154.046,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41898,Q#3149 - >seq9796,superfamily,351117,9,234,4.57651e-42,154.046,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41899,Q#3149 - >seq9796,specific,333820,513,737,3.84582e-33,126.63799999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41900,Q#3149 - >seq9796,superfamily,333820,513,737,3.84582e-33,126.63799999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41901,Q#3149 - >seq9796,non-specific,197306,9,234,1.43376e-19,89.0776,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41902,Q#3149 - >seq9796,specific,335306,10,227,2.32614e-15,76.5149,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41903,Q#3149 - >seq9796,non-specific,238828,513,734,5.61184e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41904,Q#3149 - >seq9796,non-specific,223780,9,235,1.4432700000000002e-12,69.1643,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41905,Q#3149 - >seq9796,non-specific,197320,9,227,2.72184e-12,67.9254,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41906,Q#3149 - >seq9796,non-specific,197307,9,234,4.04411e-12,67.3129,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41907,Q#3149 - >seq9796,non-specific,273186,9,235,3.1398200000000004e-09,58.8296,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41908,Q#3149 - >seq9796,non-specific,197321,7,234,1.15303e-08,57.1768,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41909,Q#3149 - >seq9796,non-specific,275209,584,796,4.50945e-08,56.312,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41910,Q#3149 - >seq9796,superfamily,275209,584,796,4.50945e-08,56.312,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41911,Q#3149 - >seq9796,non-specific,197319,13,234,1.90702e-07,53.4345,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41912,Q#3149 - >seq9796,non-specific,235175,261,465,8.0756e-07,53.5291,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41913,Q#3149 - >seq9796,superfamily,235175,261,465,8.0756e-07,53.5291,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41914,Q#3149 - >seq9796,non-specific,272954,9,234,5.77127e-06,48.9185,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41915,Q#3149 - >seq9796,non-specific,197336,9,74,1.63761e-05,47.6071,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
41916,Q#3149 - >seq9796,non-specific,238185,653,738,0.000292843,41.1824,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs4_gibbon,marg,CompleteHit
41917,Q#3149 - >seq9796,non-specific,224117,262,467,0.000689996,43.9348,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41918,Q#3149 - >seq9796,superfamily,224117,262,467,0.000689996,43.9348,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41919,Q#3149 - >seq9796,non-specific,334125,210,409,0.0007544510000000001,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41920,Q#3149 - >seq9796,superfamily,334125,210,409,0.0007544510000000001,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41921,Q#3149 - >seq9796,non-specific,274009,292,471,0.00180356,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41922,Q#3149 - >seq9796,superfamily,274009,292,471,0.00180356,42.3623,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41923,Q#3149 - >seq9796,non-specific,224117,261,498,0.00404054,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,N-TerminusTruncated
41924,Q#3149 - >seq9796,non-specific,223496,318,497,0.00530067,40.8991,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41925,Q#3149 - >seq9796,superfamily,223496,318,497,0.00530067,40.8991,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41926,Q#3149 - >seq9796,non-specific,274475,253,446,0.00545715,40.8224,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41927,Q#3149 - >seq9796,superfamily,274475,253,446,0.00545715,40.8224,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB4,ORF2,hs4_gibbon,marg,BothTerminiTruncated
41928,Q#3149 - >seq9796,non-specific,223496,259,470,0.0070111999999999996,40.5139,COG0419,SbcC,C,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
41929,Q#3149 - >seq9796,non-specific,224117,220,484,0.00941167,40.0828,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB4.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs4_gibbon,marg,C-TerminusTruncated
41930,Q#3151 - >seq9798,specific,311990,1182,1200,7.0813e-05,40.7332,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41931,Q#3151 - >seq9798,superfamily,311990,1182,1200,7.0813e-05,40.7332,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs5_gmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41932,Q#3152 - >seq9799,specific,238827,505,766,1.1740299999999998e-64,218.31400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41933,Q#3152 - >seq9799,superfamily,295487,505,766,1.1740299999999998e-64,218.31400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41934,Q#3152 - >seq9799,specific,197310,9,232,7.201419999999999e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41935,Q#3152 - >seq9799,superfamily,351117,9,232,7.201419999999999e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41936,Q#3152 - >seq9799,specific,333820,511,735,1.10541e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41937,Q#3152 - >seq9799,superfamily,333820,511,735,1.10541e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41938,Q#3152 - >seq9799,non-specific,197306,9,232,1.4498099999999999e-30,121.04899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41939,Q#3152 - >seq9799,non-specific,197307,9,232,6.14905e-20,90.4249,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41940,Q#3152 - >seq9799,non-specific,223780,9,233,3.28267e-18,85.7279,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41941,Q#3152 - >seq9799,specific,335306,10,225,1.54826e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41942,Q#3152 - >seq9799,non-specific,197320,9,225,3.2203300000000003e-16,79.4813,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41943,Q#3152 - >seq9799,non-specific,197319,13,232,3.6659e-15,76.5465,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41944,Q#3152 - >seq9799,non-specific,197321,7,232,3.79656e-14,73.3552,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41945,Q#3152 - >seq9799,non-specific,273186,9,233,5.24529e-14,73.082,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41946,Q#3152 - >seq9799,non-specific,272954,9,232,6.5296e-12,67.0229,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41947,Q#3152 - >seq9799,non-specific,238828,511,732,2.73552e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41948,Q#3152 - >seq9799,non-specific,275209,462,794,3.96732e-09,59.7788,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41949,Q#3152 - >seq9799,superfamily,275209,462,794,3.96732e-09,59.7788,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41950,Q#3152 - >seq9799,non-specific,197336,9,225,9.828480000000001e-06,48.3775,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41951,Q#3152 - >seq9799,non-specific,236970,9,233,1.8101300000000002e-05,47.5814,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41952,Q#3152 - >seq9799,non-specific,197311,7,143,2.54342e-05,46.5161,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,pars,C-TerminusTruncated
41953,Q#3152 - >seq9799,non-specific,223496,316,495,0.00030345400000000004,45.1363,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41954,Q#3152 - >seq9799,superfamily,223496,316,495,0.00030345400000000004,45.1363,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41955,Q#3152 - >seq9799,non-specific,224117,250,462,0.00183364,42.394,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
41956,Q#3152 - >seq9799,superfamily,224117,250,462,0.00183364,42.394,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs5_gmonkey,pars,N-TerminusTruncated
41957,Q#3152 - >seq9799,non-specific,223496,260,441,0.00218756,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41958,Q#3152 - >seq9799,non-specific,274009,297,453,0.00311376,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41959,Q#3152 - >seq9799,superfamily,274009,297,453,0.00311376,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
41960,Q#3152 - >seq9799,non-specific,238185,651,736,0.00337582,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,pars,CompleteHit
41961,Q#3155 - >seq9802,specific,238827,505,765,1.1418899999999997e-62,212.53599999999997,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41962,Q#3155 - >seq9802,superfamily,295487,505,765,1.1418899999999997e-62,212.53599999999997,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41963,Q#3155 - >seq9802,specific,197310,9,232,3.3437800000000003e-56,194.878,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41964,Q#3155 - >seq9802,superfamily,351117,9,232,3.3437800000000003e-56,194.878,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41965,Q#3155 - >seq9802,specific,333820,511,735,5.93258e-31,120.475,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41966,Q#3155 - >seq9802,superfamily,333820,511,735,5.93258e-31,120.475,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41967,Q#3155 - >seq9802,non-specific,197306,9,232,1.6773699999999997e-30,121.04899999999999,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41968,Q#3155 - >seq9802,non-specific,197307,9,232,3.9897400000000004e-19,88.1137,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41969,Q#3155 - >seq9802,non-specific,223780,9,233,3.16322e-17,82.6463,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41970,Q#3155 - >seq9802,specific,335306,10,225,1.59552e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41971,Q#3155 - >seq9802,non-specific,197320,9,225,7.39402e-16,78.7109,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41972,Q#3155 - >seq9802,non-specific,197319,13,232,3.70462e-14,73.4649,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41973,Q#3155 - >seq9802,non-specific,197321,7,232,1.65753e-13,71.8144,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41974,Q#3155 - >seq9802,non-specific,273186,9,233,2.1625799999999999e-13,71.5412,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41975,Q#3155 - >seq9802,non-specific,272954,9,232,4.09181e-11,64.7117,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41976,Q#3155 - >seq9802,non-specific,238828,511,732,8.5361e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41977,Q#3155 - >seq9802,non-specific,275209,462,793,1.18686e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41978,Q#3155 - >seq9802,superfamily,275209,462,793,1.18686e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41979,Q#3155 - >seq9802,non-specific,197336,9,225,1.32929e-05,47.9923,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41980,Q#3155 - >seq9802,non-specific,197311,7,143,3.65626e-05,46.1309,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs5_gmonkey,marg,C-TerminusTruncated
41981,Q#3155 - >seq9802,non-specific,236970,9,233,4.00459e-05,46.4258,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41982,Q#3155 - >seq9802,non-specific,223496,316,495,0.00047808199999999995,44.3659,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41983,Q#3155 - >seq9802,superfamily,223496,316,495,0.00047808199999999995,44.3659,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41984,Q#3155 - >seq9802,specific,311990,1230,1248,0.000938116,37.2664,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41985,Q#3155 - >seq9802,superfamily,311990,1230,1248,0.000938116,37.2664,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41986,Q#3155 - >seq9802,non-specific,224117,250,462,0.00281264,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
41987,Q#3155 - >seq9802,superfamily,224117,250,462,0.00281264,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs5_gmonkey,marg,N-TerminusTruncated
41988,Q#3155 - >seq9802,non-specific,223496,260,441,0.00353349,41.6695,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41989,Q#3155 - >seq9802,non-specific,274009,297,453,0.00481621,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41990,Q#3155 - >seq9802,superfamily,274009,297,453,0.00481621,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
41991,Q#3155 - >seq9802,non-specific,339261,105,228,0.00930403,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs5_gmonkey,marg,CompleteHit
41992,Q#3157 - >seq9804,specific,197310,22,211,1.73981e-31,123.616,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
41993,Q#3157 - >seq9804,superfamily,351117,22,211,1.73981e-31,123.616,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
41994,Q#3157 - >seq9804,non-specific,197306,42,217,1.0808900000000001e-13,71.7437,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41995,Q#3157 - >seq9804,non-specific,197320,101,201,1.9052799999999997e-10,62.5326,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41996,Q#3157 - >seq9804,non-specific,223780,86,200,1.51006e-06,50.6747,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41997,Q#3157 - >seq9804,non-specific,197307,84,211,1.29826e-05,48.0529,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41998,Q#3157 - >seq9804,non-specific,272954,85,200,7.06606e-05,45.8369,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
41999,Q#3157 - >seq9804,specific,311990,1169,1186,8.19442e-05,40.348,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42000,Q#3157 - >seq9804,superfamily,311990,1169,1186,8.19442e-05,40.348,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42001,Q#3157 - >seq9804,non-specific,197319,101,211,0.000142266,44.5749,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
42002,Q#3157 - >seq9804,specific,335306,68,203,0.00136613,41.4618,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
42003,Q#3158 - >seq9805,specific,238827,473,731,4.66737e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42004,Q#3158 - >seq9805,superfamily,295487,473,731,4.66737e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42005,Q#3158 - >seq9805,specific,333820,479,703,8.122489999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42006,Q#3158 - >seq9805,superfamily,333820,479,703,8.122489999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42007,Q#3158 - >seq9805,non-specific,238828,479,700,8.44651e-13,68.7668,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42008,Q#3158 - >seq9805,non-specific,197310,9,69,1.53551e-10,62.3689,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42009,Q#3158 - >seq9805,superfamily,351117,9,69,1.53551e-10,62.3689,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42010,Q#3158 - >seq9805,non-specific,275209,430,757,7.42732e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42011,Q#3158 - >seq9805,superfamily,275209,430,757,7.42732e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42012,Q#3158 - >seq9805,non-specific,197307,9,69,0.00019828,44.2009,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42013,Q#3158 - >seq9805,non-specific,238185,619,704,0.00039819800000000005,40.7972,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs6_sqmonkey,pars,CompleteHit
42014,Q#3158 - >seq9805,non-specific,197321,7,48,0.000546969,42.9244,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42015,Q#3158 - >seq9805,non-specific,223780,9,42,0.0006711239999999999,42.5855,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42016,Q#3158 - >seq9805,non-specific,197306,9,53,0.00140771,41.6981,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42017,Q#3158 - >seq9805,non-specific,273186,9,42,0.00325153,40.7252,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42018,Q#3160 - >seq9807,specific,238827,506,764,3.9262799999999994e-64,216.774,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42019,Q#3160 - >seq9807,superfamily,295487,506,764,3.9262799999999994e-64,216.774,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42020,Q#3160 - >seq9807,specific,197310,29,232,4.5295499999999997e-38,142.49,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42021,Q#3160 - >seq9807,superfamily,351117,29,232,4.5295499999999997e-38,142.49,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42022,Q#3160 - >seq9807,specific,333820,512,736,9.132749999999999e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42023,Q#3160 - >seq9807,superfamily,333820,512,736,9.132749999999999e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42024,Q#3160 - >seq9807,non-specific,197306,43,232,5.069640000000001e-17,81.7588,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42025,Q#3160 - >seq9807,non-specific,238828,512,733,2.0939e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42026,Q#3160 - >seq9807,non-specific,197320,102,225,3.70779e-10,61.7622,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42027,Q#3160 - >seq9807,non-specific,275209,463,790,6.480930000000001e-10,62.09,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42028,Q#3160 - >seq9807,superfamily,275209,463,790,6.480930000000001e-10,62.09,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42029,Q#3160 - >seq9807,non-specific,223780,87,233,1.0043999999999999e-08,57.6083,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42030,Q#3160 - >seq9807,non-specific,197307,85,232,4.5035999999999994e-08,55.3717,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42031,Q#3160 - >seq9807,non-specific,197319,102,232,1.11761e-07,54.2049,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42032,Q#3160 - >seq9807,specific,335306,69,225,1.20449e-05,47.625,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42033,Q#3160 - >seq9807,non-specific,273186,102,233,1.6768699999999998e-05,47.6588,TIGR00633,xth,N,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42034,Q#3160 - >seq9807,non-specific,272954,86,232,3.88982e-05,46.6073,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42035,Q#3160 - >seq9807,non-specific,197321,102,232,0.000337895,43.6948,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42036,Q#3160 - >seq9807,non-specific,238185,652,737,0.000735153,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42037,Q#3160 - >seq9807,non-specific,224117,295,463,0.00551694,40.8532,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42038,Q#3160 - >seq9807,superfamily,224117,295,463,0.00551694,40.8532,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ATPase_ChromSeg,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42039,Q#3160 - >seq9807,non-specific,274009,297,454,0.00673605,40.8215,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB4,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42040,Q#3160 - >seq9807,superfamily,274009,297,454,0.00673605,40.8215,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB4,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42041,Q#3160 - >seq9807,non-specific,236970,87,233,0.00955111,39.107,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs6_sqmonkey.marg.frame2,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42042,Q#3161 - >seq9808,non-specific,197310,9,70,3.04488e-13,70.4581,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42043,Q#3161 - >seq9808,superfamily,351117,9,70,3.04488e-13,70.4581,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42044,Q#3161 - >seq9808,non-specific,197306,9,54,5.73111e-06,48.6317,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42045,Q#3161 - >seq9808,non-specific,197307,9,70,6.54322e-06,48.8233,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42046,Q#3161 - >seq9808,non-specific,223780,9,43,7.682e-06,48.7487,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42047,Q#3161 - >seq9808,non-specific,197321,7,49,1.2249300000000001e-05,47.931999999999995,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42048,Q#3161 - >seq9808,non-specific,273186,9,43,0.000123065,44.9624,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42049,Q#3161 - >seq9808,specific,335306,10,63,0.000188513,44.1582,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42050,Q#3161 - >seq9808,non-specific,197336,9,43,0.00030339900000000004,43.7551,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42051,Q#3161 - >seq9808,specific,311990,1127,1144,0.000447564,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42052,Q#3161 - >seq9808,superfamily,311990,1127,1144,0.000447564,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs6_sqmonkey,marg,CompleteHit
42053,Q#3161 - >seq9808,non-specific,197320,9,43,0.000476494,42.8874,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42054,Q#3161 - >seq9808,non-specific,197319,13,43,0.00358884,40.3377,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PB4.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42055,Q#3162 - >seq9809,non-specific,197310,9,76,2.3375e-14,73.9249,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease,L1PB4,ORF2,hs0_human,pars,C-TerminusTruncated
42056,Q#3162 - >seq9809,superfamily,351117,9,76,2.3375e-14,73.9249,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,C-TerminusTruncated
42057,Q#3162 - >seq9809,non-specific,235175,276,449,6.81717e-06,50.4476,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42058,Q#3162 - >seq9809,superfamily,235175,276,449,6.81717e-06,50.4476,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42059,Q#3162 - >seq9809,non-specific,223496,302,426,7.2942e-05,47.0623,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42060,Q#3162 - >seq9809,superfamily,223496,302,426,7.2942e-05,47.0623,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_ATPase_DNArepair,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42061,Q#3162 - >seq9809,non-specific,197306,9,72,8.75942e-05,45.1649,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,C-TerminusTruncated
42062,Q#3162 - >seq9809,specific,335306,16,145,0.00023369799999999998,43.773,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,C-TerminusTruncated
42063,Q#3162 - >seq9809,non-specific,197307,19,84,0.00258033,40.7341,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.pars.frame1,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Exonuclease,L1PB4,ORF2,hs0_human,pars,C-TerminusTruncated
42064,Q#3163 - >seq9810,specific,197310,77,223,9.748190000000001e-33,127.08200000000001,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42065,Q#3163 - >seq9810,superfamily,351117,77,223,9.748190000000001e-33,127.08200000000001,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42066,Q#3163 - >seq9810,non-specific,197306,68,223,3.8063199999999997e-16,79.0624,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42067,Q#3163 - >seq9810,non-specific,197320,94,196,2.4899899999999996e-09,59.0658,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42068,Q#3163 - >seq9810,non-specific,223780,79,224,7.12681e-08,54.9119,COG0708,XthA,N,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42069,Q#3163 - >seq9810,non-specific,197307,77,223,5.3496e-07,51.9049,cd09073,ExoIII_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42070,Q#3163 - >seq9810,specific,335306,100,216,4.1825e-06,49.1658,pfam03372,Exo_endo_phos,N,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42071,Q#3163 - >seq9810,non-specific,197319,94,223,4.35042e-06,49.1973,cd09085,Mth212-like_AP-endo,N,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42072,Q#3163 - >seq9810,non-specific,272954,68,223,1.0661199999999999e-05,48.1481,TIGR00195,exoDNase_III,N,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42073,Q#3163 - >seq9810,specific,311990,1157,1175,0.000124917,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs0_human,pars,CompleteHit
42074,Q#3163 - >seq9810,superfamily,311990,1157,1175,0.000124917,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs0_human,pars,CompleteHit
42075,Q#3163 - >seq9810,non-specific,236970,70,223,0.00429583,40.2626,PRK11756,PRK11756,N,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42076,Q#3163 - >seq9810,non-specific,339261,96,219,0.00545451,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42077,Q#3163 - >seq9810,non-specific,197321,94,223,0.00667101,39.4576,cd09087,Ape1-like_AP-endo,N,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.pars.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PB4,ORF2,hs0_human,pars,N-TerminusTruncated
42078,Q#3164 - >seq9811,specific,238827,449,709,2.2069299999999994e-65,220.24,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42079,Q#3164 - >seq9811,superfamily,295487,449,709,2.2069299999999994e-65,220.24,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42080,Q#3164 - >seq9811,specific,333820,455,678,1.8886700000000002e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42081,Q#3164 - >seq9811,superfamily,333820,455,678,1.8886700000000002e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42082,Q#3164 - >seq9811,non-specific,238828,455,663,1.20505e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42083,Q#3164 - >seq9811,non-specific,275209,526,610,9.906770000000001e-06,48.9932,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42084,Q#3164 - >seq9811,superfamily,275209,526,610,9.906770000000001e-06,48.9932,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,BothTerminiTruncated
42085,Q#3164 - >seq9811,non-specific,238185,595,679,0.00122894,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs0_human.pars.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs0_human,pars,CompleteHit
42086,Q#3166 - >seq9813,specific,238827,495,755,1.5656399999999996e-63,215.233,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42087,Q#3166 - >seq9813,superfamily,295487,495,755,1.5656399999999996e-63,215.233,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42088,Q#3166 - >seq9813,specific,333820,501,724,2.2454499999999997e-29,115.853,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42089,Q#3166 - >seq9813,superfamily,333820,501,724,2.2454499999999997e-29,115.853,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42090,Q#3166 - >seq9813,non-specific,238828,501,709,9.06664e-11,62.9888,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42091,Q#3166 - >seq9813,non-specific,275209,452,656,8.49904e-06,49.3784,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,C-TerminusTruncated
42092,Q#3166 - >seq9813,superfamily,275209,452,656,8.49904e-06,49.3784,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,C-TerminusTruncated
42093,Q#3166 - >seq9813,non-specific,235175,281,454,2.37722e-05,48.5216,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB4,ORF2,hs0_human,marg,BothTerminiTruncated
42094,Q#3166 - >seq9813,superfamily,235175,281,454,2.37722e-05,48.5216,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ChromSeg,L1PB4,ORF2,hs0_human,marg,BothTerminiTruncated
42095,Q#3166 - >seq9813,non-specific,223496,307,431,0.000212497,45.5215,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs0_human,marg,BothTerminiTruncated
42096,Q#3166 - >seq9813,superfamily,223496,307,431,0.000212497,45.5215,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Other_ATPase_DNArepair,L1PB4,ORF2,hs0_human,marg,BothTerminiTruncated
42097,Q#3166 - >seq9813,specific,311990,1223,1241,0.000606814,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB4,ORF2,hs0_human,marg,CompleteHit
42098,Q#3166 - >seq9813,superfamily,311990,1223,1241,0.000606814,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PB4,ORF2,hs0_human,marg,CompleteHit
42099,Q#3166 - >seq9813,non-specific,238185,641,725,0.00689562,36.9452,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs0_human.marg.frame2,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42100,Q#3167 - >seq9814,specific,197310,9,235,1.0910999999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42101,Q#3167 - >seq9814,superfamily,351117,9,235,1.0910999999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42102,Q#3167 - >seq9814,non-specific,197306,9,235,9.13819e-33,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42103,Q#3167 - >seq9814,non-specific,197307,9,235,1.4301e-22,98.1289,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42104,Q#3167 - >seq9814,non-specific,223780,9,236,1.9125200000000002e-20,92.2763,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42105,Q#3167 - >seq9814,non-specific,197320,9,208,1.18081e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42106,Q#3167 - >seq9814,specific,335306,10,228,2.54579e-19,88.0709,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42107,Q#3167 - >seq9814,non-specific,197321,7,235,1.83191e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42108,Q#3167 - >seq9814,non-specific,197319,13,235,2.7593499999999998e-15,76.9317,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42109,Q#3167 - >seq9814,non-specific,273186,9,236,2.29371e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42110,Q#3167 - >seq9814,non-specific,272954,9,235,2.6478800000000003e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42111,Q#3167 - >seq9814,non-specific,236970,9,235,9.66042e-10,60.6782,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42112,Q#3167 - >seq9814,non-specific,197336,9,194,4.29788e-09,58.3927,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42113,Q#3167 - >seq9814,non-specific,197322,8,235,1.3414700000000002e-06,51.549,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42114,Q#3167 - >seq9814,non-specific,197311,26,146,0.000335554,43.0493,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs0_human,marg,C-TerminusTruncated
42115,Q#3167 - >seq9814,non-specific,197318,9,235,0.00191106,41.1279,cd09084,EEP-2, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs0_human,marg,CompleteHit
42116,Q#3167 - >seq9814,non-specific,339261,108,231,0.00300142,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs0_human.marg.frame3,1909201640_L1PB4.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs0_human,marg,CompleteHit
42117,Q#3170 - >seq9817,specific,238827,506,768,2.3652199999999997e-66,223.322,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42118,Q#3170 - >seq9817,superfamily,295487,506,768,2.3652199999999997e-66,223.322,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42119,Q#3170 - >seq9817,specific,197310,9,235,3.058299999999999e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42120,Q#3170 - >seq9817,superfamily,351117,9,235,3.058299999999999e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42121,Q#3170 - >seq9817,specific,333820,512,768,2.22966e-31,121.631,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42122,Q#3170 - >seq9817,superfamily,333820,512,768,2.22966e-31,121.631,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42123,Q#3170 - >seq9817,non-specific,197306,9,235,2.70285e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42124,Q#3170 - >seq9817,non-specific,197307,9,235,2.8350500000000002e-21,94.2769,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42125,Q#3170 - >seq9817,non-specific,197320,9,206,5.31841e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42126,Q#3170 - >seq9817,non-specific,223780,9,236,1.04515e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42127,Q#3170 - >seq9817,specific,335306,10,228,1.6011400000000002e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42128,Q#3170 - >seq9817,non-specific,197321,7,235,1.49056e-17,83.7556,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42129,Q#3170 - >seq9817,non-specific,273186,9,236,7.734669999999999e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42130,Q#3170 - >seq9817,non-specific,197319,13,235,2.7099900000000002e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42131,Q#3170 - >seq9817,non-specific,272954,9,207,3.6482e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42132,Q#3170 - >seq9817,non-specific,238828,512,733,4.16916e-11,64.1444,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42133,Q#3170 - >seq9817,non-specific,197336,9,194,1.71079e-09,59.5483,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42134,Q#3170 - >seq9817,non-specific,236970,9,194,3.61354e-07,52.9742,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42135,Q#3170 - >seq9817,non-specific,197311,7,146,2.99377e-06,49.2125,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42136,Q#3170 - >seq9817,non-specific,197314,7,192,4.94121e-06,49.2643,cd09080,TDP2,C,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42137,Q#3170 - >seq9817,non-specific,235175,289,465,8.767719999999999e-06,50.0624,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42138,Q#3170 - >seq9817,superfamily,235175,289,465,8.767719999999999e-06,50.0624,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42139,Q#3170 - >seq9817,non-specific,275209,463,667,9.63817e-06,48.9932,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42140,Q#3170 - >seq9817,superfamily,275209,463,667,9.63817e-06,48.9932,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42141,Q#3170 - >seq9817,non-specific,197322,8,235,6.50466e-05,46.1562,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB3,ORF2,hs0_human,marg,CompleteHit
42142,Q#3170 - >seq9817,non-specific,334125,213,408,0.000727898,43.292,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs0_human,marg,N-TerminusTruncated
42143,Q#3170 - >seq9817,superfamily,334125,213,408,0.000727898,43.292,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PB3,ORF2,hs0_human,marg,N-TerminusTruncated
42144,Q#3170 - >seq9817,specific,311990,1237,1255,0.000760397,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs0_human,marg,CompleteHit
42145,Q#3170 - >seq9817,superfamily,311990,1237,1255,0.000760397,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB3,ORF2,hs0_human,marg,CompleteHit
42146,Q#3170 - >seq9817,non-specific,238185,652,766,0.00153938,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42147,Q#3170 - >seq9817,non-specific,274009,292,431,0.00167023,42.7475,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42148,Q#3170 - >seq9817,superfamily,274009,292,431,0.00167023,42.7475,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42149,Q#3170 - >seq9817,non-specific,274009,309,454,0.00240256,41.9771,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42150,Q#3170 - >seq9817,non-specific,339261,108,231,0.00353431,38.4723,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB3,ORF2,hs0_human,marg,CompleteHit
42151,Q#3170 - >seq9817,non-specific,224117,281,429,0.00621355,40.8532,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42152,Q#3170 - >seq9817,superfamily,224117,281,429,0.00621355,40.8532,cl34174,Smc superfamily,C, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB3,ORF2,hs0_human,marg,C-TerminusTruncated
42153,Q#3170 - >seq9817,non-specific,223496,318,496,0.00627357,40.5139,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42154,Q#3170 - >seq9817,superfamily,223496,318,496,0.00627357,40.5139,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB3.ORF2.hs0_human.marg.frame3,1909201640_L1PB3.RM_hs_1709082029.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB3,ORF2,hs0_human,marg,BothTerminiTruncated
42155,Q#3173 - >seq9820,non-specific,335182,149,244,9.42839e-31,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42156,Q#3173 - >seq9820,superfamily,335182,149,244,9.42839e-31,111.241,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42157,Q#3173 - >seq9820,non-specific,340205,247,310,1.7399499999999997e-27,101.64399999999999,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42158,Q#3173 - >seq9820,superfamily,340205,247,310,1.7399499999999997e-27,101.64399999999999,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Transposase22,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42159,Q#3173 - >seq9820,non-specific,340204,103,145,3.9562e-05,40.0836,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42160,Q#3173 - >seq9820,superfamily,340204,103,145,3.9562e-05,40.0836,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Trimerization,L1PB2,ORF1,hs5_gmonkey,pars,CompleteHit
42161,Q#3173 - >seq9820,non-specific,223571,57,115,0.000507677,41.4311,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42162,Q#3173 - >seq9820,superfamily,223571,57,115,0.000507677,41.4311,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_NotSeenBefore,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42163,Q#3173 - >seq9820,non-specific,224117,25,142,0.00133997,40.0828,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42164,Q#3173 - >seq9820,superfamily,224117,25,142,0.00133997,40.0828,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42165,Q#3173 - >seq9820,non-specific,274008,60,141,0.00164724,40.0399,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42166,Q#3173 - >seq9820,superfamily,274008,60,141,0.00164724,40.0399,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42167,Q#3173 - >seq9820,non-specific,314569,85,134,0.00184624,38.9368,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42168,Q#3173 - >seq9820,superfamily,327698,85,134,0.00184624,38.9368,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB2,ORF1,hs5_gmonkey,pars,BothTerminiTruncated
42169,Q#3173 - >seq9820,non-specific,336852,60,117,0.00938833,35.2533,pfam07889,DUF1664,N,cl06776,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
42170,Q#3173 - >seq9820,superfamily,336852,60,117,0.00938833,35.2533,cl06776,DUF1664 superfamily,N, - ,Protein of unknown function (DUF1664); The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.,L1PB2.ORF1.hs5_gmonkey.pars.frame2,1909201640_L1PB2.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Unusual,L1PB2,ORF1,hs5_gmonkey,pars,N-TerminusTruncated
42171,Q#3175 - >seq9822,specific,197310,9,236,3.926e-60,206.048,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42172,Q#3175 - >seq9822,superfamily,351117,9,236,3.926e-60,206.048,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42173,Q#3175 - >seq9822,specific,238827,510,773,1.59238e-54,189.424,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42174,Q#3175 - >seq9822,superfamily,295487,510,773,1.59238e-54,189.424,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42175,Q#3175 - >seq9822,non-specific,197306,9,236,1.14388e-46,167.658,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42176,Q#3175 - >seq9822,specific,333820,516,773,7.426329999999999e-31,120.09,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42177,Q#3175 - >seq9822,superfamily,333820,516,773,7.426329999999999e-31,120.09,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42178,Q#3175 - >seq9822,non-specific,197307,9,236,1.2137700000000001e-22,98.5141,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42179,Q#3175 - >seq9822,non-specific,223780,9,237,8.52707e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42180,Q#3175 - >seq9822,non-specific,197320,8,229,5.25188e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42181,Q#3175 - >seq9822,specific,335306,10,229,1.5261e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42182,Q#3175 - >seq9822,non-specific,197321,7,236,7.975909999999999e-17,81.4444,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42183,Q#3175 - >seq9822,non-specific,273186,9,237,1.3463e-13,71.9264,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42184,Q#3175 - >seq9822,non-specific,272954,9,236,1.45501e-13,72.0305,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42185,Q#3175 - >seq9822,non-specific,238828,516,725,8.728939999999999e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42186,Q#3175 - >seq9822,non-specific,197319,8,236,1.28195e-11,66.1461,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42187,Q#3175 - >seq9822,non-specific,197336,7,229,7.44913e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42188,Q#3175 - >seq9822,non-specific,339261,108,232,7.1019300000000005e-09,54.6507,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42189,Q#3175 - >seq9822,non-specific,197322,9,236,8.184670000000001e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42190,Q#3175 - >seq9822,non-specific,275209,467,795,4.2998199999999997e-08,56.6972,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42191,Q#3175 - >seq9822,superfamily,275209,467,795,4.2998199999999997e-08,56.6972,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42192,Q#3175 - >seq9822,non-specific,236970,9,237,2.37256e-07,53.3594,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42193,Q#3175 - >seq9822,non-specific,197311,37,236,1.46379e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,marg,CompleteHit
42194,Q#3175 - >seq9822,non-specific,238185,657,773,0.00010109399999999999,42.338,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42195,Q#3175 - >seq9822,specific,311990,1243,1261,0.00047313199999999997,38.422,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs0_human,marg,CompleteHit
42196,Q#3175 - >seq9822,superfamily,311990,1243,1261,0.00047313199999999997,38.422,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA12,ORF2,hs0_human,marg,CompleteHit
42197,Q#3175 - >seq9822,non-specific,197317,139,229,0.00271007,40.6632,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,marg,N-TerminusTruncated
42198,Q#3175 - >seq9822,specific,225881,406,740,0.00747937,39.8221,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42199,Q#3175 - >seq9822,superfamily,225881,406,740,0.00747937,39.8221,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs0_human,marg,CompleteHit
42200,Q#3177 - >seq9824,specific,238827,482,744,6.293199999999998e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42201,Q#3177 - >seq9824,superfamily,295487,482,744,6.293199999999998e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42202,Q#3177 - >seq9824,specific,333820,488,744,3.29087e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42203,Q#3177 - >seq9824,superfamily,333820,488,744,3.29087e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42204,Q#3177 - >seq9824,non-specific,238828,488,709,1.18338e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42205,Q#3177 - >seq9824,non-specific,275209,439,772,7.601300000000001e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42206,Q#3177 - >seq9824,superfamily,275209,439,772,7.601300000000001e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42207,Q#3177 - >seq9824,non-specific,238185,628,744,8.1941e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42208,Q#3177 - >seq9824,specific,311990,1210,1228,0.00185281,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42209,Q#3177 - >seq9824,superfamily,311990,1210,1228,0.00185281,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42210,Q#3177 - >seq9824,specific,225881,454,711,0.00201387,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42211,Q#3177 - >seq9824,superfamily,225881,454,711,0.00201387,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42212,Q#3178 - >seq9825,specific,197310,9,236,1.3762999999999997e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42213,Q#3178 - >seq9825,superfamily,351117,9,236,1.3762999999999997e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42214,Q#3178 - >seq9825,non-specific,197306,9,236,7.45756e-45,162.266,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42215,Q#3178 - >seq9825,non-specific,197307,9,236,2.7250999999999995e-24,103.13600000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42216,Q#3178 - >seq9825,non-specific,223780,9,224,1.5849400000000001e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42217,Q#3178 - >seq9825,non-specific,197320,9,221,7.929390000000001e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42218,Q#3178 - >seq9825,specific,335306,10,229,5.71104e-17,81.1373,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42219,Q#3178 - >seq9825,non-specific,197321,7,236,1.9793799999999998e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42220,Q#3178 - >seq9825,non-specific,272954,9,221,4.36101e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42221,Q#3178 - >seq9825,non-specific,273186,9,237,9.116010000000001e-14,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42222,Q#3178 - >seq9825,non-specific,197319,13,236,9.52692e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42223,Q#3178 - >seq9825,non-specific,197336,9,194,1.12884e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42224,Q#3178 - >seq9825,non-specific,197322,8,236,2.87495e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42225,Q#3178 - >seq9825,non-specific,236970,9,221,5.5897300000000004e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42226,Q#3178 - >seq9825,non-specific,339261,108,232,4.1943e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42227,Q#3178 - >seq9825,non-specific,197311,30,204,5.1986099999999993e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,pars,CompleteHit
42228,Q#3178 - >seq9825,non-specific,224117,266,389,0.00124894,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42229,Q#3178 - >seq9825,superfamily,224117,266,389,0.00124894,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42230,Q#3180 - >seq9827,specific,238827,482,744,6.293199999999998e-67,224.863,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42231,Q#3180 - >seq9827,superfamily,295487,482,744,6.293199999999998e-67,224.863,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42232,Q#3180 - >seq9827,specific,333820,488,744,3.29087e-35,132.416,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42233,Q#3180 - >seq9827,superfamily,333820,488,744,3.29087e-35,132.416,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42234,Q#3180 - >seq9827,non-specific,238828,488,709,1.18338e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42235,Q#3180 - >seq9827,non-specific,275209,439,772,7.601300000000001e-08,55.5416,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42236,Q#3180 - >seq9827,superfamily,275209,439,772,7.601300000000001e-08,55.5416,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42237,Q#3180 - >seq9827,non-specific,238185,628,744,8.1941e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42238,Q#3180 - >seq9827,specific,311990,1210,1228,0.00185281,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42239,Q#3180 - >seq9827,superfamily,311990,1210,1228,0.00185281,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42240,Q#3180 - >seq9827,specific,225881,454,711,0.00201387,41.7481,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,N-TerminusTruncated
42241,Q#3180 - >seq9827,superfamily,225881,454,711,0.00201387,41.7481,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.marg.frame2,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA14,ORF2,hs4_gibbon,marg,N-TerminusTruncated
42242,Q#3181 - >seq9828,specific,197310,9,236,1.3762999999999997e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42243,Q#3181 - >seq9828,superfamily,351117,9,236,1.3762999999999997e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42244,Q#3181 - >seq9828,non-specific,197306,9,236,7.45756e-45,162.266,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42245,Q#3181 - >seq9828,non-specific,197307,9,236,2.7250999999999995e-24,103.13600000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42246,Q#3181 - >seq9828,non-specific,223780,9,224,1.5849400000000001e-21,95.3579,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42247,Q#3181 - >seq9828,non-specific,197320,9,221,7.929390000000001e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42248,Q#3181 - >seq9828,specific,335306,10,229,5.71104e-17,81.1373,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42249,Q#3181 - >seq9828,non-specific,197321,7,236,1.9793799999999998e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42250,Q#3181 - >seq9828,non-specific,272954,9,221,4.36101e-14,73.1861,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42251,Q#3181 - >seq9828,non-specific,273186,9,237,9.116010000000001e-14,72.3116,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42252,Q#3181 - >seq9828,non-specific,197319,13,236,9.52692e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42253,Q#3181 - >seq9828,non-specific,197336,9,194,1.12884e-09,60.3187,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42254,Q#3181 - >seq9828,non-specific,197322,8,236,2.87495e-09,59.6382,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42255,Q#3181 - >seq9828,non-specific,236970,9,221,5.5897300000000004e-08,55.2854,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42256,Q#3181 - >seq9828,non-specific,339261,108,232,4.1943e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42257,Q#3181 - >seq9828,non-specific,197311,30,204,5.1986099999999993e-05,45.3605,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs4_gibbon,marg,CompleteHit
42258,Q#3181 - >seq9828,non-specific,224117,266,389,0.00124894,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42259,Q#3181 - >seq9828,superfamily,224117,266,389,0.00124894,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA14.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42260,Q#3184 - >seq9831,specific,238827,510,772,6.052329999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42261,Q#3184 - >seq9831,superfamily,295487,510,772,6.052329999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42262,Q#3184 - >seq9831,non-specific,238827,510,772,6.052329999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42263,Q#3184 - >seq9831,specific,197310,9,236,5.44181e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42264,Q#3184 - >seq9831,superfamily,351117,9,236,5.44181e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42265,Q#3184 - >seq9831,non-specific,197310,9,236,5.44181e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42266,Q#3184 - >seq9831,non-specific,197306,9,236,4.98581e-44,159.954,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42267,Q#3184 - >seq9831,non-specific,197306,9,236,4.98581e-44,159.954,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42268,Q#3184 - >seq9831,specific,333820,516,772,8.938539999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42269,Q#3184 - >seq9831,superfamily,333820,516,772,8.938539999999999e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42270,Q#3184 - >seq9831,non-specific,333820,516,772,8.938539999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42271,Q#3184 - >seq9831,non-specific,197307,9,236,5.83429e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42272,Q#3184 - >seq9831,non-specific,197307,9,236,5.83429e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42273,Q#3184 - >seq9831,non-specific,223780,9,237,6.16439e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42274,Q#3184 - >seq9831,non-specific,223780,9,237,6.16439e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42275,Q#3184 - >seq9831,non-specific,197320,9,229,1.1746100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42276,Q#3184 - >seq9831,non-specific,197320,9,229,1.1746100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42277,Q#3184 - >seq9831,specific,335306,10,229,2.64007e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42278,Q#3184 - >seq9831,non-specific,335306,10,229,2.64007e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42279,Q#3184 - >seq9831,non-specific,197321,7,236,1.89576e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42280,Q#3184 - >seq9831,non-specific,197321,7,236,1.89576e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42281,Q#3184 - >seq9831,non-specific,273186,9,237,1.32743e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42282,Q#3184 - >seq9831,non-specific,273186,9,237,1.32743e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42283,Q#3184 - >seq9831,non-specific,272954,9,236,1.86554e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42284,Q#3184 - >seq9831,non-specific,272954,9,236,1.86554e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42285,Q#3184 - >seq9831,non-specific,197319,13,236,1.47191e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42286,Q#3184 - >seq9831,non-specific,197319,13,236,1.47191e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42287,Q#3184 - >seq9831,non-specific,197322,8,236,6.56834e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42288,Q#3184 - >seq9831,non-specific,197322,8,236,6.56834e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42289,Q#3184 - >seq9831,non-specific,238828,516,737,1.51777e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42290,Q#3184 - >seq9831,non-specific,238828,516,737,1.51777e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42291,Q#3184 - >seq9831,non-specific,197336,9,194,7.43575e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42292,Q#3184 - >seq9831,non-specific,197336,9,194,7.43575e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42293,Q#3184 - >seq9831,non-specific,275209,467,800,1.66566e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42294,Q#3184 - >seq9831,superfamily,275209,467,800,1.66566e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42295,Q#3184 - >seq9831,non-specific,275209,467,800,1.66566e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42296,Q#3184 - >seq9831,non-specific,339261,108,232,5.98421e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42297,Q#3184 - >seq9831,non-specific,339261,108,232,5.98421e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42298,Q#3184 - >seq9831,non-specific,236970,9,237,8.241589999999998e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42299,Q#3184 - >seq9831,non-specific,236970,9,237,8.241589999999998e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42300,Q#3184 - >seq9831,non-specific,197311,30,236,3.38502e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42301,Q#3184 - >seq9831,non-specific,197311,30,236,3.38502e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42302,Q#3184 - >seq9831,non-specific,238185,656,772,6.70251e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42303,Q#3184 - >seq9831,non-specific,238185,656,772,6.70251e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42304,Q#3184 - >seq9831,non-specific,235175,294,469,0.00063831,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42305,Q#3184 - >seq9831,superfamily,235175,294,469,0.00063831,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42306,Q#3184 - >seq9831,non-specific,235175,294,469,0.00063831,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42307,Q#3184 - >seq9831,non-specific,224117,266,391,0.0013741,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42308,Q#3184 - >seq9831,superfamily,224117,266,391,0.0013741,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42309,Q#3184 - >seq9831,non-specific,224117,266,391,0.0013741,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,pars,BothTerminiTruncated
42310,Q#3184 - >seq9831,specific,311990,1241,1259,0.004157500000000001,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42311,Q#3184 - >seq9831,superfamily,311990,1241,1259,0.004157500000000001,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42312,Q#3184 - >seq9831,non-specific,311990,1241,1259,0.004157500000000001,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,pars,CompleteHit
42313,Q#3187 - >seq9834,specific,238827,510,772,6.052329999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42314,Q#3187 - >seq9834,superfamily,295487,510,772,6.052329999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42315,Q#3187 - >seq9834,non-specific,238827,510,772,6.052329999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42316,Q#3187 - >seq9834,specific,197310,9,236,5.44181e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42317,Q#3187 - >seq9834,superfamily,351117,9,236,5.44181e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42318,Q#3187 - >seq9834,non-specific,197310,9,236,5.44181e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42319,Q#3187 - >seq9834,non-specific,197306,9,236,4.98581e-44,159.954,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42320,Q#3187 - >seq9834,non-specific,197306,9,236,4.98581e-44,159.954,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42321,Q#3187 - >seq9834,specific,333820,516,772,8.938539999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42322,Q#3187 - >seq9834,superfamily,333820,516,772,8.938539999999999e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42323,Q#3187 - >seq9834,non-specific,333820,516,772,8.938539999999999e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42324,Q#3187 - >seq9834,non-specific,197307,9,236,5.83429e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42325,Q#3187 - >seq9834,non-specific,197307,9,236,5.83429e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42326,Q#3187 - >seq9834,non-specific,223780,9,237,6.16439e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42327,Q#3187 - >seq9834,non-specific,223780,9,237,6.16439e-22,96.5135,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42328,Q#3187 - >seq9834,non-specific,197320,9,229,1.1746100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42329,Q#3187 - >seq9834,non-specific,197320,9,229,1.1746100000000001e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42330,Q#3187 - >seq9834,specific,335306,10,229,2.64007e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42331,Q#3187 - >seq9834,non-specific,335306,10,229,2.64007e-18,84.9893,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42332,Q#3187 - >seq9834,non-specific,197321,7,236,1.89576e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42333,Q#3187 - >seq9834,non-specific,197321,7,236,1.89576e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42334,Q#3187 - >seq9834,non-specific,273186,9,237,1.32743e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42335,Q#3187 - >seq9834,non-specific,273186,9,237,1.32743e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42336,Q#3187 - >seq9834,non-specific,272954,9,236,1.86554e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42337,Q#3187 - >seq9834,non-specific,272954,9,236,1.86554e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42338,Q#3187 - >seq9834,non-specific,197319,13,236,1.47191e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42339,Q#3187 - >seq9834,non-specific,197319,13,236,1.47191e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42340,Q#3187 - >seq9834,non-specific,197322,8,236,6.56834e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42341,Q#3187 - >seq9834,non-specific,197322,8,236,6.56834e-13,70.809,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42342,Q#3187 - >seq9834,non-specific,238828,516,737,1.51777e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42343,Q#3187 - >seq9834,non-specific,238828,516,737,1.51777e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42344,Q#3187 - >seq9834,non-specific,197336,9,194,7.43575e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42345,Q#3187 - >seq9834,non-specific,197336,9,194,7.43575e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42346,Q#3187 - >seq9834,non-specific,275209,467,800,1.66566e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42347,Q#3187 - >seq9834,superfamily,275209,467,800,1.66566e-08,57.8528,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42348,Q#3187 - >seq9834,non-specific,275209,467,800,1.66566e-08,57.8528,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42349,Q#3187 - >seq9834,non-specific,339261,108,232,5.98421e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42350,Q#3187 - >seq9834,non-specific,339261,108,232,5.98421e-08,52.3395,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42351,Q#3187 - >seq9834,non-specific,236970,9,237,8.241589999999998e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42352,Q#3187 - >seq9834,non-specific,236970,9,237,8.241589999999998e-08,54.9002,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42353,Q#3187 - >seq9834,non-specific,197311,30,236,3.38502e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42354,Q#3187 - >seq9834,non-specific,197311,30,236,3.38502e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42355,Q#3187 - >seq9834,non-specific,238185,656,772,6.70251e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42356,Q#3187 - >seq9834,non-specific,238185,656,772,6.70251e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42357,Q#3187 - >seq9834,non-specific,235175,294,469,0.00063831,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42358,Q#3187 - >seq9834,superfamily,235175,294,469,0.00063831,43.8992,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42359,Q#3187 - >seq9834,non-specific,235175,294,469,0.00063831,43.8992,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42360,Q#3187 - >seq9834,non-specific,224117,266,391,0.0013741,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42361,Q#3187 - >seq9834,superfamily,224117,266,391,0.0013741,42.7792,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42362,Q#3187 - >seq9834,non-specific,224117,266,391,0.0013741,42.7792,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs5_gmonkey,marg,BothTerminiTruncated
42363,Q#3187 - >seq9834,specific,311990,1241,1259,0.004157500000000001,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42364,Q#3187 - >seq9834,superfamily,311990,1241,1259,0.004157500000000001,35.7256,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42365,Q#3187 - >seq9834,non-specific,311990,1241,1259,0.004157500000000001,35.7256,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs5_gmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPC_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA14,ORF2,hs5_gmonkey,marg,CompleteHit
42366,Q#3188 - >seq9835,specific,311990,1150,1168,0.0017304000000000002,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs6_sqmonkey.pars.frame1,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42367,Q#3188 - >seq9835,superfamily,311990,1150,1168,0.0017304000000000002,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs6_sqmonkey.pars.frame1,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42368,Q#3189 - >seq9836,non-specific,238827,484,516,3.01502e-07,52.2934,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42369,Q#3189 - >seq9836,superfamily,295487,484,516,3.01502e-07,52.2934,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs6_sqmonkey.pars.frame2,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA14,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42370,Q#3190 - >seq9837,specific,197310,9,236,2.0260499999999997e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42371,Q#3190 - >seq9837,superfamily,351117,9,236,2.0260499999999997e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42372,Q#3190 - >seq9837,specific,238827,523,753,1.19387e-49,175.172,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42373,Q#3190 - >seq9837,superfamily,295487,523,753,1.19387e-49,175.172,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42374,Q#3190 - >seq9837,non-specific,197306,9,236,6.559039999999999e-44,159.569,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42375,Q#3190 - >seq9837,non-specific,333820,510,753,1.11055e-27,110.845,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42376,Q#3190 - >seq9837,superfamily,333820,510,753,1.11055e-27,110.845,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42377,Q#3190 - >seq9837,non-specific,197307,9,236,2.8636500000000006e-25,105.833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42378,Q#3190 - >seq9837,non-specific,223780,9,237,9.389650000000002e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42379,Q#3190 - >seq9837,non-specific,197320,9,229,1.46834e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42380,Q#3190 - >seq9837,specific,335306,10,229,4.75162e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42381,Q#3190 - >seq9837,non-specific,197321,7,236,1.8493500000000002e-16,80.2888,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42382,Q#3190 - >seq9837,non-specific,273186,9,237,5.77246e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42383,Q#3190 - >seq9837,non-specific,272954,9,236,1.1599200000000001e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42384,Q#3190 - >seq9837,non-specific,197319,13,236,8.49723e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42385,Q#3190 - >seq9837,non-specific,238828,563,718,9.08826e-12,66.0704,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
42386,Q#3190 - >seq9837,non-specific,197322,8,236,1.0482999999999999e-11,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42387,Q#3190 - >seq9837,non-specific,197336,9,194,3.7812e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42388,Q#3190 - >seq9837,non-specific,339261,108,232,2.93056e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42389,Q#3190 - >seq9837,non-specific,275209,565,777,5.68423e-07,52.8452,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
42390,Q#3190 - >seq9837,superfamily,275209,565,777,5.68423e-07,52.8452,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
42391,Q#3190 - >seq9837,non-specific,236970,9,237,7.65681e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42392,Q#3190 - >seq9837,non-specific,197311,30,236,2.8576400000000002e-06,49.2125,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42393,Q#3190 - >seq9837,non-specific,238185,637,753,3.3956199999999994e-06,46.5752,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,pars,CompleteHit
42394,Q#3190 - >seq9837,non-specific,224117,266,382,0.00356992,41.6236,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
42395,Q#3190 - >seq9837,superfamily,224117,266,382,0.00356992,41.6236,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
42396,Q#3190 - >seq9837,non-specific,197318,9,148,0.00570601,39.5871,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA14.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
42397,Q#3191 - >seq9838,specific,311990,1155,1173,0.00221988,36.1108,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs6_sqmonkey.marg.frame1,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42398,Q#3191 - >seq9838,superfamily,311990,1155,1173,0.00221988,36.1108,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA14.ORF2.hs6_sqmonkey.marg.frame1,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,DUF1725,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42399,Q#3193 - >seq9840,specific,197310,9,236,2.8514299999999994e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42400,Q#3193 - >seq9840,superfamily,351117,9,236,2.8514299999999994e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42401,Q#3193 - >seq9840,specific,238827,510,772,2.1520100000000004e-57,197.514,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42402,Q#3193 - >seq9840,superfamily,295487,510,772,2.1520100000000004e-57,197.514,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42403,Q#3193 - >seq9840,non-specific,197306,9,236,1.3291899999999998e-43,158.799,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42404,Q#3193 - >seq9840,specific,333820,516,772,1.4839799999999996e-32,124.712,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42405,Q#3193 - >seq9840,superfamily,333820,516,772,1.4839799999999996e-32,124.712,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42406,Q#3193 - >seq9840,non-specific,197307,9,236,4.76496e-25,105.448,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42407,Q#3193 - >seq9840,non-specific,223780,9,237,9.60592e-22,96.1283,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42408,Q#3193 - >seq9840,non-specific,197320,9,229,1.50191e-19,89.4965,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42409,Q#3193 - >seq9840,specific,335306,10,229,4.857359999999999e-17,81.5225,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42410,Q#3193 - >seq9840,non-specific,197321,7,236,2.75762e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42411,Q#3193 - >seq9840,non-specific,273186,9,237,5.9037500000000005e-15,75.7784,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42412,Q#3193 - >seq9840,non-specific,272954,9,236,1.91437e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42413,Q#3193 - >seq9840,non-specific,197319,13,236,1.856e-13,71.5389,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42414,Q#3193 - >seq9840,non-specific,197322,8,236,1.07277e-11,67.3422,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42415,Q#3193 - >seq9840,non-specific,238828,582,737,1.5584e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
42416,Q#3193 - >seq9840,non-specific,197336,9,194,3.86628e-10,61.4743,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42417,Q#3193 - >seq9840,non-specific,275209,467,800,4.92469e-08,56.312,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42418,Q#3193 - >seq9840,superfamily,275209,467,800,4.92469e-08,56.312,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42419,Q#3193 - >seq9840,non-specific,339261,108,232,3.2952300000000003e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42420,Q#3193 - >seq9840,non-specific,236970,9,237,1.03671e-06,51.4334,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42421,Q#3193 - >seq9840,non-specific,197311,30,236,4.2372199999999996e-06,48.8273,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42422,Q#3193 - >seq9840,non-specific,238185,656,772,5.017709999999999e-06,46.19,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA14,ORF2,hs6_sqmonkey,marg,CompleteHit
42423,Q#3193 - >seq9840,non-specific,235175,294,469,4.743979999999999e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42424,Q#3193 - >seq9840,superfamily,235175,294,469,4.743979999999999e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42425,Q#3193 - >seq9840,non-specific,224117,266,391,0.00264687,42.0088,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42426,Q#3193 - >seq9840,superfamily,224117,266,391,0.00264687,42.0088,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
42427,Q#3193 - >seq9840,non-specific,197318,9,148,0.00678764,39.5871,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA14,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42428,Q#3193 - >seq9840,non-specific,274009,307,458,0.00906668,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42429,Q#3193 - >seq9840,superfamily,274009,307,458,0.00906668,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA14.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA14.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA14,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
42430,Q#3194 - >seq9841,specific,238827,490,724,9.045030000000001e-51,178.25400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42431,Q#3194 - >seq9841,superfamily,295487,490,724,9.045030000000001e-51,178.25400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42432,Q#3194 - >seq9841,specific,333820,488,705,8.62059e-29,113.927,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42433,Q#3194 - >seq9841,superfamily,333820,488,705,8.62059e-29,113.927,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42434,Q#3194 - >seq9841,non-specific,238828,509,696,2.72408e-13,70.3076,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42435,Q#3194 - >seq9841,non-specific,275209,546,696,8.85891e-07,52.46,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,BothTerminiTruncated
42436,Q#3194 - >seq9841,superfamily,275209,546,696,8.85891e-07,52.46,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,BothTerminiTruncated
42437,Q#3194 - >seq9841,non-specific,238185,615,700,0.000546859,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs3_orang.pars.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42438,Q#3195 - >seq9842,specific,197310,9,236,4.378809999999999e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42439,Q#3195 - >seq9842,superfamily,351117,9,236,4.378809999999999e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42440,Q#3195 - >seq9842,non-specific,197306,9,236,6.112619999999999e-39,145.317,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42441,Q#3195 - >seq9842,non-specific,197307,9,236,1.7724200000000003e-21,95.0473,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42442,Q#3195 - >seq9842,non-specific,197320,9,229,4.43539e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42443,Q#3195 - >seq9842,non-specific,197321,7,236,8.54226e-20,89.9188,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42444,Q#3195 - >seq9842,non-specific,223780,9,237,8.841089999999999e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42445,Q#3195 - >seq9842,non-specific,273186,9,237,2.68523e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42446,Q#3195 - >seq9842,specific,335306,10,229,3.91164e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42447,Q#3195 - >seq9842,non-specific,197319,13,236,2.93633e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42448,Q#3195 - >seq9842,non-specific,272954,9,194,1.0276800000000001e-13,72.4157,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,C-TerminusTruncated
42449,Q#3195 - >seq9842,non-specific,197322,8,236,6.33699e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42450,Q#3195 - >seq9842,non-specific,236970,9,194,7.3238900000000004e-09,57.9818,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs3_orang,pars,C-TerminusTruncated
42451,Q#3195 - >seq9842,non-specific,197336,9,194,7.663529999999999e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42452,Q#3195 - >seq9842,non-specific,339261,108,232,1.74016e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42453,Q#3195 - >seq9842,non-specific,197311,7,236,0.000248673,43.4345,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs3_orang,pars,CompleteHit
42454,Q#3195 - >seq9842,non-specific,235175,291,469,0.000452953,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA15-16,ORF2,hs3_orang,pars,BothTerminiTruncated
42455,Q#3195 - >seq9842,superfamily,235175,291,469,0.000452953,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA15-16,ORF2,hs3_orang,pars,BothTerminiTruncated
42456,Q#3195 - >seq9842,non-specific,224117,299,467,0.00486781,41.2384,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1PA15-16,ORF2,hs3_orang,pars,N-TerminusTruncated
42457,Q#3195 - >seq9842,superfamily,224117,299,467,0.00486781,41.2384,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs3_orang.pars.frame2,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_ChromSeg,L1PA15-16,ORF2,hs3_orang,pars,N-TerminusTruncated
42458,Q#3197 - >seq9844,specific,238827,474,715,5.70485e-54,187.88400000000001,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42459,Q#3197 - >seq9844,superfamily,295487,474,715,5.70485e-54,187.88400000000001,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42460,Q#3197 - >seq9844,specific,333820,469,715,2.7838599999999995e-28,112.771,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42461,Q#3197 - >seq9844,superfamily,333820,469,715,2.7838599999999995e-28,112.771,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42462,Q#3197 - >seq9844,non-specific,238828,493,680,5.79139e-13,69.5372,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42463,Q#3197 - >seq9844,non-specific,275209,530,739,6.4146199999999995e-09,59.0084,TIGR04416,group_II_RT_mat,N,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,N-TerminusTruncated
42464,Q#3197 - >seq9844,superfamily,275209,530,739,6.4146199999999995e-09,59.0084,cl37441,group_II_RT_mat superfamily,N, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,N-TerminusTruncated
42465,Q#3197 - >seq9844,non-specific,238185,599,684,0.00146145,38.8712,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs3_orang.marg.frame1,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42466,Q#3200 - >seq9847,specific,197310,9,236,5.26344e-60,205.66299999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42467,Q#3200 - >seq9847,superfamily,351117,9,236,5.26344e-60,205.66299999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42468,Q#3200 - >seq9847,non-specific,197306,9,236,3.7170199999999997e-47,168.81400000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42469,Q#3200 - >seq9847,non-specific,197307,9,236,3.5869e-24,102.751,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42470,Q#3200 - >seq9847,non-specific,223780,9,237,7.80746e-23,99.2099,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42471,Q#3200 - >seq9847,non-specific,197320,8,229,3.15217e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42472,Q#3200 - >seq9847,non-specific,197321,7,236,5.9547599999999996e-18,84.52600000000001,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42473,Q#3200 - >seq9847,specific,335306,10,229,1.42049e-17,82.6781,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42474,Q#3200 - >seq9847,non-specific,272954,9,236,2.09549e-14,74.3417,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42475,Q#3200 - >seq9847,non-specific,273186,9,237,3.4026099999999996e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42476,Q#3200 - >seq9847,non-specific,197319,8,236,2.61561e-13,71.1537,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42477,Q#3200 - >seq9847,non-specific,197336,7,229,6.92736e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42478,Q#3200 - >seq9847,non-specific,197322,9,236,7.60024e-09,58.4826,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42479,Q#3200 - >seq9847,non-specific,339261,108,232,3.73305e-08,52.7247,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42480,Q#3200 - >seq9847,non-specific,236970,9,237,1.6201499999999999e-07,53.7446,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42481,Q#3200 - >seq9847,non-specific,197311,37,236,1.22128e-05,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs0_human,pars,CompleteHit
42482,Q#3200 - >seq9847,non-specific,197317,139,229,0.00252655,40.6632,cd09083,EEP-1,N,cl00490,"Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1PA12.ORF2.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs0_human,pars,N-TerminusTruncated
42483,Q#3201 - >seq9848,specific,238827,484,747,2.01553e-56,194.817,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42484,Q#3201 - >seq9848,superfamily,295487,484,747,2.01553e-56,194.817,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42485,Q#3201 - >seq9848,specific,333820,490,747,5.559249999999999e-32,123.171,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42486,Q#3201 - >seq9848,superfamily,333820,490,747,5.559249999999999e-32,123.171,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42487,Q#3201 - >seq9848,non-specific,238828,490,699,1.1883e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42488,Q#3201 - >seq9848,non-specific,275209,441,769,2.0959e-08,57.4676,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42489,Q#3201 - >seq9848,superfamily,275209,441,769,2.0959e-08,57.4676,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42490,Q#3201 - >seq9848,non-specific,238185,631,747,2.68121e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42491,Q#3201 - >seq9848,specific,225881,380,714,0.00043716699999999997,43.6741,COG3344,YkfC, - ,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42492,Q#3201 - >seq9848,superfamily,225881,380,714,0.00043716699999999997,43.6741,cl34590,YkfC superfamily, - , - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,RT,L1PA12,ORF2,hs0_human,pars,CompleteHit
42493,Q#3201 - >seq9848,non-specific,224117,157,441,0.00272351,42.0088,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA12,ORF2,hs0_human,pars,N-TerminusTruncated
42494,Q#3201 - >seq9848,superfamily,224117,157,441,0.00272351,42.0088,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ATPase_ChromSeg,L1PA12,ORF2,hs0_human,pars,N-TerminusTruncated
42495,Q#3201 - >seq9848,non-specific,235175,268,438,0.009063799999999999,40.0472,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA12,ORF2,hs0_human,pars,BothTerminiTruncated
42496,Q#3201 - >seq9848,superfamily,235175,268,438,0.009063799999999999,40.0472,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,ChromSeg,L1PA12,ORF2,hs0_human,pars,BothTerminiTruncated
42497,Q#3203 - >seq9850,specific,238827,503,745,1.8119e-58,200.21,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42498,Q#3203 - >seq9850,superfamily,295487,503,745,1.8119e-58,200.21,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42499,Q#3203 - >seq9850,specific,333820,509,732,3.63177e-31,120.86,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42500,Q#3203 - >seq9850,superfamily,333820,509,732,3.63177e-31,120.86,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42501,Q#3203 - >seq9850,non-specific,238828,509,729,1.6669599999999998e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42502,Q#3203 - >seq9850,non-specific,275209,460,729,3.4250599999999998e-09,59.7788,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
42503,Q#3203 - >seq9850,superfamily,275209,460,729,3.4250599999999998e-09,59.7788,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
42504,Q#3203 - >seq9850,non-specific,235175,300,457,0.00290235,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42505,Q#3203 - >seq9850,superfamily,235175,300,457,0.00290235,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ChromSeg,L1M1,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42506,Q#3203 - >seq9850,non-specific,238185,650,733,0.00303118,38.1008,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42507,Q#3203 - >seq9850,non-specific,334125,212,404,0.00583717,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
42508,Q#3203 - >seq9850,superfamily,334125,212,404,0.00583717,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1M1.ORF2.hs2_gorilla.pars.frame2,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_Chrom,L1M1,ORF2,hs2_gorilla,pars,N-TerminusTruncated
42509,Q#3204 - >seq9851,specific,197310,9,227,5.251299999999999e-56,193.722,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42510,Q#3204 - >seq9851,superfamily,351117,9,227,5.251299999999999e-56,193.722,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42511,Q#3204 - >seq9851,non-specific,197306,9,210,1.01529e-32,127.212,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42512,Q#3204 - >seq9851,non-specific,197320,7,207,2.1574000000000005e-22,97.5857,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42513,Q#3204 - >seq9851,non-specific,223780,7,206,3.63475e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42514,Q#3204 - >seq9851,non-specific,197307,9,207,6.74323e-19,87.3433,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42515,Q#3204 - >seq9851,specific,335306,10,209,1.00009e-17,83.0633,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42516,Q#3204 - >seq9851,non-specific,272954,7,206,1.6352e-17,83.2012,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42517,Q#3204 - >seq9851,non-specific,197321,7,206,2.44916e-16,79.9036,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42518,Q#3204 - >seq9851,non-specific,273186,7,207,1.25571e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42519,Q#3204 - >seq9851,non-specific,197336,7,203,8.04113e-13,69.5635,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42520,Q#3204 - >seq9851,non-specific,197319,7,217,4.29497e-11,64.2201,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42521,Q#3204 - >seq9851,non-specific,197311,7,203,4.1502300000000006e-08,54.6053,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,pars,CompleteHit
42522,Q#3204 - >seq9851,non-specific,339261,108,204,0.000298265,41.5539,pfam14529,Exo_endo_phos_2,C,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs2_gorilla.pars.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs2_gorilla,pars,C-TerminusTruncated
42523,Q#3207 - >seq9854,specific,197310,9,236,3.9714699999999996e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42524,Q#3207 - >seq9854,superfamily,351117,9,236,3.9714699999999996e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42525,Q#3207 - >seq9854,specific,238827,509,770,4.093159999999999e-62,210.61,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42526,Q#3207 - >seq9854,superfamily,295487,509,770,4.093159999999999e-62,210.61,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42527,Q#3207 - >seq9854,non-specific,197306,9,236,1.33583e-34,132.605,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42528,Q#3207 - >seq9854,specific,333820,515,770,2.43882e-30,118.54899999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42529,Q#3207 - >seq9854,superfamily,333820,515,770,2.43882e-30,118.54899999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42530,Q#3207 - >seq9854,non-specific,197320,7,229,2.87241e-23,100.28200000000001,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42531,Q#3207 - >seq9854,non-specific,223780,7,229,2.9809299999999998e-21,94.5875,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42532,Q#3207 - >seq9854,specific,335306,10,229,8.74646e-20,89.2265,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42533,Q#3207 - >seq9854,non-specific,197307,9,236,5.582260000000001e-19,87.7285,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42534,Q#3207 - >seq9854,non-specific,197321,7,236,2.45259e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42535,Q#3207 - >seq9854,non-specific,272954,7,207,3.3447300000000004e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42536,Q#3207 - >seq9854,non-specific,273186,7,237,2.69254e-15,76.934,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42537,Q#3207 - >seq9854,non-specific,197319,7,236,8.565700000000001e-14,72.3093,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42538,Q#3207 - >seq9854,non-specific,197336,7,229,9.01722e-12,66.4819,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42539,Q#3207 - >seq9854,non-specific,238828,515,735,2.68301e-11,64.5296,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42540,Q#3207 - >seq9854,non-specific,275209,466,735,2.2667700000000002e-08,57.0824,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42541,Q#3207 - >seq9854,superfamily,275209,466,735,2.2667700000000002e-08,57.0824,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42542,Q#3207 - >seq9854,non-specific,197311,7,236,6.1497e-08,54.2201,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42543,Q#3207 - >seq9854,non-specific,339261,108,232,6.9735e-06,46.1763,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42544,Q#3207 - >seq9854,non-specific,238185,656,770,0.000180172,41.5676,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42545,Q#3207 - >seq9854,non-specific,197314,7,236,0.00150766,41.5603,cd09080,TDP2, - ,cl00490,"Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_DNARepair,L1M1,ORF2,hs2_gorilla,marg,CompleteHit
42546,Q#3207 - >seq9854,non-specific,235175,306,463,0.00293081,41.588,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42547,Q#3207 - >seq9854,superfamily,235175,306,463,0.00293081,41.588,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1M1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42548,Q#3207 - >seq9854,non-specific,274475,255,427,0.00776238,40.052,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1M1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42549,Q#3207 - >seq9854,superfamily,274475,255,427,0.00776238,40.052,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1M1.ORF2.hs2_gorilla.marg.frame3,1909201640_L1M1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1M1,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42550,Q#3209 - >seq9856,specific,238827,485,743,7.454369999999998e-64,215.618,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42551,Q#3209 - >seq9856,superfamily,295487,485,743,7.454369999999998e-64,215.618,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42552,Q#3209 - >seq9856,specific,333820,491,711,6.73421e-34,128.564,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42553,Q#3209 - >seq9856,superfamily,333820,491,711,6.73421e-34,128.564,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42554,Q#3209 - >seq9856,non-specific,238828,491,699,1.0862e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42555,Q#3209 - >seq9856,non-specific,275209,442,766,1.75706e-10,63.6308,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42556,Q#3209 - >seq9856,superfamily,275209,442,766,1.75706e-10,63.6308,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42557,Q#3209 - >seq9856,non-specific,238185,631,747,6.8328300000000004e-06,45.4196,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42558,Q#3209 - >seq9856,specific,225881,457,714,0.00205046,41.3629,COG3344,YkfC,N,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,N-TerminusTruncated
42559,Q#3209 - >seq9856,superfamily,225881,457,714,0.00205046,41.3629,cl34590,YkfC superfamily,N, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PA12.ORF2.hs1_chimp.pars.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA12,ORF2,hs1_chimp,pars,N-TerminusTruncated
42560,Q#3210 - >seq9857,specific,197310,9,236,1.35637e-60,206.81900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42561,Q#3210 - >seq9857,superfamily,351117,9,236,1.35637e-60,206.81900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42562,Q#3210 - >seq9857,non-specific,197306,9,236,5.267619999999999e-44,159.569,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42563,Q#3210 - >seq9857,non-specific,197307,9,236,1.0047000000000001e-23,101.21,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42564,Q#3210 - >seq9857,non-specific,223780,9,224,3.60957e-21,94.2023,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42565,Q#3210 - >seq9857,non-specific,197320,9,221,1.74069e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42566,Q#3210 - >seq9857,specific,335306,10,229,7.53681e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42567,Q#3210 - >seq9857,non-specific,197321,7,236,1.85893e-15,77.2072,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42568,Q#3210 - >seq9857,non-specific,273186,9,237,1.81507e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42569,Q#3210 - >seq9857,non-specific,272954,9,221,3.38045e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42570,Q#3210 - >seq9857,non-specific,197319,13,236,1.65027e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42571,Q#3210 - >seq9857,non-specific,197336,9,194,2.25049e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42572,Q#3210 - >seq9857,non-specific,197322,8,236,2.19936e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42573,Q#3210 - >seq9857,non-specific,236970,9,221,4.43495e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42574,Q#3210 - >seq9857,non-specific,339261,108,232,3.4540699999999997e-06,46.9467,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42575,Q#3210 - >seq9857,non-specific,197311,30,204,2.30462e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,pars,CompleteHit
42576,Q#3210 - >seq9857,non-specific,224117,263,398,0.00719686,40.468,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF2,hs1_chimp,pars,N-TerminusTruncated
42577,Q#3210 - >seq9857,superfamily,224117,263,398,0.00719686,40.468,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs1_chimp.pars.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF2,hs1_chimp,pars,N-TerminusTruncated
42578,Q#3212 - >seq9859,specific,311990,1185,1203,0.000533798,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs1_chimp.marg.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42579,Q#3212 - >seq9859,superfamily,311990,1185,1203,0.000533798,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs1_chimp.marg.frame2,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42580,Q#3213 - >seq9860,specific,311990,1145,1162,0.00010747899999999999,39.9628,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs0_human.pars.frame2,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA12,ORF2,hs0_human,pars,CompleteHit
42581,Q#3213 - >seq9860,superfamily,311990,1145,1162,0.00010747899999999999,39.9628,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs0_human.pars.frame2,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PA12,ORF2,hs0_human,pars,CompleteHit
42582,Q#3214 - >seq9861,specific,238827,510,768,1.2049999999999999e-61,209.84,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42583,Q#3214 - >seq9861,superfamily,295487,510,768,1.2049999999999999e-61,209.84,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42584,Q#3214 - >seq9861,specific,197310,9,236,1.2219599999999998e-59,204.50799999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42585,Q#3214 - >seq9861,superfamily,351117,9,236,1.2219599999999998e-59,204.50799999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42586,Q#3214 - >seq9861,non-specific,197306,9,236,1.36693e-43,158.799,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42587,Q#3214 - >seq9861,specific,333820,516,736,2.2222499999999996e-32,124.32700000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42588,Q#3214 - >seq9861,superfamily,333820,516,736,2.2222499999999996e-32,124.32700000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42589,Q#3214 - >seq9861,non-specific,197307,9,236,2.95275e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42590,Q#3214 - >seq9861,non-specific,223780,9,224,1.18432e-20,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42591,Q#3214 - >seq9861,non-specific,197320,9,221,2.0502500000000002e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42592,Q#3214 - >seq9861,specific,335306,10,229,8.83525e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42593,Q#3214 - >seq9861,non-specific,197321,7,236,2.81956e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42594,Q#3214 - >seq9861,non-specific,273186,9,237,3.81924e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42595,Q#3214 - >seq9861,non-specific,272954,9,221,8.414969999999999e-14,72.4157,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42596,Q#3214 - >seq9861,non-specific,197319,13,236,3.94298e-12,67.6869,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42597,Q#3214 - >seq9861,non-specific,238828,516,724,7.8358e-12,66.0704,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42598,Q#3214 - >seq9861,non-specific,197336,9,194,2.6433699999999996e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42599,Q#3214 - >seq9861,non-specific,275209,467,796,3.3595e-10,63.2456,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42600,Q#3214 - >seq9861,superfamily,275209,467,796,3.3595e-10,63.2456,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42601,Q#3214 - >seq9861,non-specific,197322,8,236,2.59407e-09,60.0234,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42602,Q#3214 - >seq9861,non-specific,236970,9,221,9.13159e-07,51.8186,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42603,Q#3214 - >seq9861,non-specific,339261,108,232,6.1833100000000004e-06,46.5615,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42604,Q#3214 - >seq9861,non-specific,197311,30,204,2.9228200000000002e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42605,Q#3214 - >seq9861,non-specific,238185,656,772,7.02006e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA12,ORF2,hs1_chimp,marg,CompleteHit
42606,Q#3214 - >seq9861,non-specific,235175,294,469,0.000908893,43.513999999999996,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs1_chimp,marg,BothTerminiTruncated
42607,Q#3214 - >seq9861,superfamily,235175,294,469,0.000908893,43.513999999999996,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs1_chimp,marg,BothTerminiTruncated
42608,Q#3214 - >seq9861,non-specific,224117,266,391,0.00112819,43.1644,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs1_chimp,marg,BothTerminiTruncated
42609,Q#3214 - >seq9861,superfamily,224117,266,391,0.00112819,43.1644,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs1_chimp.marg.frame3,1909201640_L1PA12.RM_HP_1707271643.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF2,hs1_chimp,marg,BothTerminiTruncated
42610,Q#3216 - >seq9863,specific,238827,507,765,1.1049899999999997e-64,218.31400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42611,Q#3216 - >seq9863,superfamily,295487,507,765,1.1049899999999997e-64,218.31400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42612,Q#3216 - >seq9863,specific,197310,9,236,6.221399999999999e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42613,Q#3216 - >seq9863,superfamily,351117,9,236,6.221399999999999e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42614,Q#3216 - >seq9863,non-specific,197306,9,236,9.88514e-44,159.184,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42615,Q#3216 - >seq9863,specific,333820,513,734,4.9711e-34,128.94899999999998,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42616,Q#3216 - >seq9863,superfamily,333820,513,734,4.9711e-34,128.94899999999998,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42617,Q#3216 - >seq9863,non-specific,197307,9,236,5.80651e-24,102.366,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42618,Q#3216 - >seq9863,non-specific,223780,9,224,2.0555900000000002e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42619,Q#3216 - >seq9863,non-specific,197320,9,221,6.10113e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42620,Q#3216 - >seq9863,specific,335306,10,229,5.9468e-17,81.1373,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42621,Q#3216 - >seq9863,non-specific,197321,7,236,1.23512e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42622,Q#3216 - >seq9863,non-specific,273186,9,237,2.04232e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42623,Q#3216 - >seq9863,non-specific,272954,9,221,3.46311e-14,73.5713,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42624,Q#3216 - >seq9863,non-specific,197319,13,236,9.47097e-13,69.2277,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42625,Q#3216 - >seq9863,non-specific,238828,579,734,1.71612e-11,65.3,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,N-TerminusTruncated
42626,Q#3216 - >seq9863,non-specific,197336,9,194,2.55289e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42627,Q#3216 - >seq9863,non-specific,197322,8,236,7.87659e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42628,Q#3216 - >seq9863,non-specific,275209,464,734,8.82575e-08,55.5416,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,C-TerminusTruncated
42629,Q#3216 - >seq9863,superfamily,275209,464,734,8.82575e-08,55.5416,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,C-TerminusTruncated
42630,Q#3216 - >seq9863,non-specific,236970,9,221,4.23113e-07,52.589,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42631,Q#3216 - >seq9863,non-specific,339261,108,232,1.4876199999999998e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42632,Q#3216 - >seq9863,non-specific,197311,30,204,2.6003400000000002e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42633,Q#3216 - >seq9863,non-specific,238185,653,769,5.3836400000000005e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42634,Q#3216 - >seq9863,non-specific,224117,266,388,0.000119802,46.246,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42635,Q#3216 - >seq9863,superfamily,224117,266,388,0.000119802,46.246,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42636,Q#3216 - >seq9863,non-specific,235175,263,407,0.00189884,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42637,Q#3216 - >seq9863,superfamily,235175,263,407,0.00189884,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs2_gorilla.pars.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,pars,BothTerminiTruncated
42638,Q#3218 - >seq9865,specific,238827,487,745,4.36268e-65,219.47,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42639,Q#3218 - >seq9865,superfamily,295487,487,745,4.36268e-65,219.47,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42640,Q#3218 - >seq9865,specific,333820,493,714,4.746009999999999e-34,129.334,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42641,Q#3218 - >seq9865,superfamily,333820,493,714,4.746009999999999e-34,129.334,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42642,Q#3218 - >seq9865,non-specific,238828,559,714,2.25951e-11,64.9148,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,N-TerminusTruncated
42643,Q#3218 - >seq9865,non-specific,275209,444,714,2.88714e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42644,Q#3218 - >seq9865,superfamily,275209,444,714,2.88714e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42645,Q#3218 - >seq9865,non-specific,238185,633,749,4.84179e-05,43.1084,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42646,Q#3218 - >seq9865,specific,311990,1213,1231,0.000221752,39.1924,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42647,Q#3218 - >seq9865,superfamily,311990,1213,1231,0.000221752,39.1924,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs2_gorilla.marg.frame2,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,DUF1725,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42648,Q#3219 - >seq9866,specific,197310,9,236,1.0264499999999998e-60,207.58900000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42649,Q#3219 - >seq9866,superfamily,351117,9,236,1.0264499999999998e-60,207.58900000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42650,Q#3219 - >seq9866,non-specific,197306,9,236,1.2714600000000001e-44,161.495,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42651,Q#3219 - >seq9866,non-specific,197307,9,236,5.304159999999999e-25,105.06200000000001,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42652,Q#3219 - >seq9866,non-specific,223780,9,224,1.9595000000000003e-21,94.9727,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42653,Q#3219 - >seq9866,non-specific,197320,9,221,5.81759e-21,93.3485,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42654,Q#3219 - >seq9866,specific,335306,10,229,5.67814e-17,81.1373,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42655,Q#3219 - >seq9866,non-specific,197321,7,236,4.1037e-16,79.1332,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42656,Q#3219 - >seq9866,non-specific,272954,9,221,1.25707e-14,75.1121,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42657,Q#3219 - >seq9866,non-specific,273186,9,237,1.9481e-14,74.2376,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42658,Q#3219 - >seq9866,non-specific,197319,13,236,1.1748800000000002e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42659,Q#3219 - >seq9866,non-specific,197336,9,194,2.43622e-10,62.2447,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42660,Q#3219 - >seq9866,non-specific,197322,8,236,7.506730000000001e-10,61.5642,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42661,Q#3219 - >seq9866,non-specific,236970,9,221,1.4726800000000002e-07,54.1298,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42662,Q#3219 - >seq9866,non-specific,339261,108,232,1.6641300000000003e-05,45.0207,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42663,Q#3219 - >seq9866,non-specific,197311,30,204,2.4862399999999998e-05,46.5161,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF2,hs2_gorilla,marg,CompleteHit
42664,Q#3219 - >seq9866,non-specific,235175,263,394,0.000191366,45.44,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42665,Q#3219 - >seq9866,superfamily,235175,263,394,0.000191366,45.44,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42666,Q#3219 - >seq9866,non-specific,224117,266,386,0.00021915400000000002,45.4756,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA12,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42667,Q#3219 - >seq9866,superfamily,224117,266,386,0.00021915400000000002,45.4756,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA12,ORF2,hs2_gorilla,marg,BothTerminiTruncated
42668,Q#3219 - >seq9866,non-specific,224259,301,400,0.00359354,40.4348,COG1340,COG1340,C,cl34231,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42669,Q#3219 - >seq9866,superfamily,224259,301,400,0.00359354,40.4348,cl34231,COG1340 superfamily,C, - ,"Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Uncharacterized archaeal coiled-coil protein [Function unknown].",L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42670,Q#3219 - >seq9866,non-specific,234767,158,389,0.00366338,41.361999999999995,PRK00448,polC,C,cl35100,DNA polymerase III PolC; Validated,L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42671,Q#3219 - >seq9866,superfamily,234767,158,389,0.00366338,41.361999999999995,cl35100,polC superfamily,C, - ,DNA polymerase III PolC; Validated,L1PA12.ORF2.hs2_gorilla.marg.frame3,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_Chrom,L1PA12,ORF2,hs2_gorilla,marg,C-TerminusTruncated
42672,Q#3220 - >seq9867,non-specific,335182,147,236,1.68633e-35,123.95200000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs0_human,pars,CompleteHit
42673,Q#3220 - >seq9867,superfamily,335182,147,236,1.68633e-35,123.95200000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs0_human,pars,CompleteHit
42674,Q#3220 - >seq9867,non-specific,340205,239,302,3.2950999999999997e-29,106.266,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs0_human,pars,CompleteHit
42675,Q#3220 - >seq9867,superfamily,340205,239,302,3.2950999999999997e-29,106.266,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs0_human.pars.frame1,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Transposase22,L1PA12,ORF1,hs0_human,pars,CompleteHit
42676,Q#3222 - >seq9869,non-specific,313299,64,128,0.00298141,36.025999999999996,pfam10046,BLOC1_2,N,cl10824,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PA12,ORF1,hs0_human,pars,N-TerminusTruncated
42677,Q#3222 - >seq9869,superfamily,313299,64,128,0.00298141,36.025999999999996,cl10824,BLOC1_2 superfamily,N, - ,"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.",L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA12,ORF1,hs0_human,pars,N-TerminusTruncated
42678,Q#3222 - >seq9869,non-specific,222878,51,123,0.00595388,38.0717,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs0_human,pars,BothTerminiTruncated
42679,Q#3222 - >seq9869,superfamily,222878,51,123,0.00595388,38.0717,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA12,ORF1,hs0_human,pars,BothTerminiTruncated
42680,Q#3222 - >seq9869,non-specific,224117,33,122,0.00741591,37.7716,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA12,ORF1,hs0_human,pars,BothTerminiTruncated
42681,Q#3222 - >seq9869,superfamily,224117,33,122,0.00741591,37.7716,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA12.ORF1.hs0_human.pars.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA12,ORF1,hs0_human,pars,BothTerminiTruncated
42682,Q#3225 - >seq9872,non-specific,335182,154,250,1.57627e-38,132.041,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs0_human,marg,CompleteHit
42683,Q#3225 - >seq9872,superfamily,335182,154,250,1.57627e-38,132.041,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs0_human,marg,CompleteHit
42684,Q#3225 - >seq9872,non-specific,340205,253,316,1.6196399999999997e-30,110.118,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs0_human,marg,CompleteHit
42685,Q#3225 - >seq9872,superfamily,340205,253,316,1.6196399999999997e-30,110.118,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA12,ORF1,hs0_human,marg,CompleteHit
42686,Q#3225 - >seq9872,non-specific,340204,110,151,0.000143055,38.5428,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs0_human,marg,CompleteHit
42687,Q#3225 - >seq9872,superfamily,340204,110,151,0.000143055,38.5428,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA12,ORF1,hs0_human,marg,CompleteHit
42688,Q#3225 - >seq9872,non-specific,222878,51,140,0.0025684,39.2273,PHA02562,46,NC,cl33686,endonuclease subunit; Provisional,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs0_human,marg,BothTerminiTruncated
42689,Q#3225 - >seq9872,superfamily,222878,51,140,0.0025684,39.2273,cl33686,46 superfamily,NC, - ,endonuclease subunit; Provisional,L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA12,ORF1,hs0_human,marg,BothTerminiTruncated
42690,Q#3225 - >seq9872,non-specific,275316,51,148,0.00833896,37.6924,TIGR04523,Mplasa_alph_rch,NC,cl37461,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs0_human,marg,BothTerminiTruncated
42691,Q#3225 - >seq9872,superfamily,275316,51,148,0.00833896,37.6924,cl37461,Mplasa_alph_rch superfamily,NC, - ,"helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.",L1PA12.ORF1.hs0_human.marg.frame3,1909201640_L1PA12.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Mycoplasma,L1PA12,ORF1,hs0_human,marg,BothTerminiTruncated
42692,Q#3226 - >seq9873,specific,311990,1127,1145,5.9042799999999997e-05,40.7332,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs2_gorilla.pars.frame1,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42693,Q#3226 - >seq9873,superfamily,311990,1127,1145,5.9042799999999997e-05,40.7332,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA12.ORF2.hs2_gorilla.pars.frame1,1909201640_L1PA12.RM_HPG_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,DUF1725,L1PA12,ORF2,hs2_gorilla,pars,CompleteHit
42694,Q#3227 - >seq9874,specific,197310,9,236,7.848669999999998e-60,205.278,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42695,Q#3227 - >seq9874,superfamily,351117,9,236,7.848669999999998e-60,205.278,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42696,Q#3227 - >seq9874,non-specific,197306,9,236,6.78649e-39,145.317,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42697,Q#3227 - >seq9874,non-specific,197307,9,236,9.7426e-22,95.8177,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42698,Q#3227 - >seq9874,non-specific,197321,7,236,3.09913e-20,91.4596,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42699,Q#3227 - >seq9874,non-specific,197320,9,229,4.92723e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42700,Q#3227 - >seq9874,non-specific,223780,9,237,8.77188e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42701,Q#3227 - >seq9874,non-specific,273186,9,237,3.2773400000000005e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42702,Q#3227 - >seq9874,specific,335306,10,229,4.3332100000000003e-16,78.8261,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42703,Q#3227 - >seq9874,non-specific,197319,13,236,1.36135e-14,75.0057,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42704,Q#3227 - >seq9874,non-specific,272954,9,194,1.16229e-13,72.4157,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,C-TerminusTruncated
42705,Q#3227 - >seq9874,non-specific,197322,8,236,7.04394e-09,58.8678,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42706,Q#3227 - >seq9874,non-specific,197336,9,194,8.49584e-09,57.6223,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42707,Q#3227 - >seq9874,non-specific,236970,9,194,9.58085e-09,57.5966,PRK11756,PRK11756,C,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs3_orang,marg,C-TerminusTruncated
42708,Q#3227 - >seq9874,non-specific,339261,108,232,4.27182e-05,44.2503,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42709,Q#3227 - >seq9874,non-specific,235175,291,469,0.000107465,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs3_orang,marg,BothTerminiTruncated
42710,Q#3227 - >seq9874,superfamily,235175,291,469,0.000107465,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs3_orang,marg,BothTerminiTruncated
42711,Q#3227 - >seq9874,non-specific,197311,7,236,0.000342635,43.0493,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs3_orang,marg,CompleteHit
42712,Q#3227 - >seq9874,non-specific,224117,299,467,0.00391326,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs3_orang,marg,N-TerminusTruncated
42713,Q#3227 - >seq9874,superfamily,224117,299,467,0.00391326,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15-16.ORF2.hs3_orang.marg.frame3,1909201640_L1PA15-16.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15-16,ORF2,hs3_orang,marg,N-TerminusTruncated
42714,Q#3229 - >seq9876,specific,238827,476,583,4.80129e-34,130.10399999999998,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42715,Q#3229 - >seq9876,superfamily,295487,476,583,4.80129e-34,130.10399999999998,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42716,Q#3229 - >seq9876,non-specific,333820,482,609,2.14266e-13,69.2434,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42717,Q#3229 - >seq9876,superfamily,333820,482,609,2.14266e-13,69.2434,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.pars.frame2,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PA15-16,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42718,Q#3232 - >seq9879,non-specific,335182,156,251,1.42102e-30,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42719,Q#3232 - >seq9879,superfamily,335182,156,251,1.42102e-30,111.241,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42720,Q#3232 - >seq9879,non-specific,335182,156,251,1.42102e-30,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42721,Q#3232 - >seq9879,non-specific,340205,254,317,1.76564e-27,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42722,Q#3232 - >seq9879,superfamily,340205,254,317,1.76564e-27,102.029,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42723,Q#3232 - >seq9879,non-specific,340205,254,317,1.76564e-27,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42724,Q#3232 - >seq9879,non-specific,340204,110,152,2.37892e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42725,Q#3232 - >seq9879,superfamily,340204,110,152,2.37892e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42726,Q#3232 - >seq9879,non-specific,340204,110,152,2.37892e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,pars,CompleteHit
42727,Q#3232 - >seq9879,non-specific,274009,32,154,0.000113776,43.5179,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,N-TerminusTruncated
42728,Q#3232 - >seq9879,superfamily,274009,32,154,0.000113776,43.5179,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,N-TerminusTruncated
42729,Q#3232 - >seq9879,non-specific,274009,32,154,0.000113776,43.5179,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,N-TerminusTruncated
42730,Q#3232 - >seq9879,non-specific,237177,42,149,0.000531125,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42731,Q#3232 - >seq9879,superfamily,237177,42,149,0.000531125,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42732,Q#3232 - >seq9879,non-specific,237177,42,149,0.000531125,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42733,Q#3232 - >seq9879,non-specific,235175,38,242,0.00438765,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42734,Q#3232 - >seq9879,superfamily,235175,38,242,0.00438765,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42735,Q#3232 - >seq9879,non-specific,235175,38,242,0.00438765,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42736,Q#3232 - >seq9879,non-specific,274008,28,148,0.00444253,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42737,Q#3232 - >seq9879,superfamily,274008,28,148,0.00444253,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42738,Q#3232 - >seq9879,non-specific,274008,28,148,0.00444253,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42739,Q#3232 - >seq9879,non-specific,188306,43,149,0.00475766,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42740,Q#3232 - >seq9879,superfamily,188306,43,149,0.00475766,38.3682,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42741,Q#3232 - >seq9879,non-specific,188306,43,149,0.00475766,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,pars,C-TerminusTruncated
42742,Q#3232 - >seq9879,non-specific,235943,36,131,0.00836545,37.4898,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42743,Q#3232 - >seq9879,superfamily,235943,36,131,0.00836545,37.4898,cl35548,PRK07133 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42744,Q#3232 - >seq9879,non-specific,235943,36,131,0.00836545,37.4898,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42745,Q#3232 - >seq9879,non-specific,223571,63,121,0.00946362,37.5791,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42746,Q#3232 - >seq9879,superfamily,223571,63,121,0.00946362,37.5791,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42747,Q#3232 - >seq9879,non-specific,223571,63,121,0.00946362,37.5791,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42748,Q#3232 - >seq9879,non-specific,314569,92,141,0.00998687,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42749,Q#3232 - >seq9879,superfamily,327698,92,141,0.00998687,37.0108,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42750,Q#3232 - >seq9879,non-specific,314569,92,141,0.00998687,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,pars,BothTerminiTruncated
42751,Q#3235 - >seq9882,non-specific,335182,156,251,1.42102e-30,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42752,Q#3235 - >seq9882,superfamily,335182,156,251,1.42102e-30,111.241,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42753,Q#3235 - >seq9882,non-specific,335182,156,251,1.42102e-30,111.241,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42754,Q#3235 - >seq9882,non-specific,340205,254,317,1.76564e-27,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42755,Q#3235 - >seq9882,superfamily,340205,254,317,1.76564e-27,102.029,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42756,Q#3235 - >seq9882,non-specific,340205,254,317,1.76564e-27,102.029,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42757,Q#3235 - >seq9882,non-specific,340204,110,152,2.37892e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42758,Q#3235 - >seq9882,superfamily,340204,110,152,2.37892e-05,40.854,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42759,Q#3235 - >seq9882,non-specific,340204,110,152,2.37892e-05,40.854,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs3_orang,marg,CompleteHit
42760,Q#3235 - >seq9882,non-specific,274009,32,154,0.000113776,43.5179,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,N-TerminusTruncated
42761,Q#3235 - >seq9882,superfamily,274009,32,154,0.000113776,43.5179,cl37070,SMC_prok_A superfamily,N, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,N-TerminusTruncated
42762,Q#3235 - >seq9882,non-specific,274009,32,154,0.000113776,43.5179,TIGR02169,SMC_prok_A,N,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,N-TerminusTruncated
42763,Q#3235 - >seq9882,non-specific,237177,42,149,0.000531125,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42764,Q#3235 - >seq9882,superfamily,237177,42,149,0.000531125,41.3022,cl36166,PRK12704 superfamily,C, - ,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42765,Q#3235 - >seq9882,non-specific,237177,42,149,0.000531125,41.3022,PRK12704,PRK12704,C,cl36166,phosphodiesterase; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42766,Q#3235 - >seq9882,non-specific,235175,38,242,0.00438765,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42767,Q#3235 - >seq9882,superfamily,235175,38,242,0.00438765,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42768,Q#3235 - >seq9882,non-specific,235175,38,242,0.00438765,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42769,Q#3235 - >seq9882,non-specific,274008,28,148,0.00444253,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42770,Q#3235 - >seq9882,superfamily,274008,28,148,0.00444253,38.4991,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42771,Q#3235 - >seq9882,non-specific,274008,28,148,0.00444253,38.4991,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42772,Q#3235 - >seq9882,non-specific,188306,43,149,0.00475766,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42773,Q#3235 - >seq9882,superfamily,188306,43,149,0.00475766,38.3682,cl33207,RNase_Y superfamily,C, - ,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42774,Q#3235 - >seq9882,non-specific,188306,43,149,0.00475766,38.3682,TIGR03319,RNase_Y,C,cl33207,"ribonuclease Y; Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA]",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF1,hs3_orang,marg,C-TerminusTruncated
42775,Q#3235 - >seq9882,non-specific,235943,36,131,0.00836545,37.4898,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42776,Q#3235 - >seq9882,superfamily,235943,36,131,0.00836545,37.4898,cl35548,PRK07133 superfamily,NC, - ,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42777,Q#3235 - >seq9882,non-specific,235943,36,131,0.00836545,37.4898,PRK07133,PRK07133,NC,cl35548,DNA polymerase III subunits gamma and tau; Validated,L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42778,Q#3235 - >seq9882,non-specific,223571,63,121,0.00946362,37.5791,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42779,Q#3235 - >seq9882,superfamily,223571,63,121,0.00946362,37.5791,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42780,Q#3235 - >seq9882,non-specific,223571,63,121,0.00946362,37.5791,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42781,Q#3235 - >seq9882,non-specific,314569,92,141,0.00998687,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42782,Q#3235 - >seq9882,superfamily,327698,92,141,0.00998687,37.0108,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42783,Q#3235 - >seq9882,non-specific,314569,92,141,0.00998687,37.0108,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs3_orang,marg,BothTerminiTruncated
42784,Q#3237 - >seq9884,specific,311990,1197,1214,6.56312e-05,40.7332,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs3_orang.pars.frame2,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42785,Q#3237 - >seq9884,superfamily,311990,1197,1214,6.56312e-05,40.7332,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs3_orang.pars.frame2,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42786,Q#3238 - >seq9885,specific,238827,502,755,2.1588199999999996e-63,214.46200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42787,Q#3238 - >seq9885,superfamily,295487,502,755,2.1588199999999996e-63,214.46200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42788,Q#3238 - >seq9885,specific,197310,3,230,7.0008199999999986e-62,211.05599999999998,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42789,Q#3238 - >seq9885,superfamily,351117,3,230,7.0008199999999986e-62,211.05599999999998,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42790,Q#3238 - >seq9885,specific,333820,508,732,2.75962e-32,123.94200000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42791,Q#3238 - >seq9885,superfamily,333820,508,732,2.75962e-32,123.94200000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42792,Q#3238 - >seq9885,non-specific,197306,3,230,1.7794099999999999e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42793,Q#3238 - >seq9885,non-specific,197307,3,230,1.40822e-21,95.4325,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42794,Q#3238 - >seq9885,non-specific,197320,3,223,2.74553e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42795,Q#3238 - >seq9885,non-specific,223780,3,231,9.358200000000002e-21,93.0467,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42796,Q#3238 - >seq9885,non-specific,197321,1,230,4.13639e-18,85.2964,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42797,Q#3238 - >seq9885,non-specific,273186,3,231,3.08792e-17,82.712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42798,Q#3238 - >seq9885,non-specific,272954,3,230,4.270350000000001e-17,82.4308,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42799,Q#3238 - >seq9885,specific,335306,4,223,1.52331e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42800,Q#3238 - >seq9885,non-specific,197319,7,230,2.21221e-15,77.3169,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42801,Q#3238 - >seq9885,non-specific,238828,508,729,1.4828799999999998e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42802,Q#3238 - >seq9885,non-specific,197336,3,188,7.28894e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42803,Q#3238 - >seq9885,non-specific,236970,3,231,1.63555e-08,56.8262,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42804,Q#3238 - >seq9885,non-specific,275209,458,663,5.14476e-08,56.312,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42805,Q#3238 - >seq9885,superfamily,275209,458,663,5.14476e-08,56.312,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42806,Q#3238 - >seq9885,non-specific,197322,2,230,9.19515e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42807,Q#3238 - >seq9885,non-specific,197311,1,140,3.83127e-06,48.8273,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42808,Q#3238 - >seq9885,non-specific,235175,284,461,4.20852e-05,47.7512,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,pars,BothTerminiTruncated
42809,Q#3238 - >seq9885,superfamily,235175,284,461,4.20852e-05,47.7512,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,pars,BothTerminiTruncated
42810,Q#3238 - >seq9885,non-specific,339261,102,226,6.92037e-05,43.4799,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs3_orang,pars,CompleteHit
42811,Q#3238 - >seq9885,non-specific,274009,300,450,0.000273308,45.0587,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42812,Q#3238 - >seq9885,superfamily,274009,300,450,0.000273308,45.0587,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42813,Q#3238 - >seq9885,non-specific,238185,648,725,0.000652062,40.0268,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,C-TerminusTruncated
42814,Q#3238 - >seq9885,non-specific,274009,287,439,0.00213415,42.3623,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,pars,BothTerminiTruncated
42815,Q#3238 - >seq9885,specific,225881,475,672,0.00297943,40.9777,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,BothTerminiTruncated
42816,Q#3238 - >seq9885,superfamily,225881,475,672,0.00297943,40.9777,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs3_orang,pars,BothTerminiTruncated
42817,Q#3238 - >seq9885,non-specific,334125,206,402,0.0068468999999999995,40.2104,pfam00521,DNA_topoisoIV,N,cl29575,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB2,ORF2,hs3_orang,pars,N-TerminusTruncated
42818,Q#3238 - >seq9885,superfamily,334125,206,402,0.0068468999999999995,40.2104,cl29575,DNA_topoisoIV superfamily,N, - ,"DNA gyrase/topoisomerase IV, subunit A; DNA gyrase/topoisomerase IV, subunit A.  ",L1PB2.ORF2.hs3_orang.pars.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_Chrom,L1PB2,ORF2,hs3_orang,pars,N-TerminusTruncated
42819,Q#3241 - >seq9888,non-specific,335182,67,162,1.3041299999999999e-33,116.633,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42820,Q#3241 - >seq9888,superfamily,335182,67,162,1.3041299999999999e-33,116.633,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42821,Q#3241 - >seq9888,non-specific,340205,165,228,1.51073e-29,105.111,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42822,Q#3241 - >seq9888,superfamily,340205,165,228,1.51073e-29,105.111,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42823,Q#3241 - >seq9888,non-specific,340204,21,63,0.00160931,35.076,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42824,Q#3241 - >seq9888,superfamily,340204,21,63,0.00160931,35.076,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs2_gorilla.marg.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs2_gorilla,marg,CompleteHit
42825,Q#3242 - >seq9889,specific,238827,502,765,6.224939999999999e-65,219.085,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42826,Q#3242 - >seq9889,superfamily,295487,502,765,6.224939999999999e-65,219.085,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42827,Q#3242 - >seq9889,specific,197310,3,230,1.64202e-61,209.9,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42828,Q#3242 - >seq9889,superfamily,351117,3,230,1.64202e-61,209.9,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42829,Q#3242 - >seq9889,specific,333820,508,765,8.724719999999999e-32,122.786,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42830,Q#3242 - >seq9889,superfamily,333820,508,765,8.724719999999999e-32,122.786,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42831,Q#3242 - >seq9889,non-specific,197306,3,230,2.2483899999999996e-31,123.36,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42832,Q#3242 - >seq9889,non-specific,197320,3,223,3.8077600000000006e-21,94.1189,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42833,Q#3242 - >seq9889,non-specific,197307,3,230,2.4434300000000002e-20,91.5805,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42834,Q#3242 - >seq9889,non-specific,223780,3,231,1.01199e-19,89.9651,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42835,Q#3242 - >seq9889,non-specific,197321,1,230,4.01006e-17,82.2148,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42836,Q#3242 - >seq9889,non-specific,273186,3,231,1.3254200000000001e-16,80.786,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42837,Q#3242 - >seq9889,specific,335306,4,223,1.5725e-16,79.9817,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42838,Q#3242 - >seq9889,non-specific,272954,3,230,4.1970999999999997e-16,79.3493,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42839,Q#3242 - >seq9889,non-specific,197319,7,230,4.93101e-14,73.0797,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42840,Q#3242 - >seq9889,non-specific,238828,508,729,1.1269e-11,65.6852,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42841,Q#3242 - >seq9889,non-specific,197336,3,188,7.52745e-11,63.7855,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42842,Q#3242 - >seq9889,non-specific,236970,3,231,3.44395e-08,56.0558,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42843,Q#3242 - >seq9889,non-specific,197322,2,230,9.500069999999999e-08,55.0158,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42844,Q#3242 - >seq9889,non-specific,275209,458,663,2.79281e-07,54.0008,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42845,Q#3242 - >seq9889,superfamily,275209,458,663,2.79281e-07,54.0008,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42846,Q#3242 - >seq9889,non-specific,197311,1,140,5.1762099999999995e-06,48.4421,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42847,Q#3242 - >seq9889,non-specific,339261,102,226,4.79412e-05,43.8651,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42848,Q#3242 - >seq9889,non-specific,235175,284,461,0.00045955800000000005,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,marg,BothTerminiTruncated
42849,Q#3242 - >seq9889,superfamily,235175,284,461,0.00045955800000000005,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,marg,BothTerminiTruncated
42850,Q#3242 - >seq9889,non-specific,274009,300,450,0.0005696459999999999,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42851,Q#3242 - >seq9889,superfamily,274009,300,450,0.0005696459999999999,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42852,Q#3242 - >seq9889,specific,311990,1235,1252,0.000655483,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42853,Q#3242 - >seq9889,superfamily,311990,1235,1252,0.000655483,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs3_orang,marg,CompleteHit
42854,Q#3242 - >seq9889,non-specific,238185,648,725,0.00224737,38.486,cd00304,RT_like,C,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs3_orang,marg,C-TerminusTruncated
42855,Q#3242 - >seq9889,non-specific,274009,287,439,0.00500435,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs3_orang.marg.frame3,1909201640_L1PB2.RM_HPGP_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs3_orang,marg,BothTerminiTruncated
42856,Q#3244 - >seq9891,non-specific,335182,67,162,3.3009e-33,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42857,Q#3244 - >seq9891,superfamily,335182,67,162,3.3009e-33,115.478,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42858,Q#3244 - >seq9891,non-specific,335182,67,162,3.3009e-33,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42859,Q#3244 - >seq9891,non-specific,340205,165,228,2.9139899999999994e-29,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42860,Q#3244 - >seq9891,superfamily,340205,165,228,2.9139899999999994e-29,104.34,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42861,Q#3244 - >seq9891,non-specific,340205,165,228,2.9139899999999994e-29,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42862,Q#3244 - >seq9891,non-specific,340204,21,63,6.60317e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42863,Q#3244 - >seq9891,superfamily,340204,21,63,6.60317e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42864,Q#3244 - >seq9891,non-specific,340204,21,63,6.60317e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,pars,CompleteHit
42865,Q#3244 - >seq9891,non-specific,314569,3,52,0.00314461,37.7812,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
42866,Q#3244 - >seq9891,superfamily,327698,3,52,0.00314461,37.7812,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
42867,Q#3244 - >seq9891,non-specific,314569,3,52,0.00314461,37.7812,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,pars,BothTerminiTruncated
42868,Q#3247 - >seq9894,non-specific,335182,67,162,3.3009e-33,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42869,Q#3247 - >seq9894,superfamily,335182,67,162,3.3009e-33,115.478,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42870,Q#3247 - >seq9894,non-specific,335182,67,162,3.3009e-33,115.478,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42871,Q#3247 - >seq9894,non-specific,340205,165,228,2.9139899999999994e-29,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42872,Q#3247 - >seq9894,superfamily,340205,165,228,2.9139899999999994e-29,104.34,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42873,Q#3247 - >seq9894,non-specific,340205,165,228,2.9139899999999994e-29,104.34,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42874,Q#3247 - >seq9894,non-specific,340204,21,63,6.60317e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42875,Q#3247 - >seq9894,superfamily,340204,21,63,6.60317e-06,42.0096,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42876,Q#3247 - >seq9894,non-specific,340204,21,63,6.60317e-06,42.0096,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PB2,ORF1,hs4_gibbon,marg,CompleteHit
42877,Q#3247 - >seq9894,non-specific,314569,3,52,0.00314461,37.7812,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
42878,Q#3247 - >seq9894,superfamily,327698,3,52,0.00314461,37.7812,cl19916,ISG65-75 superfamily,NC, - ,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
42879,Q#3247 - >seq9894,non-specific,314569,3,52,0.00314461,37.7812,pfam11727,ISG65-75,NC,cl19916,"Invariant surface glycoprotein; This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.",L1PB2.ORF1.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PB2,ORF1,hs4_gibbon,marg,BothTerminiTruncated
42880,Q#3249 - >seq9896,specific,238827,502,764,2.22658e-67,226.018,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42881,Q#3249 - >seq9896,superfamily,295487,502,764,2.22658e-67,226.018,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42882,Q#3249 - >seq9896,specific,197310,3,230,8.454459999999998e-61,207.97400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42883,Q#3249 - >seq9896,superfamily,351117,3,230,8.454459999999998e-61,207.97400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42884,Q#3249 - >seq9896,specific,333820,508,764,6.675479999999999e-33,125.868,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42885,Q#3249 - >seq9896,superfamily,333820,508,764,6.675479999999999e-33,125.868,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42886,Q#3249 - >seq9896,non-specific,197306,3,230,1.5728799999999999e-31,123.74600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42887,Q#3249 - >seq9896,non-specific,197320,3,223,2.64764e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42888,Q#3249 - >seq9896,non-specific,197307,3,230,1.8685099999999997e-20,91.9657,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42889,Q#3249 - >seq9896,non-specific,223780,3,231,1.41885e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42890,Q#3249 - >seq9896,non-specific,197321,1,230,2.87447e-17,82.6,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42891,Q#3249 - >seq9896,non-specific,273186,3,231,5.76588e-17,81.9416,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42892,Q#3249 - >seq9896,specific,335306,4,223,7.83709e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42893,Q#3249 - >seq9896,non-specific,272954,3,230,9.766869999999999e-16,78.1937,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42894,Q#3249 - >seq9896,non-specific,197319,7,230,1.6253e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42895,Q#3249 - >seq9896,non-specific,238828,508,729,2.13101e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42896,Q#3249 - >seq9896,non-specific,197336,3,188,4.67493e-11,64.5559,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42897,Q#3249 - >seq9896,non-specific,275209,457,663,8.79253e-09,58.6232,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42898,Q#3249 - >seq9896,superfamily,275209,457,663,8.79253e-09,58.6232,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42899,Q#3249 - >seq9896,non-specific,236970,3,231,1.05404e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42900,Q#3249 - >seq9896,non-specific,197322,2,230,1.1847000000000001e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42901,Q#3249 - >seq9896,non-specific,197311,1,140,4.01767e-06,48.8273,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42902,Q#3249 - >seq9896,non-specific,238185,648,762,6.65802e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42903,Q#3249 - >seq9896,non-specific,235175,284,461,8.04942e-05,46.9808,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42904,Q#3249 - >seq9896,superfamily,235175,284,461,8.04942e-05,46.9808,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42905,Q#3249 - >seq9896,non-specific,339261,102,226,0.00020618,41.9391,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42906,Q#3249 - >seq9896,specific,311990,1222,1239,0.0005129430000000001,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42907,Q#3249 - >seq9896,superfamily,311990,1222,1239,0.0005129430000000001,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB2,ORF2,hs4_gibbon,pars,CompleteHit
42908,Q#3249 - >seq9896,non-specific,274009,300,450,0.00956447,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42909,Q#3249 - >seq9896,superfamily,274009,300,450,0.00956447,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,pars,C-TerminusTruncated
42910,Q#3252 - >seq9899,specific,238827,502,764,1.8013999999999997e-67,226.40400000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42911,Q#3252 - >seq9899,superfamily,295487,502,764,1.8013999999999997e-67,226.40400000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42912,Q#3252 - >seq9899,specific,197310,3,230,2.2983699999999994e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42913,Q#3252 - >seq9899,superfamily,351117,3,230,2.2983699999999994e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42914,Q#3252 - >seq9899,specific,333820,508,764,9.91827e-33,125.48299999999999,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42915,Q#3252 - >seq9899,superfamily,333820,508,764,9.91827e-33,125.48299999999999,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42916,Q#3252 - >seq9899,non-specific,197306,3,230,1.2500199999999998e-31,124.131,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42917,Q#3252 - >seq9899,non-specific,197320,3,223,4.55214e-21,93.7337,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42918,Q#3252 - >seq9899,non-specific,197307,3,230,3.8098500000000005e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42919,Q#3252 - >seq9899,non-specific,223780,3,231,3.1421e-19,88.8095,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42920,Q#3252 - >seq9899,non-specific,197321,1,230,5.16446e-17,81.8296,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42921,Q#3252 - >seq9899,specific,335306,4,223,7.91505e-17,80.7521,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42922,Q#3252 - >seq9899,non-specific,273186,3,231,1.02568e-16,81.1712,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42923,Q#3252 - >seq9899,non-specific,272954,3,230,2.09381e-15,77.4233,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42924,Q#3252 - >seq9899,non-specific,197319,7,230,3.28825e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42925,Q#3252 - >seq9899,non-specific,238828,508,729,2.36424e-11,64.9148,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42926,Q#3252 - >seq9899,non-specific,197336,3,188,5.47899e-11,64.1707,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42927,Q#3252 - >seq9899,non-specific,275209,457,663,1.25519e-08,58.238,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
42928,Q#3252 - >seq9899,superfamily,275209,457,663,1.25519e-08,58.238,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
42929,Q#3252 - >seq9899,non-specific,197322,2,230,1.19678e-07,54.6306,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42930,Q#3252 - >seq9899,non-specific,236970,3,231,1.2093400000000002e-07,54.515,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42931,Q#3252 - >seq9899,non-specific,197311,1,140,3.3988599999999995e-06,49.2125,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
42932,Q#3252 - >seq9899,non-specific,238185,648,762,8.08546e-05,42.7232,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42933,Q#3252 - >seq9899,non-specific,235175,284,461,0.00010488,46.5956,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42934,Q#3252 - >seq9899,superfamily,235175,284,461,0.00010488,46.5956,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42935,Q#3252 - >seq9899,non-specific,339261,102,226,0.000134688,42.7095,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42936,Q#3252 - >seq9899,specific,311990,1233,1250,0.000623187,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42937,Q#3252 - >seq9899,superfamily,311990,1233,1250,0.000623187,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB2,ORF2,hs4_gibbon,marg,CompleteHit
42938,Q#3252 - >seq9899,non-specific,274009,300,450,0.009338500000000001,40.0511,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
42939,Q#3252 - >seq9899,superfamily,274009,300,450,0.009338500000000001,40.0511,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PB2.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PB2.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB2,ORF2,hs4_gibbon,marg,C-TerminusTruncated
42940,Q#3257 - >seq9904,non-specific,335182,156,251,5.71725e-31,112.01100000000001,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42941,Q#3257 - >seq9904,superfamily,335182,156,251,5.71725e-31,112.01100000000001,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42942,Q#3257 - >seq9904,non-specific,340205,254,317,6.8438e-28,102.8,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42943,Q#3257 - >seq9904,superfamily,340205,254,317,6.8438e-28,102.8,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42944,Q#3257 - >seq9904,non-specific,223571,63,122,0.000588157,41.0459,COG0497,RecN,NC,cl33912,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
42945,Q#3257 - >seq9904,superfamily,223571,63,122,0.000588157,41.0459,cl33912,RecN superfamily,NC, - ,"DNA repair ATPase RecN [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_NotSeenBefore,L1PB2,ORF1,hs2_gorilla,pars,BothTerminiTruncated
42946,Q#3257 - >seq9904,non-specific,340204,110,152,0.00902174,33.5352,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42947,Q#3257 - >seq9904,superfamily,340204,110,152,0.00902174,33.5352,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PB2.ORF1.hs2_gorilla.pars.frame3,1909201640_L1PB2.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PB2,ORF1,hs2_gorilla,pars,CompleteHit
42948,Q#3258 - >seq9905,specific,197310,9,236,3.0935699999999998e-61,208.36,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42949,Q#3258 - >seq9905,superfamily,351117,9,236,3.0935699999999998e-61,208.36,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42950,Q#3258 - >seq9905,non-specific,197306,9,236,2.4178899999999997e-39,146.08700000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42951,Q#3258 - >seq9905,specific,238827,644,760,1.56707e-26,108.53299999999999,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42952,Q#3258 - >seq9905,superfamily,295487,644,760,1.56707e-26,108.53299999999999,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42953,Q#3258 - >seq9905,non-specific,197307,9,236,2.43464e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42954,Q#3258 - >seq9905,non-specific,223780,9,237,8.16925e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42955,Q#3258 - >seq9905,non-specific,197320,9,229,2.36875e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42956,Q#3258 - >seq9905,non-specific,197321,7,236,3.0636500000000004e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42957,Q#3258 - >seq9905,non-specific,273186,9,237,2.7876799999999996e-18,85.4084,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42958,Q#3258 - >seq9905,specific,335306,10,229,3.6245e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42959,Q#3258 - >seq9905,non-specific,197319,13,236,5.26116e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42960,Q#3258 - >seq9905,non-specific,333820,596,760,4.31599e-14,71.5546,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42961,Q#3258 - >seq9905,superfamily,333820,596,760,4.31599e-14,71.5546,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42962,Q#3258 - >seq9905,non-specific,272954,9,207,9.914329999999999e-14,72.0305,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42963,Q#3258 - >seq9905,non-specific,197322,8,236,3.37878e-11,65.4162,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42964,Q#3258 - >seq9905,non-specific,197336,9,194,4.0283600000000004e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42965,Q#3258 - >seq9905,non-specific,236970,9,237,1.12523e-09,60.293,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42966,Q#3258 - >seq9905,non-specific,238828,599,726,2.3498699999999999e-07,52.5884,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,N-TerminusTruncated
42967,Q#3258 - >seq9905,non-specific,339261,108,232,1.03179e-06,48.4875,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42968,Q#3258 - >seq9905,non-specific,197311,30,236,4.10532e-06,48.4421,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42969,Q#3258 - >seq9905,non-specific,235175,291,468,0.0008339830000000001,43.1288,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42970,Q#3258 - >seq9905,superfamily,235175,291,468,0.0008339830000000001,43.1288,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42971,Q#3258 - >seq9905,non-specific,238185,645,730,0.000855976,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,pars,CompleteHit
42972,Q#3258 - >seq9905,non-specific,274009,294,468,0.00315457,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42973,Q#3258 - >seq9905,superfamily,274009,294,468,0.00315457,41.2067,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42974,Q#3258 - >seq9905,non-specific,274009,305,457,0.00334725,41.2067,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.pars.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,pars,BothTerminiTruncated
42975,Q#3261 - >seq9908,specific,197310,9,236,2.0551299999999997e-60,206.43400000000003,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42976,Q#3261 - >seq9908,superfamily,351117,9,236,2.0551299999999997e-60,206.43400000000003,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42977,Q#3261 - >seq9908,specific,238827,508,757,1.8781700000000003e-55,191.736,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42978,Q#3261 - >seq9908,superfamily,295487,508,757,1.8781700000000003e-55,191.736,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42979,Q#3261 - >seq9908,non-specific,197306,9,236,3.25766e-39,146.08700000000002,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42980,Q#3261 - >seq9908,specific,333820,514,739,1.02762e-31,122.40100000000001,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42981,Q#3261 - >seq9908,superfamily,333820,514,739,1.02762e-31,122.40100000000001,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42982,Q#3261 - >seq9908,non-specific,197307,9,236,3.0344599999999996e-23,100.055,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42983,Q#3261 - >seq9908,non-specific,223780,9,237,9.538419999999999e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42984,Q#3261 - >seq9908,non-specific,197320,9,229,2.7625399999999996e-21,94.5041,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42985,Q#3261 - >seq9908,non-specific,197321,7,236,2.89877e-21,94.156,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42986,Q#3261 - >seq9908,non-specific,273186,9,237,3.2495799999999998e-18,85.4084,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42987,Q#3261 - >seq9908,specific,335306,10,229,4.20658e-18,84.2189,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42988,Q#3261 - >seq9908,non-specific,197319,13,236,6.1284199999999995e-16,78.8577,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42989,Q#3261 - >seq9908,non-specific,272954,9,207,1.41841e-13,71.6453,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42990,Q#3261 - >seq9908,non-specific,238828,514,730,5.8016e-12,66.4556,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42991,Q#3261 - >seq9908,non-specific,197322,8,236,3.95206e-11,65.4162,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42992,Q#3261 - >seq9908,non-specific,197336,9,194,4.68334e-10,61.0891,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42993,Q#3261 - >seq9908,non-specific,236970,9,237,2.21039e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42994,Q#3261 - >seq9908,non-specific,339261,108,232,2.5165900000000003e-06,47.3319,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42995,Q#3261 - >seq9908,non-specific,275209,580,730,5.461e-06,49.7636,TIGR04416,group_II_RT_mat,NC,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42996,Q#3261 - >seq9908,superfamily,275209,580,730,5.461e-06,49.7636,cl37441,group_II_RT_mat superfamily,NC, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42997,Q#3261 - >seq9908,non-specific,197311,30,236,5.984149999999999e-06,48.0569,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
42998,Q#3261 - >seq9908,non-specific,235175,291,468,0.000496212,44.2844,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
42999,Q#3261 - >seq9908,superfamily,235175,291,468,0.000496212,44.2844,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
43000,Q#3261 - >seq9908,non-specific,238185,649,734,0.000643681,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs4_gibbon,marg,CompleteHit
43001,Q#3261 - >seq9908,non-specific,274009,305,457,0.00320072,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
43002,Q#3261 - >seq9908,superfamily,274009,305,457,0.00320072,41.5919,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
43003,Q#3261 - >seq9908,non-specific,274009,294,468,0.00320072,41.5919,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15-16.ORF2.hs4_gibbon.marg.frame3,1909201640_L1PA15-16.RM_HPGPN_1708181204.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs4_gibbon,marg,BothTerminiTruncated
43004,Q#3263 - >seq9910,specific,197310,9,236,1.0060799999999998e-62,212.982,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43005,Q#3263 - >seq9910,superfamily,351117,9,236,1.0060799999999998e-62,212.982,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43006,Q#3263 - >seq9910,non-specific,197306,9,236,3.37428e-41,151.48,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43007,Q#3263 - >seq9910,non-specific,197307,9,236,3.31081e-25,105.833,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43008,Q#3263 - >seq9910,non-specific,223780,9,237,9.1764e-23,98.8247,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43009,Q#3263 - >seq9910,non-specific,197321,7,236,1.45145e-22,98.008,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43010,Q#3263 - >seq9910,non-specific,197320,9,229,5.33868e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43011,Q#3263 - >seq9910,specific,335306,10,229,1.0933399999999998e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43012,Q#3263 - >seq9910,non-specific,273186,9,237,8.20201e-18,84.2528,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43013,Q#3263 - >seq9910,non-specific,197319,13,236,1.79924e-17,83.0949,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43014,Q#3263 - >seq9910,non-specific,272954,9,207,2.24295e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43015,Q#3263 - >seq9910,non-specific,236970,9,237,2.74937e-11,65.3006,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Exonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43016,Q#3263 - >seq9910,non-specific,197322,8,236,3.47465e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43017,Q#3263 - >seq9910,non-specific,197336,9,194,1.12729e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43018,Q#3263 - >seq9910,non-specific,197311,30,236,9.91418e-06,47.2865,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43019,Q#3263 - >seq9910,non-specific,339261,108,232,2.03645e-05,44.6355,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs0_human.pars.frame2,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Endonuclease_RT,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43020,Q#3264 - >seq9911,specific,238827,465,701,2.56416e-46,165.542,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs0_human.pars.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43021,Q#3264 - >seq9911,superfamily,295487,465,701,2.56416e-46,165.542,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs0_human.pars.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43022,Q#3264 - >seq9911,non-specific,333820,471,686,1.0020199999999999e-21,93.5109,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs0_human.pars.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43023,Q#3264 - >seq9911,superfamily,333820,471,686,1.0020199999999999e-21,93.5109,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs0_human.pars.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,pars,CompleteHit
43024,Q#3264 - >seq9911,non-specific,238828,513,677,4.06791e-06,48.7364,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs0_human.pars.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,pars,N-TerminusTruncated
43025,Q#3268 - >seq9915,non-specific,239242,1073,1139,0.00150206,42.0954,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs6_sqmonkey.pars.frame1,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43026,Q#3268 - >seq9915,superfamily,355772,1073,1139,0.00150206,42.0954,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs6_sqmonkey.pars.frame1,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43027,Q#3270 - >seq9917,specific,197310,9,236,4.35589e-62,211.44099999999997,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43028,Q#3270 - >seq9917,superfamily,351117,9,236,4.35589e-62,211.44099999999997,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43029,Q#3270 - >seq9917,specific,238827,510,754,9.932059999999999e-53,184.032,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43030,Q#3270 - >seq9917,superfamily,295487,510,754,9.932059999999999e-53,184.032,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43031,Q#3270 - >seq9917,non-specific,197306,9,236,8.309119999999999e-40,147.628,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43032,Q#3270 - >seq9917,non-specific,333820,516,739,3.0466699999999997e-27,109.689,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43033,Q#3270 - >seq9917,superfamily,333820,516,739,3.0466699999999997e-27,109.689,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43034,Q#3270 - >seq9917,non-specific,197307,9,236,8.795869999999999e-24,101.596,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43035,Q#3270 - >seq9917,non-specific,223780,9,237,3.3407e-22,97.2839,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43036,Q#3270 - >seq9917,non-specific,197320,9,229,5.76123e-22,96.4301,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43037,Q#3270 - >seq9917,non-specific,197321,7,236,1.31754e-21,95.3116,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43038,Q#3270 - >seq9917,specific,335306,10,229,1.17719e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43039,Q#3270 - >seq9917,non-specific,273186,9,237,2.17015e-17,83.0972,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43040,Q#3270 - >seq9917,non-specific,197319,13,236,3.82626e-16,79.2429,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43041,Q#3270 - >seq9917,non-specific,272954,9,207,2.72707e-14,73.9565,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43042,Q#3270 - >seq9917,non-specific,236970,9,237,2.1979e-10,62.6042,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43043,Q#3270 - >seq9917,non-specific,197322,8,236,3.7532499999999994e-10,62.3346,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43044,Q#3270 - >seq9917,non-specific,197336,9,194,1.21453e-09,59.9335,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43045,Q#3270 - >seq9917,non-specific,238828,516,730,7.814999999999999e-09,57.2108,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43046,Q#3270 - >seq9917,non-specific,339261,108,232,8.35962e-06,45.7911,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43047,Q#3270 - >seq9917,non-specific,197311,30,236,9.61436e-06,47.6717,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15-16,ORF2,hs0_human,marg,CompleteHit
43048,Q#3270 - >seq9917,non-specific,275209,466,730,3.78077e-05,47.0672,TIGR04416,group_II_RT_mat,C,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,C-TerminusTruncated
43049,Q#3270 - >seq9917,superfamily,275209,466,730,3.78077e-05,47.0672,cl37441,group_II_RT_mat superfamily,C, - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15-16,ORF2,hs0_human,marg,C-TerminusTruncated
43050,Q#3270 - >seq9917,non-specific,235175,291,469,0.00458129,40.8176,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs0_human,marg,BothTerminiTruncated
43051,Q#3270 - >seq9917,superfamily,235175,291,469,0.00458129,40.8176,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15-16.ORF2.hs0_human.marg.frame3,1909201640_L1PA15-16.RM_hs_1709082029.200longest.o3000.out.fa.ch.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15-16,ORF2,hs0_human,marg,BothTerminiTruncated
43052,Q#3271 - >seq9918,non-specific,239242,1073,1139,0.00150206,42.0954,cd02932,OYE_YqiM_FMN,NC,cl28888,"Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis.  Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent.   The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.",L1PA15.ORF2.hs6_sqmonkey.marg.frame1,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43053,Q#3271 - >seq9918,superfamily,355772,1073,1139,0.00150206,42.0954,cl28888,TIM_phosphate_binding superfamily,NC, - ,"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.",L1PA15.ORF2.hs6_sqmonkey.marg.frame1,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,Other_NotSeenBefore,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43054,Q#3274 - >seq9921,specific,238827,507,769,9.867279999999999e-66,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43055,Q#3274 - >seq9921,superfamily,295487,507,769,9.867279999999999e-66,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43056,Q#3274 - >seq9921,specific,197310,9,235,2.3323099999999995e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43057,Q#3274 - >seq9921,superfamily,351117,9,235,2.3323099999999995e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43058,Q#3274 - >seq9921,non-specific,197306,9,235,3.5292299999999996e-41,151.865,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43059,Q#3274 - >seq9921,specific,333820,513,769,9.43078e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43060,Q#3274 - >seq9921,superfamily,333820,513,769,9.43078e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43061,Q#3274 - >seq9921,non-specific,197307,9,235,6.943800000000001e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43062,Q#3274 - >seq9921,non-specific,223780,9,222,5.64524e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43063,Q#3274 - >seq9921,non-specific,197321,7,235,1.76281e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43064,Q#3274 - >seq9921,non-specific,197320,9,193,2.1274800000000002e-19,89.1113,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
43065,Q#3274 - >seq9921,specific,335306,10,228,2.26075e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43066,Q#3274 - >seq9921,non-specific,197319,13,235,2.0671099999999997e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43067,Q#3274 - >seq9921,non-specific,273186,9,236,2.49294e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43068,Q#3274 - >seq9921,non-specific,238828,513,734,1.7075e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43069,Q#3274 - >seq9921,non-specific,272954,9,193,1.1326799999999998e-10,63.1709,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
43070,Q#3274 - >seq9921,non-specific,197336,9,193,1.67521e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43071,Q#3274 - >seq9921,non-specific,197322,8,222,8.547739999999999e-08,55.401,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43072,Q#3274 - >seq9921,non-specific,275209,466,797,2.0920200000000002e-07,54.386,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43073,Q#3274 - >seq9921,superfamily,275209,466,797,2.0920200000000002e-07,54.386,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43074,Q#3274 - >seq9921,non-specific,339261,108,231,3.12574e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43075,Q#3274 - >seq9921,non-specific,197311,7,235,4.14009e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43076,Q#3274 - >seq9921,non-specific,235175,262,466,1.67072e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43077,Q#3274 - >seq9921,superfamily,235175,262,466,1.67072e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43078,Q#3274 - >seq9921,non-specific,238185,653,769,3.21359e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43079,Q#3274 - >seq9921,non-specific,223496,303,497,0.000402685,44.7511,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43080,Q#3274 - >seq9921,superfamily,223496,303,497,0.000402685,44.7511,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43081,Q#3274 - >seq9921,non-specific,274009,306,455,0.00103148,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
43082,Q#3274 - >seq9921,superfamily,274009,306,455,0.00103148,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
43083,Q#3274 - >seq9921,non-specific,274475,254,425,0.00171219,42.3632,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43084,Q#3274 - >seq9921,superfamily,274475,254,425,0.00171219,42.3632,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Unusual,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43085,Q#3274 - >seq9921,specific,311990,1237,1255,0.00212695,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43086,Q#3274 - >seq9921,superfamily,311990,1237,1255,0.00212695,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PA15,ORF2,hs6_sqmonkey,pars,CompleteHit
43087,Q#3274 - >seq9921,non-specific,224117,262,464,0.00305426,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
43088,Q#3274 - >seq9921,superfamily,224117,262,464,0.00305426,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,N-TerminusTruncated
43089,Q#3274 - >seq9921,non-specific,274008,266,461,0.00315318,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43090,Q#3274 - >seq9921,superfamily,274008,266,461,0.00315318,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43091,Q#3274 - >seq9921,non-specific,274008,262,433,0.00514866,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,BothTerminiTruncated
43092,Q#3274 - >seq9921,non-specific,224117,262,445,0.00793996,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.pars.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,pars,C-TerminusTruncated
43093,Q#3277 - >seq9924,non-specific,335182,147,244,2.50372e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43094,Q#3277 - >seq9924,superfamily,335182,147,244,2.50372e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43095,Q#3277 - >seq9924,non-specific,340205,247,311,6.963979999999999e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43096,Q#3277 - >seq9924,superfamily,340205,247,311,6.963979999999999e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43097,Q#3277 - >seq9924,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43098,Q#3277 - >seq9924,superfamily,340204,102,144,8.91821e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Trimerization,L1PA8A,ORF1,hs6_sqmonkey,marg,CompleteHit
43099,Q#3277 - >seq9924,non-specific,224117,56,173,0.00251603,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43100,Q#3277 - >seq9924,superfamily,224117,56,173,0.00251603,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43101,Q#3277 - >seq9924,non-specific,235461,38,165,0.00293021,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
43102,Q#3277 - >seq9924,superfamily,235461,38,165,0.00293021,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
43103,Q#3277 - >seq9924,non-specific,179385,49,136,0.00365936,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43104,Q#3277 - >seq9924,superfamily,179385,49,136,0.00365936,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43105,Q#3277 - >seq9924,non-specific,235175,25,147,0.00439985,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43106,Q#3277 - >seq9924,superfamily,235175,25,147,0.00439985,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43107,Q#3277 - >seq9924,non-specific,235175,31,147,0.00510345,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,C-TerminusTruncated
43108,Q#3277 - >seq9924,non-specific,179877,26,186,0.00958512,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43109,Q#3277 - >seq9924,superfamily,179877,26,186,0.00958512,37.5078,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43110,Q#3277 - >seq9924,non-specific,274009,57,138,0.00966517,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43111,Q#3277 - >seq9924,superfamily,274009,57,138,0.00966517,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs6_sqmonkey.marg.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,marg,BothTerminiTruncated
43112,Q#3280 - >seq9927,specific,238827,507,769,9.867279999999999e-66,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43113,Q#3280 - >seq9927,superfamily,295487,507,769,9.867279999999999e-66,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43114,Q#3280 - >seq9927,specific,197310,9,235,2.3323099999999995e-61,209.515,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43115,Q#3280 - >seq9927,superfamily,351117,9,235,2.3323099999999995e-61,209.515,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43116,Q#3280 - >seq9927,non-specific,197306,9,235,3.5292299999999996e-41,151.865,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43117,Q#3280 - >seq9927,specific,333820,513,769,9.43078e-34,128.179,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43118,Q#3280 - >seq9927,superfamily,333820,513,769,9.43078e-34,128.179,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43119,Q#3280 - >seq9927,non-specific,197307,9,235,6.943800000000001e-23,99.2844,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43120,Q#3280 - >seq9927,non-specific,223780,9,222,5.64524e-21,93.8171,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43121,Q#3280 - >seq9927,non-specific,197321,7,235,1.76281e-19,89.1484,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43122,Q#3280 - >seq9927,non-specific,197320,9,193,2.1274800000000002e-19,89.1113,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
43123,Q#3280 - >seq9927,specific,335306,10,228,2.26075e-16,79.5965,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43124,Q#3280 - >seq9927,non-specific,197319,13,235,2.0671099999999997e-12,68.4573,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43125,Q#3280 - >seq9927,non-specific,273186,9,236,2.49294e-12,68.0744,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43126,Q#3280 - >seq9927,non-specific,238828,513,734,1.7075e-11,65.3,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43127,Q#3280 - >seq9927,non-specific,272954,9,193,1.1326799999999998e-10,63.1709,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
43128,Q#3280 - >seq9927,non-specific,197336,9,193,1.67521e-10,62.6299,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43129,Q#3280 - >seq9927,non-specific,197322,8,222,8.547739999999999e-08,55.401,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43130,Q#3280 - >seq9927,non-specific,275209,466,797,2.0920200000000002e-07,54.386,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43131,Q#3280 - >seq9927,superfamily,275209,466,797,2.0920200000000002e-07,54.386,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43132,Q#3280 - >seq9927,non-specific,339261,108,231,3.12574e-07,50.0283,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43133,Q#3280 - >seq9927,non-specific,197311,7,235,4.14009e-07,51.9089,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43134,Q#3280 - >seq9927,non-specific,235175,262,466,1.67072e-05,49.292,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43135,Q#3280 - >seq9927,superfamily,235175,262,466,1.67072e-05,49.292,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43136,Q#3280 - >seq9927,non-specific,238185,653,769,3.21359e-05,43.8788,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43137,Q#3280 - >seq9927,non-specific,223496,303,497,0.000402685,44.7511,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43138,Q#3280 - >seq9927,superfamily,223496,303,497,0.000402685,44.7511,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43139,Q#3280 - >seq9927,non-specific,274009,306,455,0.00103148,43.5179,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
43140,Q#3280 - >seq9927,superfamily,274009,306,455,0.00103148,43.5179,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
43141,Q#3280 - >seq9927,non-specific,274475,254,425,0.00171219,42.3632,TIGR03185,DNA_S_dndD,NC,cl25734,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43142,Q#3280 - >seq9927,superfamily,274475,254,425,0.00171219,42.3632,cl25734,DNA_S_dndD superfamily,NC, - ,"DNA sulfur modification protein DndD; This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Unusual,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43143,Q#3280 - >seq9927,specific,311990,1237,1255,0.00212695,36.496,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43144,Q#3280 - >seq9927,superfamily,311990,1237,1255,0.00212695,36.496,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PA15,ORF2,hs6_sqmonkey,marg,CompleteHit
43145,Q#3280 - >seq9927,non-specific,224117,262,464,0.00305426,41.6236,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
43146,Q#3280 - >seq9927,superfamily,224117,262,464,0.00305426,41.6236,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,N-TerminusTruncated
43147,Q#3280 - >seq9927,non-specific,274008,266,461,0.00315318,41.5807,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43148,Q#3280 - >seq9927,superfamily,274008,266,461,0.00315318,41.5807,cl37069,SMC_prok_B superfamily,NC, - ,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43149,Q#3280 - >seq9927,non-specific,274008,262,433,0.00514866,41.1955,TIGR02168,SMC_prok_B,NC,cl37069,"chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,BothTerminiTruncated
43150,Q#3280 - >seq9927,non-specific,224117,262,445,0.00793996,40.468,COG1196,Smc,C,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA15.ORF2.hs6_sqmonkey.marg.frame3,1909201640_L1PA15.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF2.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PA15,ORF2,hs6_sqmonkey,marg,C-TerminusTruncated
43151,Q#3282 - >seq9929,non-specific,335182,147,244,2.50372e-46,152.072,pfam02994,Transposase_22, - ,cl25509,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43152,Q#3282 - >seq9929,superfamily,335182,147,244,2.50372e-46,152.072,cl25509,Transposase_22 superfamily, - , - ,L1 transposable element RBD-like domain; This entry represents the RBD-like domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43153,Q#3282 - >seq9929,non-specific,340205,247,311,6.963979999999999e-33,116.28200000000001,pfam17490,Tnp_22_dsRBD, - ,cl38762,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43154,Q#3282 - >seq9929,superfamily,340205,247,311,6.963979999999999e-33,116.28200000000001,cl38762,Tnp_22_dsRBD superfamily, - , - ,L1 transposable element dsRBD-like domain; This entry represents the double stranded RNA-binding-like domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Transposase22,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43155,Q#3282 - >seq9929,non-specific,340204,102,144,8.91821e-08,47.7876,pfam17489,Tnp_22_trimer, - ,cl38761,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43156,Q#3282 - >seq9929,superfamily,340204,102,144,8.91821e-08,47.7876,cl38761,Tnp_22_trimer superfamily, - , - ,L1 transposable element trimerization domain; This entry represents the trimerization domain.,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Trimerization,L1PA8A,ORF1,hs6_sqmonkey,pars,CompleteHit
43157,Q#3282 - >seq9929,non-specific,224117,56,173,0.00251603,39.3124,COG1196,Smc,NC,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43158,Q#3282 - >seq9929,superfamily,224117,56,173,0.00251603,39.3124,cl34174,Smc superfamily,NC, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43159,Q#3282 - >seq9929,non-specific,235461,38,165,0.00293021,38.8958,PRK05431,PRK05431,C,cl35319,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
43160,Q#3282 - >seq9929,superfamily,235461,38,165,0.00293021,38.8958,cl35319,PRK05431 superfamily,C, - ,seryl-tRNA synthetase; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_tRNAsynthetase,L1PA8A,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
43161,Q#3282 - >seq9929,non-specific,179385,49,136,0.00365936,38.8678,PRK02224,PRK02224,NC,cl32023,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43162,Q#3282 - >seq9929,superfamily,179385,49,136,0.00365936,38.8678,cl32023,PRK02224 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43163,Q#3282 - >seq9929,non-specific,235175,25,147,0.00439985,38.5064,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43164,Q#3282 - >seq9929,superfamily,235175,25,147,0.00439985,38.5064,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43165,Q#3282 - >seq9929,non-specific,235175,31,147,0.00510345,38.5064,PRK03918,PRK03918,C,cl35229,chromosome segregation protein; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,C-TerminusTruncated
43166,Q#3282 - >seq9929,non-specific,179877,26,186,0.00958512,37.5078,PRK04778,PRK04778,NC,cl32064,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43167,Q#3282 - >seq9929,superfamily,179877,26,186,0.00958512,37.5078,cl32064,PRK04778 superfamily,NC, - ,septation ring formation regulator EzrA; Provisional,L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_CellDiv,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43168,Q#3282 - >seq9929,non-specific,274009,57,138,0.00966517,37.7399,TIGR02169,SMC_prok_A,NC,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43169,Q#3282 - >seq9929,superfamily,274009,57,138,0.00966517,37.7399,cl37070,SMC_prok_A superfamily,NC, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1PA8A.ORF1.hs6_sqmonkey.pars.frame3,1909201640_L1PA8A.RM_HPGPNRMPCCS_1709081336.200longest.o3000.out.fa.ch.100longest.fa.ORF1.fa.manual.macse_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PA8A,ORF1,hs6_sqmonkey,pars,BothTerminiTruncated
43170,Q#3283 - >seq9930,specific,238827,508,769,8.953839999999998e-66,221.396,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43171,Q#3283 - >seq9930,superfamily,295487,508,769,8.953839999999998e-66,221.396,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43172,Q#3283 - >seq9930,specific,197310,9,235,1.3182299999999997e-60,207.204,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43173,Q#3283 - >seq9930,superfamily,351117,9,235,1.3182299999999997e-60,207.204,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43174,Q#3283 - >seq9930,specific,333820,514,769,2.70237e-33,127.023,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43175,Q#3283 - >seq9930,superfamily,333820,514,769,2.70237e-33,127.023,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43176,Q#3283 - >seq9930,non-specific,197306,9,235,1.1177e-30,121.434,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43177,Q#3283 - >seq9930,non-specific,197320,9,208,4.2077e-20,91.0373,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43178,Q#3283 - >seq9930,specific,335306,10,228,1.19572e-19,88.8413,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43179,Q#3283 - >seq9930,non-specific,197307,9,235,2.0103999999999998e-19,88.8841,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43180,Q#3283 - >seq9930,non-specific,223780,9,236,2.35256e-19,89.1947,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43181,Q#3283 - >seq9930,non-specific,197321,7,235,1.47063e-15,77.5924,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43182,Q#3283 - >seq9930,non-specific,273186,9,236,8.18297e-15,75.3932,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43183,Q#3283 - >seq9930,non-specific,197319,13,235,3.1786900000000005e-14,73.8501,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43184,Q#3283 - >seq9930,non-specific,272954,9,207,7.436710000000001e-14,72.8009,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43185,Q#3283 - >seq9930,non-specific,238828,514,735,1.7333700000000001e-12,67.9964,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43186,Q#3283 - >seq9930,non-specific,275209,465,797,1.3644399999999998e-08,58.238,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43187,Q#3283 - >seq9930,superfamily,275209,465,797,1.3644399999999998e-08,58.238,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43188,Q#3283 - >seq9930,non-specific,197336,9,194,1.38771e-08,56.8519,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43189,Q#3283 - >seq9930,non-specific,236970,9,235,2.4836800000000002e-08,56.441,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43190,Q#3283 - >seq9930,non-specific,197322,8,235,6.86552e-06,49.2378,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43191,Q#3283 - >seq9930,non-specific,197311,30,146,8.54148e-05,44.9753,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43192,Q#3283 - >seq9930,specific,311990,1236,1254,0.000855235,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43193,Q#3283 - >seq9930,superfamily,311990,1236,1254,0.000855235,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43194,Q#3283 - >seq9930,non-specific,238185,654,739,0.00143788,39.2564,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43195,Q#3283 - >seq9930,non-specific,223496,319,498,0.00217507,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
43196,Q#3283 - >seq9930,superfamily,223496,319,498,0.00217507,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
43197,Q#3283 - >seq9930,specific,225881,481,678,0.00769736,39.8221,COG3344,YkfC,NC,cl34590,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
43198,Q#3283 - >seq9930,superfamily,225881,481,678,0.00769736,39.8221,cl34590,YkfC superfamily,NC, - ,"Retron-type reverse transcriptase [Mobilome: prophages, transposons]; Retron-type reverse transcriptase [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs2_gorilla,marg,BothTerminiTruncated
43199,Q#3283 - >seq9930,non-specific,339261,108,231,0.0085807,37.3167,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs2_gorilla.marg.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs2_gorilla,marg,CompleteHit
43200,Q#3286 - >seq9933,specific,197310,9,218,4.239289999999999e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43201,Q#3286 - >seq9933,superfamily,351117,9,218,4.239289999999999e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43202,Q#3286 - >seq9933,non-specific,197306,9,224,2.62894e-29,117.197,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43203,Q#3286 - >seq9933,non-specific,197320,9,208,1.91908e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43204,Q#3286 - >seq9933,non-specific,197307,9,218,3.4205599999999995e-20,91.1953,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43205,Q#3286 - >seq9933,non-specific,223780,9,207,8.089960000000001e-20,90.3503,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43206,Q#3286 - >seq9933,specific,335306,10,210,5.77194e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43207,Q#3286 - >seq9933,non-specific,272954,9,207,2.29107e-15,77.0381,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43208,Q#3286 - >seq9933,non-specific,197321,7,194,3.40306e-15,76.4368,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43209,Q#3286 - >seq9933,non-specific,197319,13,218,1.6050700000000002e-14,74.6205,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43210,Q#3286 - >seq9933,non-specific,273186,9,208,4.1939099999999994e-14,73.4672,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43211,Q#3286 - >seq9933,non-specific,236970,9,207,1.98386e-09,59.5226,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43212,Q#3286 - >seq9933,non-specific,197336,9,194,9.61418e-09,57.2371,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43213,Q#3286 - >seq9933,non-specific,197322,8,217,1.1758299999999999e-05,48.4674,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43214,Q#3286 - >seq9933,non-specific,197311,30,146,5.6635e-05,45.3605,cd09077,R1-I-EN,C,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs2_gorilla.pars.frame3,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs2_gorilla,pars,C-TerminusTruncated
43215,Q#3288 - >seq9935,specific,238827,500,761,3.6475799999999995e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43216,Q#3288 - >seq9935,superfamily,295487,500,761,3.6475799999999995e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43217,Q#3288 - >seq9935,specific,333820,506,761,1.4463299999999998e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43218,Q#3288 - >seq9935,superfamily,333820,506,761,1.4463299999999998e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43219,Q#3288 - >seq9935,non-specific,238828,506,727,1.4388e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43220,Q#3288 - >seq9935,non-specific,275209,457,789,2.7010800000000002e-08,57.0824,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43221,Q#3288 - >seq9935,superfamily,275209,457,789,2.7010800000000002e-08,57.0824,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43222,Q#3288 - >seq9935,specific,311990,1228,1246,0.000609195,38.0368,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43223,Q#3288 - >seq9935,superfamily,311990,1228,1246,0.000609195,38.0368,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,DUF1725,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43224,Q#3288 - >seq9935,non-specific,238185,646,731,0.000765635,40.0268,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,RT,L1PB4,ORF2,hs2_gorilla,pars,CompleteHit
43225,Q#3288 - >seq9935,non-specific,223496,311,490,0.00233057,42.0547,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
43226,Q#3288 - >seq9935,superfamily,223496,311,490,0.00233057,42.0547,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs2_gorilla.pars.frame2,1909201643_L1PB4.RM_HPG_1708011910.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame2,Other_ATPase_DNArepair,L1PB4,ORF2,hs2_gorilla,pars,BothTerminiTruncated
43227,Q#3291 - >seq9938,specific,238827,507,768,4.1679699999999995e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43228,Q#3291 - >seq9938,superfamily,295487,507,768,4.1679699999999995e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43229,Q#3291 - >seq9938,specific,197310,9,234,2.12283e-58,201.041,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43230,Q#3291 - >seq9938,superfamily,351117,9,234,2.12283e-58,201.041,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43231,Q#3291 - >seq9938,specific,333820,513,768,1.5085699999999999e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43232,Q#3291 - >seq9938,superfamily,333820,513,768,1.5085699999999999e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43233,Q#3291 - >seq9938,non-specific,197306,9,234,1.78999e-28,114.88600000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43234,Q#3291 - >seq9938,non-specific,197320,9,207,1.2215700000000002e-20,92.5781,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43235,Q#3291 - >seq9938,specific,335306,10,227,6.699659999999999e-19,86.9153,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43236,Q#3291 - >seq9938,non-specific,197307,9,234,8.535849999999999e-19,87.3433,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43237,Q#3291 - >seq9938,non-specific,223780,9,235,2.55824e-18,86.1131,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43238,Q#3291 - >seq9938,non-specific,197321,7,234,2.99497e-15,76.822,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43239,Q#3291 - >seq9938,non-specific,273186,9,235,1.93351e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43240,Q#3291 - >seq9938,non-specific,197319,13,234,1.40624e-13,71.9241,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43241,Q#3291 - >seq9938,non-specific,238828,513,734,2.98325e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43242,Q#3291 - >seq9938,non-specific,272954,9,206,4.52226e-12,67.4081,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43243,Q#3291 - >seq9938,non-specific,275209,464,796,5.08135e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43244,Q#3291 - >seq9938,superfamily,275209,464,796,5.08135e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43245,Q#3291 - >seq9938,non-specific,197336,9,193,2.51417e-08,56.0815,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43246,Q#3291 - >seq9938,non-specific,236970,9,234,3.89711e-06,49.8926,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43247,Q#3291 - >seq9938,non-specific,197322,8,234,5.5776e-06,49.623000000000005,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43248,Q#3291 - >seq9938,non-specific,235175,289,466,1.92275e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,pars,BothTerminiTruncated
43249,Q#3291 - >seq9938,superfamily,235175,289,466,1.92275e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,pars,BothTerminiTruncated
43250,Q#3291 - >seq9938,non-specific,197311,30,203,4.4531000000000004e-05,45.7457,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43251,Q#3291 - >seq9938,specific,311990,1235,1253,0.0008953710000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43252,Q#3291 - >seq9938,superfamily,311990,1235,1253,0.0008953710000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,DUF1725,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43253,Q#3291 - >seq9938,non-specific,224117,261,464,0.00107563,43.1644,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
43254,Q#3291 - >seq9938,superfamily,224117,261,464,0.00107563,43.1644,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs1_chimp,pars,N-TerminusTruncated
43255,Q#3291 - >seq9938,non-specific,223496,261,497,0.00194115,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs1_chimp,pars,BothTerminiTruncated
43256,Q#3291 - >seq9938,superfamily,223496,261,497,0.00194115,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs1_chimp,pars,BothTerminiTruncated
43257,Q#3291 - >seq9938,non-specific,238185,653,738,0.00422676,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43258,Q#3291 - >seq9938,non-specific,339261,107,230,0.00587251,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs1_chimp.pars.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs1_chimp,pars,CompleteHit
43259,Q#3294 - >seq9941,specific,238827,506,767,3.949559999999999e-66,222.55200000000002,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43260,Q#3294 - >seq9941,superfamily,295487,506,767,3.949559999999999e-66,222.55200000000002,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43261,Q#3294 - >seq9941,specific,197310,9,233,4.3981400000000004e-57,197.18900000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43262,Q#3294 - >seq9941,superfamily,351117,9,233,4.3981400000000004e-57,197.18900000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43263,Q#3294 - >seq9941,specific,333820,512,767,1.30169e-33,127.794,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43264,Q#3294 - >seq9941,superfamily,333820,512,767,1.30169e-33,127.794,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43265,Q#3294 - >seq9941,non-specific,197306,9,233,2.80938e-29,117.58200000000001,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43266,Q#3294 - >seq9941,non-specific,197320,9,206,2.60208e-20,91.8077,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43267,Q#3294 - >seq9941,non-specific,223780,9,234,1.7271e-19,89.5799,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43268,Q#3294 - >seq9941,non-specific,197307,9,233,9.99918e-19,86.9581,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43269,Q#3294 - >seq9941,specific,335306,10,226,1.54627e-18,85.7597,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43270,Q#3294 - >seq9941,non-specific,197321,7,233,1.3175599999999999e-15,77.9776,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43271,Q#3294 - >seq9941,non-specific,273186,9,234,1.8056400000000002e-14,74.6228,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43272,Q#3294 - >seq9941,non-specific,197319,13,233,2.4515200000000002e-14,74.2353,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43273,Q#3294 - >seq9941,non-specific,272954,9,205,1.16617e-12,69.3341,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43274,Q#3294 - >seq9941,non-specific,238828,512,733,2.91972e-12,67.226,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43275,Q#3294 - >seq9941,non-specific,275209,463,795,5.11216e-09,59.3936,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43276,Q#3294 - >seq9941,superfamily,275209,463,795,5.11216e-09,59.3936,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43277,Q#3294 - >seq9941,non-specific,197336,9,192,4.5979199999999995e-08,55.3111,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43278,Q#3294 - >seq9941,non-specific,197322,8,233,3.10672e-07,53.475,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43279,Q#3294 - >seq9941,non-specific,236970,9,233,1.61709e-06,51.0482,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43280,Q#3294 - >seq9941,non-specific,235175,288,465,1.85342e-05,48.9068,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,marg,BothTerminiTruncated
43281,Q#3294 - >seq9941,superfamily,235175,288,465,1.85342e-05,48.9068,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,marg,BothTerminiTruncated
43282,Q#3294 - >seq9941,non-specific,197311,30,202,3.3950100000000006e-05,46.1309,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43283,Q#3294 - >seq9941,specific,311990,1232,1250,0.0008932780000000001,37.6516,pfam08333,DUF1725, - ,cl07081,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43284,Q#3294 - >seq9941,superfamily,311990,1232,1250,0.0008932780000000001,37.6516,cl07081,DUF1725 superfamily, - , - ,Protein of unknown function (DUF1725); This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.,L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,DUF1725,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43285,Q#3294 - >seq9941,non-specific,224117,260,463,0.00106366,43.1644,COG1196,Smc,N,cl34174,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1PB4,ORF2,hs1_chimp,marg,N-TerminusTruncated
43286,Q#3294 - >seq9941,superfamily,224117,260,463,0.00106366,43.1644,cl34174,Smc superfamily,N, - ,"Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]; Chromosome segregation ATPases [Cell division and chromosome partitioning].",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_ChromSeg,L1PB4,ORF2,hs1_chimp,marg,N-TerminusTruncated
43287,Q#3294 - >seq9941,non-specific,223496,260,496,0.00188728,42.4399,COG0419,SbcC,NC,cl33865,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ATPase_DNARepair_Exonuclease,L1PB4,ORF2,hs1_chimp,marg,BothTerminiTruncated
43288,Q#3294 - >seq9941,superfamily,223496,260,496,0.00188728,42.4399,cl33865,SbcC superfamily,NC, - ,"DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; ATPase involved in DNA repair [DNA replication, recombination, and repair].",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Other_ATPase_DNArepair,L1PB4,ORF2,hs1_chimp,marg,BothTerminiTruncated
43289,Q#3294 - >seq9941,non-specific,238185,652,737,0.00405521,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43290,Q#3294 - >seq9941,non-specific,339261,106,229,0.00597195,37.7019,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1PB4.ORF2.hs1_chimp.marg.frame3,1909201643_L1PB4.RM_HP_1707271643.200longest.o3000.out.fa.ch.100longest.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1PB4,ORF2,hs1_chimp,marg,CompleteHit
43291,Q#3297 - >seq9944,non-specific,197310,9,86,1.92853e-21,83.5549,cd09076,L1-EN,C,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43292,Q#3297 - >seq9944,superfamily,351117,9,86,1.92853e-21,83.5549,cl00490,EEP superfamily,C, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43293,Q#3297 - >seq9944,non-specific,197306,9,81,2.07333e-09,51.7133,cd08372,EEP,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43294,Q#3297 - >seq9944,non-specific,223780,7,83,2.1082900000000002e-08,49.1339,COG0708,XthA,C,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43295,Q#3297 - >seq9944,specific,335306,10,88,1.96858e-07,46.0842,pfam03372,Exo_endo_phos,C,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43296,Q#3297 - >seq9944,non-specific,197320,7,77,8.71061e-07,44.4282,cd09086,ExoIII-like_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43297,Q#3297 - >seq9944,non-specific,197321,7,81,1.37553e-06,43.6948,cd09087,Ape1-like_AP-endo,C,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43298,Q#3297 - >seq9944,non-specific,272954,7,77,1.8884400000000003e-06,43.5257,TIGR00195,exoDNase_III,C,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43299,Q#3297 - >seq9944,non-specific,197307,9,81,3.06622e-06,43.0453,cd09073,ExoIII_AP-endo,C,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43300,Q#3297 - >seq9944,non-specific,273186,7,77,1.12901e-05,41.4956,TIGR00633,xth,C,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43301,Q#3297 - >seq9944,non-specific,197336,7,77,0.00028211400000000003,37.2067,cd10281,Nape_like_AP-endo,C,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43302,Q#3297 - >seq9944,non-specific,197319,7,44,0.00328315,34.1746,cd09085,Mth212-like_AP-endo,C,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs2_gorilla.marg.frame3,1909201647_L1M4c.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43303,Q#3300 - >seq9947,specific,197310,9,238,7.003519999999999e-61,200.27,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43304,Q#3300 - >seq9947,superfamily,351117,9,238,7.003519999999999e-61,200.27,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43305,Q#3300 - >seq9947,non-specific,197306,9,238,1.59777e-27,110.649,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43306,Q#3300 - >seq9947,non-specific,197320,7,231,2.6623000000000004e-21,92.9633,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43307,Q#3300 - >seq9947,specific,335306,10,231,1.2587299999999999e-18,84.6041,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43308,Q#3300 - >seq9947,non-specific,223780,7,231,2.9782200000000003e-18,84.5723,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43309,Q#3300 - >seq9947,non-specific,197307,9,231,4.23608e-16,77.7133,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43310,Q#3300 - >seq9947,non-specific,273186,7,239,1.07338e-11,64.9928,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43311,Q#3300 - >seq9947,non-specific,197321,7,231,1.92915e-11,64.1104,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43312,Q#3300 - >seq9947,non-specific,272954,7,209,7.24072e-11,62.4005,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43313,Q#3300 - >seq9947,non-specific,197319,7,238,3.5919499999999998e-09,57.2865,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43314,Q#3300 - >seq9947,non-specific,197336,7,231,1.55107e-05,46.4515,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43315,Q#3300 - >seq9947,non-specific,238827,512,542,2.09215e-05,45.745,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs3_orang,marg,C-TerminusTruncated
43316,Q#3300 - >seq9947,superfamily,295487,512,542,2.09215e-05,45.745,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1M4c,ORF2,hs3_orang,marg,C-TerminusTruncated
43317,Q#3300 - >seq9947,non-specific,197311,36,206,7.01756e-05,43.8197,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43318,Q#3300 - >seq9947,non-specific,236970,9,231,0.00063923,41.4182,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43319,Q#3300 - >seq9947,non-specific,339261,110,233,0.0009496089999999999,38.8575,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1M4c.ORF2.hs3_orang.marg.frame3,1909201650_L1M4c.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1M4c,ORF2,hs3_orang,marg,CompleteHit
43320,Q#3303 - >seq9950,non-specific,197310,9,185,4.8977e-14,71.6137,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs4_gibbon.marg.frame3,1909201653_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs4_gibbon,marg,CompleteHit
43321,Q#3303 - >seq9950,superfamily,351117,9,185,4.8977e-14,71.6137,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs4_gibbon.marg.frame3,1909201653_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs4_gibbon,marg,CompleteHit
43322,Q#3303 - >seq9950,non-specific,197306,9,193,8.04147e-09,55.9505,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs4_gibbon.marg.frame3,1909201653_L1ME1.RM_HPGPN_1708181204.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs4_gibbon,marg,CompleteHit
43323,Q#3304 - >seq9951,non-specific,238827,494,691,7.73198e-26,106.221,cd01650,RT_nLTR_like,N,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs2_gorilla.marg.frame2,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43324,Q#3304 - >seq9951,superfamily,295487,494,691,7.73198e-26,106.221,cl02808,RT_like superfamily,N, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs2_gorilla.marg.frame2,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43325,Q#3304 - >seq9951,non-specific,333820,505,691,1.81989e-14,72.325,pfam00078,RVT_1,N,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs2_gorilla.marg.frame2,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43326,Q#3304 - >seq9951,superfamily,333820,505,691,1.81989e-14,72.325,cl37957,RVT_1 superfamily,N, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs2_gorilla.marg.frame2,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43327,Q#3304 - >seq9951,non-specific,238828,489,659,1.3212899999999998e-08,56.0552,cd01651,RT_G2_intron,N,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs2_gorilla.marg.frame2,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43328,Q#3305 - >seq9952,non-specific,197310,2,227,4.359380000000001e-24,101.65899999999999,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs2_gorilla,marg,CompleteHit
43329,Q#3305 - >seq9952,superfamily,351117,2,227,4.359380000000001e-24,101.65899999999999,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs2_gorilla,marg,CompleteHit
43330,Q#3305 - >seq9952,non-specific,238827,511,558,6.77403e-10,59.9974,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43331,Q#3305 - >seq9952,superfamily,295487,511,558,6.77403e-10,59.9974,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43332,Q#3305 - >seq9952,non-specific,197306,2,202,4.4180500000000003e-07,51.7133,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs2_gorilla,marg,CompleteHit
43333,Q#3305 - >seq9952,non-specific,197320,100,199,0.00159856,40.9614,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1ME1,ORF2,hs2_gorilla,marg,N-TerminusTruncated
43334,Q#3305 - >seq9952,non-specific,333820,511,550,0.00379662,39.1978,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43335,Q#3305 - >seq9952,superfamily,333820,511,550,0.00379662,39.1978,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs2_gorilla.marg.frame3,1909201659_L1ME1.RM_HPG_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs2_gorilla,marg,C-TerminusTruncated
43336,Q#3309 - >seq9956,non-specific,238827,330,541,2.95209e-19,87.3466,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs3_orang.pars.frame3,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs3_orang,pars,CompleteHit
43337,Q#3309 - >seq9956,superfamily,295487,330,541,2.95209e-19,87.3466,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs3_orang.pars.frame3,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs3_orang,pars,CompleteHit
43338,Q#3309 - >seq9956,non-specific,333820,330,531,1.4347100000000001e-09,58.4578,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs3_orang.pars.frame3,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs3_orang,pars,CompleteHit
43339,Q#3309 - >seq9956,superfamily,333820,330,531,1.4347100000000001e-09,58.4578,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs3_orang.pars.frame3,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs3_orang,pars,CompleteHit
43340,Q#3309 - >seq9956,non-specific,238828,381,466,1.11997e-05,47.5809,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs3_orang.pars.frame3,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC3,ORF2,hs3_orang,pars,BothTerminiTruncated
43341,Q#3310 - >seq9957,non-specific,238827,509,723,4.87032e-20,90.04299999999999,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC3.ORF2.hs3_orang.marg.frame1,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs3_orang,marg,CompleteHit
43342,Q#3310 - >seq9957,superfamily,295487,509,723,4.87032e-20,90.04299999999999,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC3.ORF2.hs3_orang.marg.frame1,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs3_orang,marg,CompleteHit
43343,Q#3310 - >seq9957,non-specific,333820,509,713,5.99322e-09,56.917,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs3_orang.marg.frame1,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs3_orang,marg,CompleteHit
43344,Q#3310 - >seq9957,superfamily,333820,509,713,5.99322e-09,56.917,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC3.ORF2.hs3_orang.marg.frame1,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs3_orang,marg,CompleteHit
43345,Q#3310 - >seq9957,non-specific,238828,563,648,1.62737e-05,47.1957,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC3.ORF2.hs3_orang.marg.frame1,1909201706_L1MC3.RM_HPGP_1708011910.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame1,RT,L1MC3,ORF2,hs3_orang,marg,BothTerminiTruncated
43346,Q#3313 - >seq9960,specific,238827,509,771,7.05249e-55,190.195,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43347,Q#3313 - >seq9960,superfamily,295487,509,771,7.05249e-55,190.195,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43348,Q#3313 - >seq9960,specific,197310,9,236,7.9072e-54,187.94400000000002,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43349,Q#3313 - >seq9960,superfamily,351117,9,236,7.9072e-54,187.94400000000002,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43350,Q#3313 - >seq9960,specific,333820,515,771,1.88293e-30,118.934,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43351,Q#3313 - >seq9960,superfamily,333820,515,771,1.88293e-30,118.934,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43352,Q#3313 - >seq9960,non-specific,197306,9,236,1.3063299999999998e-28,115.271,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43353,Q#3313 - >seq9960,non-specific,223780,9,229,1.2466700000000002e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43354,Q#3313 - >seq9960,specific,335306,10,229,5.78573e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43355,Q#3313 - >seq9960,non-specific,197307,9,236,6.36735e-17,81.5653,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43356,Q#3313 - >seq9960,non-specific,197320,9,221,6.77205e-17,81.7925,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43357,Q#3313 - >seq9960,non-specific,273186,9,237,1.07063e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43358,Q#3313 - >seq9960,non-specific,238828,515,749,2.20975e-12,67.6112,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43359,Q#3313 - >seq9960,non-specific,197321,7,236,3.52344e-11,64.8808,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43360,Q#3313 - >seq9960,non-specific,272954,9,207,5.47191e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43361,Q#3313 - >seq9960,non-specific,275209,468,805,2.40089e-09,60.5492,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43362,Q#3313 - >seq9960,superfamily,275209,468,805,2.40089e-09,60.5492,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43363,Q#3313 - >seq9960,non-specific,197319,9,236,4.49276e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43364,Q#3313 - >seq9960,non-specific,197322,8,236,1.69004e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43365,Q#3313 - >seq9960,non-specific,197336,9,194,2.44436e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43366,Q#3313 - >seq9960,non-specific,339261,108,232,1.2425699999999999e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43367,Q#3313 - >seq9960,non-specific,236970,9,207,0.000155369,44.885,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43368,Q#3313 - >seq9960,non-specific,197318,9,148,0.000561431,42.6687,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,pars,C-TerminusTruncated
43369,Q#3313 - >seq9960,non-specific,197311,7,236,0.0005652669999999999,42.2789,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,pars,CompleteHit
43370,Q#3313 - >seq9960,non-specific,274009,307,449,0.00287205,41.9771,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,pars,C-TerminusTruncated
43371,Q#3313 - >seq9960,superfamily,274009,307,449,0.00287205,41.9771,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,pars,C-TerminusTruncated
43372,Q#3313 - >seq9960,non-specific,238185,654,749,0.00522217,37.3304,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs0_human.pars.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_Chars_ParsimonyIndels_N1.frame3,RT,L1MC1,ORF2,hs0_human,pars,CompleteHit
43373,Q#3317 - >seq9964,non-specific,240274,194,503,0.00225289,42.2845,PTZ00112,PTZ00112,C,cl36513,origin recognition complex 1 protein; Provisional,L1MC1.ORF2.hs0_human.marg.frame2,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MC1,ORF2,hs0_human,marg,C-TerminusTruncated
43374,Q#3317 - >seq9964,superfamily,240274,194,503,0.00225289,42.2845,cl36513,PTZ00112 superfamily,C, - ,origin recognition complex 1 protein; Provisional,L1MC1.ORF2.hs0_human.marg.frame2,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Unusual,L1MC1,ORF2,hs0_human,marg,C-TerminusTruncated
43375,Q#3318 - >seq9965,specific,238827,510,772,3.0872599999999995e-55,191.35,cd01650,RT_nLTR_like, - ,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43376,Q#3318 - >seq9965,superfamily,295487,510,772,3.0872599999999995e-55,191.35,cl02808,RT_like superfamily, - , - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43377,Q#3318 - >seq9965,specific,197310,9,236,6.548759999999999e-54,188.329,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43378,Q#3318 - >seq9965,superfamily,351117,9,236,6.548759999999999e-54,188.329,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43379,Q#3318 - >seq9965,specific,333820,516,772,7.711469999999999e-31,120.09,pfam00078,RVT_1, - ,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43380,Q#3318 - >seq9965,superfamily,333820,516,772,7.711469999999999e-31,120.09,cl37957,RVT_1 superfamily, - , - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43381,Q#3318 - >seq9965,non-specific,197306,9,236,1.1543399999999998e-28,115.656,cd08372,EEP, - ,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43382,Q#3318 - >seq9965,non-specific,223780,9,229,1.69365e-20,92.6615,COG0708,XthA, - ,cl00490,"Exonuclease III [Replication, recombination and repair]; Exonuclease III [DNA replication, recombination, and repair].",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43383,Q#3318 - >seq9965,specific,335306,10,229,6.42085e-18,83.8337,pfam03372,Exo_endo_phos, - ,cl00490,"Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12, and Nocturnin.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43384,Q#3318 - >seq9965,non-specific,197307,9,236,5.91897e-17,81.9505,cd09073,ExoIII_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43385,Q#3318 - >seq9965,non-specific,197320,9,221,7.5336e-17,81.7925,cd09086,ExoIII-like_AP-endo, - ,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43386,Q#3318 - >seq9965,non-specific,273186,9,237,1.39735e-15,78.0896,TIGR00633,xth, - ,cl00490,"exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43387,Q#3318 - >seq9965,non-specific,238828,516,750,1.58936e-12,68.3816,cd01651,RT_G2_intron, - ,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43388,Q#3318 - >seq9965,non-specific,197321,7,236,3.9889e-11,64.4956,cd09087,Ape1-like_AP-endo, - ,cl00490,"Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43389,Q#3318 - >seq9965,non-specific,272954,9,207,4.77626e-11,64.3265,TIGR00195,exoDNase_III, - ,cl00490,"exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43390,Q#3318 - >seq9965,non-specific,275209,469,806,1.8776099999999997e-09,60.9344,TIGR04416,group_II_RT_mat, - ,cl37441,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43391,Q#3318 - >seq9965,superfamily,275209,469,806,1.8776099999999997e-09,60.9344,cl37441,group_II_RT_mat superfamily, - , - ,"group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43392,Q#3318 - >seq9965,non-specific,197319,9,236,4.72053e-09,58.4421,cd09085,Mth212-like_AP-endo, - ,cl00490,"Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43393,Q#3318 - >seq9965,non-specific,197322,8,236,1.88137e-08,57.327,cd09088,Ape2-like_AP-endo, - ,cl00490,"Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43394,Q#3318 - >seq9965,non-specific,197336,9,194,2.71282e-07,52.9999,cd10281,Nape_like_AP-endo, - ,cl00490,"Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43395,Q#3318 - >seq9965,non-specific,339261,108,232,1.50761e-05,45.4059,pfam14529,Exo_endo_phos_2, - ,cl00490,"Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43396,Q#3318 - >seq9965,non-specific,236970,9,207,0.00016769599999999997,44.885,PRK11756,PRK11756, - ,cl00490,exonuclease III; Provisional,L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Exonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43397,Q#3318 - >seq9965,non-specific,197318,9,148,0.000433658,43.4391,cd09084,EEP-2,C,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1MC1,ORF2,hs0_human,marg,C-TerminusTruncated
43398,Q#3318 - >seq9965,non-specific,274009,307,450,0.000509506,44.2883,TIGR02169,SMC_prok_A,C,cl37070,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,marg,C-TerminusTruncated
43399,Q#3318 - >seq9965,superfamily,274009,307,450,0.000509506,44.2883,cl37070,SMC_prok_A superfamily,C, - ,"chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,marg,C-TerminusTruncated
43400,Q#3318 - >seq9965,non-specific,197311,7,236,0.000919954,41.8937,cd09077,R1-I-EN, - ,cl00490,"Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1MC1,ORF2,hs0_human,marg,CompleteHit
43401,Q#3318 - >seq9965,non-specific,235175,307,450,0.00209144,42.3584,PRK03918,PRK03918,NC,cl35229,chromosome segregation protein; Provisional,L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,marg,BothTerminiTruncated
43402,Q#3318 - >seq9965,superfamily,235175,307,450,0.00209144,42.3584,cl35229,PRK03918 superfamily,NC, - ,chromosome segregation protein; Provisional,L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,ChromSeg,L1MC1,ORF2,hs0_human,marg,BothTerminiTruncated
43403,Q#3318 - >seq9965,non-specific,238185,655,750,0.00441555,37.7156,cd00304,RT_like, - ,cl02808,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1MC1.ORF2.hs0_human.marg.frame3,1909201710_L1MC1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1MC1,ORF2,hs0_human,marg,CompleteHit
43404,Q#3320 - >seq9967,non-specific,238827,556,644,7.05783e-24,100.05799999999999,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs0_human,marg,C-TerminusTruncated
43405,Q#3320 - >seq9967,superfamily,295487,556,644,7.05783e-24,100.05799999999999,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs0_human,marg,C-TerminusTruncated
43406,Q#3320 - >seq9967,non-specific,197310,50,264,2.37767e-17,81.6289,cd09076,L1-EN, - ,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease,L1ME1,ORF2,hs0_human,marg,CompleteHit
43407,Q#3320 - >seq9967,superfamily,351117,50,264,2.37767e-17,81.6289,cl00490,EEP superfamily, - , - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs0_human,marg,CompleteHit
43408,Q#3320 - >seq9967,non-specific,333820,556,644,3.73457e-11,62.3098,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs0_human,marg,C-TerminusTruncated
43409,Q#3320 - >seq9967,superfamily,333820,556,644,3.73457e-11,62.3098,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,RT,L1ME1,ORF2,hs0_human,marg,C-TerminusTruncated
43410,Q#3320 - >seq9967,non-specific,197306,171,264,0.000134971,43.6241,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Endonuclease_Exonuclease,L1ME1,ORF2,hs0_human,marg,N-TerminusTruncated
43411,Q#3320 - >seq9967,non-specific,197320,170,236,0.00230272,40.191,cd09086,ExoIII-like_AP-endo,N,cl00490,"Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII  are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and  3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.",L1ME1.ORF2.hs0_human.marg.frame2,1909201710_L1ME1.RM_hs_1709082029.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame2,Exonuclease,L1ME1,ORF2,hs0_human,marg,N-TerminusTruncated
43412,Q#3324 - >seq9971,non-specific,238827,496,639,8.3998e-18,82.339,cd01650,RT_nLTR_like,C,cl02808,"RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs1_chimp,marg,C-TerminusTruncated
43413,Q#3324 - >seq9971,superfamily,295487,496,639,8.3998e-18,82.339,cl02808,RT_like superfamily,C, - ,"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs1_chimp,marg,C-TerminusTruncated
43414,Q#3324 - >seq9971,non-specific,197310,94,219,2.1019499999999997e-13,70.0729,cd09076,L1-EN,N,cl00490,"Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease,L1ME1,ORF2,hs1_chimp,marg,N-TerminusTruncated
43415,Q#3324 - >seq9971,superfamily,351117,94,219,2.1019499999999997e-13,70.0729,cl00490,EEP superfamily,N, - ,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs1_chimp,marg,N-TerminusTruncated
43416,Q#3324 - >seq9971,non-specific,333820,497,639,7.8218e-11,61.1542,pfam00078,RVT_1,C,cl37957,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs1_chimp,marg,C-TerminusTruncated
43417,Q#3324 - >seq9971,superfamily,333820,497,639,7.8218e-11,61.1542,cl37957,RVT_1 superfamily,C, - ,"Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs1_chimp,marg,C-TerminusTruncated
43418,Q#3324 - >seq9971,non-specific,238828,551,636,0.0004988880000000001,41.8029,cd01651,RT_G2_intron,NC,cl02808,"RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,RT,L1ME1,ORF2,hs1_chimp,marg,BothTerminiTruncated
43419,Q#3324 - >seq9971,non-specific,197306,92,220,0.00738432,38.2313,cd08372,EEP,N,cl00490,"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.",L1ME1.ORF2.hs1_chimp.marg.frame3,1909201712_L1ME1.RM_HP_1707271643.100longest.o3000.out.fa.ORF2.macse2_nt.aln.orfreconst_macse_round5large.2.marginal_IndelAndChars_N1.frame3,Endonuclease_Exonuclease,L1ME1,ORF2,hs1_chimp,marg,N-TerminusTruncated